@article{bekele_associations_2026,
	title = {Associations between volatile fatty acid profiles, methane emissions, and rumen microbiota in sheep fed {Ethiopian} forage},
	volume = {16},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1731623/full},
	doi = {10.3389/fmicb.2025.1731623},
	abstract = {This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD\_0), 45 (SD\_45), and 90 (SD\_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9\% of ASVs were Bacteria, and 0.05\% Archaea. At the genus level, Rikenellaceae RC9 gut group (18\%), Prevotella (17\%), and Candidatus Saccharimonas (8.9\%) were the most abundant Bacteria, while Methanobrevibacter (88\%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.},
	language = {English},
	urldate = {2026-01-23},
	journal = {Frontiers in Microbiology},
	publisher = {Frontiers},
	author = {Bekele, Wondimagegne and Mahawar, Lovely and Ramin, Mohammad and Simachew, Addis and Albrectsen, Benedicte Riber and Zegeye, Abiy},
	month = jan,
	year = {2026},
	keywords = {Archaea, Bacteria, CH4 intensity, Illumina sequencing, gut microbiota, metabarcoding, ruminant, volatile fatty acids},
}

This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD_0), 45 (SD_45), and 90 (SD_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9% of ASVs were Bacteria, and 0.05% Archaea. At the genus level, Rikenellaceae RC9 gut group (18%), Prevotella (17%), and Candidatus Saccharimonas (8.9%) were the most abundant Bacteria, while Methanobrevibacter (88%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.

@article{giubilei_clearing_2026,
	title = {Clearing the {Noise}: {Seasonal} {Dynamics} of {Endophytic} {Bacteria} in {Fagus} sylvatica {Leaves} {Revealed} by {Application} of {PNA} {Clamps}},
	volume = {178},
	issn = {1399-3054},
	shorttitle = {Clearing the {Noise}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70897},
	doi = {10.1111/ppl.70897},
	abstract = {The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.},
	language = {en},
	number = {3},
	urldate = {2026-04-27},
	journal = {Physiologia Plantarum},
	author = {Giubilei, Irene and Turco, Silvia and Cardacino, Antonella and Mahawar, Lovely and Albrectsen, Benedicte Riber and Mazzaglia, Angelo},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70897},
	keywords = {Fagus sylvatica, PNA clamps, endophytes, metabarcoding, microbiome},
	pages = {e70897},
}

The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.

@article{turco_comparative_2026,
	title = {Comparative {Metabarcoding} of {ITS1}, {ITS2}, and {Full}-{Length} {ITS} {Reveals} {Marker}- and {Tissue}-{Specific} {Variation} in {Fungal} {Community} {Profiling} in {Potato}},
	volume = {7},
	copyright = {© 2026 The Author(s). Plant-Environment Interactions published by John Wiley \& Sons Ltd and New Phytologist Foundation.},
	issn = {2575-6265},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pei3.70168},
	doi = {10.1002/pei3.70168},
	abstract = {Accurate profiling of plant-associated fungal and oomycete communities depends critically on the choice of ITS marker. Using Illumina sequencing for ITS1/ITS2 and PacBio HiFi sequencing for full-length ITS (ITSf), we compared read recovery, taxonomic assignment depth, and diversity patterns across potato leaf and root tissues. ITS2 generally recovered more diverse and even community profiles in leaves, whereas ITSf recovered comparatively more even and taxonomically broad profiles in roots. In contrast, ITS1 showed high read recovery but produced strongly skewed compositional profiles and was frequently dominated by host-derived sequences. Beta-diversity analyses indicated that ITS marker choice was associated with substantial variation in observed community composition, while functional annotation highlighted communities composed of taxa associated with multiple ecological guilds, including endophytes and opportunistic pathogens such as Cladosporium and Ilyonectria. Overall, the results demonstrate that ITS marker choice strongly influences the observed structure and diversity of plant-associated communities. ITS2 was generally more suitable for phyllosphere-associated communities, whereas ITSf provided broader recovery of root-associated taxa. Combining complementary markers therefore offers a more comprehensive representation of potato-associated microbial eukaryotic communities than single-marker approaches alone.},
	language = {en},
	number = {3},
	urldate = {2026-06-05},
	journal = {Plant-Environment Interactions},
	author = {Turco, Silvia and Giubilei, Irene and Mahawar, Lovely and Mazzaglia, Angelo and Albrectsen, Benedicte Riber},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pei3.70168},
	keywords = {ITS markers, Solanum tuberosum L., amplicon sequencing, metabarcoding, mycobiome},
	pages = {e70168},
}

Accurate profiling of plant-associated fungal and oomycete communities depends critically on the choice of ITS marker. Using Illumina sequencing for ITS1/ITS2 and PacBio HiFi sequencing for full-length ITS (ITSf), we compared read recovery, taxonomic assignment depth, and diversity patterns across potato leaf and root tissues. ITS2 generally recovered more diverse and even community profiles in leaves, whereas ITSf recovered comparatively more even and taxonomically broad profiles in roots. In contrast, ITS1 showed high read recovery but produced strongly skewed compositional profiles and was frequently dominated by host-derived sequences. Beta-diversity analyses indicated that ITS marker choice was associated with substantial variation in observed community composition, while functional annotation highlighted communities composed of taxa associated with multiple ecological guilds, including endophytes and opportunistic pathogens such as Cladosporium and Ilyonectria. Overall, the results demonstrate that ITS marker choice strongly influences the observed structure and diversity of plant-associated communities. ITS2 was generally more suitable for phyllosphere-associated communities, whereas ITSf provided broader recovery of root-associated taxa. Combining complementary markers therefore offers a more comprehensive representation of potato-associated microbial eukaryotic communities than single-marker approaches alone.

@article{moazzami_farida_dopamine_2026,
	title = {Dopamine modulates antioxidant and phenolic responses to alleviate nickel stress in {Salvia} officinalis},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-08365-5},
	doi = {10.1186/s12870-026-08365-5},
	abstract = {Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.},
	language = {en},
	number = {1},
	urldate = {2026-03-27},
	journal = {BMC Plant Biology},
	author = {Moazzami Farida, Seyed Hamed and Rahmani, Nosrat and Taghizadeh, Marzieh and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2026},
	keywords = {Antioxidant defense, Dopamine, Heavy metal, Nickel stress, Phenolic metabolism, Salvia officinalis l},
	pages = {491},
}

Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.

@article{mishra_plant_2026,
	title = {Plant growth-promoting {Pseudomonas} strains modulate potato tuberization signalling and development},
	volume = {77},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag237},
	doi = {10.1093/jxb/erag237},
	abstract = {Plant growth-promoting rhizobacteria (PGPR) can influence plant development through hormone signalling, nutrient mobilization, and activation of defence pathways. While individual bacterial strains can enhance plant performance, microbial consortia may generate complementary or synergistic effects that remain poorly understood, particularly with respect to crop developmental signalling. Potato (Solanum tuberosum), the most important dicot food crop globally, represents a suitable model for investigating how beneficial microbes influence tuber development. In this study, we investigated the effects of two well-characterized PGPR strains, Pseudomonas protegens CHA0 and P. simiae WCS417, applied individually or in combination, on two potato cultivars (‘Mandel’ and ‘Désirée’) under long-day conditions. Confocal microscopy confirmed rapid root colonization by both strains within 24 h of inoculation. Metabolomic profiling of bacterial exudates revealed distinct metabolic signatures for the two strains and non-additive metabolite patterns when cultured together, suggesting metabolic interactions within the bacterial consortium. Plant responses were cultivar dependent, with bacterial treatments influencing vegetative growth and selected tuber quality traits, including starch and ascorbic acid levels. Gene expression analyses revealed strong induction of the tuberization regulator StSP6A in roots, with up to 5-fold increased expression following P. protegens and combined inoculation, accompanied by activation of jasmonic acid-related signalling pathways. Together, these results indicate that interactions between beneficial Pseudomonas strains can influence potato development through coordinated effects on root architecture and signalling pathways associated with tuberization and defence.},
	number = {13},
	urldate = {2026-07-24},
	journal = {Journal of Experimental Botany},
	author = {Mishra, Arti and Mahawar, Lovely and Tsitouri, Angeliki and Basheer, Jasim and Albrectsen, Benedicte Riber},
	month = jul,
	year = {2026},
	pages = {4177--4194},
}

Plant growth-promoting rhizobacteria (PGPR) can influence plant development through hormone signalling, nutrient mobilization, and activation of defence pathways. While individual bacterial strains can enhance plant performance, microbial consortia may generate complementary or synergistic effects that remain poorly understood, particularly with respect to crop developmental signalling. Potato (Solanum tuberosum), the most important dicot food crop globally, represents a suitable model for investigating how beneficial microbes influence tuber development. In this study, we investigated the effects of two well-characterized PGPR strains, Pseudomonas protegens CHA0 and P. simiae WCS417, applied individually or in combination, on two potato cultivars (‘Mandel’ and ‘Désirée’) under long-day conditions. Confocal microscopy confirmed rapid root colonization by both strains within 24 h of inoculation. Metabolomic profiling of bacterial exudates revealed distinct metabolic signatures for the two strains and non-additive metabolite patterns when cultured together, suggesting metabolic interactions within the bacterial consortium. Plant responses were cultivar dependent, with bacterial treatments influencing vegetative growth and selected tuber quality traits, including starch and ascorbic acid levels. Gene expression analyses revealed strong induction of the tuberization regulator StSP6A in roots, with up to 5-fold increased expression following P. protegens and combined inoculation, accompanied by activation of jasmonic acid-related signalling pathways. Together, these results indicate that interactions between beneficial Pseudomonas strains can influence potato development through coordinated effects on root architecture and signalling pathways associated with tuberization and defence.

@article{mahawar_straw_2026,
	title = {Straw {Mulching} {Differentially} {Shapes} the {Structure} and {Function} of {Below}-{Ground} {Bacterial} {Communities} in {Potato} {Depending} on {eDNA} {Source} and {Cultivar}},
	volume = {7},
	copyright = {© 2026 The Author(s). Plant-Environment Interactions published by New Phytologist Foundation and John Wiley \& Sons Ltd.},
	issn = {2575-6265},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pei3.70131},
	doi = {10.1002/pei3.70131},
	abstract = {Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Plant-Environment Interactions},
	author = {Mahawar, Lovely and Mishra, Arti and Tsitouri, Angeliki and Albrectsen, Benedicte Riber},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pei3.70131},
	keywords = {bacterial communities, cv King Edward, cv Mandel, illumina amplicon sequencing, metabarcoding},
	pages = {e70131},
}

Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.

@article{ramanathan_effects_2026,
	title = {The {Effects} of {Acorn} {Origin}, {Environmental} {Microbiomes} and {Local} {Adaptation} on the {Leaf} {Metabolome}},
	volume = {52},
	issn = {1573-1561},
	url = {https://doi.org/10.1007/s10886-026-01692-9},
	doi = {10.1007/s10886-026-01692-9},
	abstract = {Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.},
	language = {en},
	number = {1},
	urldate = {2026-02-13},
	journal = {Journal of Chemical Ecology},
	author = {Ramanathan, Chandrasekar and Goris, Lisse and Mishra, Arti and Lihavainen-Bag, Jenna and Pawlowski, Katharina and Albrectsen, Benedicte Riber and Tack, Ayco J.M.},
	month = feb,
	year = {2026},
	keywords = {GC-MS, Local adaptation, Metabolomics, Microbiome, Plant-microbe interactions, Quercus robur},
	pages = {18},
}

Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.

@article{rydman_metabolomics_2025,
	title = {A {Metabolomics} and {Transcriptomics} {Resource} for {Identifying} {Candidate} {Genes} in the {Biosynthesis} of {Specialised} {Metabolites} in {Populus} tremula},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70567},
	doi = {10.1111/ppl.70567},
	abstract = {This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.},
	language = {en},
	number = {5},
	urldate = {2025-10-13},
	journal = {Physiologia Plantarum},
	author = {Rydman, Sara M. and Lihavainen, Jenna and Robinson, Kathryn M. and Jansson, Stefan and Albrectsen, Benedicte R. and Street, Nathaniel R.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70567},
	keywords = {Populus tremula, RNA-Seq, aspen, biosynthesis, chemotype, liquid chromatography–mass spectrometry (LC–MS), metabolomics, phenolic glycosides, salicinoid, specialised metabolite},
	pages = {e70567},
}

This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.

@article{sharma_microbial_2025,
	title = {Microbial contributions to plant growth and stress tolerance: {Mechanisms} for sustainable plant production},
	volume = {17},
	issn = {2667-064X},
	shorttitle = {Microbial contributions to plant growth and stress tolerance},
	url = {https://www.sciencedirect.com/science/article/pii/S2667064X25002349},
	doi = {10.1016/j.stress.2025.100966},
	abstract = {Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.},
	urldate = {2025-08-22},
	journal = {Plant Stress},
	author = {Sharma, Neha and Mahawar, Lovely and Mishra, Arti and Albrectsen, Benedicte Riber},
	month = sep,
	year = {2025},
	keywords = {Baseline soil microflora, PGPR, Plant Growth Promotion, Plant Stress Mitigation, Plant growth promotion, Plant stress mitigation, Rethinking agricultural Practices, Rethinking agricultural practices},
	pages = {100966},
}

Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.

@article{albrectsen_nordic_2025,
	title = {Nordic {Countries} as an {Opportunity} for {Sustainable}, {Low} {Pest} {Seed} {Potato} {Production} in a {Climate} {Change} {Scenario}},
	issn = {1871-4528},
	url = {https://doi.org/10.1007/s11540-025-09935-0},
	doi = {10.1007/s11540-025-09935-0},
	abstract = {Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.},
	language = {en},
	urldate = {2025-11-07},
	journal = {Potato Research},
	author = {Albrectsen, Benedicte Riber and Mäkinen, Kristiina and Mahawar, Lovely and Mishra, Arti and Abuley, Isaac Kwesi and Veillon, Isalyne and Gopan, Apsara Indhu and Sajeevan, Radha Sivarajan and Resjö, Svante and Andreasson, Erik and Liljeroth, Erland and Marhavý, Peter and Rossmann, Simeon Lim and Hansen, Jens Grønbech},
	month = oct,
	year = {2025},
	keywords = {Climate change adaptation, Food security strategy, Potato disease management, Seed potato production, Sustainable farming},
}

Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.

@article{mikko_sequencing_2025,
	title = {Sequencing airborne {DNA} to monitor crop pathogens and pests},
	volume = {28},
	issn = {2589-0042},
	url = {https://www.cell.com/iscience/abstract/S2589-0042(25)01173-3},
	doi = {10.1016/j.isci.2025.112912},
	language = {English},
	number = {7},
	urldate = {2025-07-25},
	journal = {iScience},
	publisher = {Elsevier},
	author = {Mikko, Amanda and Villegas, Jose Antonio and Svensson, Daniel and Karlsson, Edvin and Esseen, Per-Anders and Albrectsen, Benedicte Riber and Lundin, Ola and Forsman, Mats and Berlin, Anna and Stenberg, Per},
	month = jul,
	year = {2025},
	keywords = {Agricultural science, Airborne eDNA, Environmental biotechnology, Environmental monitoring, Genomics, Omics, metagenomics, non-targeted surveillance, pathogen surveillance, plant pathogens, plant pests},
}

@article{bekele_methane_2024,
	title = {Methane production from locally available ruminant feedstuffs in {Ethiopia} – {An} \textit{in vitro} study},
	volume = {312},
	issn = {0377-8401},
	url = {https://www.sciencedirect.com/science/article/pii/S0377840124001056},
	doi = {10.1016/j.anifeedsci.2024.115977},
	abstract = {Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P{\textless}0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6\%; indigenous plants 3.1–16.9\%; crop residues 15.8–20.6\%; agro-industrial by-products 12.8–18.7\%), and within category, e.g., Trifolium acaule (3.1\%), Acacia nilotica L. (7.1\%), Ziziphus spina-christi (9.9\%), brewer’s spent grains (BSG) (12.8\%), local liquor (areki) residues (14.1\%), and local beer (tella) residues (15.1\%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P{\textless}0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.},
	urldate = {2024-05-06},
	journal = {Animal Feed Science and Technology},
	author = {Bekele, Wondimagegne and Huhtanen, Pekka and Zegeye, Abiy and Simachew, Addis and Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ramin, Mohammad},
	month = jun,
	year = {2024},
	keywords = {CH, CH gas percentage, Local feeds, condensed tannins, dry matter digestibility},
	pages = {115977},
}

Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P\textless0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6%; indigenous plants 3.1–16.9%; crop residues 15.8–20.6%; agro-industrial by-products 12.8–18.7%), and within category, e.g., Trifolium acaule (3.1%), Acacia nilotica L. (7.1%), Ziziphus spina-christi (9.9%), brewer’s spent grains (BSG) (12.8%), local liquor (areki) residues (14.1%), and local beer (tella) residues (15.1%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P\textless0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.

@article{chowdhury_fluorogenic_2023,
	title = {Fluorogenic properties of 4-dimethylaminocinnamaldehyde ({DMACA}) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1060804},
	doi = {10.3389/fpls.2022.1060804},
	abstract = {Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.},
	urldate = {2023-02-10},
	journal = {Frontiers in Plant Science},
	author = {Chowdhury, Jamil and Ferdous, Jannatul and Lihavainen, Jenna and Albrectsen, Benedicte Riber and Lundberg-Felten, Judith},
	month = feb,
	year = {2023},
	keywords = {⛔ No DOI found},
}

Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.

@article{derba-maceluch_impact_2023,
	title = {Impact of xylan on field productivity and wood saccharification properties in aspen},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1218302},
	doi = {10.3389/fpls.2023.1218302},
	abstract = {Xylan that comprises roughly 25\% of hardwood biomass is undesirable in biorefinery applications involving saccharification and fermentation. Efforts to reduce xylan levels have therefore been made in many species, usually resulting in improved saccharification. However, such modified plants have not yet been tested under field conditions. Here we evaluate the field performance of transgenic hybrid aspen lines with reduced xylan levels and assess their usefulness as short-rotation feedstocks for biorefineries. Three types of transgenic lines were tested in four-year field tests with RNAi constructs targeting either Populus GT43 clades B and C (GT43BC) corresponding to Arabidopsis clades IRX9 and IRX14, respectively, involved in xylan backbone biosynthesis, GATL1.1 corresponding to AtGALT1 involved in xylan reducing end sequence biosynthesis, or ASPR1 encoding an atypical aspartate protease. Their productivity, wood quality traits, and saccharification efficiency were analyzed. The only lines differing significantly from the wild type with respect to growth and biotic stress resistance were the ASPR1 lines, whose stems were roughly 10\% shorter and narrower and leaves showed increased arthropod damage. GT43BC lines exhibited no growth advantage in the field despite their superior growth in greenhouse experiments. Wood from the ASPR1 and GT43BC lines had slightly reduced density due to thinner cell walls and, in the case of ASPR1, larger cell diameters. The xylan was less extractable by alkali but more hydrolysable by acid, had increased glucuronosylation, and its content was reduced in all three types of transgenic lines. The hemicellulose size distribution in the GALT1.1 and ASPR1 lines was skewed towards higher molecular mass compared to the wild type. These results provide experimental evidence that GATL1.1 functions in xylan biosynthesis and suggest that ASPR1 may regulate this process. In saccharification without pretreatment, lines of all three constructs provided 8-11\% higher average glucose yields than wild-type plants. In saccharification with acid pretreatment, the GT43BC construct provided a 10\% yield increase on average. The best transgenic lines of each construct are thus predicted to modestly outperform the wild type in terms of glucose yields per hectare. The field evaluation of transgenic xylan-reduced aspen represents an important step towards more productive feedstocks for biorefineries.},
	urldate = {2023-07-18},
	journal = {Frontiers in Plant Science},
	author = {Derba-Maceluch, Marta and Sivan, Pramod and Donev, Evgeniy N. and Gandla, Madhavi Latha and Yassin, Zakiya and Vaasan, Rakhesh and Heinonen, Emilia and Andersson, Sanna and Amini, Fariba and Scheepers, Gerhard and Johansson, Ulf and Vilaplana, Francisco J. and Albrectsen, Benedicte R. and Hertzberg, Magnus and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	year = {2023},
}

Xylan that comprises roughly 25% of hardwood biomass is undesirable in biorefinery applications involving saccharification and fermentation. Efforts to reduce xylan levels have therefore been made in many species, usually resulting in improved saccharification. However, such modified plants have not yet been tested under field conditions. Here we evaluate the field performance of transgenic hybrid aspen lines with reduced xylan levels and assess their usefulness as short-rotation feedstocks for biorefineries. Three types of transgenic lines were tested in four-year field tests with RNAi constructs targeting either Populus GT43 clades B and C (GT43BC) corresponding to Arabidopsis clades IRX9 and IRX14, respectively, involved in xylan backbone biosynthesis, GATL1.1 corresponding to AtGALT1 involved in xylan reducing end sequence biosynthesis, or ASPR1 encoding an atypical aspartate protease. Their productivity, wood quality traits, and saccharification efficiency were analyzed. The only lines differing significantly from the wild type with respect to growth and biotic stress resistance were the ASPR1 lines, whose stems were roughly 10% shorter and narrower and leaves showed increased arthropod damage. GT43BC lines exhibited no growth advantage in the field despite their superior growth in greenhouse experiments. Wood from the ASPR1 and GT43BC lines had slightly reduced density due to thinner cell walls and, in the case of ASPR1, larger cell diameters. The xylan was less extractable by alkali but more hydrolysable by acid, had increased glucuronosylation, and its content was reduced in all three types of transgenic lines. The hemicellulose size distribution in the GALT1.1 and ASPR1 lines was skewed towards higher molecular mass compared to the wild type. These results provide experimental evidence that GATL1.1 functions in xylan biosynthesis and suggest that ASPR1 may regulate this process. In saccharification without pretreatment, lines of all three constructs provided 8-11% higher average glucose yields than wild-type plants. In saccharification with acid pretreatment, the GT43BC construct provided a 10% yield increase on average. The best transgenic lines of each construct are thus predicted to modestly outperform the wild type in terms of glucose yields per hectare. The field evaluation of transgenic xylan-reduced aspen represents an important step towards more productive feedstocks for biorefineries.

@article{siddique_molecular_2023,
	title = {Molecular studies of rust on {European} aspen suggest an autochthonous relationship shaped by genotype},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1111001},
	doi = {10.3389/fpls.2023.1111001},
	abstract = {Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT).  At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances.  Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.},
	urldate = {2023-02-24},
	journal = {Frontiers in Plant Science},
	author = {Siddique, Abu Bakar and Menke, Laura and Dinedurga, Melis and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2023},
}

Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.

@article{witzell_aspen_2022,
	title = {Aspen {Leaves} as a “{Chemical} {Landscape}” for {Fungal} {Endophyte} {Diversity}—{Effects} of {Nitrogen} {Addition}},
	volume = {13},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.846208},
	doi = {10/gpq8cc},
	abstract = {Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.},
	urldate = {2022-03-22},
	journal = {Frontiers in Microbiology},
	author = {Witzell, Johanna and Decker, Vicki Huizu Guo and Agostinelli, Marta and Romeralo, Carmen and Cleary, Michelle and Albrectsen, Benedicte Riber},
	month = mar,
	year = {2022},
}

Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.

@article{gaur_compensatory_2022,
	title = {Compensatory phenolic induction dynamics in aspen after aphid infestation},
	volume = {12},
	copyright = {2022 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-022-13225-x},
	doi = {10.1038/s41598-022-13225-x},
	abstract = {Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.},
	language = {en},
	number = {1},
	urldate = {2022-06-13},
	journal = {Scientific Reports},
	author = {Gaur, Rajarshi Kumar and de Abreu, Ilka Nacif and Albrectsen, Benedicte Riber},
	month = jun,
	year = {2022},
	keywords = {Biochemistry, Plant sciences},
	pages = {9582},
}

Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.

@article{rodriguez_effects_2022,
	title = {Effects of condensed tannins on behavior and performance of a specialist aphid on aspen},
	volume = {12},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.9229},
	doi = {10.1002/ece3.9229},
	abstract = {Genes involved in plant defences against herbivores and pathogens are often highly polymorphic. This is a putative sign that balancing selection may have operated reciprocally on the hosts and their herbivores. Spatial and temporal variations (for example, in soil nutrients and the plants' ontogenetic development) may also modulate resistance traits, and thus selection pressures, but have been largely overlooked in theories of plant defences. Important elements of defences in Populus tremula (hereafter aspen) are phenolic compounds, including condensed tannins (CTs). Concentrations of CTs vary considerably with both variations in external factors and time, but they are also believed to provide genotype-dependent resistance, mainly against chewing herbivores and pathogens. However, evidence of their contributions to resistance is sparse. Detailed studies of co-evolved plant–herbivore associations could provide valuable insights into these contributions. Therefore, we examined correlations between CT levels in aspen leaves and both the feeding behavior and reproduction of the specialist aspen leaf aphid (Chaitophorus tremulae) in varied conditions. We found that xylem sap intake and probing difficulties were higher on genotypes with high-CT concentrations. However, aphids engaged in more nonprobing activities on low-CT genotypes, indicating that CTs were not the only defence traits involved. Thus, high-CT genotypes were not necessarily more resistant than low-CT genotypes, but aphid reproduction was generally negatively correlated with local CT accumulation. Genotype-specific resistance ranking also depended on the experimental conditions. These results support the hypothesis that growth conditions may affect selection pressures mediated by aphids in accordance with balancing selection theory.},
	language = {en},
	number = {8},
	urldate = {2022-09-01},
	journal = {Ecology and Evolution},
	author = {Rodríguez, Bárbara Díez and Kloth, Karen J. and Albrectsen, Benedicte Riber},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.9229},
	keywords = {Chaitophorus tremulae, Populus tremula, condensed tannins, electric penetration graph (EPG), xylem feeding},
	pages = {e9229},
}

Genes involved in plant defences against herbivores and pathogens are often highly polymorphic. This is a putative sign that balancing selection may have operated reciprocally on the hosts and their herbivores. Spatial and temporal variations (for example, in soil nutrients and the plants' ontogenetic development) may also modulate resistance traits, and thus selection pressures, but have been largely overlooked in theories of plant defences. Important elements of defences in Populus tremula (hereafter aspen) are phenolic compounds, including condensed tannins (CTs). Concentrations of CTs vary considerably with both variations in external factors and time, but they are also believed to provide genotype-dependent resistance, mainly against chewing herbivores and pathogens. However, evidence of their contributions to resistance is sparse. Detailed studies of co-evolved plant–herbivore associations could provide valuable insights into these contributions. Therefore, we examined correlations between CT levels in aspen leaves and both the feeding behavior and reproduction of the specialist aspen leaf aphid (Chaitophorus tremulae) in varied conditions. We found that xylem sap intake and probing difficulties were higher on genotypes with high-CT concentrations. However, aphids engaged in more nonprobing activities on low-CT genotypes, indicating that CTs were not the only defence traits involved. Thus, high-CT genotypes were not necessarily more resistant than low-CT genotypes, but aphid reproduction was generally negatively correlated with local CT accumulation. Genotype-specific resistance ranking also depended on the experimental conditions. These results support the hypothesis that growth conditions may affect selection pressures mediated by aphids in accordance with balancing selection theory.

@article{siddique_optimization_2022,
	title = {Optimization of {Protocol} for {Construction} of {Fungal} {ITS} {Amplicon} {Library} for {High}-{Throughput} {Illumina} {Sequencing} to {Study} the {Mycobiome} of {Aspen} {Leaves}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2076-3417},
	url = {https://www.mdpi.com/2076-3417/12/3/1136},
	doi = {10.3390/app12031136},
	abstract = {High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/\µL to 1526 ng/\µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63\–2.04 and 0.26\–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.},
	language = {en},
	number = {3},
	urldate = {2022-01-24},
	journal = {Applied Sciences},
	author = {Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ilbi, Hulya and Siddique, Abu Bakar},
	month = jan,
	year = {2022},
	keywords = {ITS, NGS, amplicon, aspen, eDNA, endophytes, metabarcoding, metagenomics, rDNA},
	pages = {1136},
}

High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.

@article{van_dijk_single_2022,
	title = {Single, but not dual, attack by a biotrophic pathogen and a sap-sucking insect affects the oak leaf metabolome},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.897186},
	abstract = {Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.},
	urldate = {2022-08-12},
	journal = {Frontiers in Plant Science},
	author = {van Dijk, Laura J. A. and Regazzoni, Emilia D. E. and Albrectsen, Benedicte R. and Ehrlén, Johan and Abdelfattah, Ahmed and Stenlund, Hans and Pawlowski, Katharina and Tack, Ayco J. M.},
	month = aug,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.

@article{biniaz_transcriptome_2022,
	title = {Transcriptome {Meta}-{Analysis} {Identifies} {Candidate} {Hub} {Genes} and {Pathways} of {Pathogen} {Stress} {Responses} in {Arabidopsis} thaliana},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-7737},
	url = {https://www.mdpi.com/2079-7737/11/8/1155},
	doi = {10.3390/biology11081155},
	abstract = {Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.},
	language = {en},
	number = {8},
	urldate = {2022-08-02},
	journal = {Biology},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Biniaz, Yaser and Tahmasebi, Ahmad and Tahmasebi, Aminallah and Albrectsen, Benedicte Riber and Poczai, Péter and Afsharifar, Alireza},
	month = aug,
	year = {2022},
	note = {Number: 8},
	keywords = {\textit{Arabidopsis thaliana}, biotic stress, plant–pathogen interaction, transcriptome data},
	pages = {1155},
}

Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.

@article{bandau_european_2021,
	title = {European aspen with high compared to low constitutive tannin defenses grow taller in response to anthropogenic nitrogen enrichment},
	volume = {487},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112721000748},
	doi = {10/gjd7k2},
	language = {en},
	urldate = {2021-06-03},
	journal = {Forest Ecology and Management},
	author = {Bandau, Franziska and Albrectsen, Benedicte Riber and Robinson, Kathryn M. and Gundale, Michael J.},
	month = may,
	year = {2021},
	pages = {118985},
}

@article{siddique_mycobiomes_2021,
	title = {Mycobiomes of {Young} {Beech} {Trees} {Are} {Distinguished} by {Organ} {Rather} {Than} by {Habitat}, and {Community} {Analyses} {Suggest} {Competitive} {Interactions} {Among} {Twig} {Fungi}},
	volume = {12},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.646302/full},
	doi = {10/gjrpd2},
	abstract = {Beech trees (
              Fagus sylvatica
              ) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52\%) and Basidiomycota (26\%) taxa. Significant correlations between richness and diversity indices were observed (
              p
              \< 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.},
	urldate = {2021-06-03},
	journal = {Frontiers in Microbiology},
	author = {Siddique, Abu Bakar and Biella, Paolo and Unterseher, Martin and Albrectsen, Benedicte Riber},
	month = apr,
	year = {2021},
	pages = {646302},
}

Beech trees ( Fagus sylvatica ) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52%) and Basidiomycota (26%) taxa. Significant correlations between richness and diversity indices were observed ( p < 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.

@article{raizada_recursive_2021,
	title = {Recursive partitioning to prioritize morphometric traits that separate {Aspen} specialist {Chaitophorus} aphid by species and stage},
	issn = {1742-7592},
	url = {https://doi.org/10.1007/s42690-021-00620-6},
	doi = {10/gmtzbt},
	abstract = {Arthropod herbivore assemblages are used to gain insight into questions about evolution, ecology, diversity, and conservation. However, determination at the species level of small arthropods may be challenging risking underestimating diversity. Here we suggest morphometric analyses as a supplementary determination method, and we demonstrate its use for a study of Chaitophorus species collected from Aspen trees (Populus tremula). Although sampled as one colony, the aphids represented three species. Rearing the species separately allowed us to get estimates characteristic of the developmental stages from each of the three species for morphometric comparisons. Recursive partitioning (RP) was used to create a decision tree for choice of morphometric parameters that with significance (p {\textless} 0.05) could determine the aphids by species and developmental stage; this insight could then be used as a key for determination. Eight of fifteen morphometric traits were selected by RP to be used in the key. Body length was responsible for nine splits and was consequently the more consistent morphometric trait used in the key.},
	language = {en},
	urldate = {2021-09-09},
	journal = {International Journal of Tropical Insect Science},
	author = {Raizada, Richa and Gaur, Rajarshi Kumar and Albrectsen, Benedicte R.},
	month = aug,
	year = {2021},
}

Arthropod herbivore assemblages are used to gain insight into questions about evolution, ecology, diversity, and conservation. However, determination at the species level of small arthropods may be challenging risking underestimating diversity. Here we suggest morphometric analyses as a supplementary determination method, and we demonstrate its use for a study of Chaitophorus species collected from Aspen trees (Populus tremula). Although sampled as one colony, the aphids represented three species. Rearing the species separately allowed us to get estimates characteristic of the developmental stages from each of the three species for morphometric comparisons. Recursive partitioning (RP) was used to create a decision tree for choice of morphometric parameters that with significance (p \textless 0.05) could determine the aphids by species and developmental stage; this insight could then be used as a key for determination. Eight of fifteen morphometric traits were selected by RP to be used in the key. Body length was responsible for nine splits and was consequently the more consistent morphometric trait used in the key.

@article{kloth_sli1_2021,
	title = {{SLI1} confers broad‐spectrum resistance to phloem‐feeding insects},
	issn = {0140-7791, 1365-3040},
	shorttitle = {{\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/pce.14064},
	doi = {10/gjzng9},
	language = {en},
	urldate = {2021-06-03},
	journal = {Plant, Cell \& Environment},
	author = {Kloth, Karen J. and Shah, Parth and Broekgaarden, Colette and Ström, Cecilia and Albrectsen, Benedicte R. and Dicke, Marcel},
	month = may,
	year = {2021},
	pages = {pce.14064},
}

@article{rogers_global_2020,
	title = {A global view of aspen: {Conservation} science for widespread keystone systems},
	volume = {21},
	issn = {23519894},
	shorttitle = {A global view of aspen},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2351989419305803},
	doi = {10.1016/j.gecco.2019.e00828},
	language = {en},
	urldate = {2021-06-07},
	journal = {Global Ecology and Conservation},
	author = {Rogers, Paul C. and Pinno, Bradley D. and Šebesta, Jan and Albrectsen, Benedicte R. and Li, Guoqing and Ivanova, Natalya and Kusbach, Antonín and Kuuluvainen, Timo and Landhäusser, Simon M. and Liu, Hongyan and Myking, Tor and Pulkkinen, Pertti and Wen, Zhongming and Kulakowski, Dominik},
	month = mar,
	year = {2020},
	pages = {e00828},
}

@article{derba-maceluch_cell_2020,
	title = {Cell {Wall} {Acetylation} in {Hybrid} {Aspen} {Affects} {Field} {Performance}, {Foliar} {Phenolic} {Composition} and {Resistance} to {Biological} {Stress} {Factors} in a {Construct}-{Dependent} {Fashion}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00651/full},
	doi = {10.3389/fpls.2020.00651},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Derba-Maceluch, Marta and Amini, Fariba and Donev, Evgeniy N. and Pawar, Prashant Mohan-Anupama and Michaud, Lisa and Johansson, Ulf and Albrectsen, Benedicte R. and Mellerowicz, Ewa J.},
	month = may,
	year = {2020},
	pages = {651},
}

@article{moazzami_farida_silver_2020,
	title = {Silver nanoparticle pollutants activate oxidative stress responses and rosmarinic acid accumulation in sage},
	volume = {170},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13172},
	doi = {10.1111/ppl.13172},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Moazzami Farida, Seyed Hamed and Karamian, Roya and Albrectsen, Benedicte R},
	month = nov,
	year = {2020},
	pages = {415--432},
}

@article{pozo_three-way_2020,
	title = {Three-way {Interactions} between {Plants}, {Microbes}, and {Arthropods} ({PMA}): {Impacts}, {Mechanisms}, and {Prospects} for {Sustainable} {Plant} {Protection}},
	volume = {32},
	issn = {1040-4651, 1532-298X},
	shorttitle = {Three-way {Interactions} between {Plants}, {Microbes}, and {Arthropods} ({PMA})},
	url = {https://academic.oup.com/plcell/article/doi/10.1105/tpc.120.tt0720/6115734},
	doi = {10.1105/tpc.120.tt0720},
	abstract = {Three-way Interactions between Plants, Microbes, and Arthropods (PMA): Impacts, Mechanisms, and Prospects for Sustainable Plant Protection (By Maria J. Pozo, Benedicte R. Albrectsen, Eduardo R. Bejarano, Eduardo de la Peña, Salva Herrero, Ainhoa Martinez-Medina, Victoria Pastor, Sabine Ravnskov, Mary Williams and Arjen Biere)
            Plants constantly interact with numerous of organisms and the outcome of these interactions determines plant health and growth. In other words, the phenotype of a plant is not only the result of the plant’s interaction with abiotic conditions, but also of multiple interactions in the living environment surrounding the plant, the phytobiome. In this Teaching Tool, we have focused on interactions between plants, microbes and arthropods (PMA). The organism groups that contribute to PMA interactions are presented as well as types of interactions between them, along with multiple examples of simple and more complex PMA interactions. The underlying mechanisms of plant responses are described in detail as well as the evolutionary aspects of PMA interactions. Finally, the use of PMA interactions for crop protection in sustainable plant production that supports the UN Sustainable Development Goals for 2030 is proposed.
            (Posted July 6, 2020)
            Click HERE to access Teaching Tool Components
            RECOMMENDED CITATION STYLE:
            Pozo, M.J., Albrectsen, B.R., Bejarano, E.R., de la Peña, E., Herrero, S., Martinez-Medina, A., Pastor, V., Ravnskov, S., Williams, M., and Biere, A. (July NN, 2020). Three-way interactions between plants, microbes, and arthropods (PMA): Impacts, mechanisms, and prospects for sustainable plant protection. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/10.1105/tpc.120.tt0720},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Pozo, M. J. and Albrectsen, B. R. and Bejarano, E. and de la Pena, E. and Herrero, S. and Martinez-Medina, A. and Pastor, V. and Ravnskov, S. and Biere, A.},
	month = jul,
	year = {2020},
	pages = {tpc.120.tt0720},
}

Three-way Interactions between Plants, Microbes, and Arthropods (PMA): Impacts, Mechanisms, and Prospects for Sustainable Plant Protection (By Maria J. Pozo, Benedicte R. Albrectsen, Eduardo R. Bejarano, Eduardo de la Peña, Salva Herrero, Ainhoa Martinez-Medina, Victoria Pastor, Sabine Ravnskov, Mary Williams and Arjen Biere) Plants constantly interact with numerous of organisms and the outcome of these interactions determines plant health and growth. In other words, the phenotype of a plant is not only the result of the plant’s interaction with abiotic conditions, but also of multiple interactions in the living environment surrounding the plant, the phytobiome. In this Teaching Tool, we have focused on interactions between plants, microbes and arthropods (PMA). The organism groups that contribute to PMA interactions are presented as well as types of interactions between them, along with multiple examples of simple and more complex PMA interactions. The underlying mechanisms of plant responses are described in detail as well as the evolutionary aspects of PMA interactions. Finally, the use of PMA interactions for crop protection in sustainable plant production that supports the UN Sustainable Development Goals for 2030 is proposed. (Posted July 6, 2020) Click HERE to access Teaching Tool Components RECOMMENDED CITATION STYLE: Pozo, M.J., Albrectsen, B.R., Bejarano, E.R., de la Peña, E., Herrero, S., Martinez-Medina, A., Pastor, V., Ravnskov, S., Williams, M., and Biere, A. (July NN, 2020). Three-way interactions between plants, microbes, and arthropods (PMA): Impacts, mechanisms, and prospects for sustainable plant protection. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/10.1105/tpc.120.tt0720

@article{westman_defence_2019,
	title = {Defence priming in {Arabidopsis} – a {Meta}-{Analysis}},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-49811-9},
	doi = {10/gh92kh},
	abstract = {Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	publisher = {Nature Publishing Group},
	author = {Westman, Sara M. and Kloth, Karen J. and Hanson, Johannes and Ohlsson, Anna B. and Albrectsen, Benedicte R.},
	month = sep,
	year = {2019},
	note = {Number: 1},
	pages = {13309},
}

Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.

@article{papazian_leaf_2019,
	title = {Leaf metabolic signatures induced by real and simulated herbivory in black mustard ({Brassica} nigra)},
	volume = {15},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-019-1592-4},
	doi = {10.1007/s11306-019-1592-4},
	abstract = {Abstract
            
              Introduction
              The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response.
            
            
              Objectives
              
                We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant
                Brassica nigra
                and monitored the herbivore-induced responses in relation to leaf ontogeny.
              
            
            
              Methods
              As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites.
            
            
              Results
              Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance.
            
            
              Conclusions
              The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Papazian, Stefano and Girdwood, Tristan and Wessels, Bernard A. and Poelman, Erik H. and Dicke, Marcel and Moritz, Thomas and Albrectsen, Benedicte R.},
	month = oct,
	year = {2019},
	pages = {130},
}

Abstract Introduction The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response. Objectives We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant Brassica nigra and monitored the herbivore-induced responses in relation to leaf ontogeny. Methods As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites. Results Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance. Conclusions The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.

@article{kloth_pectin_2019,
	title = {{PECTIN} {ACETYLESTERASE9} {Affects} the {Transcriptome} and {Metabolome} and {Delays} {Aphid} {Feeding}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/4/1704-1720/6000543},
	doi = {10.1104/pp.19.00635},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Kloth, Karen J. and Abreu, Ilka N. and Delhomme, Nicolas and Petřík, Ivan and Villard, Cloé and Ström, Cecilia and Amini, Fariba and Novák, Ondřej and Moritz, Thomas and Albrectsen, Benedicte R.},
	month = dec,
	year = {2019},
	pages = {1704--1720},
}

@article{albrectsen_both_2018,
	title = {Both plant genotype and herbivory shape aspen endophyte communities},
	volume = {187},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-018-4097-3},
	doi = {10/gdrvmw},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Oecologia},
	author = {Albrectsen, Benedicte Riber and Siddique, Abu Bakar and Decker, Vicki Huizu Guo and Unterseher, Martin and Robinson, Kathryn M.},
	month = jun,
	year = {2018},
	pages = {535--545},
}

@article{randriamanana_does_2018,
	title = {Does fungal endophyte inoculation affect the responses of aspen seedlings to carbon dioxide enrichment?},
	volume = {33},
	issn = {17545048},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1754504817301861},
	doi = {10/gdkfq9},
	language = {en},
	urldate = {2021-06-07},
	journal = {Fungal Ecology},
	author = {Randriamanana, Tendry R. and Nissinen, Katri and Ovaskainen, Anu and Lavola, Anu and Peltola, Heli and Albrectsen, Benedicte and Julkunen-Tiitto, Riitta},
	month = jun,
	year = {2018},
	pages = {24--31},
}

@article{agostinelli_pedunculate_2018,
	title = {Pedunculate {Oaks} ({Quercus} robur {L}.) {Differing} in {Vitality} as {Reservoirs} for {Fungal} {Biodiversity}},
	volume = {9},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.01758/full},
	doi = {10/gd4djv},
	urldate = {2021-06-07},
	journal = {Frontiers in Microbiology},
	author = {Agostinelli, Marta and Cleary, Michelle and Martín, Juan A. and Albrectsen, Benedicte R. and Witzell, Johanna},
	month = aug,
	year = {2018},
	pages = {1758},
}

@article{ponzio_dual_2017,
	title = {Dual herbivore attack and herbivore density affect metabolic profiles of \textit{{Brassica} nigra} leaves: {Plant} metabolome during dual insect attack},
	volume = {40},
	issn = {01407791},
	shorttitle = {Dual herbivore attack and herbivore density affect metabolic profiles of \textit{{Brassica} nigra} leaves},
	url = {http://doi.wiley.com/10.1111/pce.12926},
	doi = {10.1111/pce.12926},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Ponzio, Camille and Papazian, Stefano and Albrectsen, Benedicte R. and Dicke, Marcel and Gols, Rieta},
	month = aug,
	year = {2017},
	pages = {1356--1367},
}

@article{bandau_genotypic_2017,
	title = {Genotypic variability in {Populus} tremula {L}. affects how anthropogenic nitrogen enrichment influences litter decomposition},
	volume = {410},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-016-3033-8},
	doi = {10/f9n2mz},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Bandau, Franziska and Albrectsen, Benedicte Riber and Julkunen-Tiitto, Riitta and Gundale, Michael J.},
	month = jan,
	year = {2017},
	pages = {467--481},
}

@article{kloth_sieve_2017,
	title = {{SIEVE} {ELEMENT}-{LINING} {CHAPERONE1} {Restricts} {Aphid} {Feeding} on {Arabidopsis} during {Heat} {Stress}},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/29/10/2450-2464/6100440},
	doi = {10/gckrdb},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Kloth, Karen J. and Busscher-Lange, Jacqueline and Wiegers, Gerrie L. and Kruijer, Willem and Buijs, Gonda and Meyer, Rhonda C. and Albrectsen, Benedicte R. and Bouwmeester, Harro J. and Dicke, Marcel and Jongsma, Maarten A.},
	month = oct,
	year = {2017},
	pages = {2450--2464},
}

@article{decker_aspen_2016,
	title = {Aspen phenylpropanoid genes’ expression levels correlate with genets’ tannin richness and vary both in responses to soil nitrogen and associations with phenolic profiles},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpw118},
	doi = {10.1093/treephys/tpw118},
	language = {en},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Decker, Vicki H.G. and Bandau, Franziska and Gundale, Michael J. and Cole, Christopher T. and Albrectsen, Benedicte R.},
	editor = {Tsai, Chung-Jui},
	month = dec,
	year = {2016},
	pages = {treephys;tpw118v1},
}

@article{papazian_central_2016,
	title = {Central {Metabolic} {Responses} to {Ozone} and {Herbivory} {Affect} {Photosynthesis} and {Stomatal} {Closure}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/3/2057-2078/6115987},
	doi = {10/f3vft5},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Papazian, Stefano and Khaling, Eliezer and Bonnet, Christelle and Lassueur, Steve and Reymond, Philippe and Moritz, Thomas and Blande, James D. and Albrectsen, Benedicte R.},
	month = nov,
	year = {2016},
	pages = {2057--2078},
}

@article{soolanayakanahally_comparative_2015,
	title = {Comparative physiology of allopatric {Populus} species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	shorttitle = {Comparative physiology of allopatric {Populus} species},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26236324},
	doi = {10.3389/fpls.2015.00528},
	abstract = {Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.},
	language = {English},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Soolanayakanahally, R. Y. and Guy, R. D. and Street, N. R. and Robinson, K. M. and Silim, S. N. and Albrectsen, B. R. and Jansson, S.},
	year = {2015},
	note = {Edition: 2015/08/04},
	keywords = {Photosynthesis, bud set, carbon isotope discrimination, common garden, comparative physiology, latitude, photosynthesis, poplar, water-use efficiency},
	pages = {528},
}

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.

@article{bandau_genotypic_2015,
	title = {Genotypic {Tannin} {Levels} in {Populus} tremula {Impact} the {Way} {Nitrogen} {Enrichment} {Affects} {Growth} and {Allocation} {Responses} for {Some} {Traits} and {Not} for {Others}},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26488414},
	doi = {10.1371/journal.pone.0140971},
	abstract = {Plant intraspecific variability has been proposed as a key mechanism by which plants adapt to environmental change. In boreal forests where nitrogen availability is strongly limited, nitrogen addition happens indirectly through atmospheric N deposition and directly through industrial forest fertilization. These anthropogenic inputs of N have numerous environmental consequences, including shifts in plant species composition and reductions in plant species diversity. However, we know less about how genetic differences within plant populations determine how species respond to eutrophication in boreal forests. According to plant defense theories, nitrogen addition will cause plants to shift carbon allocation more towards growth and less to chemical defense, potentially enhancing vulnerability to antagonists. Aspens are keystone species in boreal forests that produce condensed tannins to serve as chemical defense. We conducted an experiment using ten Populus tremula genotypes from the Swedish Aspen Collection that express extreme levels of baseline investment into foliar condensed tannins. We investigated whether investment into growth and phenolic defense compounds in young plants varied in response to two nitrogen addition levels, corresponding to atmospheric N deposition and industrial forest fertilization. Nitrogen addition generally caused growth to increase, and tannin levels to decrease; however, individualistic responses among genotypes were found for height growth, biomass of specific tissues, root:shoot ratios, and tissue lignin and N concentrations. A genotype's baseline ability to produce and store condensed tannins also influenced plant responses to N, although this effect was relatively minor. High-tannin genotypes tended to grow less biomass under low nitrogen levels and more at the highest fertilization level. Thus, the ability in aspen to produce foliar tannins is likely associated with a steeper reaction norm of growth responses, which suggests a higher plasticity to nitrogen addition, and potentially an advantage when adapting to higher concentrations of soil nitrogen.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Bandau, F. and Decker, V. H. and Gundale, M. J. and Albrectsen, B. R.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/10/22},
	keywords = {Adaptation, Physiological/*genetics, Biomass, Eutrophication/*physiology, Forests, Nitrogen/*metabolism, Photosynthesis/physiology, Plant Leaves/chemistry, Plant Roots/chemistry, Plant Shoots/chemistry, Populus/genetics/*growth \& development/metabolism, Soil/chemistry, Tannins/genetics/*metabolism},
	pages = {e0140971},
}

Plant intraspecific variability has been proposed as a key mechanism by which plants adapt to environmental change. In boreal forests where nitrogen availability is strongly limited, nitrogen addition happens indirectly through atmospheric N deposition and directly through industrial forest fertilization. These anthropogenic inputs of N have numerous environmental consequences, including shifts in plant species composition and reductions in plant species diversity. However, we know less about how genetic differences within plant populations determine how species respond to eutrophication in boreal forests. According to plant defense theories, nitrogen addition will cause plants to shift carbon allocation more towards growth and less to chemical defense, potentially enhancing vulnerability to antagonists. Aspens are keystone species in boreal forests that produce condensed tannins to serve as chemical defense. We conducted an experiment using ten Populus tremula genotypes from the Swedish Aspen Collection that express extreme levels of baseline investment into foliar condensed tannins. We investigated whether investment into growth and phenolic defense compounds in young plants varied in response to two nitrogen addition levels, corresponding to atmospheric N deposition and industrial forest fertilization. Nitrogen addition generally caused growth to increase, and tannin levels to decrease; however, individualistic responses among genotypes were found for height growth, biomass of specific tissues, root:shoot ratios, and tissue lignin and N concentrations. A genotype's baseline ability to produce and store condensed tannins also influenced plant responses to N, although this effect was relatively minor. High-tannin genotypes tended to grow less biomass under low nitrogen levels and more at the highest fertilization level. Thus, the ability in aspen to produce foliar tannins is likely associated with a steeper reaction norm of growth responses, which suggests a higher plasticity to nitrogen addition, and potentially an advantage when adapting to higher concentrations of soil nitrogen.

@article{blumenstein_nutritional_2015,
	title = {Nutritional niche overlap potentiates the use of endophytes in biocontrol of a tree disease},
	volume = {60},
	issn = {1386-6141},
	url = {://WOS:000360999800007},
	doi = {10.1007/s10526-015-9668-1},
	abstract = {Asymptomatic endophytic fungi are often regarded as potent biocontrol agents in plants, but the competitive interactions between endophytes and other microbes within the same host plant are poorly understood. We tested a hypothesis that as compared to asymptomatic endophytes, an aggressive pathogen inhabiting the same host is able to utilize carbon substrates more efficiently. Using phenotype microarray, we determined the carbon utilization profiles of the highly virulent Dutch elm disease (DED) pathogen Ophiostoma novo-ulmi, and four asymptomatic elm (Ulmus spp.) endophyte isolates that were selected based on their differential association to the DED-susceptibility pattern of the host elms. The competitive interactions between isolates were evaluated using a niche overlap index. In contrast to our hypothesis, the studied endophytes exhibited extensive niche overlap with the pathogen, suggesting that some endophyte strains might protect elms against DED-pathogen through competition for substrates and provide new tools for biocontrol of DED.},
	language = {English},
	number = {5},
	urldate = {2021-06-07},
	journal = {Biocontrol},
	author = {Blumenstein, K. and Albrectsen, B. R. and Martin, J. A. and Hultberg, M. and Sieber, T. N. and Helander, M. and Witzell, J.},
	month = oct,
	year = {2015},
	keywords = {aureobasidium-pullulans, biocontrol, biological-control, carbon utilization profile, competition, dutch elm disease, endophytic fungi, fungal endophytes, growth, niche differentiation hypothesis, niche tradeoff, ophiostoma-ulmi, populations, resistance, virulence},
	pages = {655--667},
}

Asymptomatic endophytic fungi are often regarded as potent biocontrol agents in plants, but the competitive interactions between endophytes and other microbes within the same host plant are poorly understood. We tested a hypothesis that as compared to asymptomatic endophytes, an aggressive pathogen inhabiting the same host is able to utilize carbon substrates more efficiently. Using phenotype microarray, we determined the carbon utilization profiles of the highly virulent Dutch elm disease (DED) pathogen Ophiostoma novo-ulmi, and four asymptomatic elm (Ulmus spp.) endophyte isolates that were selected based on their differential association to the DED-susceptibility pattern of the host elms. The competitive interactions between isolates were evaluated using a niche overlap index. In contrast to our hypothesis, the studied endophytes exhibited extensive niche overlap with the pathogen, suggesting that some endophyte strains might protect elms against DED-pathogen through competition for substrates and provide new tools for biocontrol of DED.

@article{khaling_ozone_2015,
	title = {Ozone affects growth and development of {Pieris} brassicae on the wild host plant {Brassica} nigra},
	volume = {199},
	issn = {1873-6424 (Electronic) 0269-7491 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25645061},
	doi = {10/f3n6fn},
	abstract = {When plants are exposed to ozone they exhibit changes in both primary and secondary metabolism, which may affect their interactions with herbivorous insects. Here we investigated the performance and preferences of the specialist herbivore Pieris brassicae on the wild plant Brassica nigra under elevated ozone conditions. The direct and indirect effects of ozone on the plant-herbivore system were studied. In both cases ozone exposure had a negative effect on P. brassicae development. However, in dual-choice tests larvae preferentially consumed plant material previously fumigated with the highest concentration tested, showing a lack of correlation between larval preference and performance on ozone exposed plants. Metabolomic analysis of leaf material subjected to combinations of ozone and herbivore-feeding, and focussing on known defence metabolites, indicated that P. brassicae behaviour and performance were associated with ozone-induced alterations to glucosinolate and phenolic pools.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environ Pollut},
	author = {Khaling, E. and Papazian, S. and Poelman, E. H. and Holopainen, J. K. and Albrectsen, B. R. and Blande, J. D.},
	month = apr,
	year = {2015},
	note = {Edition: 2015/02/04},
	keywords = {Air Pollutants/*toxicity, Animals, Brassica nigra, Brassica/drug effects/metabolism, Butterflies/growth \& development/*physiology, Defence compounds, Glucosinolates, Glucosinolates/metabolism, Growth and performance, Herbivory, Larva/growth \& development, Mustard Plant, Ozone exposure, Ozone/*toxicity, Phenolics, Pieris brassicae, Plant Leaves/chemistry/drug effects, Stress, Physiological},
	pages = {119--29},
}

When plants are exposed to ozone they exhibit changes in both primary and secondary metabolism, which may affect their interactions with herbivorous insects. Here we investigated the performance and preferences of the specialist herbivore Pieris brassicae on the wild plant Brassica nigra under elevated ozone conditions. The direct and indirect effects of ozone on the plant-herbivore system were studied. In both cases ozone exposure had a negative effect on P. brassicae development. However, in dual-choice tests larvae preferentially consumed plant material previously fumigated with the highest concentration tested, showing a lack of correlation between larval preference and performance on ozone exposed plants. Metabolomic analysis of leaf material subjected to combinations of ozone and herbivore-feeding, and focussing on known defence metabolites, indicated that P. brassicae behaviour and performance were associated with ozone-induced alterations to glucosinolate and phenolic pools.

@article{blumenstein_phenotype_2015,
	title = {Phenotype {MicroArrays} as a complementary tool to next generation sequencing for characterization of tree endophytes},
	volume = {6},
	issn = {1664-302X (Print) 1664-302X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26441951},
	doi = {10/f3m9xw},
	abstract = {There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.},
	urldate = {2021-06-07},
	journal = {Front Microbiol},
	author = {Blumenstein, K. and Macaya-Sanz, D. and Martin, J. A. and Albrectsen, B. R. and Witzell, J.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/10/07},
	keywords = {Biolog PM, fungal phenotype, fungus-fungus interactions, nutrient utilization, phenolic compounds},
	pages = {1033},
}

There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.

@article{robinson_relative_2015,
	title = {Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks},
	volume = {5},
	issn = {2045-7758 (Print) 2045-7758 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26306175},
	doi = {10/f3nt2b},
	abstract = {Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant-herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen-herbivore bipartite networks, the role of environmental variations is a dominant constraint.},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Ecol Evol},
	author = {Robinson, K. M. and Hauzy, C. and Loeuille, N. and Albrectsen, B. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/08/26},
	keywords = {Antagonism, arthropod, aspen, bipartite networks, degree of specialization, modularity, nestedness, trophic strength},
	pages = {2898--915},
}

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant-herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen-herbivore bipartite networks, the role of environmental variations is a dominant constraint.

@article{keefover-ring_2-z-cinnamoylsalicortin_2014,
	title = {2′-({Z})-{Cinnamoylsalicortin}: {A} novel salicinoid isolated from {Populus} tremula},
	volume = {7},
	issn = {18743900},
	shorttitle = {2′-({Z})-{Cinnamoylsalicortin}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874390013002085},
	doi = {10/f22wct},
	language = {en},
	urldate = {2021-06-08},
	journal = {Phytochemistry Letters},
	author = {Keefover-Ring, Ken and Carlsson, Marcus and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2014},
	pages = {212--216},
}

@article{keefover-ring_no_2014,
	title = {No {Evidence} of {Geographical} {Structure} of {Salicinoid} {Chemotypes} within {Populus} {Tremula}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0107189},
	doi = {10/f25fhm},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Keefover-Ring, Ken and Ahnlund, Maria and Abreu, Ilka Nacif and Jansson, Stefan and Moritz, Thomas and Albrectsen, Benedicte Riber},
	editor = {Yin, Tongming},
	month = oct,
	year = {2014},
	pages = {e107189},
}

@article{robinson_populus_2014,
	title = {Populus tremula ({European} aspen) shows no evidence of sexual dimorphism},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0276-5},
	doi = {10/f25brv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Robinson, Kathryn M and Delhomme, Nicolas and Mähler, Niklas and Schiffthaler, Bastian and Önskog, Jenny and Albrectsen, Benedicte R and Ingvarsson, Pär K and Hvidsten, Torgeir R and Jansson, Stefan and Street, Nathaniel R},
	month = dec,
	year = {2014},
	pages = {276},
}

@article{bernhardsson_geographic_2013,
	title = {Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes},
	volume = {16},
	issn = {1461023X},
	url = {http://doi.wiley.com/10.1111/ele.12114},
	doi = {10/f25rz6},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Ecology Letters},
	author = {Bernhardsson, Carolina and Robinson, Kathryn M. and Abreu, Ilka N. and Jansson, Stefan and Albrectsen, Benedicte R. and Ingvarsson, Pär K.},
	editor = {Eubanks, Micky},
	month = jun,
	year = {2013},
	pages = {791--798},
}

@article{orians_how_2013,
	title = {How slug herbivory of juvenile hybrid willows alters chemistry, growth and subsequent susceptibility to diverse plant enemies},
	volume = {112},
	issn = {1095-8290, 0305-7364},
	url = {https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mct002},
	doi = {10/f228d8},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Annals of Botany},
	author = {Orians, Colin M. and Fritz, Robert S. and Hochwender, Cris G. and Albrectsen, Benedicte R. and Czesak, Mary Ellen},
	month = aug,
	year = {2013},
	pages = {757--765},
}

@article{caseys_effects_2012,
	title = {Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing},
	volume = {5},
	issn = {1755-0874, 1755-1668},
	url = {http://www.tandfonline.com/doi/abs/10.1080/17550874.2012.748850},
	doi = {10/f24bc2},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Ecology \& Diversity},
	author = {Caseys, Celine and Glauser, Gaetan and Stölting, Kai N. and Christe, Camille and Albrectsen, Benedicte R. and Lexer, Christian},
	month = dec,
	year = {2012},
	pages = {457--471},
}

@article{robinson_genetic_2012,
	title = {Genetic {Variation} in {Functional} {Traits} {Influences} {Arthropod} {Community} {Composition} in {Aspen} ({Populus} tremula {L}.)},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0037679},
	doi = {10/f24ksj},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Robinson, Kathryn M. and Ingvarsson, Pär K. and Jansson, Stefan and Albrectsen, Benedicte R.},
	editor = {Kliebenstein, Daniel J.},
	month = may,
	year = {2012},
	pages = {e37679},
}

@article{viswanath_global_2012,
	title = {Global regulatory burden for field testing of genetically modified trees},
	volume = {8},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-011-0445-8},
	doi = {10/dsk6sw},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Viswanath, Venkatesh and Albrectsen, Benedicte R. and Strauss, Steven H.},
	month = apr,
	year = {2012},
	pages = {221--226},
}

@article{albrectsen_diversity_2012,
	title = {The diversity and identification of eulophid parasitic wasps ({Hymenoptera}: {Chalcidoidea}: {Eulophidae}) on {Phyllocnistis} labyrinthella ({Lepidoptera}: {Gracillariidae}) from {Västerbotten}, {Sweden}},
	volume = {133},
	shorttitle = {The diversity and identification of eulophid parasitic wasps ({Hymenoptera}},
	abstract = {The diversity and identification of eulophid parasitic wasps (Hymenoptera: Chalcidoidea: Eulophidae) on Phyllocnistis labyrinthella (Lepi-doptera: Gracillariidae) from Västerbotten, Sweden. [Diversitet och identifiering av fin-glanssteklar (Hymenoptera: Chalcidoidea: Eulophidae) på aspsaftmal (Phyllocnistis labyrinthella) (Lepidoptera: Gracillariidae) i Västerbotten, Sverige.] – Entomologisk Tidskrift 133(3): 111-118. Uppsala, Sweden 2012. ISSN 0013-886x. Caterpillars of the mining micro-moth Phyllocnistis labyrinthella feed on leaves of as-pen (Populus tremula) and are often parasitized by eulophid wasps. The parasitoids are a potential important cause of death for the miners. During 2009-2011 we collected mined leaves from an experimental stand of aspen trees in Västerbotten. Adults emerged from 17-35 percent of the mines and of these every second to third specimen appeared as wasps. These wasps represented seven species of eulophid parasitoids of which three were new to Västerbotten: Chrysocharis nitetis (Walker), Cirrospilus diallus (Walker) och Cirrospilus pictus (Nees). We include an identification key that may be used to identify these eulophid species. 

http://www.sef.nu/download/entomologisk\_tidskrift/et\_2012/ET2012\%20111-118.pdf},
	author = {Albrectsen, Benedicte and Hansson, Christer},
	month = jan,
	year = {2012},
}

The diversity and identification of eulophid parasitic wasps (Hymenoptera: Chalcidoidea: Eulophidae) on Phyllocnistis labyrinthella (Lepi-doptera: Gracillariidae) from Västerbotten, Sweden. [Diversitet och identifiering av fin-glanssteklar (Hymenoptera: Chalcidoidea: Eulophidae) på aspsaftmal (Phyllocnistis labyrinthella) (Lepidoptera: Gracillariidae) i Västerbotten, Sverige.] – Entomologisk Tidskrift 133(3): 111-118. Uppsala, Sweden 2012. ISSN 0013-886x. Caterpillars of the mining micro-moth Phyllocnistis labyrinthella feed on leaves of as-pen (Populus tremula) and are often parasitized by eulophid wasps. The parasitoids are a potential important cause of death for the miners. During 2009-2011 we collected mined leaves from an experimental stand of aspen trees in Västerbotten. Adults emerged from 17-35 percent of the mines and of these every second to third specimen appeared as wasps. These wasps represented seven species of eulophid parasitoids of which three were new to Västerbotten: Chrysocharis nitetis (Walker), Cirrospilus diallus (Walker) och Cirrospilus pictus (Nees). We include an identification key that may be used to identify these eulophid species. http://www.sef.nu/download/entomologisk_tidskrift/et_2012/ET2012%20111-118.pdf

@article{abreu_uhplc-esitofms_2011,
	title = {{UHPLC}-{ESI}/{TOFMS} {Determination} of salicylate-like phenolic gycosides in {Populus} tremula leaves},
	volume = {37},
	doi = {10/c8755j},
	abstract = {Associations of salicylate-like phenolic glycosides (PGs) with biological activity have been reported in Salix and Populus trees, but only for a few compounds, and in relation to a limited number of herbivores. By considering the full diversity of PGs, we may improve our ability to recognize genotypes or chemotype groups and enhance our understanding of their ecological function. Here, we present a fast and efficient general method for salicylate determination in leaves of Eurasian aspen that uses ultra-high performance liquid chromatography-electrospray ionization/time-of-flight mass spectrometry (UHPLC-ESI/TOFMS). The time required for the liquid chromatography separations was 13.5 min per sample, compared to around 60 min per sample for most HPLC protocols. In leaf samples from identical P. tremula genotypes with diverse propagation and treatment histories, we identified nine PGs. We found the compound-specific mass chromatograms to be more informative than the UV-visible chromatograms for compound identification and when quantitating samples with large variability in PG content. Signature compounds previously reported for P. tremoloides (tremulacin, tremuloidin, salicin, and salicortin) always were present, and five PGs (2'-O-cinnamoyl-salicortin, 2'-O-acetyl-salicortin, 2'-O-acetyl-salicin, acetyl-tremulacin, and salicyloyl-salicin) were detected for the first time in P. tremula. By using information about the formic acid adduct that appeared for PGs in the LTQ-Orbitrap MS environment, novel compounds like acetyl-tremulacin could be tentatively identified without the use of standards. The novel PGs were consistently either present in genotypes regardless of propagation and damage treatment or were not detectable. In some genotypes, concentrations of 2'-O-acetyl-salicortin and 2'-O-cinnamoyl-salicortin were similar to levels of biologically active PGs in other Salicaceous trees. Our study suggests that we may expect a wide variation in PG content in aspen populations which is of interest both for studies of interactions with herbivores and for mapping population structure.

Electronic supplementary material
The online version of this article (doi:10.1007/s10886-011-9991-7) contains supplementary material, which is available to authorized users.},
	journal = {Journal of chemical ecology},
	author = {Abreu, Ilka and Ahnlund, Maria and Moritz, Thomas and Albrectsen, Benedicte},
	month = aug,
	year = {2011},
	pages = {857--70},
}

Associations of salicylate-like phenolic glycosides (PGs) with biological activity have been reported in Salix and Populus trees, but only for a few compounds, and in relation to a limited number of herbivores. By considering the full diversity of PGs, we may improve our ability to recognize genotypes or chemotype groups and enhance our understanding of their ecological function. Here, we present a fast and efficient general method for salicylate determination in leaves of Eurasian aspen that uses ultra-high performance liquid chromatography-electrospray ionization/time-of-flight mass spectrometry (UHPLC-ESI/TOFMS). The time required for the liquid chromatography separations was 13.5 min per sample, compared to around 60 min per sample for most HPLC protocols. In leaf samples from identical P. tremula genotypes with diverse propagation and treatment histories, we identified nine PGs. We found the compound-specific mass chromatograms to be more informative than the UV-visible chromatograms for compound identification and when quantitating samples with large variability in PG content. Signature compounds previously reported for P. tremoloides (tremulacin, tremuloidin, salicin, and salicortin) always were present, and five PGs (2'-O-cinnamoyl-salicortin, 2'-O-acetyl-salicortin, 2'-O-acetyl-salicin, acetyl-tremulacin, and salicyloyl-salicin) were detected for the first time in P. tremula. By using information about the formic acid adduct that appeared for PGs in the LTQ-Orbitrap MS environment, novel compounds like acetyl-tremulacin could be tentatively identified without the use of standards. The novel PGs were consistently either present in genotypes regardless of propagation and damage treatment or were not detectable. In some genotypes, concentrations of 2'-O-acetyl-salicortin and 2'-O-cinnamoyl-salicortin were similar to levels of biologically active PGs in other Salicaceous trees. Our study suggests that we may expect a wide variation in PG content in aspen populations which is of interest both for studies of interactions with herbivores and for mapping population structure. Electronic supplementary material The online version of this article (doi:10.1007/s10886-011-9991-7) contains supplementary material, which is available to authorized users.

@article{albrectsen_endophytic_2010,
	title = {Endophytic fungi in {European} aspen ({Populus} tremula) leaves—diversity, detection, and a suggested correlation with herbivory resistance},
	volume = {41},
	issn = {1560-2745, 1878-9129},
	url = {http://link.springer.com/10.1007/s13225-009-0011-y},
	doi = {10/cg5zgd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Fungal Diversity},
	author = {Albrectsen, Benedicte R. and Björkén, Lars and Varad, Akkamahadevi and Hagner, Åsa and Wedin, Mats and Karlsson, Jan and Jansson, Stefan},
	month = mar,
	year = {2010},
	pages = {17--28},
}

@article{saona_environmental_2010,
	title = {Environmental stresses mediate endophyte-grass interactions in a boreal archipelago},
	volume = {98},
	issn = {00220477, 13652745},
	url = {http://doi.wiley.com/10.1111/j.1365-2745.2009.01613.x},
	doi = {10/cbcwrq},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Ecology},
	author = {Saona, Nora M. and Albrectsen, Benedicte Riber and Ericson, Lars and Bazely, Dawn R.},
	month = mar,
	year = {2010},
	pages = {470--479},
}

@article{gundale_variation_2010,
	title = {Variation in protein complexation capacity among and within six plant species across a boreal forest chronosequence},
	volume = {211},
	issn = {1385-0237, 1573-5052},
	url = {http://link.springer.com/10.1007/s11258-010-9787-9},
	doi = {10/fb7xxd},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Ecology},
	author = {Gundale, Michael J. and Sverker, Jennie and Albrectsen, Benedicte R. and Nilsson, Marie-Charlotte and Wardle, David A.},
	month = dec,
	year = {2010},
	pages = {253--266},
}

@article{albrectsen_large_2009,
	title = {Large scale geographic clines of parasite damage to \textit{{Populus} tremula} {L}},
	issn = {09067590, 16000587},
	url = {http://doi.wiley.com/10.1111/j.1600-0587.2009.05982.x},
	doi = {10/c38874},
	language = {en},
	urldate = {2021-06-08},
	journal = {Ecography},
	author = {Albrectsen, Benedicte R. and Witzell, Johanna and Robinson, Kathryn M. and Wulff, Sören and Luquez, Virginia M. C. and Ågren, Rickard and Jansson, Stefan},
	month = oct,
	year = {2009},
}

@article{crutsinger_ecosystem_2008,
	title = {Ecosystem retrogression leads to increased insect abundance and herbivory across an island chronosequence},
	volume = {22},
	issn = {02698463, 13652435},
	url = {http://doi.wiley.com/10.1111/j.1365-2435.2008.01435.x},
	doi = {10/b3g3tc},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Functional Ecology},
	author = {Crutsinger, G. M. and Sanders, N. J. and Albrectsen, B. R. and Abreu, I. N. and Wardle, D. A.},
	month = oct,
	year = {2008},
	pages = {816--823},
}

@article{luquez_natural_2008,
	title = {Natural phenological variation in aspen ({Populus} tremula): the {SwAsp} collection},
	volume = {4},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Natural phenological variation in aspen ({Populus} tremula)},
	url = {http://link.springer.com/10.1007/s11295-007-0108-y},
	doi = {10/bwk27s},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Luquez, Virginia and Hall, David and Albrectsen, Benedicte R. and Karlsson, Jan and Ingvarsson, Pär and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {279--292},
}

@article{albrectsen_nutrient_2008,
	title = {Nutrient addition extends flowering display, which gets tracked by seed predators, but not by their parasitoids},
	volume = {117},
	issn = {00301299},
	url = {http://doi.wiley.com/10.1111/j.2008.0030-1299.16381.x},
	doi = {10/dp76wq},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Oikos},
	author = {Albrectsen, Benedicte Riber and Ericson, Lars and Lundberg, Per},
	month = mar,
	year = {2008},
	pages = {473--480},
}

@article{albrectsen_does_2007,
	title = {Does the differential seedling mortality caused by slugs alter the foliar traits and subsequent susceptibility of hybrid willows to a generalist herbivore?},
	volume = {0},
	issn = {0307-6946, 1365-2311},
	url = {http://doi.wiley.com/10.1111/j.1365-2311.2006.00860.x},
	doi = {10/bzhmrr},
	language = {en},
	number = {0},
	urldate = {2021-06-10},
	journal = {Ecological Entomology},
	author = {Albrectsen, Benedicte R. and Guiterrez, Laura and Fritz, Robert S. and Fritz, Robert D. and Orians, Colin M.},
	month = jan,
	year = {2007},
	pages = {070130195410003--???},
}

@article{fritz_fitness_2006,
	title = {Fitness and genetic architecture of parent and hybrid willows in common gardens},
	volume = {60},
	issn = {0014-3820},
	doi = {10.1554/05-343.1},
	abstract = {Models of hybrid zone dynamics incorporate different patterns of hybrid fitness relative to parental species fitness. An important but understudied source of variation underlying these fitness differences is the environment. We investigated the performance of two willow species and their F-1, F-2, and backcross hybrids using a common-garden experiment with six replicated gardens that differed in soil moisture. Aboveground biomass, catkin production, seed production per catkin, and seed germination rate were significantly different among genetic classes. For aboveground biomass and catkin production, hybrids generally had intermediate or inferior performance compared to parent species. Salix eriocephala had the highest performance for all performance measures, but in two gardens F, plants had superior or equal performance for aboveground biomass and female catkin production. Salix eriocephala and backcrosses to S. eriocephala had the highest numbers of filled seeds per catkin and the highest estimates of total fitness in all gardens. Measures of filled seeds per catkin and germination rate tend to support the model of endogenous hybrid unfitness, and these two measures had major effects on estimates of total seed production per catkin. We also estimated how the two willow species differ genetically in these fitness measures using line cross analysis. We found a complex genetic architecture underlying the fitness differences between species that involved additive, dominance, and epistatic genetic effects for all fitness measures. The environment was important in the expression of these genetic differences, because the type of epistasis differed among the gardens for aboveground biomass and for female catkin production. These findings suggest that fine-scale environmental variation can have a significant impact on hybrid fitness in hybrid zones where parents and hybrids are widely interspersed.},
	language = {English},
	number = {6},
	journal = {Evolution},
	publisher = {Wiley},
	author = {Fritz, Robert S. and Hochwender, Cris G. and Albrectsen, Benedicte R. and Czesak, Mary Ellen},
	month = jun,
	year = {2006},
	note = {Place: Hoboken
WOS:000238969900010},
	keywords = {epistasis, evolution, fitness, genetic architecture, growth, herbivores, hybrid, hybrid zone, inbreeding depression, natural   hybridization, nutrition, pinus-radiata, responses, sagebrush artemisia-tridentata, willow, zone},
	pages = {1215--1227},
}

Models of hybrid zone dynamics incorporate different patterns of hybrid fitness relative to parental species fitness. An important but understudied source of variation underlying these fitness differences is the environment. We investigated the performance of two willow species and their F-1, F-2, and backcross hybrids using a common-garden experiment with six replicated gardens that differed in soil moisture. Aboveground biomass, catkin production, seed production per catkin, and seed germination rate were significantly different among genetic classes. For aboveground biomass and catkin production, hybrids generally had intermediate or inferior performance compared to parent species. Salix eriocephala had the highest performance for all performance measures, but in two gardens F, plants had superior or equal performance for aboveground biomass and female catkin production. Salix eriocephala and backcrosses to S. eriocephala had the highest numbers of filled seeds per catkin and the highest estimates of total fitness in all gardens. Measures of filled seeds per catkin and germination rate tend to support the model of endogenous hybrid unfitness, and these two measures had major effects on estimates of total seed production per catkin. We also estimated how the two willow species differ genetically in these fitness measures using line cross analysis. We found a complex genetic architecture underlying the fitness differences between species that involved additive, dominance, and epistatic genetic effects for all fitness measures. The environment was important in the expression of these genetic differences, because the type of epistasis differed among the gardens for aboveground biomass and for female catkin production. These findings suggest that fine-scale environmental variation can have a significant impact on hybrid fitness in hybrid zones where parents and hybrids are widely interspersed.

@article{albrectsen_micro_2006,
	title = {From micro towards the macro scale},
	volume = {172},
	issn = {0028-646X},
	doi = {10.1111/j.1469-8137.2006.01869.x},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	publisher = {Wiley},
	author = {Albrectsen, Benedicte R. and Jansson, Stefan},
	year = {2006},
	note = {Place: Hoboken
WOS:000239988100003},
	keywords = {arabidopsis, biofuel, coevolution, developmental biology, diversity, genes, plant defence   strategy, plants, scientific outreach, small RNA},
	pages = {7--10},
}

@article{albrectsen_slugs_2004,
	title = {Slugs, willow seedlings and nutrient fertilization: intrinsic vigor inversely affects palatability},
	volume = {105},
	issn = {0030-1299},
	shorttitle = {Slugs, willow seedlings and nutrient fertilization},
	doi = {10/fccj89},
	abstract = {This study evaluates how preference by a generalist slug herbivore Arion subfuscus changes inversely with seedling size across three levels of fertilization for three full-sib families of willow seedlings. We analyzed seedlings for condensed tannin and protein concentration, and related these data to changes in palatability. In preference tests over time, leaf discs from more fertilized seedlings experienced an extended window of vulnerability compared to discs from less fertilized seedlings, which were also more tannin-rich. In a whole seedling selection study, slugs readily attacked smaller seedlings ({\textless}5 cm) but rarely attacked taller seedlings ({\textgreater}10 cm). However, a general difference in risk of damage close to 50\% existed when comparing shorter and taller individuals within each family and level of fertilizer. The decrease in palatability with height of the seedlings was positively correlated with an increase in condensed tannin concentration. We found no effect of seedling size on protein concentration. Akaiki index criterion model comparisons suggested that only main effects were important for explaining seedling choice by slugs as well as the ratio between proteins and condensed tannins. Seedling size, had the largest effect, followed by fertilizer level and family. Surprisingly, seedling size and fertilizer treatment had opposite effects on palatability to slugs. Size decreased probability of damage, whereas fertilization extended the window of susceptibility. Because the seedlings were even-aged, differences in size are interpreted as differences in growth rate or vigor. The positive phenotypic correlation found between size and tannin production in the less preferred willow seedlings confirms that several plant defense traits may be selected for simultaneously, because fast growth may allow an early development of plant defenses. We discuss these results in the light of plant-defense theories that predict a negative correlation between the allocation to growth and the production of secondary defense compounds.},
	language = {English},
	number = {2},
	journal = {Oikos},
	publisher = {Wiley-Blackwell},
	author = {Albrectsen, B. R. and Gardfjell, H. and Orians, C. M. and Murray, B. and Fritz, R. S.},
	month = may,
	year = {2004},
	note = {Place: Hoboken
WOS:000220383100007},
	keywords = {chemical defense, deroceras-reticulatum, grassland, herbivory, hybrid, hypothesis, performance, plants, resource availability, tannin},
	pages = {268--278},
}

This study evaluates how preference by a generalist slug herbivore Arion subfuscus changes inversely with seedling size across three levels of fertilization for three full-sib families of willow seedlings. We analyzed seedlings for condensed tannin and protein concentration, and related these data to changes in palatability. In preference tests over time, leaf discs from more fertilized seedlings experienced an extended window of vulnerability compared to discs from less fertilized seedlings, which were also more tannin-rich. In a whole seedling selection study, slugs readily attacked smaller seedlings (\textless5 cm) but rarely attacked taller seedlings (\textgreater10 cm). However, a general difference in risk of damage close to 50% existed when comparing shorter and taller individuals within each family and level of fertilizer. The decrease in palatability with height of the seedlings was positively correlated with an increase in condensed tannin concentration. We found no effect of seedling size on protein concentration. Akaiki index criterion model comparisons suggested that only main effects were important for explaining seedling choice by slugs as well as the ratio between proteins and condensed tannins. Seedling size, had the largest effect, followed by fertilizer level and family. Surprisingly, seedling size and fertilizer treatment had opposite effects on palatability to slugs. Size decreased probability of damage, whereas fertilization extended the window of susceptibility. Because the seedlings were even-aged, differences in size are interpreted as differences in growth rate or vigor. The positive phenotypic correlation found between size and tannin production in the less preferred willow seedlings confirms that several plant defense traits may be selected for simultaneously, because fast growth may allow an early development of plant defenses. We discuss these results in the light of plant-defense theories that predict a negative correlation between the allocation to growth and the production of secondary defense compounds.

@article{gowda_spines_2003,
	title = {Spines as a mechanical defence: the effects of fertiliser treatment on juvenile {Acacia} tortilis plants},
	volume = {24},
	issn = {1146-609X},
	shorttitle = {Spines as a mechanical defence},
	doi = {10/c5c6n4},
	abstract = {Using growth of different tissues in Acacia tortilis as a model, we tested current hypotheses on how nutrients affect mechanical plant defence. In a greenhouse experiment we applied a balanced commercial fertiliser (NPK) at three treatment levels to juvenile potted Acacias. As expected, plants increased in size with nutrient addition. More importantly, however, the relative mass of long spines increased significantly more than other structural components (leaves and twigs). This effect is not predicted by current nutrient availability hypotheses; which suggest either equal or proportionally lower investment in mechanical defence with increasing nutrient availability. Our results suggest that investment in spine size is nutrient limited in Acacia tortilis. It is commonly observed that the risk of damage by herbivores is highest on plants growing in nutrient-rich soils. If spines act as an effective form of anti-herbivore protection, then these plants might be expected to increase their production of physical defences (long spines) under such circumstances. Plants growing under higher nutrient conditions might therefore invest more in constitutive defences. These changes in allocation pattern are consistent with the increase in production of long spines, which are also induced by browsing. (C) 2003 Editions scientifiques et medicales Elsevier SAS. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Acta Oecologica-International Journal of Ecology},
	publisher = {Gauthier-Villars/Editions Elsevier},
	author = {Gowda, J. H. and Albrectsen, B. R. and Ball, J. P. and Sjoberg, M. and Palo, R. T.},
	month = mar,
	year = {2003},
	note = {Place: Paris
WOS:000182473100001},
	keywords = {balance, carbon-nutrient balance, growth pattern, herbivory, mammalian herbivores, nitrogen fertilisation, nutrient addition, plant-herbivore interactions, resistance, resource availability, thorns, trees},
	pages = {1--4},
}

Using growth of different tissues in Acacia tortilis as a model, we tested current hypotheses on how nutrients affect mechanical plant defence. In a greenhouse experiment we applied a balanced commercial fertiliser (NPK) at three treatment levels to juvenile potted Acacias. As expected, plants increased in size with nutrient addition. More importantly, however, the relative mass of long spines increased significantly more than other structural components (leaves and twigs). This effect is not predicted by current nutrient availability hypotheses; which suggest either equal or proportionally lower investment in mechanical defence with increasing nutrient availability. Our results suggest that investment in spine size is nutrient limited in Acacia tortilis. It is commonly observed that the risk of damage by herbivores is highest on plants growing in nutrient-rich soils. If spines act as an effective form of anti-herbivore protection, then these plants might be expected to increase their production of physical defences (long spines) under such circumstances. Plants growing under higher nutrient conditions might therefore invest more in constitutive defences. These changes in allocation pattern are consistent with the increase in production of long spines, which are also induced by browsing. (C) 2003 Editions scientifiques et medicales Elsevier SAS. All rights reserved.

@article{albrectsen_female-biased_2001,
	title = {Female-biased density-dependent dispersal of a tephritid fly in a fragmented habitat and its implications for population regulation},
	volume = {94},
	issn = {1600-0706},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1600-0706.2001.940206.x},
	doi = {10.1034/j.1600-0706.2001.940206.x},
	abstract = {The aim of this study was to quantify the rate of dispersal as a response to density in the specialist tephritid fly Paroxyna plantaginis (the main seed predator on its patchily distributed host plant, Tripolium vulgare, Asteraceae). Marked flies were released at three different fly densities in artificial host patches. The individual histories of recaptures were recorded as well as migration between patches and invasion by unmarked flies. The loss of marked flies relative to initial density was analysed using maximum likelihood estimation. Females generally had the highest loss rate. When comparing a density-independent model with a density-dependent model of the loss rate, the density-dependent model won four times out of six for the females but not a single time for the males. A stronger immigration rate of females relative to males supported the suggested female-biased dispersal. This indicates a sit-and-wait strategy for the territorial males and a pre-emptive competition strategy for egg-laying substrates for the females. These results may be of general importance for non-frugivorous tephritid systems with unpredictable and almost ephemeral accessibility to host plants and with a dynamics characterised by a high turnover rate and high attack levels. The study presents a method for measuring the propensity of individuals to leave an area as a response to local density. It is further an example of the consequences individual behavioural responses may have on the population dynamics of a patchy population.},
	language = {en},
	number = {2},
	urldate = {2021-11-02},
	journal = {Oikos},
	author = {Albrectsen, Benedicte and Nachman, Gösta},
	year = {2001},
	pages = {263--272},
}

The aim of this study was to quantify the rate of dispersal as a response to density in the specialist tephritid fly Paroxyna plantaginis (the main seed predator on its patchily distributed host plant, Tripolium vulgare, Asteraceae). Marked flies were released at three different fly densities in artificial host patches. The individual histories of recaptures were recorded as well as migration between patches and invasion by unmarked flies. The loss of marked flies relative to initial density was analysed using maximum likelihood estimation. Females generally had the highest loss rate. When comparing a density-independent model with a density-dependent model of the loss rate, the density-dependent model won four times out of six for the females but not a single time for the males. A stronger immigration rate of females relative to males supported the suggested female-biased dispersal. This indicates a sit-and-wait strategy for the territorial males and a pre-emptive competition strategy for egg-laying substrates for the females. These results may be of general importance for non-frugivorous tephritid systems with unpredictable and almost ephemeral accessibility to host plants and with a dynamics characterised by a high turnover rate and high attack levels. The study presents a method for measuring the propensity of individuals to leave an area as a response to local density. It is further an example of the consequences individual behavioural responses may have on the population dynamics of a patchy population.

@article{sjoberg_truncated_2000,
	title = {Truncated power laws: a tool for understanding aggregation patterns in animals?},
	volume = {3},
	issn = {1461-0248},
	shorttitle = {Truncated power laws},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1461-0248.2000.00113.x},
	doi = {10.1046/j.1461-0248.2000.00113.x},
	abstract = {Statistical distributions like the negative binomial distribution are commonly used to describe aggregation patterns in animals. However, recently it has been suggested that truncated power laws (TPLs) may also be used for this kind of analysis. A TPL consists of two power functions separated by a cut-off size (C*). The cut-off size and the slope of power function one (β1) for the smallest group sizes have been suggested to have a biological explanatory value. We applied TPLs to aggregation data of tephritid seed predators on a composite plant, aphids on willows and grey seals on a haulout site. β1 varied between 0.60 and and −0.72, which is higher than predicted. In addition, resource distribution and animal density influenced β1 and C*. This indicates that environmental dimensionality suggested to affect β1 is masked by ecological factors. We conclude that TPLs are useful due to their simplicity and, in comparison with traditional methods, provide additional biologically relevant information. Truncated power laws can therefore prove to be useful in studies of animal behaviour and population dynamics.},
	language = {en},
	number = {2},
	urldate = {2021-11-08},
	journal = {Ecology Letters},
	author = {Sjöberg, Mikael and Albrectsen, Benedicte and Hjältén, Joakim},
	year = {2000},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1461-0248.2000.00113.x},
	keywords = {Aggregation patterns, frequency distribution, group size, truncated power law},
	pages = {90--94},
}

Statistical distributions like the negative binomial distribution are commonly used to describe aggregation patterns in animals. However, recently it has been suggested that truncated power laws (TPLs) may also be used for this kind of analysis. A TPL consists of two power functions separated by a cut-off size (C*). The cut-off size and the slope of power function one (β1) for the smallest group sizes have been suggested to have a biological explanatory value. We applied TPLs to aggregation data of tephritid seed predators on a composite plant, aphids on willows and grey seals on a haulout site. β1 varied between 0.60 and and −0.72, which is higher than predicted. In addition, resource distribution and animal density influenced β1 and C*. This indicates that environmental dimensionality suggested to affect β1 is masked by ecological factors. We conclude that TPLs are useful due to their simplicity and, in comparison with traditional methods, provide additional biologically relevant information. Truncated power laws can therefore prove to be useful in studies of animal behaviour and population dynamics.