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Foley MM, Stone BWG, Caro TA, Sokol NW, Koch BJ, Blazewicz SJ, Dijkstra P, Hayer M, Hofmockel K, Finley BK, Mack M, Marks J, Mau RL, Monsaint-Queeney V, Morrissey E, Propster J, Purcell A, Schwartz E, Pett-Ridge J, Fierer N, Hungate BA. Growth rate as a link between microbial diversity and soil biogeochemistry. Nat Ecol Evol 2024:10.1038/s41559-024-02520-7. [PMID: 39294403 DOI: 10.1038/s41559-024-02520-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/25/2024] [Indexed: 09/20/2024]
Abstract
Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation-some of the many ways in which organisms affect Earth's ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.
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Affiliation(s)
- 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.
| | - Bram W G Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tristan A Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - Noah W Sokol
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 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
| | - 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
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brianna K Finley
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michelle Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, 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
| | - 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
| | - Victoria Monsaint-Queeney
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ember 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
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biology, New Mexico Highlands University, Las Vegas, NM, USA
| | - Alicia 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
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, Merced, CA, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 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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2
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da Silva VG, Smith NW, Mullaney JA, Wall C, Roy NC, McNabb WC. Food-breastmilk combinations alter the colonic microbiome of weaning infants: an in silico study. mSystems 2024; 9:e0057724. [PMID: 39191378 PMCID: PMC11406890 DOI: 10.1128/msystems.00577-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
The introduction of solid foods to infants, also known as weaning, is a critical point for the development of the complex microbial community inhabiting the human colon, impacting host physiology in infancy and later in life. This research investigated in silico the impact of food-breastmilk combinations on growth and metabolite production by colonic microbes of New Zealand weaning infants using the metagenome-scale metabolic model named Microbial Community. Eighty-nine foods were individually combined with breastmilk, and the 12 combinations with the strongest influence on the microbial production of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were identified. Fiber-rich and polyphenol-rich foods, like pumpkin and blackcurrant, resulted in the greatest increase in predicted fluxes of total SCFAs and individual fluxes of propionate and acetate when combined, respectively, with breastmilk. Identified foods were further combined with other foods and breastmilk, resulting in 66 multiple food-breastmilk combinations. These combinations altered in silico the impact of individual foods on the microbial production of SCFAs and BCFAs, suggesting that the interaction between the dietary compounds composing a meal is the key factor influencing colonic microbes. Blackcurrant combined with other foods and breastmilk promoted the greatest increase in the production of acetate and total SCFAs, while pork combined with other foods and breastmilk decreased the production of total BCFAs.IMPORTANCELittle is known about the influence of complementary foods on the colonic microbiome of weaning infants. Traditional in vitro and in vivo microbiome methods are limited by their resource-consuming concerns. Modeling approaches represent a promising complementary tool to provide insights into the behavior of microbial communities. This study evaluated how foods combined with other foods and human milk affect the production of short-chain fatty acids and branched-chain fatty acids by colonic microbes of weaning infants using a rapid and inexpensive in silico approach. Foods and food combinations identified here are candidates for future experimental investigations, helping to fill a crucial knowledge gap in infant nutrition.
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Affiliation(s)
- Vitor G da Silva
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nick W Smith
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jane A Mullaney
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- AgResearch, Palmerston North, New Zealand
| | - Clare Wall
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Nutrition and Dietetics, The University of Auckland, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
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3
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Caro TA, Kashyap S, Brown G, Chen C, Kopf SH, Templeton AS. Single-cell measurement of microbial growth rate with Raman microspectroscopy. FEMS Microbiol Ecol 2024; 100:fiae110. [PMID: 39113275 PMCID: PMC11347945 DOI: 10.1093/femsec/fiae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 07/12/2024] [Accepted: 08/05/2024] [Indexed: 08/28/2024] Open
Abstract
Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.
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Affiliation(s)
- Tristan A Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Srishti Kashyap
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
| | - George Brown
- Department of Applied Mathematics, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Claudia Chen
- Department of Applied Mathematics, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Alexis S Templeton
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
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4
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Sampara P, Lawson CE, Scarborough MJ, Ziels RM. Advancing environmental biotechnology with microbial community modeling rooted in functional 'omics. Curr Opin Biotechnol 2024; 88:103165. [PMID: 39033648 DOI: 10.1016/j.copbio.2024.103165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024]
Abstract
Emerging biotechnologies that solve pressing environmental and climate emergencies will require harnessing the vast functional diversity of the underlying microbiomes driving such engineered processes. Modeling is a critical aspect of process engineering that informs system design as well as aids diagnostic optimization of performance. 'Conventional' bioprocess models assume homogenous biomass within functional guilds and thus fail to predict emergent properties of diverse microbial physiologies, such as product specificity and community interactions. Yet, recent advances in functional 'omics-based approaches can provide a 'lens' through which we can probe and measure in situ ecophysiologies of environmental microbiomes. Here, we overview microbial community modeling approaches that incorporate functional 'omics data, which we posit can advance our ability to design and control new environmental biotechnologies going forward.
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Affiliation(s)
- Pranav Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher E Lawson
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada.
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5
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Kakouridis A, Yuan M, Nuccio EE, Hagen JA, Fossum CA, Moore ML, Estera-Molina KY, Nico PS, Weber PK, Pett-Ridge J, Firestone MK. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. THE NEW PHYTOLOGIST 2024; 242:1661-1675. [PMID: 38358052 DOI: 10.1111/nph.19560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/04/2023] [Indexed: 02/16/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.
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Affiliation(s)
- Anne Kakouridis
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mengting Yuan
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - John A Hagen
- University of California Berkeley, Berkeley, CA, 94720, USA
| | | | - Madeline L Moore
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katerina Y Estera-Molina
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
- University of California Merced, Merced, 95343, CA, USA
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6
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Ruan Y, Ling N, Jiang S, Jing X, He JS, Shen Q, Nan Z. Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment. eLife 2024; 12:RP89392. [PMID: 38647539 PMCID: PMC11034942 DOI: 10.7554/elife.89392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the 18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members in Solirubrobacter and Pseudonocardia genera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors.
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Affiliation(s)
- Yang Ruan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Shengjing Jiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
| | - Jin-Sheng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking UniversityBeijingChina
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhouChina
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7
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Xu Q, Li L, Guo J, Guo H, Liu M, Guo S, Kuzyakov Y, Ling N, Shen Q. Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils. mBio 2024; 15:e0017724. [PMID: 38376207 PMCID: PMC10936188 DOI: 10.1128/mbio.00177-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ling Li
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Junjie Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hanyue Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Manqiang Liu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shiwei Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Gottingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Gottingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ning Ling
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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8
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Tian J, Dungait JAJ, Hou R, Deng Y, Hartley IP, Yang Y, Kuzyakov Y, Zhang F, Cotrufo MF, Zhou J. Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming. Nat Commun 2024; 15:377. [PMID: 38191568 PMCID: PMC10774409 DOI: 10.1038/s41467-023-44647-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, PR China.
| | - Jennifer A J Dungait
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Rennes Drive, Exeter, EX4 4RJ, UK
- Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - Ruixing Hou
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), 100101, Beijing, PR China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, PR China
| | - Iain P Hartley
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Rennes Drive, Exeter, EX4 4RJ, UK
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, PR China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, 37077, Göttingen, Germany
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, PR China.
| | - M Francesca Cotrufo
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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9
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Simpson A, Wood-Charlson EM, Smith M, Koch BJ, Beilsmith K, Kimbrel JA, Kellom M, Hunter CI, Walls RL, Schriml LM, Wilhelm RC. MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment. Gigascience 2024; 13:giae071. [PMID: 39399973 DOI: 10.1093/gigascience/giae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/29/2024] [Accepted: 08/27/2024] [Indexed: 10/15/2024] Open
Abstract
DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.
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Affiliation(s)
- Abigayle Simpson
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Montana Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Kathleen Beilsmith
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Matthew Kellom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Ramona L Walls
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Lynn M Schriml
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD 21201, USA
| | - Roland C Wilhelm
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, IN 47907, USA
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10
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Wattenburger CJ, Buckley DH. Land use alters bacterial growth dynamics in soil. Environ Microbiol 2023; 25:3239-3254. [PMID: 37783513 DOI: 10.1111/1462-2920.16514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Microbial growth and mortality are major determinants of soil carbon cycling. We measured in situ growth dynamics of individual bacterial taxa in cropped and successional soils in response to a resource pulse. We hypothesized that land use imposes selection pressures on growth characteristics. We estimated growth and death for 453 and 73 taxa, respectively. The average generation time was 5.04 ± 6.28 (SD; range 0.7-63.5) days. Lag times were shorter in cultivated than successional soils and resource amendment decreased lag times. Taxa exhibiting the greatest growth response also exhibited the greatest mortality, indicative of boom-and-bust dynamics. We observed a bimodal growth rate distribution, representing fast- and slow-growing clusters. Both clusters grew more rapidly in successional soils, which had more organic matter, than cultivated soils. Resource amendment increased the growth rate of the slower growing but not the faster-growing cluster via a mixture of increased growth rates and species turnover, indicating that competitive dynamics constrain growth rates in situ. These two clusters show that copiotrophic bacteria in soils may be subdivided into different life history groups and that these subgroups respond independently to land use and resource availability.
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Affiliation(s)
- Cassandra J Wattenburger
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
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11
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Purcell AM, Dijkstra P, Hungate BA, McMillen K, Schwartz E, van Gestel N. Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula. THE ISME JOURNAL 2023; 17:2290-2302. [PMID: 37872274 PMCID: PMC10689830 DOI: 10.1038/s41396-023-01536-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site-likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink-indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.
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Affiliation(s)
- Alicia M Purcell
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
- 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
| | - 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
| | - Kelly McMillen
- 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
| | - Natasja van Gestel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- TTU Climate Center, Texas Tech University, Lubbock, TX, USA
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12
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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: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [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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13
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Nicolas AM, Sieradzki ET, Pett-Ridge J, Banfield JF, Taga ME, Firestone MK, Blazewicz SJ. A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil. Nat Commun 2023; 14:5835. [PMID: 37730729 PMCID: PMC10511743 DOI: 10.1038/s41467-023-40835-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/09/2023] [Indexed: 09/22/2023] Open
Abstract
Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following "wet-up", when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils.
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Affiliation(s)
- Alexa M Nicolas
- Plant & Microbial Biology Department, University of California Berkeley, Berkeley, CA, USA
| | - Ella T Sieradzki
- Environmental Science, Policy & Management Department, University of California Berkeley, Berkeley, CA, USA.
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Jillian F Banfield
- Environmental Science, Policy & Management Department, University of California Berkeley, Berkeley, CA, USA
- Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michiko E Taga
- Plant & Microbial Biology Department, University of California Berkeley, Berkeley, CA, USA
| | - Mary K Firestone
- Environmental Science, Policy & Management Department, University of California Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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14
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Vyshenska D, Sampara P, Singh K, Tomatsu A, Kauffman WB, Nuccio EE, Blazewicz SJ, Pett-Ridge J, Louie KB, Varghese N, Kellom M, Clum A, Riley R, Roux S, Eloe-Fadrosh EA, Ziels RM, Malmstrom RR. A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems 2023; 8:e0128022. [PMID: 37377419 PMCID: PMC10469821 DOI: 10.1128/msystems.01280-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/19/2023] [Indexed: 06/29/2023] Open
Abstract
Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.
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Affiliation(s)
- Dariia Vyshenska
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pranav Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kanwar Singh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Andy Tomatsu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - W. Berkeley Kauffman
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Steven J. Blazewicz
- 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
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Katherine B. Louie
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Neha Varghese
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew Kellom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alicia Clum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert Riley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Emiley A. Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ryan M. Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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15
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Maillard F, Michaud TJ, See CR, DeLancey LC, Blazewicz SJ, Kimbrel JA, Pett-Ridge J, Kennedy PG. Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils. mSystems 2023; 8:e0039023. [PMID: 37338274 PMCID: PMC10469842 DOI: 10.1128/msystems.00390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/21/2023] Open
Abstract
Microbial necromass contributes significantly to both soil carbon (C) persistence and ecosystem nitrogen (N) availability, but quantitative estimates of C and N movement from necromass into soils and decomposer communities are lacking. Additionally, while melanin is known to slow fungal necromass decomposition, how it influences microbial C and N acquisition as well as elemental release into soils remains unclear. Here, we tracked decomposition of isotopically labeled low and high melanin fungal necromass and measured 13C and 15N accumulation in surrounding soils and microbial communities over 77 d in a temperate forest in Minnesota, USA. Mass loss was significantly higher from low melanin necromass, corresponding with greater 13C and 15N soil inputs. A taxonomically and functionally diverse array of bacteria and fungi was enriched in 13C and/or 15N at all sampling points, with enrichment being consistently higher on low melanin necromass and earlier in decomposition. Similar patterns of preferential C and N enrichment of many bacterial and fungal genera early in decomposition suggest that both microbial groups co-contribute to the rapid assimilation of resource-rich soil organic matter inputs. While overall richness of taxa enriched in C was higher than in N for both bacteria and fungi, there was a significant positive relationship between C and N in co-enriched taxa. Collectively, our results demonstrate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate but also necromass C and N release and that both elements are rapidly co-utilized by diverse bacterial and fungal decomposers in natural settings. IMPORTANCE Recent studies indicate that microbial dead cells, particularly those of fungi, play an important role in long-term carbon persistence in soils. Despite this growing recognition, how the resources within dead fungal cells (also known as fungal necromass) move into decomposer communities and soils are poorly quantified, particularly in studies based in natural environments. In this study, we found that the contribution of fungal necromass to soil carbon and nitrogen availability was slowed by the amount of melanin present in fungal cell walls. Further, despite the overall rapid acquisition of carbon and nitrogen from necromass by a diverse range of both bacteria and fungi, melanization also slowed microbial uptake of both elements. Collectively, our results indicate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate, but also necromass carbon and nitrogen release into soil as well as microbial resource acquisition.
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Affiliation(s)
- François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Talia J. Michaud
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Craig R. See
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jeffrey A. Kimbrel
- 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
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Peter G. Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
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16
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Caro TA, McFarlin J, Jech S, Fierer N, Kopf S. Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil. Proc Natl Acad Sci U S A 2023; 120:e2211625120. [PMID: 37036980 PMCID: PMC10120080 DOI: 10.1073/pnas.2211625120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/06/2023] [Indexed: 04/12/2023] Open
Abstract
The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.
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Affiliation(s)
- Tristan A. Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Jamie McFarlin
- Department of Geology and Geophysics, University of Wyoming, Laramie, WY82071
| | - Sierra Jech
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO80309
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO80309
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Sebastian Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO80309
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17
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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. THE ISME JOURNAL 2023; 17:611-619. [PMID: 36732614 PMCID: PMC10030646 DOI: 10.1038/s41396-022-01354-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [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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18
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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] [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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19
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Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming. Appl Environ Microbiol 2023; 89:e0154322. [PMID: 36847530 PMCID: PMC10056963 DOI: 10.1128/aem.01543-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using 18O-labeled water, from which taxon-specific rates of 18O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.
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20
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Elevated temperature and CO 2 strongly affect the growth strategies of soil bacteria. Nat Commun 2023; 14:391. [PMID: 36693873 PMCID: PMC9873651 DOI: 10.1038/s41467-023-36086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
The trait-based strategies of microorganisms appear to be phylogenetically conserved, but acclimation to climate change may complicate the scenario. To study the roles of phylogeny and environment on bacterial responses to sudden moisture increases, we determine bacterial population-specific growth rates by 18O-DNA quantitative stable isotope probing (18O-qSIP) in soils subjected to a free-air CO2 enrichment (FACE) combined with warming. We find that three growth strategies of bacterial taxa - rapid, intermediate and slow responders, defined by the timing of the peak growth rates - are phylogenetically conserved, even at the sub-phylum level. For example, members of class Bacilli and Sphingobacteriia are mainly rapid responders. Climate regimes, however, modify the growth strategies of over 90% of species, partly confounding the initial phylogenetic pattern. The growth of rapid bacterial responders is more influenced by phylogeny, whereas the variance for slow responders is primarily explained by environmental conditions. Overall, these results highlight the role of phylogenetic and environmental constraints in understanding and predicting the growth strategies of soil microorganisms under global change scenarios.
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21
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Beauchemin ET, Hunter C, Maurice CF. Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting. Gut Microbes 2023; 15:2180317. [PMID: 36823031 PMCID: PMC9980609 DOI: 10.1080/19490976.2023.2180317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2'-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal that Prevotella UCG-001 and Ileibacterium are enriched in the replicating fraction. Finally, we labeled the actively replicating murine gut bacteria during exposure to cell wall-specific antibiotics in vitro. We show that regardless of the antibiotic used, the actively replicating bacteria largely consist of Ileibacterium, suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidating in situ bacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities.
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Affiliation(s)
- Eve T. Beauchemin
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Claire Hunter
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada,McGill Centre for Microbiome Research, McGill University, Montreal, Quebec, Canada,CONTACT Corinne F. Maurice Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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22
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Orsi WD. Quantitative microbial ecology: Future challenges and opportunities. Environ Microbiol 2023; 25:91-96. [PMID: 36163700 DOI: 10.1111/1462-2920.16204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 01/21/2023]
Affiliation(s)
- William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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23
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Greenlon A, Sieradzki E, Zablocki O, Koch BJ, Foley MM, Kimbrel JA, Hungate BA, Blazewicz SJ, Nuccio EE, Sun CL, Chew A, Mancilla CJ, Sullivan MB, Firestone M, Pett-Ridge J, Banfield JF. Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems. mSystems 2022; 7:e0041722. [PMID: 36300946 PMCID: PMC9765451 DOI: 10.1128/msystems.00417-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/02/2022] [Indexed: 12/25/2022] Open
Abstract
The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are shaped by both current and historical soil environmental conditions. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) with an H218O labeling experiment to identify actively growing soil microorganisms and their genomic capacities. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies. We studied three Mediterranean grassland soils across a rainfall gradient to evaluate the hypothesis that historic precipitation levels are an important factor controlling trait selection. We used qSIP-informed genome-resolved metagenomics to resolve the active subset of soil community members and identify their characteristic ecophysiological traits. Higher year-round precipitation levels correlated with higher activity and growth rates of flagellar motile microorganisms. In addition to heavily isotopically labeled bacteria, we identified abundant isotope-labeled phages, suggesting phage-induced cell lysis likely contributed to necromass production at all three sites. Further, there was a positive correlation between phage activity and the activity of putative phage hosts. Contrary to our expectations, the capacity to decompose the diverse complex carbohydrates common in soil organic matter or oxidize methanol and carbon monoxide were broadly distributed across active and inactive bacteria in all three soils, implying that these traits are not highly selected for by historical precipitation. IMPORTANCE Soil moisture is a critical factor that strongly shapes the lifestyle of soil organisms by changing access to nutrients, controlling oxygen diffusion, and regulating the potential for mobility. We identified active microorganisms in three grassland soils with similar mineral contexts, yet different historic rainfall inputs, by adding water labeled with a stable isotope and tracking that isotope in DNA of growing microbes. By examining the genomes of active and inactive microorganisms, we identified functions that are enriched in growing organisms, and showed that different functions were selected for in different soils. Wetter soil had higher activity of motile organisms, but activity of pathways for degradation of soil organic carbon compounds, including simple carbon substrates, were comparable for all three soils. We identified many labeled, and thus active bacteriophages (viruses that infect bacteria), implying that the cells they killed contributed to soil organic matter. The activity of these bacteriophages was significantly correlated with activity of their hosts.
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Affiliation(s)
- Alex Greenlon
- Department of Environmental Science, Policy and Management, University California, Berkeley, Berkley, California, USA
| | - Ella Sieradzki
- Department of Environmental Science, Policy and Management, University California, Berkeley, Berkley, California, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, Ohio State University, Columbus, Ohio, 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
| | - Megan M. Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, 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
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Christine L. Sun
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Aaron Chew
- Department of Environmental Science, Policy and Management, University California, Berkeley, Berkley, California, USA
| | - Cynthia-Jeanette Mancilla
- Department of Environmental Science, Policy and Management, University California, Berkeley, Berkley, California, USA
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio, USA
| | - Mary Firestone
- Department of Environmental Science, Policy and Management, University California, Berkeley, Berkley, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California, Merced, Merced, California, USA
| | - Jillian F. Banfield
- Department of Environmental Science, Policy and Management, University California, Berkeley, Berkley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeley, Berkley, California, USA
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24
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Hestrin R, Kan M, Lafler M, Wollard J, Kimbrel JA, Ray P, Blazewicz SJ, Stuart R, Craven K, Firestone M, Nuccio EE, Pett-Ridge J. Plant-associated fungi support bacterial resilience following water limitation. THE ISME JOURNAL 2022; 16:2752-2762. [PMID: 36085516 PMCID: PMC9666503 DOI: 10.1038/s41396-022-01308-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H218O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis compared to S. bescii-inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought susceptible. Overall, H218O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.
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Affiliation(s)
- Rachel Hestrin
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA.
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA.
| | - Megan Kan
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Marissa Lafler
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jessica Wollard
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jeffrey A Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Prasun Ray
- Department of Natural Resources, University of Maryland Eastern Shore, Princess Anne, MD, USA
- Plant Biology Division, Noble Research Institute, Ardmore, OK, USA
| | - Steven J Blazewicz
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Rhona Stuart
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Kelly Craven
- Plant Biology Division, Noble Research Institute, Ardmore, OK, USA
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, USA.
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA.
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25
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Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. MICROBIOME 2022; 10:199. [PMID: 36434737 PMCID: PMC9700909 DOI: 10.1186/s40168-022-01391-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. RESULTS Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera. CONCLUSIONS Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.
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Affiliation(s)
- Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Marissa Lafler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ashley N. Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Anne Kakouridis
- Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | | | | | | | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA USA
| | | | - Mary Firestone
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA USA
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26
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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? THE ISME JOURNAL 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] [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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27
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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. GLOBAL CHANGE BIOLOGY 2022; 28:128-139. [PMID: 34587352 PMCID: PMC9293287 DOI: 10.1111/gcb.15911] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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28
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Abstract
High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.
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Affiliation(s)
- Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
| | - Peter K Weber
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
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Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. mSphere 2021; 6:e0008521. [PMID: 34468166 PMCID: PMC8550312 DOI: 10.1128/msphere.00085-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. IMPORTANCE Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO2-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.
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Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. MICROBIOME 2021; 9:208. [PMID: 34663463 PMCID: PMC8522061 DOI: 10.1186/s40168-021-01154-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). RESULTS We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. CONCLUSIONS Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jose Liquet-Gonzalez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark P Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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31
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Martinović T, Odriozola I, Mašínová T, Doreen Bahnmann B, Kohout P, Sedlák P, Merunková K, Větrovský T, Tomšovský M, Ovaskainen O, Baldrian P. Temporal turnover of the soil microbiome composition is guild-specific. Ecol Lett 2021; 24:2726-2738. [PMID: 34595822 DOI: 10.1111/ele.13896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023]
Abstract
Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.
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Affiliation(s)
- Tijana Martinović
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic.,Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Sedlák
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Kristina Merunková
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
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32
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Zhang L, Yin W, Wang C, Zhang A, Zhang H, Zhang T, Ju F. Untangling Microbiota Diversity and Assembly Patterns in the World's Largest Water Diversion Canal. WATER RESEARCH 2021; 204:117617. [PMID: 34555587 DOI: 10.1016/j.watres.2021.117617] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Large water diversion projects are important constructions for reallocation of human-essential water resources. Deciphering microbiota dynamics and assembly mechanisms underlying canal water ecosystem services especially during long-distance diversion is a prerequisite for water quality monitoring, biohazard warning and sustainable management. Using a 1432-km canal of the South-to-North Water Diversion Projects as a model system, we answer three central questions: how bacterial and micro-eukaryotic communities spatio-temporally develop, how much ecological stochasticity contributes to microbiota assembly, and which immigrating populations better survive and navigate across the canal. We applied quantitative ribosomal RNA gene sequence analyses to investigate canal water microbial communities sampled over a year, as well as null model- and neutral model-based approaches to disentangle the microbiota assembly processes. Our results showed clear microbiota dynamics in community composition driven by seasonality more than geographic location, and seasonally dependent influence of environmental parameters. Overall, bacterial community was largely shaped by deterministic processes, whereas stochasticity dominated micro-eukaryotic community assembly. We defined a local growth factor (LGF) and demonstrated its innovative use to quantitatively infer microbial proliferation, unraveling taxonomically dependent population response to local environmental selection across canal sections. Using LGF as a quantitative indicator of immigrating capacities, we also found that most micro-eukaryotic populations (82%) from the source water sustained growth in the canal and better acclimated to the hydrodynamical water environment than bacteria (67%). Taxa inferred to largely propagate include Limnohabitans sp. and Cryptophyceae, potentially contributing to water auto-purification. Combined, our work poses first and unique insights into the microbiota assembly patterns and dynamics in the world's largest water diversion canal, providing important ecological knowledge for long-term sustainable water quality maintenance in such a giant engineered system.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Wei Yin
- Changjiang Water Resources Protection Institute, 515 Qintai Street, Wuhan 430051, Hubei Province, China
| | - Chao Wang
- Changjiang Water Resources Protection Institute, 515 Qintai Street, Wuhan 430051, Hubei Province, China
| | - Aijing Zhang
- Construction and Administration Bureau of South-to-North Water Diversion Middle Route Project, 1 Yuyuantan South Road, Beijing 100038, China
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Pokfulam Road, The University of Hong Kong, Hong Kong 999077, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
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33
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Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community. Nat Commun 2021; 12:3381. [PMID: 34099669 PMCID: PMC8184982 DOI: 10.1038/s41467-021-23676-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/11/2021] [Indexed: 01/04/2023] Open
Abstract
Nutrient amendment diminished bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Here, we show strong differences in the bacterial taxa responsible for respiration from four ecosystems, indicating the potential for taxon-specific control over soil carbon cycling. Trends in functional diversity, defined as the richness of bacteria contributing to carbon flux and their equitability of carbon use, paralleled trends in taxonomic diversity although functional diversity was lower overall. Among genera common to all ecosystems, Bradyrhizobium, the Acidobacteria genus RB41, and Streptomyces together composed 45–57% of carbon flow through bacterial productivity and respiration. Bacteria that utilized the most carbon amendment (glucose) were also those that utilized the most native soil carbon, suggesting that the behavior of key soil taxa may influence carbon balance. Mapping carbon flow through different microbial taxa as demonstrated here is crucial in developing taxon-sensitive soil carbon models that may reduce the uncertainty in climate change projections. The fate of soil carbon depends on microbial processes, but whether different microbial taxa have individualistic effects on carbon fluxes is unknown. Here the authors use 16 S amplicon sequencing and stable isotopes to show how taxonomic differences influence bacterial respiration and carbon cycling across four ecosystems.
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34
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Microbial Community Resilience across Ecosystems and Multiple Disturbances. Microbiol Mol Biol Rev 2021; 85:85/2/e00026-20. [PMID: 33789927 DOI: 10.1128/mmbr.00026-20] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.
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35
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Abstract
CRISPR-Cas gene editing tools have brought us to an era of synthetic biology that will change the world. Excitement over the breakthroughs these tools have enabled in biology and medicine is balanced, justifiably, by concern over how their applications might go wrong in open environments. We do not know how genomic processes (including regulatory and epigenetic processes), evolutionary change, ecosystem interactions, and other higher order processes will affect traits, fitness, and impacts of edited organisms in nature. However, anticipating the spread, change, and impacts of edited traits or organisms in heterogeneous, changing environments is particularly important with "gene drives on the horizon." To anticipate how "synthetic threads" will affect the web of life on Earth, scientists must confront complex system interactions across many levels of biological organization. Currently, we lack plans, infrastructure, and funding for field science and scientists to track new synthetic organisms, with or without gene drives, as they move through open environments.
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36
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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: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [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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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 JOURNAL 2021; 15:2738-2747. [PMID: 33782569 DOI: 10.1038/s41396-021-00959-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [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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38
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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] [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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Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. Methods Mol Biol 2020; 2046:137-149. [PMID: 31407302 DOI: 10.1007/978-1-4939-9721-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.
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40
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Stable Isotope Probing of Microorganisms in Environmental Samples with H 218O. Methods Mol Biol 2019; 2046:129-136. [PMID: 31407301 DOI: 10.1007/978-1-4939-9721-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
We describe a protocol for investigating microbial growth in environmental samples via stable isotope probing (SIP) with H218O. Water is a universal substrate for all microorganisms and replication is required for DNA to become labeled with 18O. By measuring how much the DNA of each taxon becomes enriched with 18O when an environmental sample is incubated with H218O, it is feasible to quantify that population's DNA replication rate, which is a proxy for growth.
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41
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Predictive genomic traits for bacterial growth in culture versus actual growth in soil. ISME JOURNAL 2019; 13:2162-2172. [PMID: 31053828 DOI: 10.1038/s41396-019-0422-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/12/2022]
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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42
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de Nijs EA, Hicks LC, Leizeaga A, Tietema A, Rousk J. Soil microbial moisture dependences and responses to drying-rewetting: The legacy of 18 years drought. GLOBAL CHANGE BIOLOGY 2019; 25:1005-1015. [PMID: 30387912 DOI: 10.1111/gcb.14508] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/27/2018] [Accepted: 10/27/2018] [Indexed: 05/25/2023]
Abstract
Climate change will alter precipitation patterns with consequences for soil C cycling. An understanding of how fluctuating soil moisture affects microbial processes is therefore critical to predict responses to future global change. We investigated how long-term experimental field drought influences microbial tolerance to lower moisture levels ("resistance") and ability to recover when rewetted after drought ("resilience"), using soils from a heathland which had been subjected to experimental precipitation reduction during the summer for 18 years. We tested whether drought could induce increased resistance, resilience, and changes in the balance between respiration and bacterial growth during perturbation events, by following a two-tiered approach. We first evaluated the effects of the long-term summer drought on microbial community functioning to drought and drying-rewetting (D/RW), and second tested the ability to alter resistance and resilience through additional perturbation cycles. A history of summer drought in the field selected for increased resilience but not resistance, suggesting that rewetting after drought, rather than low moisture levels during drought, was the selective pressure shaping the microbial community functions. Laboratory D/RW cycles also selected for communities with a higher resilience rather than increased resistance. The ratio of respiration to bacterial growth during D/RW perturbation was lower for the field drought-exposed communities and decreased for both field treatments during the D/RW cycles. This suggests that cycles of D/RW also structure microbial communities to respond quickly and efficiently to rewetting after drought. Our findings imply that microbial communities can adapt to changing climatic conditions and that this might slow the rate of soil C loss predicted to be induced by future cyclic drought.
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Affiliation(s)
- Evy A de Nijs
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Lettice C Hicks
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Ainara Leizeaga
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Albert Tietema
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Johannes Rousk
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
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43
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Quantifying population-specific growth in benthic bacterial communities under low oxygen using H 218O. ISME JOURNAL 2019; 13:1546-1559. [PMID: 30783213 PMCID: PMC6776007 DOI: 10.1038/s41396-019-0373-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 01/09/2023]
Abstract
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.
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44
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Margesin R, Collins T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl Microbiol Biotechnol 2019; 103:2537-2549. [PMID: 30719551 PMCID: PMC6443599 DOI: 10.1007/s00253-019-09631-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/28/2022]
Abstract
Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria.
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
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