1
|
Trejos-Espeleta JC, Marin-Jaramillo JP, Schmidt SK, Sommers P, Bradley JA, Orsi WD. Principal role of fungi in soil carbon stabilization during early pedogenesis in the high Arctic. Proc Natl Acad Sci U S A 2024; 121:e2402689121. [PMID: 38954550 DOI: 10.1073/pnas.2402689121] [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: 02/07/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Climate warming is causing widespread deglaciation and pioneer soil formation over glacial deposits. Melting glaciers expose rocky terrain and glacial till sediment that is relatively low in biomass, oligotrophic, and depleted in nutrients. Following initial colonization by microorganisms, glacial till sediments accumulate organic carbon and nutrients over time. However, the mechanisms driving soil nutrient stabilization during early pedogenesis after glacial retreat remain unclear. Here, we traced amino acid uptake by microorganisms in recently deglaciated high-Arctic soils and show that fungi play a critical role in the initial stabilization of the assimilated carbon. Pioneer basidiomycete yeasts were among the predominant taxa responsible for carbon assimilation, which were associated with overall high amino acid use efficiency and reduced respiration. In intermediate- and late-stage soils, lichenized ascomycete fungi were prevalent, but bacteria increasingly dominated amino acid assimilation, with substantially decreased fungal:bacterial amino acid assimilation ratios and increased respiration. Together, these findings demonstrate that fungi are important drivers of pedogenesis in high-Arctic ecosystems that are currently subject to widespread deglaciation from global warming.
Collapse
Affiliation(s)
- Juan Carlos Trejos-Espeleta
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| | - Juan P Marin-Jaramillo
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - James A Bradley
- Aix Marseille University, University of Toulon, Centre national de la recherche scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO), Marseille, France 13009
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom, E1 4NS
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| |
Collapse
|
2
|
Nwoba ST, Carere CR, Wigley K, Baronian K, Weaver L, Gostomski PA. Using RNA-Stable isotope probing to investigate methane oxidation metabolites and active microbial communities in methane oxidation coupled to denitrification. CHEMOSPHERE 2024; 357:142067. [PMID: 38643845 DOI: 10.1016/j.chemosphere.2024.142067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/26/2024] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
The active denitrifying communities performing methane oxidation coupled to denitrification (MOD) were investigated using samples from an aerobic reactor (∼20% O2 and 2% CH4) and a microaerobic reactor (2% O2, 2% CH4) undertaking denitrification. The methane oxidation metabolites excreted in the reactors were acetate, methanol, formate and acetaldehyde. Using anaerobic batch experiments supplemented with exogenously supplied 13C-labelled metabolites, the active denitrifying bacteria were identified using 16S rRNA amplicon sequencing and RNA-stable isotope probing (RNA-SIP). With the aerobic reactor (AR) samples, the maximum NO3- removal rates were 0.43 mmol g-1 d-1, 0.40 mmol g-1 d-1, 0.33 mmol g-1 d-1 and 0.10 mmol g-1 d-1 for exogenously supplied acetate, formate, acetaldehyde and methanol batch treatments respectively, while with the microaerobic reactor (MR) samples, the maximum NO3- removal rates were 0.41 mmol g-1 d-1, 0.33 mmol g-1 d-1, 0.38 mmol g-1 d-1 and 0.14 mmol g-1 d-1 for exogenously supplied acetate, formate, acetaldehyde and methanol batch treatments respectively. The RNA-SIP experiments with 13C-labelled acetate, formate, and methanol identified Methyloversatilis, and Hyphomicrobium as the active methane-driven denitrifying bacteria in the AR samples, while Pseudoxanthomonas, Hydrogenophaga and Hyphomicrobium were the active MOD bacteria in the MR samples. Collectively, all the data indicate that formate is a key cross-feeding metabolite excreted by methanotrophs and consumed by denitrifiers performing MOD.
Collapse
Affiliation(s)
- Sunday T Nwoba
- Dept. of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand.
| | - Carlo R Carere
- Dept. of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Kathryn Wigley
- Dept. of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Kim Baronian
- Dept. of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
| | - Peter A Gostomski
- Dept. of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand.
| |
Collapse
|
3
|
Lee KK, Liu S, Crocker K, Huggins DR, Tikhonov M, Mani M, Kuehn S. Functional regimes define the response of the soil microbiome to environmental change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.584851. [PMID: 38559185 PMCID: PMC10980070 DOI: 10.1101/2024.03.15.584851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The metabolic activity of soil microbiomes plays a central role in carbon and nitrogen cycling. Given the changing climate, it is important to understand how the metabolism of natural communities responds to environmental change. However, the ecological, spatial, and chemical complexity of soils makes understanding the mechanisms governing the response of these communities to perturbations challenging. Here, we overcome this complexity by using dynamic measurements of metabolism in microcosms and modeling to reveal regimes where a few key mechanisms govern the response of soils to environmental change. We sample soils along a natural pH gradient, construct >1500 microcosms to perturb the pH, and quantify the dynamics of respiratory nitrate utilization, a key process in the nitrogen cycle. Despite the complexity of the soil microbiome, a minimal mathematical model with two variables, the quantity of active biomass in the community and the availability of a growth-limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. Across environmental perturbations, changes in these two variables give rise to three functional regimes each with qualitatively distinct dynamics of nitrate utilization over time: a regime where acidic perturbations induce cell death that limits metabolic activity, a nutrient-limiting regime where nitrate uptake is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth regime in basic conditions, where excess nutrients enable growth of initially rare taxa. The underlying mechanism of each regime is predicted by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. Further, our data suggest that the long-term history of environmental variation in the wild influences the transitions between functional regimes. Therefore, quantitative measurements and a mathematical model reveal the existence of qualitative regimes that capture the mechanisms and dynamics of a community responding to environmental change.
Collapse
Affiliation(s)
- Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| | - Siqi Liu
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| | - Kyle Crocker
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| | - David R. Huggins
- USDA-ARS, Northwest Sustainable Agroecosystems Research Unit, Pullman, WA 99164, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL
| | - Seppe Kuehn
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
4
|
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.
Collapse
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
| | | |
Collapse
|
5
|
Peng Z, Qian X, Liu Y, Li X, Gao H, An Y, Qi J, Jiang L, Zhang Y, Chen S, Pan H, Chen B, Liang C, van der Heijden MGA, Wei G, Jiao S. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat Commun 2024; 15:3624. [PMID: 38684659 PMCID: PMC11058813 DOI: 10.1038/s41467-024-47348-8] [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: 09/16/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.
Collapse
Affiliation(s)
- Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yining An
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Lan Jiang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Coskun ÖK, Gomez-Saez GV, Beren M, Özcan D, Günay SD, Elkin V, Hoşgörmez H, Einsiedl F, Eisenreich W, Orsi WD. Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community. FEMS Microbiol Ecol 2024; 100:fiae062. [PMID: 38632042 DOI: 10.1093/femsec/fiae062] [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: 11/13/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
Collapse
Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Doğacan Özcan
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Suna D Günay
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Viktor Elkin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Hakan Hoşgörmez
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Florian Einsiedl
- Chair of Hydrogeology, School of Engineering and Design, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstraße, 85748 Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. SCIENCE ADVANCES 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
Collapse
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
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - 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
| | - 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
| |
Collapse
|
10
|
Tao X, Yang Z, Feng J, Jian S, Yang Y, Bates CT, Wang G, Guo X, Ning D, Kempher ML, Liu XJA, Ouyang Y, Han S, Wu L, Zeng Y, Kuang J, Zhang Y, Zhou X, Shi Z, Qin W, Wang J, Firestone MK, Tiedje JM, Zhou J. Experimental warming accelerates positive soil priming in a temperate grassland ecosystem. Nat Commun 2024; 15:1178. [PMID: 38331994 PMCID: PMC10853207 DOI: 10.1038/s41467-024-45277-0] [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: 05/04/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Unravelling biosphere feedback mechanisms is crucial for predicting the impacts of global warming. Soil priming, an effect of fresh plant-derived carbon (C) on native soil organic carbon (SOC) decomposition, is a key feedback mechanism that could release large amounts of soil C into the atmosphere. However, the impacts of climate warming on soil priming remain elusive. Here, we show that experimental warming accelerates soil priming by 12.7% in a temperate grassland. Warming alters bacterial communities, with 38% of unique active phylotypes detected under warming. The functional genes essential for soil C decomposition are also stimulated, which could be linked to priming effects. We incorporate lab-derived information into an ecosystem model showing that model parameter uncertainty can be reduced by 32-37%. Model simulations from 2010 to 2016 indicate an increase in soil C decomposition under warming, with a 9.1% rise in priming-induced CO2 emissions. If our findings can be generalized to other ecosystems over an extended period of time, soil priming could play an important role in terrestrial C cycle feedbacks and climate change.
Collapse
Affiliation(s)
- Xuanyu Tao
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhifeng Yang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiajie Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Siyang Jian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China.
| | - Colin T Bates
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Gangsheng Wang
- Institute for Water-Carbon Cycles and Carbon Neutrality, and State Key Laboratory of Water Resources Engineering and Management, Wuhan University, 430072, Wuhan, China
| | - Xue Guo
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Megan L Kempher
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiao Jun A Liu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Shun Han
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Linwei Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Jialiang Kuang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Ya Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Xishu Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Zheng Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Wei Qin
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, 210008, Nanjing, China
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- School of Computer Sciences, University of Oklahoma, Norman, OK, 73019, USA.
| |
Collapse
|
11
|
Egbadon EO, Wigley K, Nwoba ST, Carere CR, Weaver L, Baronian K, Burbery L, Gostomski PA. Microaerobic methane-driven denitrification in a biotrickle bed - Investigating the active microbial biofilm community composition using RNA-stable isotope probing. CHEMOSPHERE 2024; 346:140528. [PMID: 37907168 DOI: 10.1016/j.chemosphere.2023.140528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 10/01/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023]
Abstract
A microaerobic (2% O2 v/v) biotrickle bed reactor supplied continuously with 2% methane to drive nitrate removal (MAME-D) was investigated using 16S rDNA and rRNA amplicon sequencing in combination with RNA-stable isotope probing (RNA-SIP) to identify the active microorganisms. Methane removal rates varied from 500 to 1000 mmol m-3h-1 and nitrate removal rates from 25 to 58 mmol m-3h-1 over 55 days of operation. Biofilm samples from the column were incubated in serum bottles supplemented with 13CH4. 16S rDNA analysis indicated a simple community structure in which four taxa accounted for 45% of the total relative abundance (RA). Dominant genera included the methanotroph Methylosinus and known denitrifiers Nubsella and Pseudoxanthomonas; along with a probable denitrifier assigned to the order Obscuribacterales. The 16S rRNA results revealed the methanotrophs Methylocystis (15% RA) and Methylosinus (10% RA) and the denitrifiers Arenimonas (10% RA) and Pseudoxanthomonas (7% RA) were the most active genera. Obscuribacterales was the most active taxa in the community at 22% RA. Activity was confirmed by the Δ buoyant density changes with time for the taxa, indicating most of the community activity was associated with methane oxidation and subsequent consumption of methanotrophic metabolic intermediates by the denitrifiers. This is the first report of RNA stable isotope probing within a microaerobic methane driven denitrification system and the active community was markedly different from the full community identified via 16S-rDNA analysis.
Collapse
Affiliation(s)
- Emmanuel O Egbadon
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Kathryn Wigley
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Sunday T Nwoba
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Carlo R Carere
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
| | - Kim Baronian
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Lee Burbery
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
| | - Peter A Gostomski
- Department of Chemical & Process Engineering, University of Canterbury, Christchurch, New Zealand.
| |
Collapse
|
12
|
Thomas SC, Miller G, Li X, Saxena D. Getting off tract: contributions of intraorgan microbiota to cancer in extraintestinal organs. Gut 2023; 73:175-185. [PMID: 37918889 PMCID: PMC10842768 DOI: 10.1136/gutjnl-2022-328834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The gastrointestinal ecosystem has received the most attention when examining the contributions of the human microbiome to health and disease. This concentration of effort is logical due to the overwhelming abundance of microbes in the gut coupled with the relative ease of sampling compared with other organs. However, the intestines are intimately connected to multiple extraintestinal organs, providing an opportunity for homeostatic microbial colonisation and pathogenesis in organs traditionally thought to be sterile or only transiently harbouring microbiota. These habitats are challenging to sample, and their low microbial biomass among large amounts of host tissue can make study challenging. Nevertheless, recent findings have shown that many extraintestinal organs that are intimately linked to the gut harbour stable microbiomes, which are colonised from the gut in selective manners and have highlighted not just the influence of the bacteriome but that of the mycobiome and virome on oncogenesis and health.
Collapse
Affiliation(s)
- Scott C Thomas
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
| | - George Miller
- Cancer Center, Holy Name Medical Center, Teaneck, NJ, USA
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
- Perlmutter Cancer Institute, New York University Langone Medical Center, New York, NY, USA
- Department of Urology, New York University Grossman School of Medicine, New York, NY, USA
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
- Perlmutter Cancer Institute, New York University Langone Medical Center, New York, NY, USA
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
13
|
Revillini D, David AS, Reyes AL, Knecht LD, Vigo C, Allen P, Searcy CA, Afkhami ME. Allelopathy-selected microbiomes mitigate chemical inhibition of plant performance. THE NEW PHYTOLOGIST 2023; 240:2007-2019. [PMID: 37737029 DOI: 10.1111/nph.19249] [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: 07/11/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023]
Abstract
Allelopathy is a common and important stressor that shapes plant communities and can alter soil microbiomes, yet little is known about the direct effects of allelochemical addition on bacterial and fungal communities or the potential for allelochemical-selected microbiomes to mediate plant performance responses, especially in habitats naturally structured by allelopathy. Here, we present the first community-wide investigation of microbial mediation of allelochemical effects on plant performance by testing how allelopathy affects soil microbiome structure and how these microbial changes impact germination and productivity across 13 plant species. The soil microbiome exhibited significant changes to 'core' bacterial and fungal taxa, bacterial composition, abundance of functionally important bacterial and fungal taxa, and predicted bacterial functional genes after the addition of the dominant allelochemical native to this habitat. Furthermore, plant performance was mediated by the allelochemical-selected microbiome, with allelopathic inhibition of plant productivity moderately mitigated by the microbiome. Through our findings, we present a potential framework to understand the strength of plant-microbial interactions in the presence of environmental stressors, in which frequency of the ecological stress may be a key predictor of microbiome-mediation strength.
Collapse
Affiliation(s)
- Daniel Revillini
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| | - Aaron S David
- Archbold Biological Station, 123 Main Drive, Venus, Florida, 33960, USA
| | - Alma L Reyes
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| | - Leslie D Knecht
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| | - Carolina Vigo
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| | - Preston Allen
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| | - Christopher A Searcy
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| | - Michelle E Afkhami
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA
| |
Collapse
|
14
|
Mahmoudi N, Wilhelm RC. Can we manage microbial systems to enhance carbon storage? Environ Microbiol 2023; 25:3011-3018. [PMID: 37431673 DOI: 10.1111/1462-2920.16462] [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: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.
Collapse
Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montréal, Quebec, Canada
| | - Roland C Wilhelm
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
15
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
16
|
Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. THE ISME JOURNAL 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
Collapse
Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| |
Collapse
|
17
|
Han X, Beck K, Bürgmann H, Frey B, Stierli B, Frossard A. Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes. Front Microbiol 2023; 14:1279041. [PMID: 37942081 PMCID: PMC10627841 DOI: 10.3389/fmicb.2023.1279041] [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: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.
Collapse
Affiliation(s)
- Xingguo Han
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| |
Collapse
|
18
|
Gruppuso L, Receveur JP, Fenoglio S, Bona F, Benbow ME. Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways. MICROBIAL ECOLOGY 2023; 86:1499-1512. [PMID: 36646914 PMCID: PMC10497695 DOI: 10.1007/s00248-023-02169-y] [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: 06/20/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.
Collapse
Affiliation(s)
- L Gruppuso
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy.
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy.
| | - J P Receveur
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - S Fenoglio
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - F Bona
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - M E Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
19
|
Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
20
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
21
|
Kim J, Hwangbo M, Shih CH, Chu KH. Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation. WATER RESEARCH X 2023; 20:100187. [PMID: 37671037 PMCID: PMC10477051 DOI: 10.1016/j.wroa.2023.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 09/07/2023]
Abstract
Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.
Collapse
Affiliation(s)
- Jinha Kim
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
- School of Earth, Environmental and Marine Sciences, The University of Texas – Rio Grande Valley, Brownsville, TX, USA
| | - Chih-Hsuan Shih
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Walkup J, Dang C, Mau RL, Hayer M, Schwartz E, Stone BW, Hofmockel KS, Koch BJ, Purcell AM, Pett-Ridge J, Wang C, Hungate BA, Morrissey EM. The predictive power of phylogeny on growth rates in soil bacterial communities. ISME COMMUNICATIONS 2023; 3:73. [PMID: 37454187 PMCID: PMC10349831 DOI: 10.1038/s43705-023-00281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.
Collapse
Affiliation(s)
- Jeth Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA
- University of California Merced, Life & Environmental Sciences Department, Merced, CA, 95343, USA
| | - Chao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, LN, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA.
| |
Collapse
|
25
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
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: 0] [Impact Index Per Article: 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.
Collapse
|
29
|
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.
Collapse
|
30
|
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
| |
Collapse
|
31
|
Jameson E, Taubert M, Angel R, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol 2023; 2555:261-282. [PMID: 36306091 DOI: 10.1007/978-1-0716-2795-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.
Collapse
Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martin Taubert
- Aquatic Geochemistry, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Roey Angel
- Soil & Water Research Infrastructure and Institute of Soil Biology, Biology Centre CAS, České Budějovice, Czechia
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Özge Eyice
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK.
| |
Collapse
|
32
|
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
|
33
|
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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
|
34
|
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: 12] [Impact Index Per Article: 6.0] [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.
Collapse
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
| |
Collapse
|
35
|
Dong W, Yang Q, George TS, Yin H, Wang S, Bi J, Zhang J, Liu X, Song A, Fan F. Investigating bacterial coupled assimilation of fertilizer‑nitrogen and crop residue‑carbon in upland soils by DNA-qSIP. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157279. [PMID: 35830916 DOI: 10.1016/j.scitotenv.2022.157279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Microbial immobilization of fertilizer nitrogen (N) can effectively reduce N losses in soil. However, the effects of crop residue on microbial assimilation of fertilizer-N and the underlying microbial mechanisms in upland soils are unclear. We evaluated the influence of maize residue (13C) addition on the microbial assimilation of ammonium-N (15N) in DNA from fertilizer, and quantified the bacterial 13C or 15N assimilation by quantitative stable isotope probing (DNA-qSIP). We found that the straw addition did increase total microbial assimilation of ammonium from fertilizer during the 2-week incubation. However, bacterial taxa varied in their responses to straw addition: Bacteriodetes and Proteobacteria accounted for large fractions of ammonium assimilation and their N assimilations were increased, while N assimilations of Acidobacteria were decreased. We revealed that highly 13C-labeled taxa were the main contributors of N assimilation under straw addition. The straw primarily enhanced the contributions of bacterial taxa to ammonium assimilation through increasing the extent of N assimilation, or enhancing the abundance of the N-assimilating bacterial taxa. Overall, our study elucidated an interaction between microbial assimilation of fertilizer-N and straw-C, showing a close element coupling of the keystone functional microbial taxa in N immobilization driven by organic carbon.
Collapse
Affiliation(s)
- Weiling Dong
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Qin Yang
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Timothy S George
- Ecological Sciences Group, The James Hutton Institute, Dundee, UK
| | - Huaqun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Sai Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingjing Bi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiayin Zhang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Alin Song
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
36
|
Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil. Appl Environ Microbiol 2022; 88:e0083922. [PMID: 36300927 PMCID: PMC9680644 DOI: 10.1128/aem.00839-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking
13
C from supplied carbon sources into metabolite pools and biomass.
Collapse
|
37
|
Biodegradation of poly(butylene succinate) in soil laboratory incubations assessed by stable carbon isotope labelling. Nat Commun 2022; 13:5691. [PMID: 36171185 PMCID: PMC9519748 DOI: 10.1038/s41467-022-33064-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 08/30/2022] [Indexed: 11/20/2022] Open
Abstract
Using biodegradable instead of conventional plastics in agricultural applications promises to help overcome plastic pollution of agricultural soils. However, analytical limitations impede our understanding of plastic biodegradation in soils. Utilizing stable carbon isotope (13C-)labelled poly(butylene succinate) (PBS), a synthetic polyester, we herein present an analytical approach to continuously quantify PBS mineralization to 13CO2 during soil incubations and, thereafter, to determine non-mineralized PBS-derived 13C remaining in the soil. We demonstrate extensive PBS mineralization (65 % of added 13C) and a closed mass balance on PBS−13C over 425 days of incubation. Extraction of residual PBS from soils combined with kinetic modeling of the biodegradation data and results from monomer (i.e., butanediol and succinate) mineralization experiments suggest that PBS hydrolytic breakdown controlled the overall PBS biodegradation rate. Beyond PBS biodegradation in soil, the presented methodology is broadly applicable to investigate biodegradation of other biodegradable polymers in various receiving environments. This study applies stable carbon isotope labelling to study polymer biodegradation in soils. This labelling enables accurate and precise tracking of polymer carbon during biodegradation and, thereby, provides a holistic picture of this process.
Collapse
|
38
|
Maltz MR, Carey CJ, Freund HL, Botthoff JK, Hart SC, Stajich JE, Aarons SM, Aciego SM, Blakowski M, Dove NC, Barnes ME, Pombubpa N, Aronson EL. Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California. Front Microbiol 2022; 13:856454. [PMID: 35836417 PMCID: PMC9274194 DOI: 10.3389/fmicb.2022.856454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.
Collapse
Affiliation(s)
- Mia R. Maltz
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, United States
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
- Center for Conservation Biology, University of California, Riverside, Riverside, CA, United States
- BREATHE Center, University of California, Riverside, Riverside, CA, United States
| | - Chelsea J. Carey
- Point Blue Conservation Sciences, Petaluma, CA, United States
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, Riverside, CA, United States
| | - Hannah L. Freund
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, Riverside, CA, United States
| | - Jon K. Botthoff
- Center for Conservation Biology, University of California, Riverside, Riverside, CA, United States
| | - Stephen C. Hart
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA, United States
- Department of Life and Environmental Sciences, University of California, Merced, Merced, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, Riverside, CA, United States
| | - Sarah M. Aarons
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Sarah M. Aciego
- Department of Geology and Geophysics, University of Wyoming, Laramie, WY, United States
- Noctilucent Aviation, Bridgeport, TX, United States
| | - Molly Blakowski
- Department of Watershed Science, Utah State University, Logan, UT, United States
| | - Nicholas C. Dove
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA, United States
- Environmental Systems Graduate Group, University of California, Merced, Merced, CA, United States
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Morgan E. Barnes
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA, United States
- Environmental Systems Graduate Group, University of California, Merced, Merced, CA, United States
- Pacific Northwest National Laboratory, Biological Sciences, Richland, WA, United States
| | - Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Emma L. Aronson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
- Center for Conservation Biology, University of California, Riverside, Riverside, CA, United States
- BREATHE Center, University of California, Riverside, Riverside, CA, United States
| |
Collapse
|
39
|
Wang J, Hu A, Meng F, Zhao W, Yang Y, Soininen J, Shen J, Zhou J. Embracing mountain microbiome and ecosystem functions under global change. THE NEW PHYTOLOGIST 2022; 234:1987-2002. [PMID: 35211983 DOI: 10.1111/nph.18051] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.
Collapse
Affiliation(s)
- Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqian Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Ji Shen
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| |
Collapse
|
40
|
Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf. Appl Environ Microbiol 2022; 88:e0021622. [PMID: 35404072 PMCID: PMC9088280 DOI: 10.1128/aem.00216-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.
Collapse
|
41
|
Finley BK, Mau RL, Hayer M, Stone BW, Morrissey EM, Koch BJ, Rasmussen C, Dijkstra P, Schwartz E, Hungate BA. Soil minerals affect taxon-specific bacterial growth. THE ISME JOURNAL 2022; 16:1318-1326. [PMID: 34931028 PMCID: PMC9038713 DOI: 10.1038/s41396-021-01162-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 01/01/2023]
Abstract
Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages-particularly short-range order minerals-affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with 18O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25-36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.
Collapse
Affiliation(s)
- Brianna K. Finley
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.266093.80000 0001 0668 7243Present Address: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 USA
| | - Rebecca L. Mau
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Michaela Hayer
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Bram W. Stone
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.451303.00000 0001 2218 3491Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Ember M. Morrissey
- grid.268154.c0000 0001 2156 6140Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506 USA
| | - Benjamin J. Koch
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Craig Rasmussen
- grid.134563.60000 0001 2168 186XDepartment of Environmental Science, University of Arizona, Tucson, AZ 85721 USA
| | - Paul Dijkstra
- grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Egbert Schwartz
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - Bruce A. Hungate
- grid.261120.60000 0004 1936 8040Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 USA ,grid.261120.60000 0004 1936 8040Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011 USA
| |
Collapse
|
42
|
Orsi WD, Vuillemin A, Coskun ÖK, Rodriguez P, Oertel Y, Niggemann J, Mohrholz V, Gomez-Saez GV. Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis. THE ISME JOURNAL 2022; 16:1245-1261. [PMID: 34893690 PMCID: PMC9038920 DOI: 10.1038/s41396-021-01169-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
Fungi are ubiquitous in the ocean and hypothesized to be important members of marine ecosystems, but their roles in the marine carbon cycle are poorly understood. Here, we use 13C DNA stable isotope probing coupled with phylogenetic analyses to investigate carbon assimilation within diverse communities of planktonic and benthic fungi in the Benguela Upwelling System (Namibia). Across the redox stratified water column and in the underlying sediments, assimilation of 13C-labeled carbon from diatom extracellular polymeric substances (13C-dEPS) by fungi correlated with the expression of fungal genes encoding carbohydrate-active enzymes. Phylogenetic analysis of genes from 13C-labeled metagenomes revealed saprotrophic lineages related to the facultative yeast Malassezia were the main fungal foragers of pelagic dEPS. In contrast, fungi living in the underlying sulfidic sediments assimilated more 13C-labeled carbon from chemosynthetic bacteria compared to dEPS. This coincided with a unique seafloor fungal community and dissolved organic matter composition compared to the water column, and a 100-fold increased fungal abundance within the subseafloor sulfide-nitrate transition zone. The subseafloor fungi feeding on 13C-labeled chemolithoautotrophs under anoxic conditions were affiliated with Chytridiomycota and Mucoromycota that encode cellulolytic and proteolytic enzymes, revealing polysaccharide and protein-degrading fungi that can anaerobically decompose chemosynthetic necromass. These subseafloor fungi, therefore, appear to be specialized in organic matter that is produced in the sediments. Our findings reveal that the phylogenetic diversity of fungi across redox stratified marine ecosystems translates into functionally relevant mechanisms helping to structure carbon flow from primary producers in marine microbiomes from the surface ocean to the subseafloor.
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat Rev Microbiol 2022; 20:415-430. [DOI: 10.1038/s41579-022-00695-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 12/18/2022]
|
45
|
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: 13] [Impact Index Per Article: 6.5] [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.
Collapse
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
| |
Collapse
|
46
|
Polerecky L, Eichner M, Masuda T, Zavřel T, Rabouille S, Campbell DA, Halsey K. Calculation and Interpretation of Substrate Assimilation Rates in Microbial Cells Based on Isotopic Composition Data Obtained by nanoSIMS. Front Microbiol 2021; 12:621634. [PMID: 34917040 PMCID: PMC8670600 DOI: 10.3389/fmicb.2021.621634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Stable isotope probing (SIP) combined with nano-scale secondary ion mass spectrometry (nanoSIMS) is a powerful approach to quantify assimilation rates of elements such as C and N into individual microbial cells. Here, we use mathematical modeling to investigate how the derived rate estimates depend on the model used to describe substrate assimilation by a cell during a SIP incubation. We show that the most commonly used model, which is based on the simplifying assumptions of linearly increasing biomass of individual cells over time and no cell division, can yield underestimated assimilation rates when compared to rates derived from a model that accounts for cell division. This difference occurs because the isotopic labeling of a dividing cell increases more rapidly over time compared to a non-dividing cell and becomes more pronounced as the labeling increases above a threshold value that depends on the cell cycle stage of the measured cell. Based on the modeling results, we present formulae for estimating assimilation rates in cells and discuss their underlying assumptions, conditions of applicability, and implications for the interpretation of intercellular variability in assimilation rates derived from nanoSIMS data, including the impacts of storage inclusion metabolism. We offer the formulae as a Matlab script to facilitate rapid data evaluation by nanoSIMS users.
Collapse
Affiliation(s)
- Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Meri Eichner
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Takako Masuda
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Tomáš Zavřel
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Sophie Rabouille
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-mer, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-mer, France
| | | | - Kimberly Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
47
|
Barnett SE, Youngblut ND, Koechli CN, Buckley DH. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proc Natl Acad Sci U S A 2021; 118:e2115292118. [PMID: 34799453 PMCID: PMC8617410 DOI: 10.1073/pnas.2115292118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/10/2021] [Indexed: 11/18/2022] Open
Abstract
Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. We employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil. We identified and tracked 1,286 bacterial taxa that assimilated 13C in an agricultural soil over a period of 48 d. Overall 13C-assimilation dynamics of bacterial taxa, defined by the source and timing of the 13C they assimilated, exhibited low phylogenetic conservation. We identified bacterial guilds composed of taxa that had similar 13C assimilation dynamics. We show that C-source bioavailability explained significant variation in both C mineralization dynamics and guild structure, and that the growth dynamics of bacterial guilds differed significantly in response to C addition. We also demonstrate that the guild structure explains significant variation in the biogeographical distribution of bacteria at continental and global scales. These results suggest that an understanding of in situ growth dynamics is essential for understanding microbial contributions to soil C cycling. We interpret these findings in the context of bacterial life history strategies and their relationship to terrestrial C cycling.
Collapse
Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Nicholas D Youngblut
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chantal N Koechli
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853;
| |
Collapse
|
48
|
Dang C, Walkup JGV, Hungate BA, Franklin RB, Schwartz E, Morrissey EM. Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria. Environ Microbiol 2021; 24:357-369. [PMID: 34811865 DOI: 10.1111/1462-2920.15843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022]
Abstract
Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.
Collapse
Affiliation(s)
- Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jeth G V Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rima B Franklin
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| |
Collapse
|
49
|
The Threat of Pests and Pathogens and the Potential for Biological Control in Forest Ecosystems. FORESTS 2021. [DOI: 10.3390/f12111579] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Forests are an essential component of the natural environment, as they support biodiversity, sequester carbon, and play a crucial role in biogeochemical cycles—in addition to producing organic matter that is necessary for the function of terrestrial organisms. Forests today are subject to threats ranging from natural occurrences, such as lightning-ignited fires, storms, and some forms of pollution, to those caused by human beings, such as land-use conversion (deforestation or intensive agriculture). In recent years, threats from pests and pathogens, particularly non-native species, have intensified in forests. The damage, decline, and mortality caused by insects, fungi, pathogens, and combinations of pests can lead to sizable ecological, economic, and social losses. To combat forest pests and pathogens, biocontrol may be an effective alternative to chemical pesticides and fertilizers. This review of forest pests and potential adversaries in the natural world highlights microbial inoculants, as well as research efforts to further develop biological control agents against forest pests and pathogens. Recent studies have shown promising results for the application of microbial inoculants as preventive measures. Other studies suggest that these species have potential as fertilizers.
Collapse
|
50
|
Blagodatskaya E, Tarkka M, Knief C, Koller R, Peth S, Schmidt V, Spielvogel S, Uteau D, Weber M, Razavi BS. Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces. Front Microbiol 2021; 12:625697. [PMID: 34777265 PMCID: PMC8581545 DOI: 10.3389/fmicb.2021.625697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
Collapse
Affiliation(s)
- Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig, Leipzig, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Peth
- Institute of Soil Science, University of Hannover, Hanover, Germany
| | | | - Sandra Spielvogel
- Department Soil Science, Institute for Plant Nutrition and Soil Science, Christian-Albrechts University Kiel, Kiel, Germany
| | - Daniel Uteau
- Department of Soil Science, Faculty of Organic Agricultural Sciences, University of Kassel, Kassel, Germany
| | | | - Bahar S. Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel, Germany
| |
Collapse
|