151
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Bouskill NJ, Wood TE, Baran R, Ye Z, Bowen BP, Lim H, Zhou J, Nostrand JDV, Nico P, Northen TR, Silver WL, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Front Microbiol 2016; 7:525. [PMID: 27148214 PMCID: PMC4837414 DOI: 10.3389/fmicb.2016.00525] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/30/2016] [Indexed: 11/15/2022] Open
Abstract
Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated drought in the typically aseasonal Luquillo Experimental Forest, Puerto Rico, by intercepting precipitation falling through the forest canopy. This approach reduced soil moisture by 13% and water potential by 0.14 MPa (from -0.2 to -0.34). Previous results from this experiment have demonstrated that the diversity and composition of these soil microbial communities are sensitive to even small changes in soil water. Here, we show prolonged drought significantly alters the functional potential of the community and provokes a clear osmotic stress response, including the production of compatible solutes that increase intracellular C demand. Subsequently, a microbial population emerges with a greater capacity for extracellular enzyme production targeting macromolecular carbon. Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history.
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Affiliation(s)
- Nicholas J Bouskill
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Tana E Wood
- International Institute of Tropical Forestry, USDA Forest ServiceRio Piedras, PR, USA; Fundación Puertorriqueña de ConservaciónSan Juan, PR, USA
| | - Richard Baran
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zaw Ye
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Benjamin P Bowen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - HsiaoChien Lim
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jizhong Zhou
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
| | - Peter Nico
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy and Management, University of California-Berkeley Berkeley, CA, USA
| | - Eoin L Brodie
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California-BerkeleyBerkeley, CA, USA
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152
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Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Front Microbiol 2016; 7:323. [PMID: 27014243 PMCID: PMC4791749 DOI: 10.3389/fmicb.2016.00323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/29/2016] [Indexed: 01/29/2023] Open
Abstract
Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots.
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Affiliation(s)
- Nicholas J Bouskill
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Tana E Wood
- International Institute of Tropical Forestry, United States Department of Agriculture Forest ServiceRio Piedras, PR, USA; Fundación Puertorriqueña de ConservaciónSan Juan, PR, USA
| | - Richard Baran
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zhao Hao
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zaw Ye
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ben P Bowen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hsiao Chien Lim
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Peter S Nico
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Benjamin Gilbert
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
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153
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Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, Hayer M, McHugh TA, Marks JC, Price LB, Hungate BA. Phylogenetic organization of bacterial activity. ISME JOURNAL 2016; 10:2336-40. [PMID: 26943624 PMCID: PMC4989319 DOI: 10.1038/ismej.2016.28] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 11/25/2022]
Abstract
Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with 13C and 18O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.
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Affiliation(s)
- Ember M Morrissey
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.,Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Natasja van Gestel
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Cindy M Liu
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.,Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, AZ, USA.,Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Theresa A McHugh
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Lance B Price
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, AZ, USA.,Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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154
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Villa F, Stewart PS, Klapper I, Jacob JM, Cappitelli F. Subaerial Biofilms on Outdoor Stone Monuments: Changing the Perspective Toward an Ecological Framework. Bioscience 2016. [DOI: 10.1093/biosci/biw006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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155
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Comparative Toxicities of Salts on Microbial Processes in Soil. Appl Environ Microbiol 2016; 82:2012-2020. [PMID: 26801570 DOI: 10.1128/aem.04052-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 01/13/2016] [Indexed: 11/20/2022] Open
Abstract
Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO4(2-) than Cl(-) salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO4(2-) salts but not to Cl(-) salts; no evidence was found to distinguish K(+) and Na(+) salts.
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156
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Wu J, Pang Z, Sun T, Kan H, Hu W, Li X. Soil respiration simulation based on soil temperature and water content in artificial smooth brome grassland. RANGELAND JOURNAL 2016. [DOI: 10.1071/rj16023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Correctly quantifying the relationships between soil respiration and environmental factors and their sources of variability is essential to predict future carbon fluxes and climate feedback. Soil water conditions and soil temperature strongly affect soil respiration and the dynamics of soil organic matter. Despite this, simulation of soil respiration (Rs) based on soil temperature (Ts) and soil volumetric water content (θ) must still be improved, as demonstrated by its discrepant model performance among different seasons. With the objective of gaining a further understanding of the relationships of Rs with Ts and θ and providing an improved model to simulate Rs variations, we measured hourly Rs, Ts and θ using the chamber technique in artificial smooth brome grassland for analysis. We began by dividing the four seasons of a year according to the daily mean air temperature, followed by representing the seasonal variation of Rs, Ts and θ. We found that Rs correlated significantly with Ts in an exponential relationship and with θ in a parabolic relationship seasonally, where the determination coefficient of the Rs-θ relationship was significantly larger than that of the Rs-Ts relationship. We also discovered that the shape of the Rs-θ relationship was seasonally dependent because the optimal θ and the width of the peak Rs around the optimal θ were seasonally specific. Finally, by considering seasonality, the combinational simulation model explained more variation of soil respiration. Thus, seasonality should be considered for more reliable model simulations of soil respiration. These findings are relevant for more accurate predictions and modelling of soil respiration, particularly in temperate artificial grasslands with a continental monsoon climate, where the ‘Birch effect’ strengthens seasonality, and these findings further our understanding of changes in the rates of soil carbon losses as artificial grassland is established.
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157
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Martiny JBH, Jones SE, Lennon JT, Martiny AC. Microbiomes in light of traits: A phylogenetic perspective. Science 2015; 350:aac9323. [PMID: 26542581 DOI: 10.1126/science.aac9323] [Citation(s) in RCA: 399] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A focus on the phenotypic characteristics of microorganisms-their traits-offers a path for interpreting the growing amount of microbiome data. We review key aspects of microbial traits, as well as approaches used to assay their phylogenetic distribution. Recent studies reveal that microbial traits are differentially conserved across the tree of life and appear to be conserved in a hierarchical fashion, possibly linked to their biochemical complexity. These results suggest a predictive framework whereby the genetic (or taxonomic) resolution of microbiome variation among samples provides information about the traits under selection. The organizational parallels seen among human and free-living microbiomes seem to support this idea. Developments in this framework may offer predictions not only for how microbial composition responds to changing environmental conditions, but also for how these changes may alter the health or functioning in human, engineered, and environmental systems.
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Affiliation(s)
- Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Stuart E Jones
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA. Department of Earth System Science, University of California, Irvine, CA, USA
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158
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Erlandson SR, Savage JA, Cavender-Bares JM, Peay KG. Soil moisture and chemistry influence diversity of ectomycorrhizal fungal communities associating with willow along an hydrologic gradient. FEMS Microbiol Ecol 2015; 92:fiv148. [DOI: 10.1093/femsec/fiv148] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2015] [Indexed: 11/13/2022] Open
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159
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Ruiz-González C, Salazar G, Logares R, Proia L, Gasol JM, Sabater S. Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River. Front Microbiol 2015; 6:1293. [PMID: 26635761 PMCID: PMC4659902 DOI: 10.3389/fmicb.2015.01293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated whether the changes in abundance of six dominant bacterial classes (Actinobacteria, Beta-/Alpha-/Gamma-proteobacteria, Flavobacteria, and Sphingobacteria) along a large dam-regulated river are reflected by those of their constituent Operational Taxonomic Units (OTUs; 97% similarity level). The environmental impact generated by the reservoirs promoted clear compositional shifts in all bacterial classes that resulted from changes in the abundance of individual OTUs rather than from the appearance of new taxa along the river. Abundance patterns at the class level represented the dynamics of only a small but variable proportion of their constituting OTUs, which were not necessarily the most abundant ones. Within most classes, we detected sub-groups of OTUs showing contrasting responses to reservoir-induced environmental changes. Overall, we show that the patterns observed at the class level fail to capture the dynamics of a significant fraction of their constituent members, calling for caution when the ecological attributes of high-ranks are to be interpreted.
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Affiliation(s)
- Clara Ruiz-González
- Institute of Aquatic Ecology, University of Girona Girona, Spain ; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain ; Département des Sciences Biologiques, Université du Québec à Montréal Montréal, QC, Canada
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain
| | - Lorenzo Proia
- Institute of Aquatic Ecology, University of Girona Girona, Spain ; Catalan Institute for Water Research, Scienfitic and Technological Parc of the University of Girona Girona, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC) Barcelona, Spain
| | - Sergi Sabater
- Institute of Aquatic Ecology, University of Girona Girona, Spain ; Catalan Institute for Water Research, Scienfitic and Technological Parc of the University of Girona Girona, Spain
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160
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Veresoglou SD, Halley JM, Rillig MC. Extinction risk of soil biota. Nat Commun 2015; 6:8862. [PMID: 26593272 PMCID: PMC4673489 DOI: 10.1038/ncomms9862] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023] Open
Abstract
No species lives on earth forever. Knowing when and why species go extinct is crucial for a complete understanding of the consequences of anthropogenic activity, and its impact on ecosystem functioning. Even though soil biota play a key role in maintaining the functioning of ecosystems, the vast majority of existing studies focus on aboveground organisms. Many questions about the fate of belowground organisms remain open, so the combined effort of theorists and applied ecologists is needed in the ongoing development of soil extinction ecology.
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Affiliation(s)
- Stavros D. Veresoglou
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, Altensteinstrasse 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - John M. Halley
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Matthias C. Rillig
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, Altensteinstrasse 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
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161
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Nemergut DR, Knelman JE, Ferrenberg S, Bilinski T, Melbourne B, Jiang L, Violle C, Darcy JL, Prest T, Schmidt SK, Townsend AR. Decreases in average bacterial community rRNA operon copy number during succession. ISME JOURNAL 2015; 10:1147-56. [PMID: 26565722 PMCID: PMC5029226 DOI: 10.1038/ismej.2015.191] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 07/27/2015] [Accepted: 09/25/2015] [Indexed: 02/01/2023]
Abstract
Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.
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Affiliation(s)
- Diana R Nemergut
- Department of Biology, Duke University, Durham, NC, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
| | - Joseph E Knelman
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Scott Ferrenberg
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,U.S. Geological Survey, Canyonlands Research Station, Moab, UT, USA
| | - Teresa Bilinski
- Department of Biological Sciences, St Edward's University, Austin, TX, USA
| | - Brett Melbourne
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Lin Jiang
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cyrille Violle
- Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
| | - John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Tiffany Prest
- Department of Biology, Duke University, Durham, NC, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Alan R Townsend
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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162
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Riquelme C, Rigal F, Hathaway JJM, Northup DE, Spilde MN, Borges PAV, Gabriel R, Amorim IR, Dapkevicius MDLNE. Cave microbial community composition in oceanic islands: disentangling the effect of different colored mats in diversity patterns of Azorean lava caves. FEMS Microbiol Ecol 2015; 91:fiv141. [PMID: 26564959 DOI: 10.1093/femsec/fiv141] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 11/14/2022] Open
Abstract
Processes determining diversity and composition of bacterial communities in island volcanic caves are still poorly understood. Here, we characterized colored microbial mats in 14 volcanic caves from two oceanic islands of the Azores using 16S rRNA gene sequences. Factors determining community diversity (α) and composition (β) were explored, namely colored mats, caves and islands, as well as environmental and chemical characteristics of caves. Additive partitioning of diversity using OTU occurrence showed a greater influence of β-diversity between islands and caves that may relate to differences in rare OTUs (singletons and doubletons) across scales. In contrast, Shannon diversity partitioning revealed the importance of the lowest hierarchical level (α diversity, colored mat), suggesting a dominance of cosmopolitan OTUs (>1%) in most samples. Cosmopolitan OTUs included members involved in nitrogen cycling, supporting the importance of this process in Azorean caves. Environmental and chemical conditions in caves did not show any significant relationship to OTU diversity and composition. The absence of clear differences between mat colors and across scales may be explained by (1) the geological youth of the cave system (cave communities have not had enough time to diverge) or/and (2) community convergence, as the result of selection pressure in extreme environments.
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Affiliation(s)
- Cristina Riquelme
- Food Science and Health Group (CITA-A), Universidade dos Açores, Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - François Rigal
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal Environment and Microbiology Team, MELODY group, Université of Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| | - Jennifer J M Hathaway
- Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Diana E Northup
- Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael N Spilde
- Institute of Meteoritics, MSC03 2050, University of New Mexico, Albuquerque, NM 87131, USA
| | - Paulo A V Borges
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - Rosalina Gabriel
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - Isabel R Amorim
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - Maria de Lurdes N E Dapkevicius
- Food Science and Health Group (CITA-A), Universidade dos Açores, Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
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163
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Toward Modeling the Resistance and Resilience of "Below-ground" Fungal Communities: A Mechanistic and Trait-Based Approach. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:1-44. [PMID: 26505687 DOI: 10.1016/bs.aambs.2015.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The role of fungi in shaping ecosystems is well evidenced and there is growing recognition of their importance among scientists and the general public. Establishing and separating the role of key local (soil chemical, biological, and physical properties) and global (climate, dispersal limitation) drivers in fungal community structure and functioning is currently a source of frustration to mycologists. The quest to determine niche processes and environmental characteristics shaping fungal community structure, known to be important for plant and animal communities, is proving difficult, resulting in the acknowledgment that niche neutral processes (climate, dispersal limitations) may dominate. The search for predictable patterns in fungal community structure may have been restricted as the "appropriate" scales at which to measure community structure and characterize the environment have not been fully determined yet, and the focus on taxonomy makes it difficult to link environmental characteristics to fungal traits. While key determinants of microbial community composition have been uncovered for some functional groups, the differential response of functional groups is largely unknown. Before we can truly understand what drives the development of microbial community structure, an understanding of the autecology of major fungal taxa and how they interact with their immediate environment (from the micro- up to kilometer scale) is urgently needed. Furthermore, key information and empirical data is missing at the microscale due to experimental difficulties in mapping this heterogeneous and opaque environment. We therefore present a framework that would help generate this much-needed empirical data and information at the microscale, together with modeling approaches to link the spatial and temporal scales. The latter is important as we propose that there is much to be gained by linking our understanding of fungal community responses across scales, in order to develop species and community-environment-function predictive models.
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164
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Bier RL, Bernhardt ES, Boot CM, Graham EB, Hall EK, Lennon JT, Nemergut DR, Osborne BB, Ruiz-González C, Schimel JP, Waldrop MP, Wallenstein MD. Linking microbial community structure and microbial processes: an empirical and conceptual overview. FEMS Microbiol Ecol 2015; 91:fiv113. [DOI: 10.1093/femsec/fiv113] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 01/20/2023] Open
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165
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Larsen PE, Collart FR, Dai Y. Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PLoS One 2015; 10:e0132837. [PMID: 26332409 PMCID: PMC4557938 DOI: 10.1371/journal.pone.0132837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/18/2015] [Indexed: 12/17/2022] Open
Abstract
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. However, new algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad's ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism's transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
| | - Yang Dai
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
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166
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Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons. mBio 2015; 6:e00746. [PMID: 26242625 PMCID: PMC4526712 DOI: 10.1128/mbio.00746-15] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/20/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. IMPORTANCE We document the successional patterns of rhizosphere bacterial communities associated with a "wild" annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address "domesticated" plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable over two growing seasons. There are few studies assessing the reproducibility over multiple seasons. Through the growing season, the rhizosphere community became progressively less diverse, likely reflecting root homogenization of soil microniches. Phylogenetic clustering of the rhizosphere dynamic taxa suggests evolutionary adaptation to Avena roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.
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Affiliation(s)
- Shengjing Shi
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Erin Nuccio
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Donald J Herman
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruud Rijkers
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Katerina Estera
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Jiabao Li
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulisses Nunes da Rocha
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Eoin L Brodie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Mary Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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167
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Classen AT, Sundqvist MK, Henning JA, Newman GS, Moore JAM, Cregger MA, Moorhead LC, Patterson CM. Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? Ecosphere 2015. [DOI: 10.1890/es15-00217.1] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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168
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Wang L, Manzoni S, Ravi S, Riveros-Iregui D, Caylor K. Dynamic interactions of ecohydrological and biogeochemical processes in water-limited systems. Ecosphere 2015. [DOI: 10.1890/es15-00122.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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169
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Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00689-15. [PMID: 26089434 PMCID: PMC4472911 DOI: 10.1128/genomea.00689-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments.
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170
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Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils. J Microbiol Methods 2015; 115:112-20. [PMID: 26055315 DOI: 10.1016/j.mimet.2015.05.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/30/2015] [Accepted: 05/30/2015] [Indexed: 01/05/2023]
Abstract
We tested a method of estimating the activity of detectable individual bacterial and archaeal OTUs within a community by calculating ratios of absolute 16S rRNA to rDNA copy numbers. We investigated phylogenetically coherent patterns of activity among soil prokaryotes in non-growing soil communities. 'Activity ratios' were calculated for bacteria and archaea in soil sampled from a tropical rainforest and temperate agricultural field and incubated for one year at two levels of moisture availability and with and without carbon additions. Prior to calculating activity ratios, we corrected the relative abundances of OTUs to account for multiple copies of the 16S gene per genome. Although necessary to ensure accurate activity ratios, this correction did not change our interpretation of differences in microbial community composition across treatments. Activity ratios in this study were lower than those previously published (0.0003-210, logarithmic mean=0.24), suggesting significant extracellular DNA preservation. After controlling for the influence of individual incubation jars, significant differences in activity ratios between all members of each phylum were observed. Planctomycetes and Firmicutes had the highest activity ratios and Crenarchaeota had the lowest activity overall. Our results suggest that greater caution should be taken in interpreting soil microbial community data derived from extracted DNA. Indirect extraction methods may be useful in ensuring that microbes identified from extracellular DNA are not erroneously interpreted as components of an active microbial community.
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171
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Microbial response to simulated global change is phylogenetically conserved and linked with functional potential. ISME JOURNAL 2015; 10:109-18. [PMID: 26046258 DOI: 10.1038/ismej.2015.96] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/30/2015] [Accepted: 05/03/2015] [Indexed: 11/08/2022]
Abstract
The high diversity of microbial communities hampers predictions about their responses to global change. Here we investigate the potential for using a phylogenetic, trait-based framework to capture the response of bacteria and fungi to global change manipulations. Replicated grassland plots were subjected to 3+ years of drought and nitrogen fertilization. The responses of leaf litter bacteria and fungi to these simulated changes were significantly phylogenetically conserved. Proportional changes in abundance were highly correlated among related organisms, such that relatives with approximately 5% ribosomal DNA genetic distance showed similar responses to the treatments. A microbe's change in relative abundance was significantly correlated between the treatments, suggesting a compromise between numerical abundance in undisturbed environments and resistance to change in general, independent of disturbance type. Lineages in which at least 90% of the microbes shared the same response were circumscribed at a modest phylogenetic depth (τD 0.014-0.021), but significantly larger than randomized simulations predict. In several clades, phylogenetic depth of trait consensus was higher. Fungal response to drought was more conserved than was response to nitrogen fertilization, whereas bacteria responded equally to both treatments. Finally, we show that a bacterium's response to the manipulations is correlated with its potential functional traits (measured here as the number of glycoside hydrolase genes encoding the capacity to degrade different types of carbohydrates). Together, these results suggest that a phylogenetic, trait-based framework may be useful for predicting shifts in microbial composition and functioning in the face of global change.
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172
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Freedman ZB, Zak DR. Atmospheric N deposition alters connectance, but not functional potential among saprotrophic bacterial communities. Mol Ecol 2015; 24:3170-80. [PMID: 25943298 DOI: 10.1111/mec.13224] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 11/28/2022]
Abstract
The use of co-occurrence patterns to investigate interactions between micro-organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co-occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.
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Affiliation(s)
- Zachary B Freedman
- School of Natural Resources & Environment, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Donald R Zak
- School of Natural Resources & Environment, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, 48109, USA
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173
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Abstract
Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance-β-glucan synthesis, trehalose production, and cold-induced RNA helicases-were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter-lignin peroxidases, cellobiohydrolases, and crystalline cellulases-were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.
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Affiliation(s)
- Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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174
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Wilhelm L, Besemer K, Fragner L, Peter H, Weckwerth W, Battin TJ. Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms. ISME JOURNAL 2015; 9:2454-64. [PMID: 25978543 DOI: 10.1038/ismej.2015.56] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/04/2015] [Accepted: 03/09/2015] [Indexed: 01/18/2023]
Abstract
Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.
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Affiliation(s)
- Linda Wilhelm
- Department of Limnology and Oceanography, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | | | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Hannes Peter
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Tom J Battin
- Department of Limnology and Oceanography, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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175
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Huerta AI, Milling A, Allen C. Tropical strains of Ralstonia solanacearum Outcompete race 3 biovar 2 strains at lowland tropical temperatures. Appl Environ Microbiol 2015; 81:3542-51. [PMID: 25769835 PMCID: PMC4407210 DOI: 10.1128/aem.04123-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/10/2015] [Indexed: 01/21/2023] Open
Abstract
Bacterial wilt, caused by members of the heterogenous Ralstonia solanacearum species complex, is an economically important vascular disease affecting many crops. Human activity has widely disseminated R. solanacearum strains, increasing their global agricultural impact. However, tropical highland race 3 biovar 2 (R3bv2) strains do not cause disease in tropical lowlands, even though they are virulent at warm temperatures. We tested the hypothesis that differences in temperature adaptation and competitive fitness explain the uneven geographic distribution of R. solanacearum strains. Using three phylogenetically and ecologically distinct strains, we measured competitive fitness at two temperatures following paired-strain inoculations of their shared host, tomato. Lowland tropical strain GMI1000 was only weakly virulent on tomato under temperate conditions (24°C for day and 19°C for night [24/19°C]), but highland tropical R3bv2 strain UW551 and U.S. warm temperate strain K60 were highly virulent at both 24/19°C and 28°C. Strain K60 was significantly more competitive than both GMI1000 and UW551 in tomato rhizospheres and stems at 28°C, and GMI1000 also outcompeted UW551 at 28°C. The results were reversed at cooler temperatures, at which highland strain UW551 generally outcompeted GMI1000 and K60 in planta. The superior competitive index of UW551 at 24/19°C suggests that adaptation to cool temperatures could explain why only R3bv2 strains threaten highland agriculture. Strains K60 and GMI1000 each produced different bacteriocins that inhibited growth of UW551 in culture. Such interstrain inhibition could explain why R3bv2 strains do not cause disease in tropical lowlands.
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Affiliation(s)
- Alejandra I Huerta
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Annett Milling
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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176
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Hawkes CV, Keitt TH. Resilience vs. historical contingency in microbial responses to environmental change. Ecol Lett 2015; 18:612-25. [PMID: 25950733 DOI: 10.1111/ele.12451] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/17/2015] [Accepted: 04/13/2015] [Indexed: 12/30/2022]
Abstract
How soil processes such as carbon cycling will respond to future climate change depends on the responses of complex microbial communities, but most ecosystem models assume that microbial functional responses are resilient and can be predicted from simple parameters such as biomass and temperature. Here, we consider how historical contingencies might alter those responses because function depends on prior conditions or biota. Functional resilience can be driven by physiological, community or adaptive shifts; historical contingencies can result from the influence of historical environments or a combination of priority effects and biotic resistance. By modelling microbial population responses to environmental change, we demonstrate that historical environments can constrain soil function with the degree of constraint depending on the magnitude of change in the context of the prior environment. For example microbial assemblages from more constant environments were more sensitive to change leading to poorer functional acclimatisation compared to microbial assemblages from more fluctuating environments. Such historical contingencies can lead to deviations from expected functional responses to climate change as well as local variability in those responses. Our results form a set of interrelated hypotheses regarding soil microbial responses to climate change that warrant future empirical attention.
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Affiliation(s)
- Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Timothy H Keitt
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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177
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Waring BG, Hawkes CV. Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest. MICROBIAL ECOLOGY 2015; 69:843-854. [PMID: 24889286 DOI: 10.1007/s00248-014-0436-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
Many wet tropical forests, which contain a quarter of global terrestrial biomass carbon stocks, will experience changes in precipitation regime over the next century. Soil microbial responses to altered rainfall are likely to be an important feedback on ecosystem carbon cycling, but the ecological mechanisms underpinning these responses are poorly understood. We examined how reduced rainfall affected soil microbial abundance, activity, and community composition using a 6-month precipitation exclusion experiment at La Selva Biological Station, Costa Rica. Thereafter, we addressed the persistent effects of field moisture treatments by exposing soils to a controlled soil moisture gradient in the lab for 4 weeks. In the field, compositional and functional responses to reduced rainfall were dependent on initial conditions, consistent with a large degree of spatial heterogeneity in tropical forests. However, the precipitation manipulation significantly altered microbial functional responses to soil moisture. Communities with prior drought exposure exhibited higher respiration rates per unit microbial biomass under all conditions and respired significantly more CO2 than control soils at low soil moisture. These functional patterns suggest that changes in microbial physiology may drive positive feedbacks to rising atmospheric CO2 concentrations if wet tropical forests experience longer or more intense dry seasons in the future.
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Affiliation(s)
- Bonnie G Waring
- Section of Integrative Biology, University of Texas at Austin, Austin, TX, USA,
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178
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Biancalani T, DeVille L, Goldenfeld N. Framework for analyzing ecological trait-based models in multidimensional niche spaces. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052107. [PMID: 26066119 DOI: 10.1103/physreve.91.052107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Indexed: 06/04/2023]
Abstract
We develop a theoretical framework for analyzing ecological models with a multidimensional niche space. Our approach relies on the fact that ecological niches are described by sequences of symbols, which allows us to include multiple phenotypic traits. Ecological drivers, such as competitive exclusion, are modeled by introducing the Hamming distance between two sequences. We show that a suitable transform diagonalizes the community interaction matrix of these models, making it possible to predict the conditions for niche differentiation and, close to the instability onset, the asymptotically long time population distributions of niches. We exemplify our method using the Lotka-Volterra equations with an exponential competition kernel.
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Affiliation(s)
- Tommaso Biancalani
- Department of Physics and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Loomis Laboratory of Physics, 1110 West Green Street, Urbana, Illinois 61801-3080, USA
| | - Lee DeVille
- Department of Mathematics and Institute for Genomic Biology, 1409 West Green Street, Urbana, Illinois 61801, USA
| | - Nigel Goldenfeld
- Department of Physics and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Loomis Laboratory of Physics, 1110 West Green Street, Urbana, Illinois 61801-3080, USA
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179
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Amend AS, Matulich KL, Martiny JBH. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities. Front Microbiol 2015; 6:109. [PMID: 25741330 PMCID: PMC4332350 DOI: 10.3389/fmicb.2015.00109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/28/2015] [Indexed: 11/15/2022] Open
Abstract
Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context.
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Affiliation(s)
- Anthony S Amend
- Department of Botany, University of Hawaii at Manoa Honolulu, HI, USA
| | - Kristin L Matulich
- Department of Ecology and Evolutionary Biology, University of California at Irvine Irvine, CA USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California at Irvine Irvine, CA USA
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180
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DeAngelis KM, Pold G, Topçuoğlu BD, van Diepen LTA, Varney RM, Blanchard JL, Melillo J, Frey SD. Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol 2015; 6:104. [PMID: 25762989 PMCID: PMC4327730 DOI: 10.3389/fmicb.2015.00104] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/27/2015] [Indexed: 01/24/2023] Open
Abstract
Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
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Affiliation(s)
| | - Grace Pold
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Begüm D Topçuoğlu
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Linda T A van Diepen
- Department of Natural Resources and the Environment, University of New Hampshire Durham, NH, USA
| | - Rebecca M Varney
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | | | | | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire Durham, NH, USA
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181
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Lawrence DJ, Beauchamp DA, Olden JD. Life-stage-specific physiology defines invasion extent of a riverine fish. J Anim Ecol 2015; 84:879-888. [DOI: 10.1111/1365-2656.12332] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 01/07/2015] [Indexed: 11/28/2022]
Affiliation(s)
- David J. Lawrence
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA 98195 USA
| | - David A. Beauchamp
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA 98195 USA
- U.S. Geological Survey; Washington Cooperative Fisheries and Wildlife Research Unit; School of Aquatic and Fishery Science; University of Washington; Seattle WA 98195 USA
| | - Julian D. Olden
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA 98195 USA
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182
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Aanderud ZT, Jones SE, Fierer N, Lennon JT. Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Front Microbiol 2015; 6:24. [PMID: 25688238 PMCID: PMC4311709 DOI: 10.3389/fmicb.2015.00024] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/08/2015] [Indexed: 11/13/2022] Open
Abstract
Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H(18) 2O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69-74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5-20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.
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Affiliation(s)
- Zachary T Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University Provo, UT, USA
| | - Stuart E Jones
- Department of Biological Sciences, University of Notre Dame South Bend, IN, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and CIRES, University of Colorado Boulder, CO, USA ; Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Jay T Lennon
- Department of Biology, Indiana University Bloomington, IN, USA
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183
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Zhang X, Barberán A, Zhu X, Zhang G, Han X. Water content differences have stronger effects than plant functional groups on soil bacteria in a steppe ecosystem. PLoS One 2014; 9:e115798. [PMID: 25546333 PMCID: PMC4278768 DOI: 10.1371/journal.pone.0115798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/26/2014] [Indexed: 12/14/2022] Open
Abstract
Many investigations across natural and artificial plant diversity gradients have reported that both soil physicochemical factors and plant community composition affect soil microbial communities. To test the effect of plant diversity loss on soil bacterial communities, we conducted a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia (China). We found that the number and composition type of plant functional groups had no effect on bacterial diversity and community composition, or on the relative abundance of major taxa. In contrast, bacterial community patterns were significantly structured by soil water content differences among plots. Our results support researches that suggest that water availability is the key factor structuring soil bacterial communities in this semi-arid ecosystem.
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Affiliation(s)
- Ximei Zhang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Albert Barberán
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, United States of America
| | - Xunzhi Zhu
- School of Biology and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Guangming Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- * E-mail: (GZ); (XH)
| | - Xingguo Han
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- * E-mail: (GZ); (XH)
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184
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Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK. Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. Front Microbiol 2014; 5:698. [PMID: 25566214 PMCID: PMC4269115 DOI: 10.3389/fmicb.2014.00698] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022] Open
Abstract
Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75-78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56-72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.
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Affiliation(s)
- Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - John L. Darcy
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Diana R. Nemergut
- Environmental Studies Program, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
- Department of Biology, Duke UniversityDurham, NC, USA
| | - Steve K. Schmidt
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
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185
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Mackie KA, Schmidt HP, Müller T, Kandeler E. Cover crops influence soil microorganisms and phytoextraction of copper from a moderately contaminated vineyard. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 500-501:34-43. [PMID: 25217742 DOI: 10.1016/j.scitotenv.2014.08.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/03/2014] [Accepted: 08/25/2014] [Indexed: 06/03/2023]
Abstract
We investigated the ability of summer (Avena sativa [oat], Trifolium incarnatum [crimson clover], Chenopodium [goosefoot]) and winter (Vicia villosa [hairy vetch], Secale Cereale L. [Rye], Brassica napus L. partim [rape]) cover crops, including a mixed species treatment, to extract copper from an organic vineyard soil in situ and the microbial communities that may support it. Clover had the highest copper content (14.3mgCukg(-1) DM). However, it was the amount of total biomass production that determined which species was most effective at overall copper removal per hectare. The winter crop rye produced significantly higher amounts of biomass (3532kgDMha(-1)) and, therefore, removed significantly higher amounts of copper (14,920mgCuha(-1)), despite less accumulation of copper in plant shoots. The maximum annual removal rate, a summation of best performing summer and winter crops, would be 0.033kgCuha(-1)y(-1). Due to this low annual extraction efficiency, which is less than the 6kgCuha(-1)y(-1) permitted for application, phytoextraction cannot be recommended as a general method of copper extraction from vineyards. Copper concentration did not influence aboveground or belowground properties, as indicated by sampling at two distances from the grapevine row with different soil copper concentrations. Soil microorganisms may have become tolerant to the copper levels at this site. Microbial biomass and soil enzyme activities (arylsulfatase and phosphatase) were instead driven by seasonal fluxes of resource pools. Gram+ bacteria were associated with high soil moisture, while fungi seemed to be driven by extractable carbon, which was linked to high plant biomass. There was no microbial group associated with the increased phytoextraction of copper. Moreover, treatment did not influence the abundance, activity or community structure of soil microorganisms.
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Affiliation(s)
- K A Mackie
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Emil-Wolff-Strasse 27, 70599 Stuttgart, Germany.
| | - H P Schmidt
- Ithaka Institute, La Place 92, 1966 Ayent, Switzerland
| | - T Müller
- Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 20, 70599 Stuttgart, Germany
| | - E Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Emil-Wolff-Strasse 27, 70599 Stuttgart, Germany
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186
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Fierer N, Barberán A, Laughlin DC. Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Front Microbiol 2014; 5:614. [PMID: 25429288 PMCID: PMC4228856 DOI: 10.3389/fmicb.2014.00614] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 02/03/2023] Open
Abstract
Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.
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Affiliation(s)
- Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
| | - Albert Barberán
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Daniel C Laughlin
- Environmental Research Institute, School of Science, University of Waikato Hamilton, New Zealand
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187
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Crowther TW, Maynard DS, Crowther TR, Peccia J, Smith JR, Bradford MA. Untangling the fungal niche: the trait-based approach. Front Microbiol 2014; 5:579. [PMID: 25400630 PMCID: PMC4215788 DOI: 10.3389/fmicb.2014.00579] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/14/2014] [Indexed: 11/26/2022] Open
Abstract
Fungi are prominent components of most terrestrial ecosystems, both in terms of biomass and ecosystem functioning, but the hyper-diverse nature of most communities has obscured the search for unifying principles governing community organization. In particular, unlike plants and animals, observational studies provide little evidence for the existence of niche processes in structuring fungal communities at broad spatial scales. This limits our capacity to predict how communities, and their functioning, vary across landscapes. We outline how a shift in focus, from taxonomy toward functional traits, might prove to be valuable in the search for general patterns in fungal ecology. We build on theoretical advances in plant and animal ecology to provide an empirical framework for a trait-based approach in fungal community ecology. Drawing upon specific characteristics of the fungal system, we highlight the significance of drought stress and combat in structuring free-living fungal communities. We propose a conceptual model to formalize how trade-offs between stress-tolerance and combative dominance are likely to organize communities across environmental gradients. Given that the survival of a fungus in a given environment is contingent on its ability to tolerate antagonistic competitors, measuring variation in combat trait expression along environmental gradients provides a means of elucidating realized, from fundamental niche spaces. We conclude that, using a trait-based understanding of how niche processes structure fungal communities across time and space, we can ultimately link communities with ecosystem functioning. Our trait-based framework highlights fundamental uncertainties that require testing in the fungal system, given their potential to uncover general mechanisms in fungal ecology.
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Affiliation(s)
- Thomas W. Crowther
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
| | - Daniel S. Maynard
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
| | | | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale UniversityNew Haven, CT, USA
| | - Jeffrey R. Smith
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
| | - Mark A. Bradford
- Yale School of Forestry and Environmental Studies, Yale UniversityNew Haven, CT, USA
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188
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Peralta AL, Matthews JW, Kent AD. Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms. MICROBIAL ECOLOGY 2014; 68:339-350. [PMID: 24658457 DOI: 10.1007/s00248-014-0407-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/27/2014] [Indexed: 06/03/2023]
Abstract
Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.
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189
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Lentendu G, Wubet T, Chatzinotas A, Wilhelm C, Buscot F, Schlegel M. Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach. Mol Ecol 2014; 23:3341-55. [DOI: 10.1111/mec.12819] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Guillaume Lentendu
- Plant Physiology; Institute of Biology; University of Leipzig; Johannisallee 21-23 Leipzig 04103 Germany
- Molecular Evolution and Animal Systematics; Institute of Biology; University of Leipzig; Talstraße 33 Leipzig 04103 Germany
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 Halle/Saale 06120 Germany
| | - Tesfaye Wubet
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 Halle/Saale 06120 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology; UFZ - Helmholtz Centre for Environmental Research; Permoserstraße 15 Leipzig 04318 Germany
| | - Christian Wilhelm
- Plant Physiology; Institute of Biology; University of Leipzig; Johannisallee 21-23 Leipzig 04103 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
| | - François Buscot
- Department of Soil Ecology; UFZ - Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 Halle/Saale 06120 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics; Institute of Biology; University of Leipzig; Talstraße 33 Leipzig 04103 Germany
- German Centre for Integrative Biodiversity Research (iDiv); Halle-Jena-Leipzig; Deutscher Platz 5e Leipzig 04103 Germany
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190
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Krause S, Le Roux X, Niklaus PA, Van Bodegom PM, Lennon JT, Bertilsson S, Grossart HP, Philippot L, Bodelier PLE. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Front Microbiol 2014; 5:251. [PMID: 24904563 PMCID: PMC4033906 DOI: 10.3389/fmicb.2014.00251] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/07/2014] [Indexed: 11/13/2022] Open
Abstract
In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Chemical Engineering, University of Washington Seattle, WA, USA
| | - Xavier Le Roux
- Ecologie Microbienne, CNRS, INRA, Université de Lyon, Université Lyon 1, UMR 5557, USC 1193 Villeurbanne, France
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich Zurich, Switzerland
| | - Peter M Van Bodegom
- Subdepartment of Systems Ecology, Department of Ecological Sciences, VU University Amsterdam Amsterdam, Netherlands
| | - Jay T Lennon
- Department of Biology, Indiana University Bloomington, IN, USA
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University Uppsala, Sweden
| | - Hans-Peter Grossart
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries Berlin, Germany ; Institute for Biochemistry and Biology, Potsdam University Potsdam, Germany
| | | | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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191
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Barberán A, Ramirez KS, Leff JW, Bradford MA, Wall DH, Fierer N. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecol Lett 2014; 17:794-802. [DOI: 10.1111/ele.12282] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/22/2014] [Accepted: 03/22/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Albert Barberán
- Cooperative Institute for Research in Environmental Sciences; University of Colorado; Boulder USA
| | - Kelly S. Ramirez
- School of Global Environmental Sustainability and Department of Biology; Colorado State University; Fort Collins USA
| | - Jonathan W. Leff
- Cooperative Institute for Research in Environmental Sciences; University of Colorado; Boulder USA
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder USA
| | - Mark A. Bradford
- School of Forestry and Environmental Studies; Yale University; New Haven CT 06511 USA
| | - Diana H. Wall
- School of Global Environmental Sustainability and Department of Biology; Colorado State University; Fort Collins USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences; University of Colorado; Boulder USA
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder USA
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192
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Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microbiol 2014; 80:3034-43. [PMID: 24610850 DOI: 10.1128/aem.03414-13] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.
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193
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Fuchslueger L, Bahn M, Fritz K, Hasibeder R, Richter A. Experimental drought reduces the transfer of recently fixed plant carbon to soil microbes and alters the bacterial community composition in a mountain meadow. THE NEW PHYTOLOGIST 2014; 201:916-927. [PMID: 24171922 PMCID: PMC3908363 DOI: 10.1111/nph.12569] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/24/2013] [Indexed: 05/19/2023]
Abstract
Drought affects plants and soil microorganisms, but it is still not clear how it alters the carbon (C) transfer at the plant-microbial interface. Here, we tested direct and indirect effects of drought on soil microbes and microbial turnover of recent plant-derived C in a mountain meadow. Microbial community composition was assessed using phospholipid fatty acids (PLFAs); the allocation of recent plant-derived C to microbial groups was analysed by pulse-labelling of canopy sections with (13) CO2 and the subsequent tracing of the label into microbial PLFAs. Microbial biomass was significantly higher in plots exposed to a severe experimental drought. In addition, drought induced a shift of the microbial community composition, mainly driven by an increase of Gram-positive bacteria. Drought reduced belowground C allocation, but not the transfer of recently plant-assimilated C to fungi, and in particular reduced tracer uptake by bacteria. This was accompanied by an increase of (13) C in the extractable organic C pool during drought, which was even more pronounced after plots were mown. We conclude that drought weakened the link between plant and bacterial, but not fungal, C turnover, and facilitated the growth of potentially slow-growing, drought-adapted soil microbes, such as Gram-positive bacteria.
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Affiliation(s)
- Lucia Fuchslueger
- Department of Microbiology and Ecosystem Science, University of ViennaAlthanstr. 14, A-1090, Vienna, Austria
| | - Michael Bahn
- Institute of Ecology, University of InnsbruckInnsbruck, Austria
| | - Karina Fritz
- Institute of Ecology, University of InnsbruckInnsbruck, Austria
| | | | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of ViennaAlthanstr. 14, A-1090, Vienna, Austria
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194
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Evans SE, Wallenstein MD, Burke IC. Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought? Ecology 2014; 95:110-22. [DOI: 10.1890/13-0500.1] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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195
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Trivedi P, Anderson IC, Singh BK. Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol 2013; 21:641-51. [DOI: 10.1016/j.tim.2013.09.005] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 09/12/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
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196
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Evans SE, Wallenstein MD. Climate change alters ecological strategies of soil bacteria. Ecol Lett 2013; 17:155-64. [PMID: 24261594 DOI: 10.1111/ele.12206] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/03/2013] [Accepted: 10/02/2013] [Indexed: 11/30/2022]
Abstract
The timing and magnitude of rainfall events are expected to change in future decades, resulting in longer drought periods and larger rainfall events. Although microbial community composition and function are both sensitive to changes in rainfall, it is unclear whether this is because taxa adopt strategies that maximise fitness under new regimes. We assessed whether bacteria exhibited phylogenetically conserved ecological strategies in response to drying-rewetting, and whether these strategies were altered by historical exposure to experimentally intensified rainfall patterns. By clustering relative abundance patterns, we identified three discrete ecological strategies and found that tolerance to drying-rewetting increased with exposure to intensified rainfall patterns. Changes in strategy were primarily due to changes in community composition, but also to strategy shifts within taxa. These moisture regime-selected ecological strategies may be predictable from disturbance history, and are likely to be linked to traits that influence the functional potential of microbial communities.
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Affiliation(s)
- Sarah E Evans
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA; Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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197
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Zhang X, Zhang G, Chen Q, Han X. Soil bacterial communities respond to climate changes in a temperate steppe. PLoS One 2013; 8:e78616. [PMID: 24250803 PMCID: PMC3826739 DOI: 10.1371/journal.pone.0078616] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 09/14/2013] [Indexed: 11/18/2022] Open
Abstract
Climate warming and shifting precipitation regimes are affecting biodiversity and ecosystem functioning. Most studies have focused on the influence of warming and altered precipitation on macro-organisms, whereas the responses of soil microbial communities have been neglected. We studied the changes in the abundance, richness, and composition of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to increased precipitation, warming, and their combination, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Watering had a greater effect than warming on almost all the bacterial groups as indicated by changes in all the three attributes (abundance, richness, and composition). The 16 phyla/classes responded differentially to the experimental treatments, with Acidobacteria and Gamma-proteobacteria being the most sensitive. Stepwise regression analyses further revealed that climate changes altered the abundance and richness of bacterial groups primarily through direct routes (e.g., increasing soil water content), and changed the community composition through both direct and indirect routes (e.g., reducing soil total nitrogen content and increasing soil pH). The diverse responses of various bacterial groups could imply some potential shift in their ecosystem functions under climate changes; meanwhile, the indirect routes that are important in altering bacterial composition suggest that specific strategies (e.g., adding NH4NO3 to maintain soil nitrogen content and pH) could be adopted to maintain soil microbial composition under climate changes.
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Affiliation(s)
- Ximei Zhang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guangming Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Quansheng Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xingguo Han
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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198
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Barnard RL, Osborne CA, Firestone MK. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. THE ISME JOURNAL 2013; 7:2229-41. [PMID: 23823489 PMCID: PMC3806258 DOI: 10.1038/ismej.2013.104] [Citation(s) in RCA: 386] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/22/2013] [Accepted: 05/28/2013] [Indexed: 11/09/2022]
Abstract
The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities.
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Affiliation(s)
- Romain L Barnard
- Department of Environmental Science, Policy and Management, University of California, Berkeley CA, USA
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Catherine A Osborne
- Department of Environmental Science, Policy and Management, University of California, Berkeley CA, USA
- Monash University, Clayton, Victoria, Australia
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley CA, USA
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199
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Yuan Y, Si G, Wang J, Luo T, Zhang G. Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau. FEMS Microbiol Ecol 2013; 87:121-32. [PMID: 23991911 DOI: 10.1111/1574-6941.12197] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/07/2013] [Accepted: 08/23/2013] [Indexed: 11/28/2022] Open
Abstract
The Tibetan Plateau, 'the third pole', is a region that is very sensitive to climate change. A better understanding of response of soil microorganisms to climate warming is important to predict soil organic matter preservation in future scenario. We selected a typically altitudinal gradient (4400 m-5200 m a.s.l) along south-facing slope of Nyainqentanglha Mountains on central Tibetan Plateau. Bacterial communities were investigated using terminal restriction fragment length polymorphism analysis (T-RFLP) combined with sequencing methods. Acidobacteria and Proteobacteria were dominant bacteria in this alpine soil. Redundancy analysis revealed that soil bacterial communities were significantly different along the large altitudinal gradient, although the dominant environmental driving factors varied at different soil depth. Specifically, our results showed that precipitation and soil NH4 + were dominant environmental factors that influence bacterial communities at 0-5 cm depth along the altitudinal gradients, whereas pH was a major influential factor at 5-20 cm soil. In this semi-arid region, precipitation rather than temperature was a main driving force on soil bacterial communities as well as on plant communities. We speculate that an increase in temperature might not significantly change soil bacterial community structures along the large altitudinal gradient, whereas precipitation change would play a more important role in affecting soil bacterial communities.
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Affiliation(s)
- Yanli Yuan
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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200
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Székely AJ, Langenheder S. The importance of species sorting differs between habitat generalists and specialists in bacterial communities. FEMS Microbiol Ecol 2013; 87:102-12. [PMID: 23991811 DOI: 10.1111/1574-6941.12195] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 08/14/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022] Open
Abstract
Recent studies have shown that the spatial turnover of bacterial communities, that is, beta-diversity, is determined by a combination of different assembly mechanisms, such as species sorting, that is, environmental filtering, and dispersal-related mechanisms. However, it is currently unclear to what extent the importance of the different mechanisms depends on community traits. Here, we implemented a study using a rock pool metacommunity to test whether habitat specialization of bacterial taxa and groups or their phylogenetic identity influenced by which mechanisms communities were assembled. In general, our results show that species sorting was the most important assembly mechanism. However, we found that a larger fraction of the variation in bacterial community composition between pools could be explained by environmental factors in case of habitat generalists, that is, taxa that were widespread and abundant in the metacommunity, compared with habitat specialists, that is, taxa that had a more restricted distribution range and tended to be rare. Differences in assembly mechanisms were observed between different major phyla and classes. However, also here, a larger fraction of the variation in community composition among pools could be explained for taxonomic groups that contained on average more habitat generalists. In summary, our results show that species sorting is stronger for the most common taxa, indicating that beta-diversity along environmental gradients can be adequately described without considering rare taxa.
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Affiliation(s)
- Anna J Székely
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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