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Park DE, Aziz M, Koch BJ, Roach K, Clabots C, Johnson JR, Price LB, Liu CM. Gut microbiome predictors of Escherichia coli sequence type 131 colonization and loss. EBioMedicine 2024; 99:104909. [PMID: 38096689 PMCID: PMC10758731 DOI: 10.1016/j.ebiom.2023.104909] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Escherichia coli sequence type 131 (ST131), specifically its fluoroquinolone-resistant H30R clade (ST131-H30R), is a global multidrug-resistant pathogen. The gut microbiome's role in ST131-H30R intestinal carriage is undefined. METHODS Veterans and their household members underwent longitudinal fecal swab surveillance for ST131 in 2014-2018. The fecal microbiome was characterized by 16S rRNA qPCR and sequencing. We evaluated associations between ST131-H30R carriage and gut microbiome at baseline by random forest models to identify the most informative gut bacterial phyla and genera attributes for ST131 and ST131-H30R carriage status. Next, we assessed longitudinal associations between fecal microbiome and ST131-H30R carriage using a mixed-effects logistic regression with longitudinal measures. FINDINGS Of the 519 participants, 78 were carriers of ST131, among whom 49 had ST131-H30R. At the baseline timepoint, H30R-positive participants had higher proportional abundances of Actinobacteria phylum (mean: 4.9% vs. 3.1%) than ST131-negative participants. H30R-positive participants also had higher abundances of Collinsella (mean: 2.3% vs. 1.1%) and lower abundances of Alistipes (mean: 2.1% vs. 2.6%) than ST131-negative participants. In the longitudinal analysis, Collinsella abundance correlated positively with ST131-H30R carriage status and negatively with the loss of ST131-H30R. Conversely, Alistipes corresponded with the loss and persistent absence of ST131-H30R even in the presence of a household exposure. INTERPRETATION Abundances of specific fecal bacteria correlated with ST131-H30R carriage, persistence, and loss, suggesting their potential as targets for microbiome-based strategies to reduce carriage of ST131-H30R, a significant risk factor for invasive infections. FUNDING This work was supported in part by National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R21AI117654 and UM1AI104681 and the Office of Research and Development, Department of Veterans Affairs. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the Department of Veterans Affairs.
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Affiliation(s)
- Daniel E Park
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, P.O. Box 5620, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, 617 S Beaver St., Flagstaff, AZ, 86011, USA
| | - Kelsey Roach
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Connie Clabots
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA
| | - James R Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA; Department of Medicine, University of Minnesota, 401 East River Parkway, VCRC 1st, UK Floor, Suite 131, Minneapolis, MN, 55455, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
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2
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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3
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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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4
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Liu CM, Aziz M, Park DE, Wu Z, Stegger M, Li M, Wang Y, Schmidlin K, Johnson TJ, Koch BJ, Hungate BA, Nordstrom L, Gauld L, Weaver B, Rolland D, Statham S, Hall B, Sariya S, Davis GS, Keim PS, Johnson JR, Price LB. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections. One Health 2023; 16:100518. [PMID: 37363239 PMCID: PMC10288061 DOI: 10.1016/j.onehlt.2023.100518] [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: 09/30/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.
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Affiliation(s)
- Cindy M. Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
| | - Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Daniel E. Park
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, 500 Church Street, Suite 600, Ann Arbor, MI 48109, USA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Mengbing Li
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Yashan Wang
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Kara Schmidlin
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Ave, St Paul, MN 55108, USA
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Lora Nordstrom
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Lori Gauld
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Brett Weaver
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Diana Rolland
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Sally Statham
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sanjeev Sariya
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Gregg S. Davis
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - James R. Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN 55417, USA
| | - Lance B. Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
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5
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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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6
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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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7
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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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8
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Hayer M, Wymore AS, Hungate BA, Schwartz E, Koch BJ, Marks JC. Microbes on decomposing litter in streams: entering on the leaf or colonizing in the water? ISME J 2022; 16:717-725. [PMID: 34580429 PMCID: PMC8857200 DOI: 10.1038/s41396-021-01114-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 08/29/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023]
Abstract
When leaves fall in rivers, microbial decomposition commences within hours. Microbial assemblages comprising hundreds of species of fungi and bacteria can vary with stream conditions, leaf litter species, and decomposition stage. In terrestrial ecosystems, fungi and bacteria that enter soils with dead leaves often play prominent roles in decomposition, but their role in aquatic decomposition is less known. Here, we test whether fungi and bacteria that enter streams on senesced leaves are growing during decomposition and compare their abundances and growth to bacteria and fungi that colonize leaves in the water. We employ quantitative stable isotope probing to identify growing microbes across four leaf litter species and two decomposition times. We find that most of the growing fungal species on decomposing leaves enter the water with the leaf, whereas most growing bacteria colonize from the water column. Results indicate that the majority of bacteria found on litter are growing, whereas the majority of fungi are dormant. Both bacterial and fungal assemblages differed with leaf type on the dried leaves and throughout decomposition. This research demonstrates the importance of fungal species that enter with the leaf on aquatic decomposition and the prominence of bacteria that colonize decomposing leaves in the water.
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Affiliation(s)
- Michaela Hayer
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Adam S. Wymore
- grid.167436.10000 0001 2192 7145Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824 USA
| | - Bruce A. Hungate
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Egbert Schwartz
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Benjamin J. Koch
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Jane C. Marks
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA
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9
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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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10
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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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11
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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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12
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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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13
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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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14
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Blazewicz SJ, Hungate BA, Koch BJ, Nuccio EE, Morrissey E, Brodie EL, Schwartz E, Pett-Ridge J, Firestone MK. Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J 2020; 14:1520-1532. [PMID: 32203117 PMCID: PMC7242442 DOI: 10.1038/s41396-020-0617-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 03/25/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 02/01/2023]
Abstract
Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H218O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3 h, and continued throughout the 168 h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3 h of wet-up but had contrasting characteristics; growth at 3 h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO2 production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.
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Affiliation(s)
- Steven J Blazewicz
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA.
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA.
- Lawrence Livermore National Laboratory, 7000 East Ave L-231, Livermore, CA, 94550, 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
| | - 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
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Ember Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26505, USA
| | - Eoin L Brodie
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd. MS70A-3317, Berkeley, CA, 94720, 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
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd. MS70A-3317, Berkeley, CA, 94720, USA
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15
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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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16
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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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17
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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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18
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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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19
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Affiliation(s)
- Lance B. Price
- Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- * E-mail:
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Gregg S. Davis
- Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
| | - Cindy M. Liu
- Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
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20
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Vanni MJ, McIntyre PB, Allen D, Arnott DL, Benstead JP, Berg DJ, Brabrand Å, Brosse S, Bukaveckas PA, Caliman A, Capps KA, Carneiro LS, Chadwick NE, Christian AD, Clarke A, Conroy JD, Cross WF, Culver DA, Dalton CM, Devine JA, Domine LM, Evans-White MA, Faafeng BA, Flecker AS, Gido KB, Godinot C, Guariento RD, Haertel-Borer S, Hall RO, Henry R, Herwig BR, Hicks BJ, Higgins KA, Hood JM, Hopton ME, Ikeda T, James WF, Jansen HM, Johnson CR, Koch BJ, Lamberti GA, Lessard-Pilon S, Maerz JC, Mather ME, McManamay RA, Milanovich JR, Morgan DKJ, Moslemi JM, Naddafi R, Nilssen JP, Pagano M, Pilati A, Post DM, Roopin M, Rugenski AT, Schaus MH, Shostell J, Small GE, Solomon CT, Sterrett SC, Strand Ø, Tarvainen M, Taylor JM, Torres-Gerald LE, Turner CB, Urabe J, Uye SI, Ventelä AM, Villeger S, Whiles MR, Wilhelm FM, Wilson HF, Xenopoulos MA, Zimmer KD. A global database of nitrogen and phosphorus excretion rates of aquatic animals. Ecology 2017; 98:1475. [PMID: 28263380 DOI: 10.1002/ecy.1792] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/30/2017] [Accepted: 02/07/2017] [Indexed: 11/06/2022]
Abstract
Animals can be important in modulating ecosystem-level nutrient cycling, although their importance varies greatly among species and ecosystems. Nutrient cycling rates of individual animals represent valuable data for testing the predictions of important frameworks such as the Metabolic Theory of Ecology (MTE) and ecological stoichiometry (ES). They also represent an important set of functional traits that may reflect both environmental and phylogenetic influences. Over the past two decades, studies of animal-mediated nutrient cycling have increased dramatically, especially in aquatic ecosystems. Here we present a global compilation of aquatic animal nutrient excretion rates. The dataset includes 10,534 observations from freshwater and marine animals of N and/or P excretion rates. These observations represent 491 species, including most aquatic phyla. Coverage varies greatly among phyla and other taxonomic levels. The dataset includes information on animal body size, ambient temperature, taxonomic affiliations, and animal body N:P. This data set was used to test predictions of MTE and ES, as described in Vanni and McIntyre (2016; Ecology DOI: 10.1002/ecy.1582).
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21
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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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22
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Hayer M, Schwartz E, Marks JC, Koch BJ, Morrissey EM, Schuettenberg AA, Hungate BA. Identification of growing bacteria during litter decomposition in freshwater through H218O quantitative stable isotope probing. Environ Microbiol Rep 2016; 8:975-982. [PMID: 27657357 DOI: 10.1111/1758-2229.12475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using H218O quantitative stable isotope probing. During 8 day incubations in 97 atom % H218O, 54% of the taxa grew. The most abundant phyla among growing taxa were Proteobacteria (45%), Bacteroidetes (30%) and Firmicutes (10%). Taxa differed in isotopic enrichment, reflecting variation in DNA replication of bacterial populations. At the class level, the highest atom fraction excess was observed for OPB41 and δ-Proteobacteria. There was no linear relationship between 18 O incorporation and abundance of taxa. δ-Proteobacteria and OPB41 were not abundant, yet the DNA of both taxa was highly enriched in 18 O. Bacteriodetes, in contrast, were abundant but not highly enriched. Our study shows that a large proportion of the bacterial taxa found on decomposing leaf litter grew slowly, and several low abundance taxa were highly enriched. These findings indicating that rare organisms may be important for the decomposition of leaf litter in streams, and that quantitative stable isotope probing with H218O can be used to advance our understanding of microorganisms in freshwater by identifying species that are growing in complex communities.
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Affiliation(s)
- Michaela Hayer
- Center for Ecosystem Science and Society, 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, 86001, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86001, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil, West Virginia University, Morgantown, WV, 26506, USA
| | - Alexa A Schuettenberg
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86001, 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, 86001, USA
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23
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Schwartz E, Hayer M, Hungate BA, Koch BJ, McHugh TA, Mercurio W, Morrissey EM, Soldanova K. Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples. Curr Opin Biotechnol 2016; 41:14-18. [DOI: 10.1016/j.copbio.2016.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/27/2016] [Accepted: 03/01/2016] [Indexed: 11/17/2022]
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24
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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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25
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Abstract
Ecological restoration has grown rapidly and now encompasses not only classic ecological theory but also utilitarian concerns, such as preparedness for climate change and provisioning of ecosystem services. Three dominant perspectives compete to influence the science and practice of river restoration. A strong focus on channel morphology has led to approaches that involve major Earth-moving activities, such as channel reconfiguration with the unmet assumption that ecological recovery will follow. Functional perspectives of river restoration aim to regain the full suite of biogeochemical, ecological, and hydrogeomorphic processes that make up a healthy river, and though there is well-accepted theory to support this, research on methods to implement and assess functional restoration projects is in its infancy. A plethora of new studies worldwide provide data on why and how rivers are being restored as well as the project outcomes. Measurable improvements postrestoration vary by restoration method and measure of outcome.
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Affiliation(s)
- Margaret A. Palmer
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, Maryland 20688
- National Socio-Environmental Synthesis Center, University of Maryland, Annapolis, Maryland 21401
| | - Kelly L. Hondula
- National Socio-Environmental Synthesis Center, University of Maryland, Annapolis, Maryland 21401
| | - Benjamin J. Koch
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, Maryland 20688
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona 86011
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26
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Taylor BW, Keep CF, Hall RO, Koch BJ, Tronstad LM, Flecker AS, Ulseth AJ. Improving the fluorometric ammonium method: matrix effects, background fluorescence, and standard additions. ACTA ACUST UNITED AC 2007. [DOI: 10.1899/0887-3593(2007)26[167:itfamm]2.0.co;2] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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