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42 results for “microbial traits”
Effect of Warming on Thermal Adaptation of Soil Microbial Growth Traits at Harvard Forest 2013-2023
Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5ºC above ambient temperature with unheated controls for thirty years. We hypothesized that Alphaproteobacteria from warmed plots have (1) less temperature sensitive growth rates; (2) higher optimum growth temperatures; and (3) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22-37ºC in 2-3ºC increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range.
Effects of Long-Term Soil Warming on Microbial Yield, Acquisition, and Stress Traits at Harvard Forest 2014
Soil microbial traits drive ecosystem functions. This relationship can explain why microbial functional diversity is typically positively correlated with ecosystem function. However, microbial adaptation to climate change related warming stress can shift microbial traits with direct implications for carbon cycling in the soil. Here, we investigated how long-term warming affects the relationship between microbial trait diversity and ecosystem function. Soils were sampled after 24 years of +5\degree C warming alongside unheated control soils from the Harvard Forest Long-Term Ecological Research site. Ecosystem function was estimated from six different enzyme activities and microbial biomass. This data was coupled with metatranscriptomics sequencing, where reads were assigned to yield, acquisition, or stress trait categories. We found that in organic horizon soils, warming decreased the richness of acquisition-related traits. In the mineral soils, we observed that heated soils exhibited a negative relationship with the richness of acquisition related traits. These results suggest that the microbial communities exposed to long-term warming is shifting away from a resource acquisition life history strategy.
Data for manuscript: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry
<p>Support manuscript: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry. </p> <p>Dataset includes 1) model and analysis, and 2) supplemental data. </p> <p>In the "model_analysis" file, we include the ecosys model source code, the modeling runs, and the modeling results. The detailed introduction is in README.md file. </p> <p><strong>Acknowledgments</strong></p> <p>We thank the EMERGE Biology Integration Institute Coordinators (members listed in Supplementary Information) for project guidance and management. This research is a contribution of the EMERGE Biology Integration Institute, funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070 (V.I.R., R.K.V., S.R.S., M.B.S., E.L.B., and the EMERGE Coordinators). Additional support for individual contributors included the following. Z.L. was additionally supported by Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy under contract DE-AC52-07NA27344. W.J.R. was supported by the Belowground Biogeochemistry Scientific Focus Area and U.K. was supported by the Watershed Function Science Area, both funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under contract no. DE-AC02-05CH11231. G.L.M. was supported by the LLNL "Microbes Persist" Soil Microbiome Scientific Focus Area SCW1632 and an associated KBase award SCW1746. N.J.B. was supported by the US Department of Energy, Office of Science (BER), Early Career Research Program (#FP00005182). B.J.W. was supported by an Australian Research Council Future Fellowship (#FT210100521). J.T. was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory. </p> <p>We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council’s grant 4.3-2021-00164. This research used resources of the National Energy Research Scientific Computing Center (NERSC) which is a U.S. Department of Energy Office of Science user facility. This research used the Lawrencium computational cluster resource provided by the IT Division at the Lawrence Berkeley National Laboratory (Supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231). </p> <p><strong>Full list of the EMERGE Biology Integration Institute Coordinators and Affiliations</strong></p> <p>Eoin L. Brodie1,2, Sarah C. Bagby3, Jeffrey P. Chanton4, Jessica G. Ernakovich5, Regis Ferriere6,7, Suzanne B. Hodgkins8, William J. Riley1, Virginia I. Rich8,9, Scott R. Saleska6, Matthew B. Sullivan8,9,10, Ruth K. Varner11, Gene W. Tyson12, Malak M. Tfaily13, Ahmed A. Zayed8,9<br> 1Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory; Berkeley, CA 94720, USA.<br>2Department of Environmental Science, Policy and Management, University of California; Berkeley, CA 94720, USA.<br>3Department of Biology, Case Western Reserve University; Cleveland, OH, USA, 44106<br>4Earth Ocean and Atmospheric Sciences, Florida State University; Tallahassee, FL, USA<br>5Department of Natural Resources and the Environment, University of New Hampshire;<br>Durham, NH, USA 03824<br>6Department of Ecology and Evolutionary Biology, University of Arizona; Tucson, AZ,<br>85721, USA<br>7Institut de Biologie de l’ENS, Université Paris Sciences & Lettres; Paris, 75005, France<br>8Department of Microbiology, The Ohio State University; Columbus, OH, USA, 43210<br>9Center of Microbiome Science, The Ohio State University; Columbus, Ohio 43210, USA.<br>10Department of Civil, Environmental and Geodetic engineering, The Ohio State University; Columbus, Ohio 43210, USA.<br>11Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire; Durham, NH 03824, USA.<br>12Centre for Microbiome Research, School of Biomedical Sciences, Queensland University<br>of Technology (QUT), Translational Research Institute; Woolloongabba, QLD, Australia<br>13Department of Environmental Science, University of Arizona; Tucson, AZ, 85721, USA</p>
Soil properties in agricultural systems affect microbial genomic traits
<p>Code and supplementary table </p>
Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits
Climate change will increase soil drying, altering microbial communities via increasing water stress and decreasing resource availability. The responses of these microbial communities to changing environments is likely governed by physiological tradeoffs between high yield, resource acquisition, and stress tolerance (Y-A-S framework). We leveraged a unique field experiment that manipulates both drought and carbon availability across two years and three land uses, and we used both metagenomic and bioassay indicators of the three microbial community traits to test the following hypotheses: 1. Drought increases microbial allocation to stress tolerance functions, at the expense of growth and resource acquisition. 2. Because microbes are resource-limited under drought, increased carbon will enable greater expression of stress tolerance. 3. All three key life history traits described in the YAS framework will trade off, especially when resources are limited. Drought did increase microbial physiological investment in stress tolerance (measured via trehalose production), but we saw few other changes in microbial communities under drought. Carbon addition increased resource acquisition (measured via enzyme activity and resource acquisition gene abundance) and stress tolerance (trehalose assay), but did so in both drought and average rainfall environments. We found no evidence of trait tradeoffs, as we found no significant negative correlations between traits (measured via bioassay and metagenomics). In summary, we found C addition, and to a lesser extent, drought, both altered microbial community function and functional genes. However, resources did not alter drought response in a way that was consistent with theory of life history tradeoffs.
Data from: Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands
<p>This dataset contains data and code that support the results in Weil, S.-S., Martinez-Almoyna, C., Piton, G., Renaud, J., Boulangeat, L., Foulquier, A., ... & Thuiller, W. (2021) Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands (accepted in Journal of Biogeography).</p> <p>We used an extensive plant-soil dataset that covers 14 elevational gradients (between 1500 and 2800 m of elevation) distributed over the whole French Alps to analyse the spatial co-dependencies between the plant and soil compartments. We ran a Graphical Lasso that extracts the direct and indirect linkages between plant functional composition, soil microbial activities, and environmental conditions (local climate and soil properties).</p> <p>Our main results are 1) that plant traits are tightly associated with microbial activities, the former being driven by climate and the latter by soil properties; 2) that the dominance of specific plant traits was more important than their diversity to determine plant-soil linkages; and 3) that soil microbes invested strongly in nutrient acquisition in sites with conservative plant traits and reduced organic matter quality.</p>
Data supporting the manuscript entitled: 'Intermittent soil water stress history favors microbial traits that better mitigate wheat biomass losses during subsequent water stress.'
<p>Data living in this data repository supports the scientific article entitled: Intermittent soil water stress history favors microbial traits that better mitigate wheat biomass losses during subsequent water stress.</p> <p> </p> <p> </p> <p> </p>
Evolution in interacting species alters predator life history traits, behavior and morphology in experimental microbial communities
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Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands
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Data from: Functional diversity enhances, but exploitative traits reduce tree mixture effects on microbial biomass
1. Soil microorganisms play key roles in terrestrial biodiversity and ecosystem functions. Despite recent progress in elucidating the association between plant diversity and soil microorganisms, it remains unclear whether the functional properties of plant mixtures might alter this association. 2. We examined whether the effects of tree species mixtures on soil microbial biomass were impacted by the functional diversity (FD) and community-weighted-mean (CWM) of tree mixtures, by conducting a global meta-analysis involving 123 paired observations of tree mixtures and the corresponding monocultures from 38 studies in forests. 3. We found that the tree mixture effect on microbial biomass increased with the FD of specific leaf area (SLA), leaf N and P content, as well as the FD based on all of these traits plus leaf dry matter content. Meanwhile, the responses of microbial biomass to tree mixtures decreased with the CWM of SLA, leaf N, and P content. The effects of FD and CWM remained consistent, despite variable tree species richness, stand age and climatic factors. 4. Our results provide a new insight that the functional properties of plants may alter the magnitude of the association between plant diversity and soil microorganisms.
Data from: Relationships between rhizosphere microbial communities, soil abiotic properties and root trait variation within a pine species
<p>Rhizosphere microbes play important roles in plant performance and ecosystem functioning. It is becoming increasingly clear that rhizosphere communities vary with soil properties and variation in root traits among plant species. However, less is known about whether and how variation in root traits within plant species influences the rhizosphere microbial communities.</p> <p>We evaluated the intraspecific root traits variation and explored their associations with bacterial and fungal communities in rhizosphere by focusing on an ectomycorrhizal tree<em> </em>species, i.e., <em>Pinus massoniana</em>, in 22 sites in subtropical China.</p> <p>The first dimension of the principal component analysis on root traits revealed evidence for the 'conservation' gradient of the root economics space. Overall, root traits explained more variation in fungal communities than in bacterial communities in the rhizosphere. Functional composition of rhizosphere microbial communities changed significantly along the 'conservation' gradient, with fast-growing copiotrophic bacteria and symbiotic ectomycorrhizal fungi were significantly enriched on the 'acquisition' side, while slow-growing oligotrophic bacteria were significantly enriched on the 'conservation' side of the gradient.</p> <p><strong><em>Synthesis</em></strong>: Our study demonstrates that intraspecific variation in plant roots significantly influence rhizosphere microbial communities, which in turn can influence plant nutrition and therefore plant performance within the community.</p>
Trait Spreadsheet to DwCA: Trophic guild data for microbial eukaryotes
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Updated: 2022-05-31 02:59
Trait Spreadsheet to DwCA: Habitat data for microbial eukaryotes
<p></p>https://eol-jira.bibalex.org/browse/DATA-1882<p></p>Updated: 2022-09-28 15:15
Abiotic and biotic drivers of tree trait effects on soil microbial biomass and soil carbon concentration
<p>Forests are critical ecosystems to understand the global carbon budget, due to their carbon sequestration potential in both above- and belowground compartments, especially in species-rich forests. Soil carbon sequestration is strongly linked to soil microbial communities, and this link is mediated by the tree community, likely due to modifications of micro-environmental conditions (i.e., biotic conditions, soil properties, and microclimate). We studied soil carbon concentration and the soil microbial biomass of 180 local neighborhoods along a gradient of tree species richness ranging from 1 to 16 tree species per plot in a Chinese subtropical forest experiment (BEF-China). Tree productivity and different tree functional traits were measured at the neighborhood level. We tested the effects of tree productivity, functional trait identity and dissimilarity on soil carbon concentrations, and their mediation by the soil microbial biomass and micro-environmental conditions. Our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentrations. Besides, soil carbon concentration increased with tree productivity and tree root diameter while it decreased with litterfall C:N content. Moreover, tree productivity and tree functional traits (e.g. root fungal association and litterfall C:N ratio) modulated micro-environmental conditions with substantial consequences for soil microbial biomass. We also showed that soil history and topography should be considered in future experiments and tree plantations, as soil carbon concentrations were higher where historical (i.e., at the beginning of the experiment) carbon concentrations were high, themselves being strongly affected by the topography. Altogether, these results imply that the quantification of the different soil carbon pools is critical for understanding microbial community–soil carbon stock relationships and their dependence on tree diversity and micro-environmental conditions.</p>
Microbial traits dictate soil neromass accumulation coefficient: A global synthesis
<p><span>The accumulation of microbial necromass carbon has drawn mounting attention due to the slow decomposition. However, it remains unclear what determines the microbial necromass carbon accumulation via reiterated community turnover on large spatial scales. This study aimed to explore the characteristics of soil necromass carbon accumulation in terrestrial ecosystems. A dataset was compiled with 993 observations on the coefficient of microbial carbon accumulation in the equilibrium from 82 peer-reviewed papers. The linear mixed-effect models and structural equation models were used to ascertain the controlling factors of NAC on a global scale.</span><span> The average NAC was higher in croplands (28.2) and forests (26.8) than that in grasslands (21.1). Although the edaphic factors seemingly affect the NAC whereby the NAC lowered in soils with high levels of pH and clay content on a global scale, the biotic factors, particularly for the living microorganism abundance and microbial biomass nitrogen content, were the pivotal drivers of NAC that accounted for approximately 42.5% of the geographic variances in NAC. More organic carbon was likely to be preserved in soil with a higher NAC regardless of ecosystem types. Novel findings on the overriding controls from the living microorganism abundance and microbial biomass nitrogen in driving NAC raise an urgent need for viable strategies in manipulating microbial characteristics for carbon sequestrations.</span></p>
Data from: Relationships between rhizosphere microbial communities, soil abiotic properties and root trait variation within a pine species
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Microbial traits dictate soil neromass accumulation coefficient: A global synthesis
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Data from: Foundational kelp species reveal links between host traits, the environment, and the associated microbial community
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Data from: Functional diversity enhances, but exploitative traits reduce tree mixture effects on microbial biomass
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Abiotic and biotic drivers of tree trait effects on soil microbial biomass and soil carbon concentration
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