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2. Environmental microbiome engineering for the mitigation of climate change

Author

Silverstein, Michael R, Segrè, Daniel, and Bhatnagar, Jennifer M

Subjects
Microbiology, Biological Sciences, Human Genome, Genetics, Climate Action, Ecosystem, Bacteria, Climate Change, Microbiota, Carbon, bioinoculant, climate change mitigation, microbial inoculum, microbiome engineering, microbiome transplant, Environmental Sciences, Ecology, Biological sciences, Earth sciences, Environmental sciences
Abstract

Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

Published
2023

3. Contributors

Author

Allison, Steven D., primary, Balestrini, R., additional, Bandopadhyay, Sreejata, additional, Barré, Pierre, additional, Bhatnagar, Jennifer M., additional, Bianciotto, V., additional, Blackwood, Christopher B., additional, Brodie, Eoin L., additional, Chenu, Claire, additional, Chung, Brian, additional, Coleman, D.C., additional, Duan, Elizabeth, additional, Emerson, Joanne B., additional, Frey, Serita D., additional, Frossard, Emmanuel, additional, Geisen, S., additional, Geyer, Kevin, additional, Ghignone, S., additional, Groffman, P.M., additional, Heck, Richard J., additional, Horwath, William R., additional, Kandeler, Ellen, additional, Karaoz, Ulas, additional, Kertesz, Michael A., additional, Kuzyakov, Yakov, additional, Lumini, E., additional, McGill, William B., additional, Mello, A., additional, Moore, John C., additional, Morris, Sherri J., additional, Mueller, Nathaniel, additional, Paul, Eldor A., additional, Plante, Alain F., additional, Robertson, G.P., additional, Rumpel, Cornelia, additional, Shade, Ashley, additional, Sillo, F., additional, Slocum, Maura, additional, Taylor, D. Lee, additional, Védère, Charlotte, additional, Voroney, R. Paul, additional, Wall, D.H., additional, Xie, Wally, additional, and Zampieri, E., additional

Published
2024
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5. Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives.

Author

Iwata, Mana, Gutiérrez, Ana, Marques, Gisela, Sabat, Grzegorz, Kersten, Philip J, Cullen, Daniel, Bhatnagar, Jennifer M, Yadav, Jagjit, Lipzen, Anna, Yoshinaga, Yuko, Sharma, Aditi, Adam, Catherine, Daum, Christopher, Ng, Vivian, Grigoriev, Igor V, and Hori, Chiaki

Abstract

Wood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efficiently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defined media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was significantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi.

Published
2021

7. Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change

Author

Garcia, Maria O, Templer, Pamela H, Sorensen, Patrick O, Sanders-DeMott, Rebecca, Groffman, Peter M, and Bhatnagar, Jennifer M

Subjects
Microbiology, Biological Sciences, Ecology, Climate Action, climate change, forest ecology, microbial communities, soil freezing, warming, winter, Environmental Science and Management, Soil Sciences, Medical microbiology
Abstract

Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.

Published
2020

10. Roots Mediate the Effects of Snowpack Decline on Soil Bacteria, Fungi, and Nitrogen Cycling in a Northern Hardwood Forest

Author

Sorensen, Patrick O, Bhatnagar, Jennifer M, Christenson, Lynn, Duran, Jorge, Fahey, Timothy, Fisk, Melany C, Finzi, Adrien C, Groffman, Peter M, Morse, Jennifer L, and Templer, Pamela H

Subjects
Microbiology, Biological Sciences, Ecology, elevation gradient, plant roots, soil N cycle, snowpack, soil bacteria and fungi, Environmental Science and Management, Soil Sciences, Medical microbiology
Abstract

Rising winter air temperature will reduce snow depth and duration over the next century in northern hardwood forests. Reductions in snow depth may affect soil bacteria and fungi directly, but also affect soil microbes indirectly through effects of snowpack loss on plant roots. We incubated root exclusion and root ingrowth cores across a winter climate-elevation gradient in a northern hardwood forest for 29 months to identify direct (i.e., winter snow-mediated) and indirect (i.e., root-mediated) effects of winter snowpack decline on soil bacterial and fungal communities, as well as on potential nitrification and net N mineralization rates. Both winter snowpack decline and root exclusion increased bacterial richness and phylogenetic diversity. Variation in bacterial community composition was best explained by differences in winter snow depth or soil frost across elevation. Root ingrowth had a positive effect on the relative abundance of several bacterial taxonomic orders (e.g., Acidobacterales and Actinomycetales). Nominally saprotrophic (e.g., Saccharomycetales and Mucorales) or mycorrhizal (e.g., Helotiales, Russalales, Thelephorales) fungal taxonomic orders were also affected by both root ingrowth and snow depth variation. However, when grouped together, the relative abundance of saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal fungi were not affected by root ingrowth or snow depth, suggesting that traits in addition to trophic mode will mediate fungal community responses to snowpack decline in northern hardwood forests. Potential soil nitrification rates were positively related to ammonia-oxidizing bacteria and archaea abundance (e.g., Nitrospirales, Nitrosomondales, Nitrosphaerales). Rates of N mineralization were positively and negatively correlated with ectomycorrhizal and saprotrophic fungi, respectively, and these relationships were mediated by root exclusion. The results from this study suggest that a declining winter snowpack and its effect on plant roots each have direct effects on the diversity and abundance of soil bacteria and fungal communities that interact to determine rates of soil N cycling in northern hardwood forests.

Published
2019

11. Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes

Author

Hori, Chiaki, Gaskell, Jill, Cullen, Dan, Sabat, Grzegorz, Stewart, Philip E, Lail, Kathleen, Peng, Yi, Barry, Kerrie, Grigoriev, Igor V, Kohler, Annegret, Fauchery, Laure, Martin, Francis, Zeiner, Carolyn A, and Bhatnagar, Jennifer M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Basidiomycota, Cellulases, Gene Expression Profiling, Genome, Fungal, Glycoside Hydrolases, Hydrolysis, Lignin, Oxidation-Reduction, Pinus, Proteomics, Wood, brown rot, metaproteome, metatranscriptome, white rot, Microbiology, Medical microbiology
Abstract

Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.

Published
2018

12. Detecting macroecological patterns in bacterial communities across independent studies of global soils.

Author

Ramirez, Kelly S, Knight, Christopher G, de Hollander, Mattias, Brearley, Francis Q, Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W, Davison, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R, Fox, Graeme, Griffiths, Robert I, Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L, Krab, Eveline J, Maestre, Fernando T, McGuire, Krista L, Monteux, Sylvain, Orr, Caroline H, van der Putten, Wim H, Roberts, Ian S, Robinson, David A, Rocca, Jennifer D, Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K, Straathof, Angela L, Bhatnagar, Jennifer M, Thion, Cécile, van der Heijden, Marcel GA, and de Vries, Franciska T

Subjects
Bacteria, DNA, Bacterial, RNA, Ribosomal, 16S, Soil, Ecology, Soil Microbiology, Ecosystem, Biodiversity, Phylogeny, Bacterial Physiological Phenomena, Microbial Interactions, High-Throughput Nucleotide Sequencing, Microbiota, Machine Learning
Abstract

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Published
2018

16. Ectomycorrhizal fungi enhance pine growth by stimulating iron‐dependent mechanisms with trade‐offs in symbiotic performance.

Author

Zhang, Kaile, Wang, Haihua, Tappero, Ryan, Bhatnagar, Jennifer M., Vilgalys, Rytas, Barry, Kerrie, Keymanesh, Keykhosrow, Tejomurthula, Sravanthi, Grigoriev, Igor V., Kew, William R., Eder, Elizabeth K., Nicora, Carrie D., and Liao, Hui‐Ling

Subjects
ECTOMYCORRHIZAL fungi, X-ray spectroscopy, NUCLEAR magnetic resonance spectroscopy, PLANT metabolites, PLANT roots
Abstract

Summary: Iron (Fe) is crucial for metabolic functions of living organisms. Plants access occluded Fe through interactions with rhizosphere microorganisms and symbionts. Yet, the interplay between Fe addition and plant–mycorrhizal interactions, especially the molecular mechanisms underlying mycorrhiza‐assisted Fe processing in plants, remains largely unexplored.We conducted mesocosms in Pinus plants inoculated with different ectomycorrhizal fungi (EMF) Suillus species under conditions with and without Fe coatings. Meta‐transcriptomic, biogeochemical, and X‐ray fluorescence imaging analyses were applied to investigate early‐stage mycorrhizal roots.While Fe addition promoted Pinus growth, it concurrently reduced mycorrhiza formation rate, symbiosis‐related metabolites in plant roots, and aboveground plant carbon and macronutrient content. This suggested potential trade‐offs between Fe‐enhanced plant growth and symbiotic performance. However, the extent of this trade‐off may depend on interactions between host plants and EMF species. Interestingly, dual EMF species were more effective at facilitating plant Fe uptake by inducing diverse Fe‐related functions than single‐EMF species. This subsequently triggered various Fe‐dependent physiological and biochemical processes in Pinus roots, significantly contributing to Pinus growth. However, this resulted in a greater carbon allocation to roots, relatively reducing the aboveground plant carbon content.Our study offers critical insights into how EMF communities rebalance benefits of Fe‐induced effects on symbiotic partners. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Restoring ecological complexity in a changing environment.

Author

Mateos, David Moreno and Bhatnagar, Jennifer M.

Subjects
*ECOLOGICAL disturbances, *ECOSYSTEM dynamics, *VACANT lands, *CLIMATE change, *LAND use, *ECOSYSTEMS, *PHYSIOLOGICAL adaptation
Abstract

As land use leaves massive tracts of land vacant for recovery, restoration must undergo a substantial shift to incorporate a complexity perspective beyond the traditional community, biodiversity or functional views. With an interaction–function perspective, we may be able to achieve ecosystems with better chances to adapt to current environmental changes and, especially, to climate change. We explore combined approaches that include still unused and underexplored techniques that will soon go mainstream and produce massive amounts of information to address the complexity gap. As we understand how complexity reassembles after the end of agriculture, we will be able to design actions to restore or enhance it at unprecedented spatial scales while increasing its adaptability to environmental changes. Moreno and Bhatnagar argue in favor of using an 'interaction–function' perspective to understand the dynamics of ecosystem recovery after land-use change, especially in the light of climate change. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Ectomycorrhizal fungi enhance pine growth by stimulating iron‐dependent mechanisms with trade‐offs in symbiotic performance

Author

Zhang, Kaile, primary, Wang, Haihua, additional, Tappero, Ryan, additional, Bhatnagar, Jennifer M., additional, Vilgalys, Rytas, additional, Barry, Kerrie, additional, Keymanesh, Keykhosrow, additional, Tejomurthula, Sravanthi, additional, Grigoriev, Igor V., additional, Kew, William R., additional, Eder, Elizabeth K., additional, Nicora, Carrie D., additional, and Liao, Hui‐Ling, additional

Published
2023
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23. Unraveling the functional dark matter through global metagenomics

Author

Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, Kyrpides, Nikos C., Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, and Kyrpides, Nikos C.

Abstract

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Published
2023
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27. Urbanization and edge effects interact to drive mutualism breakdown and the rise of unstable pathogenic communities in forest soil.

Author

Chikae Tatsumi, Atherton, Kathryn F., Garvey, Sarah M., Conrad-Rooney, Emma, Morreale, Luca L., Hutyra, Lucy R., Templer, Pamela H., and Bhatnagar, Jennifer M.

Subjects
FOREST soils, COMMUNITY forests, FORESTS & forestry, URBANIZATION, TEMPERATE forests
Abstract

Temperate forests are threatened by urbanization and fragmentation, with over 20% (118,300 km2 ) of U.S. forest land projected to be subsumed by urban land development. We leveraged a unique, well-characterized urban-to-rural and forest edge-to-interior gradient to identify the combined impact of these two land use changes—urbanization and forest edge creation—on the soil microbial community in native remnant forests. We found evidence of mutualism breakdown between trees and their fungal root mutualists [ectomycorrhizal (ECM) fungi] with urbanization, where ECM fungi colonized fewer tree roots and had less connectivity in soil microbiome networks in urban forests compared to rural forests. However, urbanization did not reduce the relative abundance of ECM fungi in forest soils; instead, forest edges alone led to strong reductions in ECM fungal abundance. At forest edges, ECM fungi were replaced by plant and animal pathogens, as well as copiotrophic, xenobiotic-degrading, and nitrogen-cycling bacteria, including nitrifiers and denitrifiers. Urbanization and forest edges interacted to generate new “suites” of microbes, with urban interior forests harboring highly homogenized microbiomes, while edge forest microbiomes were more heterogeneous and less stable, showing increased vulnerability to low soil moisture. When scaled to the regional level, we found that forest soils are projected to harbor high abundances of fungal pathogens and denitrifying bacteria, even in rural areas, due to the widespread existence of forest edges. Our results highlight the potential for soil microbiome dysfunction—including increased greenhouse gas production—in temperate forest regions that are subsumed by urban expansion, both now and in the future. [ABSTRACT FROM AUTHOR]

Published
2023
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29. Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives

Author

Joint Genome Institute (US), National Science Foundation (US), Department of Energy (US), Japan Society for the Promotion of Science, Consejo Superior de Investigaciones Científicas (España), Hokkaido University, Gutiérrez Suárez, Ana [0000-0002-8823-9029], Marques, Gisela [0000-0002-6431-8267], Bhatnagar, Jennifer M. [0000-0001-6424-4133], Iwata, Mana, Gutiérrez Suárez, Ana, Marques, Gisela, Sabat, Grzegorz, Kersten, Philip J, Cullen, Daniel, Bhatnagar, Jennifer M., Yadav, Jagjit S., Lipzen, Anna, Yoshinaga, Yuko, Sharma, Aditi, Adam, Catherine, Joint Genome Institute (US), National Science Foundation (US), Department of Energy (US), Japan Society for the Promotion of Science, Consejo Superior de Investigaciones Científicas (España), Hokkaido University, Gutiérrez Suárez, Ana [0000-0002-8823-9029], Marques, Gisela [0000-0002-6431-8267], Bhatnagar, Jennifer M. [0000-0001-6424-4133], Iwata, Mana, Gutiérrez Suárez, Ana, Marques, Gisela, Sabat, Grzegorz, Kersten, Philip J, Cullen, Daniel, Bhatnagar, Jennifer M., Yadav, Jagjit S., Lipzen, Anna, Yoshinaga, Yuko, Sharma, Aditi, and Adam, Catherine

Abstract

Wood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efficiently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defined media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was significantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi. © 2021, The Author(s).

Published
2021

31. Global pine tree invasions are linked to invasive root symbionts.

Author

Policelli, Nahuel, Hoeksema, Jason D., Moyano, Jaime, Vilgalys, Rytas, Vivelo, Sasha, and Bhatnagar, Jennifer M.

Subjects
PLANT invasions, PINE, INVASIVE plants, INTRODUCED species, PLANT diversity, TREES, INTRODUCED plants, LODGEPOLE pine
Abstract

These groups did not match the I Z i -score values calculated for each pine species: some pine species predicted to be invasive based on their I Z i -score grouped with plantation and introduced EMF, while some pine species predicted to be non-invasive based on their I Z i -score grouped with invasive EMF (both early- and late-successional) (Fig. Keywords: belowground microbes; ectomycorrhizas; invasive fungi; Pinus; plant invasions; plant-soil feedbacks EN belowground microbes ectomycorrhizas invasive fungi Pinus plant invasions plant-soil feedbacks 16 21 6 12/08/22 20230101 NES 230101 Symbiotic soil microbes can facilitate plant invasions, yet it is unclear whether the invasive capacity of plants can be explained by the invasiveness of their microbial symbionts. After compiling a global dataset on associations between non-native invasive pine trees and ectomycorrhizal fungi (EMF), we found that the interaction with invasive EMF is an important predictor of pine invasion success that acts in concert with aboveground plant traits, questioning the way we currently predict plant invasions. To test the hypothesis that invasive pine species are more frequently associated with invasive EMF, we performed a principal coordinates analysis (PCoA), based on the dissimilarity among pine species in the frequency of association with each EMF species. [Extracted from the article]

Published
2023
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33. A genomic catalog of Earth’s microbiomes

Author

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium

Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Published
2021

36. Ectomycorrhizal Plant-Fungal Co-invasions as Natural Experiments for Connecting Plant and Fungal Traits to Their Ecosystem Consequences

Author

Hoeksema, Jason D., primary, Averill, Colin, additional, Bhatnagar, Jennifer M., additional, Brzostek, Edward, additional, Buscardo, Erika, additional, Chen, Ko-Hsuan, additional, Liao, Hui-Ling, additional, Nagy, Laszlo, additional, Policelli, Nahuel, additional, Ridgeway, Joanna, additional, Rojas, J. Alejandro, additional, and Vilgalys, Rytas, additional

Published
2020
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40. Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

Author

Zanne, Amy E., primary, Abarenkov, Kessy, additional, Afkhami, Michelle E., additional, Aguilar‐Trigueros, Carlos A., additional, Bates, Scott, additional, Bhatnagar, Jennifer M., additional, Busby, Posy E., additional, Christian, Natalie, additional, Cornwell, William K., additional, Crowther, Thomas W., additional, Flores‐Moreno, Habacuc, additional, Floudas, Dimitrios, additional, Gazis, Romina, additional, Hibbett, David, additional, Kennedy, Peter, additional, Lindner, Daniel L., additional, Maynard, Daniel S., additional, Milo, Amy M., additional, Nilsson, Rolf Henrik, additional, Powell, Jeff, additional, Schildhauer, Mark, additional, Schilling, Jonathan, additional, and Treseder, Kathleen K., additional

Published
2019
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43. Detecting macroecological patterns in bacterial communities across independent studies of global soils

Author

Ramirez, Kelly S., Knight, Christopher G., de Hollander, Mattias, Brearley, Francis Q., Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W., Davison, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R., Fox, Graeme, Griffiths, Robert I., Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L., Krab, Eveline J., Maestre, Fernando T., McGuire, Krista L., Monteux, Sylvain, Orr, Caroline H., van der Putten, Wim H., Roberts, Ian S., Robinson, David A., Rocca, Jennifer D., Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K., Straathof, Angela L., Bhatnagar, Jennifer M., Thion, Cecile, van der Heijden, Marcel G. A., de Vries, Franciska T., Ramirez, Kelly S., Knight, Christopher G., de Hollander, Mattias, Brearley, Francis Q., Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W., Davison, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R., Fox, Graeme, Griffiths, Robert I., Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L., Krab, Eveline J., Maestre, Fernando T., McGuire, Krista L., Monteux, Sylvain, Orr, Caroline H., van der Putten, Wim H., Roberts, Ian S., Robinson, David A., Rocca, Jennifer D., Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K., Straathof, Angela L., Bhatnagar, Jennifer M., Thion, Cecile, van der Heijden, Marcel G. A., and de Vries, Franciska T.

Abstract

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Published
2018
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44. Detecting macroecological patterns in bacterial communities across independent studies of global soils

Author

British Ecological Society, European Commission, Yorkshire Agricultural Society, Northumbria University, Wallenberg Academy, Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Griffiths, Robert [0000-0002-3341-4547], Maestre, Fernando T. [0000-0002-7434-4856], Singh, Brajesh K. [0000-0003-4413-4185], Vries, Franciska T. de [0000-0002-6822-8883], Ramirez, Kelly S., Knight, Christopher G., Hollander, Mattias de, Brearley, Francis Q., Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W., Davinson, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R., Fox, Graeme, Griffiths, Robert, Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L., Krab, Eveline J., Maestre, Fernando T., McGuire, Krista L., Monteux, Sylvain, Orr, Caroline H., Putten, Wim H. van der, Roberts. Ian S., Robinson, David A., Rocca, Jennifer, Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K., Straathof, Angela L., Bhatnagar, Jennifer M., Thion, Cécile, Heijden, Marcel G. A. van der, Vries, Franciska T. de, British Ecological Society, European Commission, Yorkshire Agricultural Society, Northumbria University, Wallenberg Academy, Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Griffiths, Robert [0000-0002-3341-4547], Maestre, Fernando T. [0000-0002-7434-4856], Singh, Brajesh K. [0000-0003-4413-4185], Vries, Franciska T. de [0000-0002-6822-8883], Ramirez, Kelly S., Knight, Christopher G., Hollander, Mattias de, Brearley, Francis Q., Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W., Davinson, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R., Fox, Graeme, Griffiths, Robert, Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L., Krab, Eveline J., Maestre, Fernando T., McGuire, Krista L., Monteux, Sylvain, Orr, Caroline H., Putten, Wim H. van der, Roberts. Ian S., Robinson, David A., Rocca, Jennifer, Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K., Straathof, Angela L., Bhatnagar, Jennifer M., Thion, Cécile, Heijden, Marcel G. A. van der, and Vries, Franciska T. de

Abstract

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Published
2018

45. Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi.

Author

Zanne, Amy E., Abarenkov, Kessy, Afkhami, Michelle E., Aguilar‐Trigueros, Carlos A., Bates, Scott, Bhatnagar, Jennifer M., Busby, Posy E., Christian, Natalie, Cornwell, William K., Crowther, Thomas W., Flores‐Moreno, Habacuc, Floudas, Dimitrios, Gazis, Romina, Hibbett, David, Kennedy, Peter, Lindner, Daniel L., Maynard, Daniel S., Milo, Amy M., Nilsson, Rolf Henrik, and Powell, Jeff

Subjects
PLANT ecology, PLANT capacity, ECOLOGY, CARBON cycle, PLANT nutrients, FUNGI
Abstract

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro‐organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait‐based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and ‐omics‐based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait‐based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology. [ABSTRACT FROM AUTHOR]

Published
2020
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49. Detecting macroecological patterns in bacterial communities across independent studies of global soils

Author

Ramirez, Kelly S., primary, Knight, Christopher G., additional, de Hollander, Mattias, additional, Brearley, Francis Q., additional, Constantinides, Bede, additional, Cotton, Anne, additional, Creer, Si, additional, Crowther, Thomas W., additional, Davison, John, additional, Delgado-Baquerizo, Manuel, additional, Dorrepaal, Ellen, additional, Elliott, David R., additional, Fox, Graeme, additional, Griffiths, Robert I., additional, Hale, Chris, additional, Hartman, Kyle, additional, Houlden, Ashley, additional, Jones, David L., additional, Krab, Eveline J., additional, Maestre, Fernando T., additional, McGuire, Krista L., additional, Monteux, Sylvain, additional, Orr, Caroline H., additional, van der Putten, Wim H., additional, Roberts, Ian S., additional, Robinson, David A., additional, Rocca, Jennifer D., additional, Rowntree, Jennifer, additional, Schlaeppi, Klaus, additional, Shepherd, Matthew, additional, Singh, Brajesh K., additional, Straathof, Angela L., additional, Bhatnagar, Jennifer M., additional, Thion, Cécile, additional, van der Heijden, Marcel G. A., additional, and de Vries, Franciska T., additional

Published
2017
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