1
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Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. ISME J 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
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Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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2
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Walkup J, Dang C, Mau RL, Hayer M, Schwartz E, Stone BW, Hofmockel KS, Koch BJ, Purcell AM, Pett-Ridge J, Wang C, Hungate BA, Morrissey EM. The predictive power of phylogeny on growth rates in soil bacterial communities. ISME Commun 2023; 3:73. [PMID: 37454187 PMCID: PMC10349831 DOI: 10.1038/s43705-023-00281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.
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Affiliation(s)
- Jeth Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA
- University of California Merced, Life & Environmental Sciences Department, Merced, CA, 95343, USA
| | - Chao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, LN, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA.
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3
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Stone BWG, Dijkstra P, Finley BK, Fitzpatrick R, Foley MM, Hayer M, Hofmockel KS, Koch BJ, Li J, Liu XJA, Martinez A, Mau RL, Marks J, Monsaint-Queeney V, Morrissey EM, Propster J, Pett-Ridge J, Purcell AM, Schwartz E, Hungate BA. Life history strategies among soil bacteria-dichotomy for few, continuum for many. ISME J 2023; 17:611-619. [PMID: 36732614 PMCID: PMC10030646 DOI: 10.1038/s41396-022-01354-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023]
Abstract
Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O-H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms' joint 18O-13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.
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Affiliation(s)
- Bram W G Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA.
- Center for Ecosystem Science and Society, 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
| | - Brianna K Finley
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Raina Fitzpatrick
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Megan M Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Xiao Jun A Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ayla Martinez
- 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
| | - Jane Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jeffrey Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 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
| | - 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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4
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Stone BW, Blazewicz SJ, Koch BJ, Dijkstra P, Hayer M, Hofmockel KS, Liu XJA, Mau RL, Pett-Ridge J, Schwartz E, Hungate BA. Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community. Oecologia 2023; 201:771-782. [PMID: 36847885 DOI: 10.1007/s00442-023-05322-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/15/2023] [Indexed: 03/01/2023]
Abstract
Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.
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Affiliation(s)
- Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, 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
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Xiao Jun Allen Liu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, 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
| | - 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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5
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Antoninka A, Chuckran PF, Mau RL, Slate ML, Mishler BD, Oliver MJ, Coe KK, Stark LR, Fisher KM, Bowker MA. Responses of Biocrust and Associated Soil Bacteria to Novel Climates Are Not Tightly Coupled. Front Microbiol 2022; 13:821860. [PMID: 35572693 PMCID: PMC9096946 DOI: 10.3389/fmicb.2022.821860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth’s terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical cycling, and water capture. Understanding how biocrusts adapt to climate change is critical to understanding how dryland ecosystems will function with altered climate. We investigated the sensitivity of biocrusts to experimentally imposed novel climates to track changes in productivity and stability under both warming and cooling scenarios. We established three common gardens along an elevational-climate gradient on the Colorado Plateau. Mature biocrusts were collected from each site and reciprocally transplanted intact. Over 20 months we monitored visible species composition and cover, chlorophyll a, and the composition of soil bacterial communities using high throughput sequencing. We hypothesized that biocrusts replanted at their home site would show local preference, and biocrusts transplanted to novel environments would maintain higher cover and stability at elevations higher than their origin, compared to at elevations lower than their origin. We expected responses of the visible biocrust cover and soil bacterial components of the biocrust community to be coupled, with later successional taxa showing higher sensitivity to novel environments. Only high elevation sourced biocrusts maintained higher biocrust cover and community stability at their site of origin. Biocrusts from all sources had higher cover and stability in the high elevation garden. Later successional taxa decreased cover in low elevation gardens, suggesting successional reversal with warming. Visible community composition was influenced by both source and transplant environment. In contrast, soil bacterial community composition was not influenced by transplant environments but retained fidelity to the source. Thus, responses of the visible and soil bacterial components of the biocrust community were not coupled. Synthesis: Our results suggest biocrust communities are sensitive to climate change, and loss of species and function can be expected, while associated soil bacteria may be buffered against rapid change.
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Affiliation(s)
- Anita Antoninka
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States
| | - Peter F Chuckran
- Department of Biological Sciences, Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, AZ, United States
| | - Rebecca L Mau
- Department of Biological Sciences, Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, AZ, United States
| | - Mandy L Slate
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Melvin J Oliver
- Interdisciplinary Plant Group, Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Kirsten K Coe
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - Llo R Stark
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, Los Angeles, CA, United States
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States
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6
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Finley BK, Mau RL, Hayer M, Stone BW, Morrissey EM, Koch BJ, Rasmussen C, Dijkstra P, Schwartz E, Hungate BA. Soil minerals affect taxon-specific bacterial growth. ISME J 2022; 16:1318-1326. [PMID: 34931028 PMCID: PMC9038713 DOI: 10.1038/s41396-021-01162-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 01/01/2023]
Abstract
Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages-particularly short-range order minerals-affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with 18O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25-36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.
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Affiliation(s)
- Brianna K. Finley
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.266093.80000 0001 0668 7243Present Address: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 USA
| | - Rebecca L. Mau
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Michaela Hayer
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Bram W. Stone
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.451303.00000 0001 2218 3491Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Ember M. Morrissey
- grid.268154.c0000 0001 2156 6140Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506 USA
| | - Benjamin J. Koch
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Craig Rasmussen
- grid.134563.60000 0001 2168 186XDepartment of Environmental Science, University of Arizona, Tucson, AZ 85721 USA
| | - Paul Dijkstra
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Egbert Schwartz
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Bruce A. Hungate
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
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7
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Purcell AM, Hayer M, Koch BJ, Mau RL, Blazewicz SJ, Dijkstra P, Mack MC, Marks JC, Morrissey EM, Pett‐Ridge J, Rubin RL, Schwartz E, van Gestel NC, Hungate BA. Decreased growth of wild soil microbes after 15 years of transplant-induced warming in a montane meadow. Glob Chang Biol 2022; 28:128-139. [PMID: 34587352 PMCID: PMC9293287 DOI: 10.1111/gcb.15911] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 05/19/2023]
Abstract
The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates to warming may be strongly idiosyncratic, varying among taxa, making ecosystem predictions difficult. Here, we show that 15 years of warming by transplanting plant-soil mesocosms down in elevation, strongly reduced the growth rates of soil microorganisms, measured in the field using undisturbed soil. The magnitude of the response to warming varied among microbial taxa. However, the direction of the response-reduced growth-was universal and warming explained twofold more variation than did the sum of taxonomic identity and its interaction with warming. For this ecosystem, most of the growth responses to warming could be explained without taxon-specific information, suggesting that in some cases microbial responses measured in aggregate may be adequate for climate modeling. Long-term experimental warming also reduced soil carbon content, likely a consequence of a warming-induced increase in decomposition, as warming-induced changes in plant productivity were negligible. The loss of soil carbon and decreased microbial biomass with warming may explain the reduced growth of the microbial community, more than the direct effects of temperature on growth. These findings show that direct and indirect effects of long-term warming can reduce growth rates of soil microbes, which may have important feedbacks to global warming.
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Affiliation(s)
- Alicia M. Purcell
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Michaela Hayer
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Benjamin J. Koch
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Rebecca L. Mau
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Steven J. Blazewicz
- Physical and Life Sciences DirectorateLawrence Livermore National LabLivermoreCaliforniaUSA
| | - Paul Dijkstra
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Michelle C. Mack
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Jane C. Marks
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Ember M. Morrissey
- Division of Plant and Soil SciencesWest Virginia UniversityMorgantownWest VirginiaUSA
| | - Jennifer Pett‐Ridge
- Physical and Life Sciences DirectorateLawrence Livermore National LabLivermoreCaliforniaUSA
- Life & Environmental Sciences DepartmentUniversity of California MercedMercedCAUSA
| | - Rachel L. Rubin
- Department of Environmental SciencesMount Holyoke CollegeSouth HadleyMassachusettsUSA
| | - Egbert Schwartz
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Natasja C. van Gestel
- Department of Biological Sciences & TTU Climate CenterTexas Tech UniversityLubbockTexasUSA
| | - Bruce A. Hungate
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
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8
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Stone BW, Li J, Koch BJ, Blazewicz SJ, Dijkstra P, Hayer M, Hofmockel KS, Liu XJA, Mau RL, Morrissey EM, Pett-Ridge J, Schwartz E, Hungate BA. Author Correction: Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community. Nat Commun 2021; 12:4052. [PMID: 34168161 PMCID: PMC8225670 DOI: 10.1038/s41467-021-24314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. .,Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
| | - Junhui Li
- 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.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 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
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Xiao-Jun Allen Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.,Life and Environmental Sciences Department, University of California Merced, Merced, CA, 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
| | - 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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9
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Hungate BA, Marks JC, Power ME, Schwartz E, van Groenigen KJ, Blazewicz SJ, Chuckran P, Dijkstra P, Finley BK, Firestone MK, Foley M, Greenlon A, Hayer M, Hofmockel KS, Koch BJ, Mack MC, Mau RL, Miller SN, Morrissey EM, Propster JR, Purcell AM, Sieradzki E, Starr EP, Stone BWG, Terrer C, Pett-Ridge J. The Functional Significance of Bacterial Predators. mBio 2021; 12:e00466-21. [PMID: 33906922 PMCID: PMC8092244 DOI: 10.1128/mbio.00466-21] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs.IMPORTANCE The word "predator" may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as Bdellovibrionales and Vampirovibrionales, increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria-along with protists, nematodes, and phages-are active and important in microbial food webs.
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Affiliation(s)
- Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mary E Power
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Peter Chuckran
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Brianna K Finley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Megan Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alex Greenlon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Jeffrey R Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ella Sieradzki
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Evan P Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Bram W G Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - César Terrer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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10
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Wang C, Morrissey EM, Mau RL, Hayer M, Piñeiro J, Mack MC, Marks JC, Bell SL, Miller SN, Schwartz E, Dijkstra P, Koch BJ, Stone BW, Purcell AM, Blazewicz SJ, Hofmockel KS, Pett-Ridge J, Hungate BA. The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization. ISME J 2021; 15:2738-2747. [PMID: 33782569 DOI: 10.1038/s41396-021-00959-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 03/04/2021] [Indexed: 11/09/2022]
Abstract
Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.
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Affiliation(s)
- Chao Wang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.,CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Juan Piñeiro
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Michelle C Mack
- 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
| | - Sheryl L Bell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, 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
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA.,Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Jennifer Pett-Ridge
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 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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11
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Sieradzki ET, Koch BJ, Greenlon A, Sachdeva R, Malmstrom RR, Mau RL, Blazewicz SJ, Firestone MK, Hofmockel KS, Schwartz E, Hungate BA, Pett-Ridge J. Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design. mSystems 2020; 5:e00151-20. [PMID: 32694124 PMCID: PMC7566279 DOI: 10.1128/msystems.00151-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.
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Affiliation(s)
- Ella T Sieradzki
- University of California Berkeley, Environmental Science and Policy Management, Berkeley, California, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alex Greenlon
- University of California Berkeley, Environmental Science and Policy Management, Berkeley, California, USA
| | - Rohan Sachdeva
- University of California Berkeley, Earth and Planetary Sciences, Berkeley, California, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Mary K Firestone
- University of California Berkeley, Environmental Science and Policy Management, Berkeley, California, USA
| | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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12
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Li J, Mau RL, Dijkstra P, Koch BJ, Schwartz E, Liu XJA, Morrissey EM, Blazewicz SJ, Pett-Ridge J, Stone BW, Hayer M, Hungate BA. Predictive genomic traits for bacterial growth in culture versus actual growth in soil. ISME J 2019. [PMID: 31053828 DOI: 10.1038/s41396‐019‐0422‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.
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Affiliation(s)
- Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Xiao-Jun Allen Liu
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
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13
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Papp K, Mau RL, Hayer M, Koch BJ, Hungate BA, Schwartz E. Quantitative stable isotope probing with H 218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA. ISME J 2018; 12:3043-3045. [PMID: 30042501 PMCID: PMC6246559 DOI: 10.1038/s41396-018-0233-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 11/09/2022]
Abstract
Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We analyzed 18O composition of RNA extracted from soil incubated with H218O and used quantitative stable isotope probing to characterize rRNA synthesis among microbial taxa. RNA was not fully labeled with 18O, peaking at a mean of 23.6 ± 6.8 atom percent excess (APE) 18O after eight days of incubation, suggesting some ribonucleotides in soil were more than eight days old. Microbial taxa varied in the degree they incorporated 18O into their rRNA over time and there was no correlation between the APE 18O of bacterial rRNA and their rRNA to DNA ratios, suggesting that the ratios were not appropriate to measure ribonucleotide synthesis. Our study indicates that, on average, 94% of soil taxa produced new rRNA and therefore were metabolically active.
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Affiliation(s)
- Katerina Papp
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
- Division of Hydrological Sciences, Desert Research Institute, Las Vegas, NV, USA.
- Department of Civil and Environmental Engineering and Construction, University of Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 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
| | - Egbert Schwartz
- 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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14
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Rubin RL, Koch GW, Martinez A, Mau RL, Bowker MA, Hungate BA. Developing climate-smart restoration: Can plant microbiomes be hardened against heat waves? Ecol Appl 2018; 28:1594-1605. [PMID: 29989265 DOI: 10.1002/eap.1763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/24/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Heat waves are increasing in frequency and intensity, presenting a challenge for the already difficult practice of ecological restoration. We investigated whether pre-heating locally sourced rhizosphere soil (inoculum) could acclimatize plants to a field-imposed heat wave in a restoration setting. Soil heating in the laboratory caused a marked shift in rhizosphere bacterial community composition, accompanied by an increase in species evenness. Furthermore, pre-heated rhizosphere soil reduced plant height, number of leaves, and shoot mass of the C4 grass, blue grama (Bouteloua gracilis), and it reduced the shoot mass of the C3 grass, Arizona fescue (Festuca arizonica) in the glasshouse. Following transplantation and the application of a field heat wave, pre-heated inoculum did not influence heat wave survival for either plant species. However, there were strong species-level responses to the field heat wave. For instance, heat wave survivorship was over four times higher in blue grama (92%) than in Arizona fescue (22%). These results suggest that the use of C4 seeds may be preferable for sites exhibiting high heat wave risk. Further research is needed to understand whether inocula are more effective in highly degraded soil in comparison with partially degraded soils.
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Affiliation(s)
- Rachel L Rubin
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - George W Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Ayla Martinez
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Rebecca L Mau
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
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15
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Morrissey EM, Mau RL, Schwartz E, Koch BJ, Hayer M, Hungate BA. Taxonomic patterns in the nitrogen assimilation of soil prokaryotes. Environ Microbiol 2018; 20:1112-1119. [PMID: 29411496 DOI: 10.1111/1462-2920.14051] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/27/2017] [Accepted: 01/14/2018] [Indexed: 11/27/2022]
Abstract
Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with 15 N. Following incubation with 15 NH4+, distinct patterns of 15 N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated 15 N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased 15 N use by Firmicutes and Bacteriodetes. While NH4+ is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with 15 N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment.
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Affiliation(s)
- Ember M Morrissey
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 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
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 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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16
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Koch BJ, McHugh TA, Hayer M, Schwartz E, Blazewicz SJ, Dijkstra P, Gestel N, Marks JC, Mau RL, Morrissey EM, Pett‐Ridge J, Hungate BA. Estimating taxon‐specific population dynamics in diverse microbial communities. Ecosphere 2018. [DOI: 10.1002/ecs2.2090] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Benjamin J. Koch
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
| | - Theresa A. McHugh
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona 86011 USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California 94550 USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona 86011 USA
| | - Natasja Gestel
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
| | - Jane C. Marks
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona 86011 USA
| | - Rebecca L. Mau
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
| | - Ember M. Morrissey
- Division of Plant and Soil Sciences West Virginia University Morgantown West Virginia 26506 USA
| | - Jennifer Pett‐Ridge
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California 94550 USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona 86011 USA
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona 86011 USA
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17
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Morrissey EM, Mau RL, Schwartz E, McHugh TA, Dijkstra P, Koch BJ, Marks JC, Hungate BA. Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter. ISME J 2017; 11:1890-1899. [PMID: 28387774 DOI: 10.1038/ismej.2017.43] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022]
Abstract
Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influence soil C cycling following the addition of labile C (glucose). Specifically, we show that increased decomposition of soil C in response to added glucose (positive priming) occurs as a phylogenetically diverse group of taxa, accounting for a large proportion of the bacterial community, shift toward additional soil C use for growth. Our findings suggest that many microbial taxa exhibit C use plasticity, as most taxa altered their use of glucose and soil organic matter depending upon environmental conditions. In contrast, bacteria that exhibit other responses to glucose (reduced growth or reliance on glucose for additional growth) clustered strongly by phylogeny. These results suggest that positive priming is likely the prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the positive priming effect in nature.
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Affiliation(s)
- Ember M Morrissey
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 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
| | - Theresa A McHugh
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, 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
| | - Benjamin J Koch
- 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
| | - 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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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 J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Ulrich W, Soliveres S, Maestre FT, Gotelli NJ, Quero JL, Delgado-Baquerizo M, Bowker MA, Eldridge DJ, Ochoa V, Gozalo B, Valencia E, Berdugo M, Escolar C, García-Gómez M, Escudero A, Prina A, Alfonso G, Arredondo T, Bran D, Cabrera O, Cea A, Chaieb M, Contreras J, Derak M, Espinosa CI, Florentino A, Gaitán J, Muro VG, Ghiloufi W, Gómez-González S, Gutiérrez JR, Hernández RM, Huber-Sannwald E, Jankju M, Mau RL, Hughes FM, Miriti M, Monerris J, Muchane M, Naseri K, Pucheta E, Ramírez-Collantes DA, Raveh E, Romão RL, Torres-Díaz C, Val J, Veiga JP, Wang D, Yuan X, Zaady E. Climate and soil attributes determine plant species turnover in global drylands. J Biogeogr 2014; 41:2307-2319. [PMID: 25914437 PMCID: PMC4407967 DOI: 10.1111/jbi.12377] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
AIM Geographic, climatic, and soil factors are major drivers of plant beta diversity, but their importance for dryland plant communities is poorly known. This study aims to: i) characterize patterns of beta diversity in global drylands, ii) detect common environmental drivers of beta diversity, and iii) test for thresholds in environmental conditions driving potential shifts in plant species composition. LOCATION 224 sites in diverse dryland plant communities from 22 geographical regions in six continents. METHODS Beta diversity was quantified with four complementary measures: the percentage of singletons (species occurring at only one site), Whittake's beta diversity (β(W)), a directional beta diversity metric based on the correlation in species occurrences among spatially contiguous sites (β(R2)), and a multivariate abundance-based metric (β(MV)). We used linear modelling to quantify the relationships between these metrics of beta diversity and geographic, climatic, and soil variables. RESULTS Soil fertility and variability in temperature and rainfall, and to a lesser extent latitude, were the most important environmental predictors of beta diversity. Metrics related to species identity (percentage of singletons and β(W)) were most sensitive to soil fertility, whereas those metrics related to environmental gradients and abundance ((β(R2)) and β(MV)) were more associated with climate variability. Interactions among soil variables, climatic factors, and plant cover were not important determinants of beta diversity. Sites receiving less than 178 mm of annual rainfall differed sharply in species composition from more mesic sites (> 200 mm). MAIN CONCLUSIONS Soil fertility and variability in temperature and rainfall are the most important environmental predictors of variation in plant beta diversity in global drylands. Our results suggest that those sites annually receiving ~ 178 mm of rainfall will be especially sensitive to future climate changes. These findings may help to define appropriate conservation strategies for mitigating effects of climate change on dryland vegetation.
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Affiliation(s)
- Werner Ulrich
- Chair of Ecology and Biogeography Nicolaus Copernicus University in Toruń Lwowska1, 87-100 Toruń, Poland
- Corresponding author: Werner Ulrich, Chair of Ecology and Biogeography Nicolaus Copernicus University in Toruń, Lwowska1, 87-100 Toruń, Poland.
| | - Santiago Soliveres
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Fernando T. Maestre
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | | | - José L. Quero
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Departamento de Ingeniería Forestal, Escuela Técnica Superior de Ingeniería Agronómica y de Montes. Universidad de Córdoba. Edificio Leonardo da Vinci, 1 planta. Campus de Rabanales. Ctra N-IV km 396. C.P. 14071, Córdoba, Spain
| | - Manuel Delgado-Baquerizo
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Carretera de Utrera kilómetro 1, 41013 Sevilla, Spain
| | - Matthew A. Bowker
- School of Forestry, Northern Arizona University, 200 East Pine Knoll Drive, AZ 86011, Flagstaff, USA
| | - David J. Eldridge
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Victoria Ochoa
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Beatriz Gozalo
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Enrique Valencia
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Miguel Berdugo
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Cristina Escolar
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Miguel García-Gómez
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Departamento de Ingeniería y Morfología del Terreno, Escuela Técnica Superior de Ingenieros de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Calle Profesor Aranguren S/N, 28040 Madrid, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación Departamento de Biología y Geología Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Aníbal Prina
- Facultad de Agronomía, Universidad Nacional de La Pampa, Casilla de Correo 300, 6300 Santa Rosa, La Pampa, Argentina
| | - Graciela Alfonso
- Facultad de Agronomía, Universidad Nacional de La Pampa, Casilla de Correo 300, 6300 Santa Rosa, La Pampa, Argentina
| | - Tulio Arredondo
- Division de Ciencias Ambientales, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT)
| | - Donaldo Bran
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental San Carlos de Bariloche, Casilla de Correo 277 (8400), Bariloche, Río Negro, Argentina
| | - Omar Cabrera
- Instituto de Ecología, Universidad Técnica Particular de Loja, San Cayetano Alto, Marcelino Champagnat, Loja, Ecuador
| | - Alex Cea
- Departamento de Biología, Universidad de La Serena, Casilla 599
| | - Mohamed Chaieb
- UR Plant Biodiversity and Ecosystems in Arid Environments, Faculty of Sciences, University of Sfax. Route de Sokra, km 3.5, Boîte Postale 802, 3018, Sfax, Tunisia
| | - Jorge Contreras
- Departamento de Suelos; Universidad Centroccidental Lizandro Alvarado, Barquisimeto, estado Lara, Venezuela
| | - Mchich Derak
- Direction Régionale des Eaux et Forêts et de la Lutte Contre la Désertification du Rif, Avenue Mohamed 5, Boîte Postale 722, 93000 Tétouan, Morocco
| | - Carlos I. Espinosa
- Instituto de Ecología, Universidad Técnica Particular de Loja, San Cayetano Alto, Marcelino Champagnat, Loja, Ecuador
| | - Adriana Florentino
- Instituto de Edafología, Facultad de Agronomía, Universidad Central de Venezuela, Campus UCV-Maracay, ZP 2101, estado Aragua, Venezuela
| | - Juan Gaitán
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental San Carlos de Bariloche, Casilla de Correo 277 (8400), Bariloche, Río Negro, Argentina
| | - Victoria García Muro
- IANIGLA, CCT Mendoza, CONICET A. Ruiz Leal s/n, Parque General San Martín, Mendoza, Argentina. CP.: M5502IRA
| | - Wahida Ghiloufi
- UR Plant Biodiversity and Ecosystems in Arid Environments, Faculty of Sciences, University of Sfax. Route de Sokra, km 3.5, Boîte Postale 802, 3018, Sfax, Tunisia
| | - Susana Gómez-González
- Instituto de Edafología, Facultad de Agronomía, Universidad Central de Venezuela, Campus UCV-Maracay, ZP 2101, estado Aragua, Venezuela
| | - Julio R. Gutiérrez
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental San Carlos de Bariloche, Casilla de Correo 277 (8400), Bariloche, Río Negro, Argentina
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Rosa M. Hernández
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile; Laboratorio de Biogeoquímica, Centro de Agroecología Tropical, Universidad Experimental Simón Rodríguez, Apdo 47925, Caracas, Venezuela
| | - Elisabeth Huber-Sannwald
- Division de Ciencias Ambientales, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT)
| | - Mohammad Jankju
- Department of Range and Watershed Management, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Rebecca L. Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Frederic Mendes Hughes
- Departamento de Biologia, Universidade Federal de Minas Gerais, Minas Gerais 31270-901, Brasil
| | - Maria Miriti
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 West 12 Avenue, Columbus, OH 43210, USA
| | - Jorge Monerris
- Université du Québec à Montréal Pavillon des sciences biologiques Département des sciences biologiques 141 Président-Kennedy Montréal, Québec H2X 3Y5, Canada
| | - Muchai Muchane
- Zoology Department of the National Museums of Kenya, Nairobi, Kenya
| | - Kamal Naseri
- Department of Range and Watershed Management, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Eduardo Pucheta
- Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, J5402DCS Rivadavia, San Juan, Argentina
| | - David A. Ramírez-Collantes
- Production Systems and the Environment Sub-Program, International Potato Center. Apartado 1558, Lima 12, Peru
| | - Eran Raveh
- Department of Natural Resources and Agronomy, Agriculture Research Organization, Ministry of Agriculture, Gilat Research Center, Mobile Post Negev 85280, Israel
| | - Roberto L. Romão
- Departamento de Ciencias Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina Sin Número, Bairro Novo Horizonte, Feira de Santana, 44036-900, Brasil
| | - Cristian Torres-Díaz
- Instituto de Edafología, Facultad de Agronomía, Universidad Central de Venezuela, Campus UCV-Maracay, ZP 2101, estado Aragua, Venezuela
| | - James Val
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - José Pablo Veiga
- Departamento de Ecología Evolutiva, Museo Nacional de CCNN (CSIC), Madrid, Spain
| | - Deli Wang
- Institute of Grassland Science, Key Laboratory for Vegetation Ecology, Northeast Normal University, Changchun, Jilin 130024, China
| | - Xia Yuan
- Institute of Grassland Science, Key Laboratory for Vegetation Ecology, Northeast Normal University, Changchun, Jilin 130024, China
| | - Eli Zaady
- Department of Natural Resources and Agronomy, Agriculture Research Organization, Ministry of Agriculture, Gilat Research Center, Mobile Post Negev 85280, Israel
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20
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Mau RL, Liu CM, Aziz M, Schwartz E, Dijkstra P, Marks JC, Price LB, Keim P, Hungate BA. Linking soil bacterial biodiversity and soil carbon stability. ISME J 2014; 9:1477-80. [PMID: 25350158 DOI: 10.1038/ismej.2014.205] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 09/05/2014] [Accepted: 09/22/2014] [Indexed: 10/24/2022]
Abstract
Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.
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Affiliation(s)
- Rebecca L Mau
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Cindy M Liu
- 1] Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA [2] Microbial Genetic and Genomics Center (MGGen), Northern Arizona University, Flagstaff, AZ, USA
| | - Maliha Aziz
- Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA
| | - Egbert Schwartz
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Lance B Price
- Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA
| | - Paul Keim
- 1] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA [2] Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA [3] Microbial Genetic and Genomics Center (MGGen), Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
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21
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Delgado-Baquerizo M, Maestre FT, Gallardo A, Bowker MA, Wallenstein MD, Quero JL, Ochoa V, Gozalo B, García-Gómez M, Soliveres S, García-Palacios P, Berdugo M, Valencia E, Escolar C, Arredondo T, Barraza-Zepeda C, Bran D, Carreira JA, Chaieb M, Conceição AA, Derak M, Eldridge DJ, Escudero A, Espinosa CI, Gaitán J, Gatica MG, Gómez-González S, Guzman E, Gutiérrez JR, Florentino A, Hepper E, Hernández RM, Huber-Sannwald E, Jankju M, Liu J, Mau RL, Miriti M, Monerris J, Naseri K, Noumi Z, Polo V, Prina A, Pucheta E, Ramírez E, Ramírez-Collantes DA, Romão R, Tighe M, Torres D, Torres-Díaz C, Ungar ED, Val J, Wamiti W, Wang D, Zaady E. Decoupling of soil nutrient cycles as a function of aridity in global drylands. Nature 2013; 502:672-6. [DOI: 10.1038/nature12670] [Citation(s) in RCA: 537] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 09/17/2013] [Indexed: 11/09/2022]
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22
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Bowker MA, Maestre FT, Mau RL. Diversity and Patch-Size Distributions of Biological Soil Crusts Regulate Dryland Ecosystem Multifunctionality. Ecosystems 2013. [DOI: 10.1007/s10021-013-9644-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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Maestre FT, Quero JL, Gotelli NJ, Escudero A, Ochoa V, Delgado-Baquerizo M, García-Gómez M, Bowker MA, Soliveres S, Escolar C, García-Palacios P, Berdugo M, Valencia E, Gozalo B, Gallardo A, Aguilera L, Arredondo T, Blones J, Boeken B, Bran D, Conceição AA, Cabrera O, Chaieb M, Derak M, Eldridge DJ, Espinosa CI, Florentino A, Gaitán J, Gatica MG, Ghiloufi W, Gómez-González S, Gutiérrez JR, Hernández RM, Huang X, Huber-Sannwald E, Jankju M, Miriti M, Monerris J, Mau RL, Morici E, Naseri K, Ospina A, Polo V, Prina A, Pucheta E, Ramírez-Collantes DA, Romão R, Tighe M, Torres-Díaz C, Val J, Veiga JP, Wang D, Zaady E. Plant species richness and ecosystem multifunctionality in global drylands. Science 2012; 335:214-8. [PMID: 22246775 PMCID: PMC3558739 DOI: 10.1126/science.1215442] [Citation(s) in RCA: 506] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Experiments suggest that biodiversity enhances the ability of ecosystems to maintain multiple functions, such as carbon storage, productivity, and the buildup of nutrient pools (multifunctionality). However, the relationship between biodiversity and multifunctionality has never been assessed globally in natural ecosystems. We report here on a global empirical study relating plant species richness and abiotic factors to multifunctionality in drylands, which collectively cover 41% of Earth's land surface and support over 38% of the human population. Multifunctionality was positively and significantly related to species richness. The best-fitting models accounted for over 55% of the variation in multifunctionality and always included species richness as a predictor variable. Our results suggest that the preservation of plant biodiversity is crucial to buffer negative effects of climate change and desertification in drylands.
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Affiliation(s)
- Fernando T Maestre
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Calle Tulipán Sin Número, 28933 Móstoles, Spain.
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Bowker MA, Mau RL, Maestre FT, Escolar C, Castillo-Monroy AP. Functional profiles reveal unique ecological roles of various biological soil crust organisms. Funct Ecol 2011. [DOI: 10.1111/j.1365-2435.2011.01835.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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