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Zhu M, Dai X. Shaping of microbial phenotypes by trade-offs. Nat Commun 2024; 15:4238. [PMID: 38762599 DOI: 10.1038/s41467-024-48591-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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2
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Xu Q, Li L, Guo J, Guo H, Liu M, Guo S, Kuzyakov Y, Ling N, Shen Q. Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils. mBio 2024; 15:e0017724. [PMID: 38376207 PMCID: PMC10936188 DOI: 10.1128/mbio.00177-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ling Li
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Junjie Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hanyue Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Manqiang Liu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shiwei Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Gottingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Gottingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ning Ling
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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3
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - 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
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4
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Marschmann GL, Tang J, Zhalnina K, Karaoz U, Cho H, Le B, Pett-Ridge J, Brodie EL. Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nat Microbiol 2024; 9:421-433. [PMID: 38316928 PMCID: PMC10847045 DOI: 10.1038/s41564-023-01582-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
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Affiliation(s)
- Gianna L Marschmann
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinyun Tang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kateryna Zhalnina
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Beatrice Le
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
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5
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Yuan M, Na M, Hicks LC, Rousk J. Limiting resources for soil microbial growth in climate change simulation treatments in the subarctic. Ecology 2024; 105:e4210. [PMID: 37989722 DOI: 10.1002/ecy.4210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/06/2023] [Accepted: 10/04/2023] [Indexed: 11/23/2023]
Abstract
The microbial use of resources to sustain life and reproduce influences for example, decomposition and plant nutrient provisioning. The study of "limiting factors" has shed light on the interaction between plants and their environment. Here, we investigated whether carbon (C), nitrogen (N), or phosphorus (P) was limiting for soil microorganisms in a subarctic tundra heath, and how changes in resource availability associated with climate change affected this. We studied samples in which changes in resource availability due to climate warming were simulated by the addition of birch litter and/or inorganic N. To these soils, we supplied factorial C (as glucose), N (as NH4 NO3 ), and P (as KH2 PO4 /K2 HPO4 ) additions ("limiting factor assays," LFA), to determine the limiting factors. The combination of C and P induced large growth responses in all soils and, combined with a systematic tendency for growth increases by C, this suggested that total microbial growth was primarily limited by C and secondarily by P. The C limitation was alleviated by the field litter treatment and strengthened by N fertilization. The microbial growth response to the LFA-C and LFA-P addition was strongest in the field-treatment that combined litter and N addition. We also found that bacteria were closer to P limitation than fungi. Our results suggest that, under a climate change scenario, increased C availability resulting from Arctic greening, treeline advance, and shrubification will reduce the microbial C limitation, while increased N availability resulting from warming will intensify the microbial C limitation. Our results also suggest that the synchronous increase of both C and N availability might lead to a progressive P limitation of microbial growth, primarily driven by bacteria being closer to P limitation. These shifts in microbial resource limitation might lead to a microbial targeting of the limiting element from organic matter, and also trigger competition for nutrients between plants and microorganisms, thus modulating the productivity of the ecosystem.
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Affiliation(s)
- Mingyue Yuan
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Meng Na
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Lettice C Hicks
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Johannes Rousk
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
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Chen L, Chen S, Xing T, Long Y, Wang Z, Kong X, Xu A, Wu Q, Sun Y. Phytoremediation with application of anaerobic fermentation residues regulate the assembly of ecological clusters within co-occurrence network in ionic rare earth tailings soil: A pot experiment. Environ Pollut 2024; 340:122790. [PMID: 37890691 DOI: 10.1016/j.envpol.2023.122790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/03/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023]
Abstract
The cultivation of energy plants (Pennisetum hybrid) with anaerobic fermentation residues has become an important phytoremediation approach in ionic rare earth elements (REEs) tailings because of its advantages in low cost and sustainability recently. In this study, a comparative pot experiment was carried out to determine the interaction pattern and key ecological clusters in microbial community respond to phytoremediation. Results showed that the application of biogas residues or slurry could effectively mitigate soil acidification, increase soil nutrients, alter REEs bioavailability and promote plant growth. Without fertilization, plant growth was restricted and soil acidification and nutrient-deficiency would be further aggravated. This difference in phytoremediation effect was associated with the assembly of seven key ecological clusters in co-occurrence network of rhizosphere soil. And such assembly pattern of cluster, determined by the environmental preference (e.g. pH, REEs), nutrient demand and interaction among clusters, could alter the microbial communities in response to the changes in soil context rapidly and exert corresponding ecological function during phytoremediation, such as participating in soil nutrient cycling, affecting plant biomass and altering REEs bioavailability. These findings provided new insights for anaerobic fermentation residues application, and can be beneficial to support for studying microbe-plant combined remediation in the future.
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Affiliation(s)
- Liumeng Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China; Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shasha Chen
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Tao Xing
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Yun Long
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Zhi Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Science and Technology of China, Hefei, 230026, China
| | - Xiaoying Kong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Science and Technology of China, Hefei, 230026, China.
| | - An Xu
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Qiangjian Wu
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yongmin Sun
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
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7
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Duan P, Fu R, Nottingham AT, Domeignoz-Horta LA, Yang X, Du H, Wang K, Li D. Tree species diversity increases soil microbial carbon use efficiency in a subtropical forest. Glob Chang Biol 2023; 29:7131-7144. [PMID: 37859578 DOI: 10.1111/gcb.16971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023]
Abstract
Plant communities strongly influence soil microbial communities and, in turn, soil carbon (C) cycling. Microbial carbon use efficiency (CUE) is an important parameter for predicting soil C accumulation, yet how plant and soil microbial community traits influence microbial CUE remains poorly understood. Here, we determined how soil microbial CUE is influenced by plant and soil microbial community traits, by studying a natural gradient of plant species diversity in a subtropical forest. Our results showed that microbial CUE increased with increasing tree species diversity, suggesting a correlation between plant community traits and soil C storage. The specific soil properties that explained the greatest variation in microbial CUE were associated with microbial communities (biomass, enzyme activities and the ratio of oligotrophic to copiotrophic taxa); there were weaker correlations with plant-input properties, soil chemistry and soil organic C quality and its mineral protection. Overall, high microbial CUE was associated with soil properties correlated with increased tree species diversity: higher substrate availability (simple SOM chemical structures and weak mineral organic associations) and high microbial growth rates despite increased community dominance by oligotrophic strategists. Our results point to a mechanism by which increased tree species diversity may increase the forest C sink by affecting carbon use with the soil microbial community.
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Affiliation(s)
- Pengpeng Duan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang, China
- Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Ruitong Fu
- Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Andrew T Nottingham
- School of Geography, University of Leeds, Leeds, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Luiz A Domeignoz-Horta
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Xinyi Yang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang, China
- Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hu Du
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang, China
- Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Kelin Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang, China
- Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Dejun Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang, China
- Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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8
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Marshall DJ, Cameron HE, Loreau M. Relationships between intrinsic population growth rate, carrying capacity and metabolism in microbial populations. ISME J 2023; 17:2140-2143. [PMID: 37891425 PMCID: PMC10689727 DOI: 10.1038/s41396-023-01543-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Dustin J Marshall
- School of Biological Sciences/Centre for Geometric Biology, Monash University, Victoria, 3800, VIC, Australia.
| | - Hayley E Cameron
- School of Biological Sciences/Centre for Geometric Biology, Monash University, Victoria, 3800, VIC, Australia
| | - Michel Loreau
- Theoretical and Experimental Ecology Station, CNRS, 2 route du CNRS, 09200, Moulis, France
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9
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Liu Y, Dai W, Yao D, Wang N, Liu M, Wang L, Tian W, Yan P, Huang Z, Wang H. Arsenic pollution from human activities drives changes in soil microbial community characteristics. Environ Microbiol 2023; 25:2592-2603. [PMID: 37349980 DOI: 10.1111/1462-2920.16442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 05/30/2023] [Indexed: 06/24/2023]
Abstract
Soil arsenic (As) pollution not only decreases plant productivity but also soil quality, in turn hampering sustainable agricultural development. Despite the negative effects of As contamination on rice yield and quality being reported widely, the responses of microbial communities and co-occurrence networks in paddy soil to As pollution have not been explored. Here, based on high-throughput sequencing technologies, we investigated bacterial abundance and diversity in paddy soils with different levels of As contamination, and constructed associated microbial co-occurrence networks. As pollution reduced soil bacterial diversity significantly (p < 0.001). In addition, bioavailable As concentrations were negatively correlated with Actinobacteria and Acidobacteria relative abundance (p < 0.05). Conversely, As pollution had a positive relationship with Chloroflexi, Betaproteobacteria, and Bacteroidetes relative abundance (p < 0.05). Firmicutes relative abundance decreased with an increase in total As concentration. The ecological clusters and key groups in bacterial co-occurrence networks exhibited distinct trends with an increase in As pollution. Notably, Acidobacteria play an important role in maintaining microbial networks in As contaminated soils. Overall, we provide empirical evidence that As contamination influences soil microbial community structure, posing a threat to soil ecosystem health and sustainable agriculture.
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Affiliation(s)
- Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
| | - Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
| | - Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
| | - Mingqing Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Lei Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Peirui Yan
- Mangshi Soil and Fertilizer Workstation, Yunnan, China
| | - Zhonglin Huang
- Guangxi Bossco Environmental Protection Technology Co., Ltd., Nanning, China
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
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10
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Li Z, Xu W, Kang L, Kuzyakov Y, Chen L, He M, Liu F, Zhang D, Zhou W, Liu X, Yang Y. Accelerated organic matter decomposition in thermokarst lakes upon carbon and phosphorus inputs. Glob Chang Biol 2023; 29:6367-6382. [PMID: 37695465 DOI: 10.1111/gcb.16938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
Mineralization of dissolved organic matter (DOM) in thermokarst lakes plays a non-negligible role in the permafrost carbon (C) cycle, but remains poorly understood due to its complex interactions with external C and nutrient inputs (i.e., aquatic priming and nutrient effects). Based on large-scale lake sampling and laboratory incubations, in combination with 13 C-stable-isotope labeling, optical spectroscopy, and high-throughput sequencing, we examined large-scale patterns and dominant drivers of priming and nutrient effects of DOM biodegradation across 30 thermokarst lakes along a 1100-km transect on the Tibetan Plateau. We observed that labile C and phosphorus (P) rather than nitrogen (N) inputs stimulated DOM biodegradation, with the priming and P effects being 172% and 451% over unamended control, respectively. We also detected significant interactive effects of labile C and nutrient supply on DOM biodegradation, with the combined labile C and nutrient additions inducing stronger microbial mineralization than C or nutrient treatment alone, illustrating that microbial activity in alpine thermokarst lakes is co-limited by both C and nutrients. We further found that the aquatic priming was mainly driven by DOM quality, with the priming intensity increasing with DOM recalcitrance, reflecting the limitation of external C as energy sources for microbial activity. Greater priming intensity was also associated with higher community-level ribosomal RNA gene operon (rrn) copy number and bacterial diversity as well as increased background soluble reactive P concentration. In contrast, the P effect decreased with DOM recalcitrance as well as with background soluble reactive P and ammonium concentrations, revealing the declining importance of P availability in mediating DOM biodegradation with enhanced C limitation but reduced nutrient limitation. Overall, the stimulation of external C and P inputs on DOM biodegradation in thermokarst lakes would amplify C-climate feedback in this alpine permafrost region.
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Affiliation(s)
- Ziliang Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weijie Xu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyao Kang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Göttingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Mei He
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Futing Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Wei Zhou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuning Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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11
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Liu J, Gang S, Wang X, Sun S, Kang J, Ge J. Quorum sensing in different subcommunities becomes the key factor affecting the humification of the aerobic composting system with sauerkraut fermentation wastewater. Bioresour Technol 2023; 387:129608. [PMID: 37544536 DOI: 10.1016/j.biortech.2023.129608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
Aerobic composting is an effective and harmless method to treat Sauerkraut fermentation wastewater (SFW). Given the limited understanding of the effect of quorum sensing (QS) on humification in subcommunities under acidic environments, a large-scale analysis was conducted to identify features that impact the response of QS to humification in different subcommunities. The results showed that the addition of SFW directly affected humification in subcommunities A and C, and the abundances of functional genes related to carbon fixation and carbon degradation were significantly increased at 7 and 15 d, respectively. In addition, subcommunity B indirectly affected humus production but regulated carbon metabolic pathways such as glycolysis/gluconeogenesis and pentose phosphate by QS with subcommunities B. These findings provide a novel perspective for analysing the regulation of humification in aerobic composting and suggest that composting has potential applications in organic wastewater treatment.
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Affiliation(s)
- Jiaxin Liu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Song Gang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; Hebei University of Environmental Engineering, Hebei Key Laboratory of Agroecological Safety, Qinhuangdao 066102, China
| | - Xu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Shanshan Sun
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; Hebei University of Environmental Engineering, Hebei Key Laboratory of Agroecological Safety, Qinhuangdao 066102, China.
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12
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Li J, Pei J, Fang C, Li B, Nie M. Thermal adaptation of microbial respiration persists throughout long-term soil carbon decomposition. Ecol Lett 2023; 26:1803-1814. [PMID: 37592863 DOI: 10.1111/ele.14296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Soil microbial respiration is expected to show adaptations to changing temperatures, greatly weakening the magnitude of feedback over time, as shown in labile carbon substrates. However, whether such thermal adaptation persists during long-term soil carbon decomposition as carbon substrates decrease in decomposability remains unknown. Here, we conducted a 6-year incubation experiment in natural and arable soils with distinct properties under three temperatures (10, 20 and 30°C). Mass-specific microbial respiration was consistently lower under higher long-term incubation temperatures, suggesting the occurrence and persistence of microbial thermal adaptation in long-term soil carbon decomposition. Furthermore, changes in microbial community composition and function largely explained the persistence of microbial respiratory thermal adaptation. If such thermal adaptation generally occurs in large low-decomposability carbon pools, warming-induced soil carbon losses may be lower than previously predicted and thus may not contribute as much as expected to greenhouse warming.
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Affiliation(s)
- Jinquan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Junmin Pei
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Changming Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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13
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López JL, Fourie A, Poppeliers SWM, Pappas N, Sánchez-Gil JJ, de Jonge R, Dutilh BE. Growth rate is a dominant factor predicting the rhizosphere effect. ISME J 2023; 17:1396-1405. [PMID: 37322285 PMCID: PMC10432406 DOI: 10.1038/s41396-023-01453-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.
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Affiliation(s)
- José L López
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Bariloche, Rio Negro, Argentina
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Arista Fourie
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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14
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Zhang S, Han S, Gao J, Yu X, Hu S. Low-temperature corn straw-degrading bacterial agent and moisture effects on indigenous microbes. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12644-8. [PMID: 37392246 PMCID: PMC10386949 DOI: 10.1007/s00253-023-12644-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/05/2023] [Accepted: 06/15/2023] [Indexed: 07/03/2023]
Abstract
While the in situ return of corn straw can improve soil fertility and farmland ecology, additional bacterial agents are required in low-temperature areas of northern China to accelerate straw degradation. Moisture is an important factor affecting microbial activity; however, owing to a lack of bacterial agents adapted to low-temperature complex soil environments, the effects of soil moisture on the interaction between exogenous bacterial agents and indigenous soil microorganisms remain unclear. To this end, we explored the effect of the compound bacterial agent CFF constructed using Pseudomonas putida and Acinetobacter lwoffii, developed to degrade corn straw in low-temperature soils (15 °C), on indigenous bacterial and fungal communities under dry (10% moisture content), slightly wet (20%), and wet (30%) soil-moisture conditions. The results showed that CFF application significantly affected the α-diversity of bacterial communities and changed both bacterial and fungal community structures, enhancing the correlation between microbial communities and soil-moisture content. CFF application also changed the network structure and the species of key microbial taxa, promoting more linkages among microbial genera. Notably, with an increase in soil moisture, CFF enhanced the rate of corn straw degradation by inducing positive interactions between bacterial and fungal genera and enriching straw degradation-related microbial taxa. Overall, our study demonstrates the alteration of indigenous microbial communities using bacterial agents (CFF) to overcome the limitations of indigenous microorganisms for in situ straw-return agriculture in low-temperature areas. KEY POINTS: • Low-temperature and variable moisture conditions (10-30%) were compared • Soil microbial network structure and linkages between genera were altered • CFF improves straw degradation via positive interactions between soil microbes.
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Affiliation(s)
- Sainan Zhang
- College of Agriculture, Inner Mongolia Agricultural University, 306 Zhaowunda Road, Saihan District, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China
| | - Shengcai Han
- Key Laboratory of Crop Cultivation and Genetic Improvement, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010000, People's Republic of China
| | - Julin Gao
- College of Agriculture, Inner Mongolia Agricultural University, 306 Zhaowunda Road, Saihan District, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China.
- Key Laboratory of Crop Cultivation and Genetic Improvement, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China.
| | - Xiaofang Yu
- College of Agriculture, Inner Mongolia Agricultural University, 306 Zhaowunda Road, Saihan District, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China.
- Key Laboratory of Crop Cultivation and Genetic Improvement, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China.
| | - Shuping Hu
- College of Agriculture, Inner Mongolia Agricultural University, 306 Zhaowunda Road, Saihan District, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China
- Key Laboratory of Crop Cultivation and Genetic Improvement, Inner Mongolia Autonomous Region, 010000, Hohhot, People's Republic of China
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15
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Li S, Yang S, Wei X, Jiao S, Luo W, Chen W, Wei G. Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands. ISME J 2023:10.1038/s41396-023-01437-6. [PMID: 37253970 PMCID: PMC10356767 DOI: 10.1038/s41396-023-01437-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/03/2023] [Accepted: 05/19/2023] [Indexed: 06/01/2023]
Abstract
Atmospheric trace gases, such as H2 and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H2 and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.
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Affiliation(s)
- Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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16
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McCully AL, Loop Yao M, Brower KK, Fordyce PM, Spormann AM. Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes. ISME Commun 2023; 3:47. [PMID: 37160952 PMCID: PMC10169782 DOI: 10.1038/s43705-023-00241-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
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Affiliation(s)
- Alexandra L McCully
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - McKenna Loop Yao
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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17
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Guan X, Guo Z, Wang X, Xiang S, Sun T, Zhao R, He J, Liu F. Transfer route and driving forces of antibiotic resistance genes from reclaimed water to groundwater. Environ Pollut 2023; 330:121800. [PMID: 37169235 DOI: 10.1016/j.envpol.2023.121800] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
The infiltration of reclaimed water has created a significant environmental risk due to the spread of antibiotic resistance genes (ARGs) in riparian groundwater. Reclaimed water from wastewater treatment plants (WWTPs) had been identified as a source of both antibiotics and ARGs in groundwater, based on their spatial and temporal distribution. The assembly process of microbial communities in the groundwater of the infiltration zone was more influenced by deterministic processes. Co-occurrence network analysis revealed that Thermotoga, Desulfotomaculum, Methanobacterium, and other such genera were dominant shared genera. These were considered core genera and hosts of ARGs for transport from reclaimed water to groundwater. The most abundant ARG in these shared genera was MacB, enriched in groundwater point G3 and potentially transferred from reclaimed water to groundwater by Acidovorax, Hydrogenophaga, Methylotenera, Dechloromonas, and Nitrospira. During the infiltration process, environmental factors and the tradeoff between energy metabolism and antibiotic defense strategy may have affected ARG transfer. Understanding the transfer route and driving forces of ARGs from reclaimed water to groundwater provided a new perspective for evaluating the spread risk of ARGs in reclaimed water infiltration.
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Affiliation(s)
- Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China.
| | - Zining Guo
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Xusheng Wang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Shizheng Xiang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Tongxin Sun
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Ruoyu Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Jiangtao He
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing, 100083, China
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18
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Yang X, Duan P, Hicks L, Wang K, Li D. Mechanisms underlying the responses of microbial carbon and nitrogen use efficiencies to nitrogen addition are mediated by topography in a subtropical forest. Sci Total Environ 2023; 880:163236. [PMID: 37030359 DOI: 10.1016/j.scitotenv.2023.163236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
Microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are key parameters determining the fate of C and N in soils. Atmospheric N deposition has been found to heavily impact multiple soil C and N transformations, but we lack understanding of the responses of CUE and NUE to N deposition, and it remains uncertain whether responses may be mediated by topography. Here, a N addition experiment with three treatment levels (0, 50 and 100 kg N ha-1 yr-1) was conducted in the valley and on the slope of a subtropical karst forest. Nitrogen addition increased microbial CUE and NUE at both topographic positions, but the underlying mechanisms differed. In the valley, the increase in CUE was associated with an increase in soil fungal richness:biomass and lower litter C:N, whereas on the slope, the response was linked with a reduced ratio of dissolved soil organic C (DOC) to available phosphorus (AVP) which reduced respiration, and increased root N:P stoichiometry. In the valley, the increase in NUE was explained by stimulated microbial N growth relative to gross N mineralization, which was associated with increased ratios of soil total dissolved N:AVP and fungal richness:biomass. In contrast, on the slope, the increase in NUE was attributed to reduced gross N mineralization, linked to increased DOC:AVP. Overall, our results highlight how topography-driven soil substrate availability and microbial properties can regulate microbial CUE and NUE.
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Affiliation(s)
- Xinyi Yang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Pengpeng Duan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Lettice Hicks
- Section of Microbial Ecology, Department of Biology, Lund University, Lund 223 62, Sweden
| | - Kelin Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Dejun Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Huanjiang 547100, China.
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19
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Ma S, Zhu W, Wang W, Li X, Sheng Z. Microbial assemblies with distinct trophic strategies drive changes in soil microbial carbon use efficiency along vegetation primary succession in a glacier retreat area of the southeastern Tibetan Plateau. Sci Total Environ 2023; 867:161587. [PMID: 36638988 DOI: 10.1016/j.scitotenv.2023.161587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Soil microbial carbon use efficiency (CUE) is a vital physiological parameter in assessing carbon turnover. Yet, how the microbial assemblies with distinct trophic strategies regulate the soil microbial CUE remains elusive. Based on the oligotrophic-copiotrophic framework, we explored the role of microbial taxa with different trophic strategies in mediating microbial CUE (determined by a 13C-labeled approach) along the vegetation primary succession in Hailuogou glacier retreat area of the southeastern Tibetan Plateau. Results showed that soil microbial CUE ranged from 0.54 to 0.72 (averaging 0.62 ± 0.01 across all samples) and increased staggeringly along the vegetation succession. Microbial assemblies with distinct trophic strategies were crucial regulators of soil microbial CUE. Specifically, microbial CUE increased with microbial oligotroph: copiotroph ratios, oligotroph-dominated stage had a higher microbial CUE than copiotroph-dominated ones. The prevalence of oligotrophic members would be the underlying microbial mechanism for the high microbial CUE. Given that oligotrophs predominate in more recalcitrant carbon soils and their higher microbial CUE, we speculate that oligotrophs are likely to potentially enhance carbon sequestration in soils. In addition, the responses of the microbial CUE to fungal oligotroph: copiotroph ratios were higher than bacterial ones. Fungal taxa may play a dominant role in shaping microbial CUE relative to bacterial members. Overall, our results constructed close associations between microbial trophic strategies and CUE and provide direct evidence regarding how microbial trophic strategies regulate microbial CUE. This study is a significant step forward for elucidating the physiological mechanisms regulating microbial CUE and has significant implications for understanding microbial-mediated carbon cycling processes.
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Affiliation(s)
- Shenglan Ma
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wanze Zhu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, PR China.
| | - Wenwu Wang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xia Li
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zheliang Sheng
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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20
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Barnett SE, Egan R, Foster B, Eloe-Fadrosh EA, Buckley DH. Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing. mBio 2023;:e0358422. [PMID: 36877031 DOI: 10.1128/mbio.03584-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.
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21
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Manzoni S, Chakrawal A, Ledder G. Decomposition rate as an emergent property of optimal microbial foraging. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1094269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Decomposition kinetics are fundamental for quantifying carbon and nutrient cycling in terrestrial and aquatic ecosystems. Several theories have been proposed to construct process-based kinetics laws, but most of these theories do not consider that microbial decomposers can adapt to environmental conditions, thereby modulating decomposition. Starting from the assumption that a homogeneous microbial community maximizes its growth rate over the period of decomposition, we formalize decomposition as an optimal control problem where the decomposition rate is a control variable. When maintenance respiration is negligible, we find that the optimal decomposition kinetics scale as the square root of the substrate concentration, resulting in growth kinetics following a Hill function with exponent 1/2 (rather than the Monod growth function). When maintenance respiration is important, optimal decomposition is a more complex function of substrate concentration, which does not decrease to zero as the substrate is depleted. With this optimality-based formulation, a trade-off emerges between microbial carbon-use efficiency (ratio of growth rate over substrate uptake rate) and decomposition rate at the beginning of decomposition. In environments where carbon substrates are easily lost due to abiotic or biotic factors, microbes with higher uptake capacity and lower efficiency are selected, compared to environments where substrates remain available. The proposed optimization framework provides an alternative to purely empirical or process-based formulations for decomposition, allowing exploration of the effects of microbial adaptation on element cycling.
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22
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Li JT, Zhang Y, Chen H, Sun H, Tian W, Li J, Liu X, Zhou S, Fang C, Li B, Nie M. Low soil moisture suppresses the thermal compensatory response of microbial respiration. Glob Chang Biol 2023; 29:874-889. [PMID: 36177515 DOI: 10.1111/gcb.16448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The thermal compensatory response of microbial respiration contributes to a decrease in warming-induced enhancement of soil respiration over time, which could weaken the positive feedback between the carbon cycle and climate warming. Climate warming is also predicted to cause a worldwide decrease in soil moisture, which has an effect on the microbial metabolism of soil carbon. However, whether and how changes in moisture affect the thermal compensatory response of microbial respiration are unexplored. Here, using soils from an 8-year warming experiment in an alpine grassland, we assayed the thermal response of microbial respiration rates at different soil moisture levels. The results showed that relatively low soil moisture suppressed the thermal compensatory response of microbial respiration, leading to an enhanced response to warming. A subsequent moisture incubation experiment involving off-plot soils also showed that the response of microbial respiration to 100 d warming shifted from a slight compensatory response to an enhanced response with decreasing incubation moisture. Further analysis revealed that such respiration regulation by moisture was associated with shifts in enzymatic activities and carbon use efficiency. Our findings suggest that future drought induced by climate warming might weaken the thermal compensatory capacity of microbial respiration, with important consequences for carbon-climate feedback.
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Affiliation(s)
- Jin-Tao Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyang Chen
- Research Centre for Northeast Asia Carbon Sink, Centre for Ecological Research, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Huiming Sun
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Weitao Tian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Jinquan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiang Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Shurong Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Changming Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
- Centre for Invasion Biology, Institute of Biodiversity, Yunnan University, Kunming, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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23
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Cooper RE, Finck J, Chan C, Küsel K. Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland. FEMS Microbiol Ecol 2023; 99:6979798. [PMID: 36623865 PMCID: PMC9925335 DOI: 10.1093/femsec/fiac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
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Affiliation(s)
- Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jessica Finck
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Clara Chan
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States,Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, United States,Department of Earth Sciences, University of Delaware, Newark, DE 19716, United States
| | - Kirsten Küsel
- Corresponding author. Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany. Tel: +49 3641 949461; Fax: +49 3641 949462; E-mail:
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24
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Wang Z, Liu X, Zhou W, Sinclair F, Shi L, Xu J, Gui H. Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO 2 production. Sci Total Environ 2022; 852:158397. [PMID: 36055510 DOI: 10.1016/j.scitotenv.2022.158397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Conversion of abandoned land (mainly savanna) into cropland generally occurs in fragile ecosystems such as dry-hot valleys (DHVs) in southwest China, with the intent of increasing land productivity and conducting ecological restoration. However, the effects of conversion on soil microbial communities and carbon turnover of savanna ecosystems remain unclear, since savannas could be a vital but overlooked carbon sink. To illustrate the ecological consequences of land-use change (LUC) for savanna ecosystems, a 1-year field experiment was conducted in DHVs of southwest China. The soil properties, microbial respiration, and metagenomics from two different land-use types (grassland and mango plantation) were examined to reveal the effects of regional LUC on soil C turnover and microbial traits. Conversion from degraded grassland into cropland increased the contribution of soil microclimate to the microbial community composition, reduced the constraints of soil water content (SWC), and further decreased nutrient availability. LUC reshaped the composition and structure of soil bacterial communities. Specifically, soil dominant microbes that belonged to Actinobacteria and Proteobacteria were significantly enriched by conversion, while rare microbes that belonged to a wider range of phyla were generally depleted, leading to an overall decrease in community diversity. In addition, LUC-induced changes in soil characteristics and microbial communities further decreased soil multifunctionality as well as the carbon use efficiency of microbes. Intensified microbial respiration and a significant increase in the soil CO2 efflux were observed following LUC, which could drive changes in soil microbial community composition and functions (such as growth and regeneration). In summary, through simultaneously reducing constraints on SWC and decreasing nutrient availability, conversion from degraded grassland to cropland in a DHV decreased soil microbial diversity and multifunctionality, and increased microbial respiration and soil CO2 efflux. Our study provides new insights for understanding the role and mechanisms of LUC in soil carbon turnover in ecologically fragile areas such as DHVs.
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Affiliation(s)
- Zhenghong Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Wenjun Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Fergus Sinclair
- World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, P.O. Box 30677-00100, Nairobi, Kenya
| | - Lingling Shi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jianchu Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Heng Gui
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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Wu W, Dijkstra P, Hungate BA, Shi L, Dippold MA. In situ diversity of metabolism and carbon use efficiency among soil bacteria. Sci Adv 2022; 8:eabq3958. [PMID: 36332015 PMCID: PMC9635821 DOI: 10.1126/sciadv.abq3958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
The central carbon (C) metabolic network harvests energy to power the cell and feed biosynthesis for growth. In pure cultures, bacteria use some but not all of the network's major pathways, such as glycolysis and pentose phosphate and Entner-Doudoroff pathways. However, how these pathways are used in microorganisms in intact soil communities is unknown. Here, we analyzed the incorporation of 13C from glucose isotopomers into phospholipid fatty acids. We showed that groups of Gram-positive and Gram-negative bacteria in an intact agricultural soil used different pathways to metabolize glucose. They also differed in C use efficiency (CUE), the efficiency with which a substrate is used for biosynthesis. Our results provide experimental evidence for diversity among microbes in the organization of their central carbon metabolic network and CUE under in situ conditions. These results have important implications for our understanding of how community composition affects soil C cycling and organic matter formation.
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Affiliation(s)
- Weichao Wu
- Biogeochemistry of Agroecosystem, University of Goettingen, Goettingen, Germany
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, China
| | - Paul Dijkstra
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Lingling Shi
- Key Laboratory of Economics Plants and Biotechnology, Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, China and East-Asia Office, Kunming, China
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Michaela A. Dippold
- Biogeochemistry of Agroecosystem, University of Goettingen, Goettingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
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26
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González-Serrano F, Abreu-Goodger C, Delaye L. Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes. J Mol Evol 2022; 90:438-451. [PMID: 36156124 DOI: 10.1007/s00239-022-10074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
Codon usage is the outcome of different evolutionary processes and can inform us about the conditions in which organisms live and evolve. Here, we present R_ENC', which is an improvement to the original S index developed by dos Reis et al. (2004). Our index is less sensitive to G+C content, which greatly affects synonymous codon usage in prokaryotes, making it better suited to detect selection acting on codon usage. We used R_ENC' to estimate the extent of selected codon usage bias in 1800 genomes representing 26 prokaryotic phyla. We found that Gammaproteobacteria, Betaproteobacteria, Actinobacteria, and Firmicutes are the phyla/subphyla showing more genomes with selected codon usage bias. In particular, we found that several lineages within Gammaproteobacteria and Firmicutes show a similar set of functional terms enriched in genes under selected codon usage bias, indicating convergent evolution. We also show that selected codon usage bias tends to evolve in genes coding for the translation machinery before other functional GO terms. Finally, we discuss the possibility to use R_ENC' to predict whether lineages evolved in copiotrophic or oligotrophic environments.
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Affiliation(s)
- Francisco González-Serrano
- Genetic Engineering Department, CINVESTAV Irapuato, Guanajuato, Mexico.,Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Luis Delaye
- Genetic Engineering Department, CINVESTAV Irapuato, Guanajuato, Mexico.
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27
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Barnett SE, Youngblut ND, Buckley DH. Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history. Environ Microbiol 2022; 24:5230-5247. [PMID: 35920035 DOI: 10.1111/1462-2920.16146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of 13 C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are associated with soil DNA content. Soil DNA yield is easy to measure and may be useful in predicting microbial community dynamics linked to soil carbon cycling. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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28
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Zhu X, Zhang Z, Wang Q, Peñuelas J, Sardans J, Lambers H, Li N, Liu Q, Yin H, Liu Z. More soil organic carbon is sequestered through the mycelium pathway than through the root pathway under nitrogen enrichment in an alpine forest. Glob Chang Biol 2022; 28:4947-4961. [PMID: 35582981 DOI: 10.1111/gcb.16263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots and associated mycorrhizae exert a large influence on soil carbon (C) cycling. Yet, little was known whether and how roots and ectomycorrhizal (ECM) extraradical mycelia differentially contribute to soil organic C (SOC) accumulation in alpine forests under increasing nitrogen (N) deposition. Using ingrowth cores, the relative contributions of the root pathway (RP; i.e., roots and rhizosphere processes) and mycelium pathway (MP; i.e., extraradical mycelia and hyphosphere processes) to SOC accumulation were distinguished and quantified in an ECM-dominated forest receiving chronic N addition (25 kg N ha-1 year-1 ). Under the non-N addition, the RP facilitated SOC accumulation, although the MP reduced SOC accumulation. Nitrogen addition enhanced the positive effect of RP on SOC accumulation from +18.02 to +20.55 mg C g-1 but counteracted the negative effect of MP on SOC accumulation from -5.62 to -0.57 mg C g-1 , compared with the non-N addition. Compared with the non-N addition, the N-induced SOC accumulation was 1.62-2.21 and 3.23-4.74 mg C g-1 , in the RP and the MP, respectively. The greater contribution of MP to SOC accumulation was mainly attributed to the higher microbial C pump (MCP) efficacy (the proportion of increased microbial residual C to the increased SOC under N addition) in the MP (72.5%) relative to the RP (57%). The higher MCP efficacy in the MP was mainly associated with the higher fungal metabolic activity (i.e., the greater fungal biomass and N-acetyl glucosidase activity) and greater binding efficiency of fungal residual C to mineral surfaces than those of RP. Collectively, our findings highlight the indispensable role of mycelia and hyphosphere processes in the formation and accumulation of stable SOC in the context of increasing N deposition.
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Affiliation(s)
- Xiaomin Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ziliang Zhang
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qitong Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CEAB-UAB, Cerdanyola del Valles, Catalonia, Spain
- CREAF, Cerdanyola del Valles, Catalonia, Spain
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CEAB-UAB, Cerdanyola del Valles, Catalonia, Spain
- CREAF, Cerdanyola del Valles, Catalonia, Spain
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Na Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Huajun Yin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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29
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Fang W, Lin M, Shi J, Liang Z, Tu X, He Z, Qiu R, Wang S. Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities. Sci Total Environ 2022; 830:154386. [PMID: 35331758 DOI: 10.1016/j.scitotenv.2022.154386] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
With rapid global urbanization, anthropogenic activities alter aquatic biota in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms-mediated global element cycles provide functions in maintaining microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, as well as their resistance and resilience, for which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate the impact of DOC on microbial ecology stability. Results showed that low (25-75 mg/L) and high DOC (100-150 mg/L) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms (e.g., PSB-M-3 and Clostridium) with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insight into the impact of DOC on aquatic microbial community stability, which may help guide sustainable urban river management.
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Affiliation(s)
- Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China; Zhongshan Municipal Ecology and Environment Bureau, Zhongshan, Guangdong 528403, China
| | - Muxing Lin
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jiangjian Shi
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China
| | - Xiang Tu
- State Environmental Protection Key Laboratory of Source Water Protection, Chinese Research Academy of Environmental Sciences, 100012 Beijing, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China
| | - Rongliang Qiu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510275 China.
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30
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Wale N. mSphere of Influence: There’s More to (a Pathogen’s) Life than Growing Fast. mSphere. [PMID: 35862792 PMCID: PMC9429926 DOI: 10.1128/msphere.00277-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nina Wale works in the field of infectious disease evolution and ecology. In this mSphere of Influence article, she reflects on how the paper by Roller and Schmidt, “The physiology and ecological implications of efficient growth” (B. R. Roller and T. M. Schmidt, ISME J 9:1481–1487, 2015,
https://doi.org/10.1038/ismej.2014.235
) broadened her thinking about how microbes acquire and allocate resources and, in so doing, set her research on pathogen virulence evolution in a new direction.
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31
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Wang Y, Wilhelm RC, Swenson TL, Silver A, Andeer PF, Golini A, Kosina SM, Bowen BP, Buckley DH, Northen TR. Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies. Front Microbiol 2022; 13:914472. [PMID: 35756023 PMCID: PMC9225577 DOI: 10.3389/fmicb.2022.914472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.
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Affiliation(s)
- Ying Wang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anita Silver
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amber Golini
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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32
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Cyle KT, Klein AR, Aristilde L, Martínez CE. Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient. J Appl Microbiol 2022; 133:1479-1495. [PMID: 35665577 DOI: 10.1111/jam.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
Abstract
AIM Low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been suggested a potential parameter for modeling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. METHODS AND RESULTS In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16-0.99 and there was no observed relationship between NOSC and SUE. CONCLUSION Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.
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Affiliation(s)
- K Taylor Cyle
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Annaleise R Klein
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC 3168, Australia
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Carmen Enid Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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33
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Piontek J, Meeske C, Hassenrück C, Engel A, Jürgens K. Organic matter availability drives the spatial variation in the community composition and activity of Antarctic marine bacterioplankton. Environ Microbiol 2022; 24:4030-4048. [PMID: 35656758 DOI: 10.1111/1462-2920.16087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO2 sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice-covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom-responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia-Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub-zero seawater temperatures. A co-occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Judith Piontek
- Leibniz Institute for Baltic Sea Research Warnemünde, Germany
| | | | | | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde, Germany
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34
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Rui Z, Lu X, Li Z, Lin Z, Lu H, Zhang D, Shen S, Liu X, Zheng J, Drosos M, Cheng K, Bian R, Zhang X, Li L, Pan G. Macroaggregates Serve as Micro-Hotspots Enriched With Functional and Networked Microbial Communities and Enhanced Under Organic/Inorganic Fertilization in a Paddy Topsoil From Southeastern China. Front Microbiol 2022; 13:831746. [PMID: 35495701 PMCID: PMC9039729 DOI: 10.3389/fmicb.2022.831746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Microbial communities of soil aggregate-size fractions were explored with molecular and networking assays for topsoil samples from a clayey rice paddy under long-term fertilization treatments. The treatments included no fertilizer (NF) as control, chemical fertilizer only (CF), chemical fertilizer with swine manure (CFM), and chemical fertilizer with rice straw return (CFS). Following a wet-sieving protocol, water-stable aggregates were separated into size fractions of large macroaggregates (L-MacA, >2,000 μm), macroaggregates (MacA, 2,000-250 μm), microaggregates (MicA, 250-53 μm), fine microaggregates (F-MicA, 53-2 μm), and fine clay (F-Clay, <2 μm). Mass proportion was 32.3-38.2% for F-MicA, 23.0-31.5% for MacA, 19.0-23.1% for MicA, 9.1-12.0% for L-MacA, and 4.9-7.5% for F-Clay, respectively. The proportion of MacA was increased, but F-Clay was reduced by fertilization, whereas the mean weight diameter was increased by 8.0-16.2% from 534.8 μm under NF to 621.5 μm under CFM. Fertilization affected bacterial 16S rRNA and fungal 18S rRNA gene abundance in F-MicA and F-Clay but not in aggregates in size larger than 53 μm. However, bacterial and fungal community α-diversities and community structures were quite more divergent among the fertilization treatments in all size fractions. Organic carbon and gene abundance of bacteria and fungi were enriched in both L-MacA and MacA but depleted in F-Clay, whereas microbial Shannon diversity was rarely changed by fraction size under the four treatments. L-MacA and MacA contained more bacteria of r-strategists and copiotrophs, whereas F-MicA and F-Clay were demonstrated with a higher abundance of K-strategists and oligotrophs. Guilds of parasitic and litter saprotrophic fungi were enriched in F-MicA but depleted in L-MacA. Furthermore, most of bacterial and fungal operational taxonomic units were strongly interacted in L-MacA and MacA rather than in MicA and F-Clay. Thus, MacA acted as micro-hotspots enriched with functional and networked microbial communities, which were enhanced with organic/inorganic fertilization in the rice paddy.
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Affiliation(s)
- Zhipeng Rui
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Xinda Lu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Zichuan Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhi Lin
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Haifei Lu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Dengxiao Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | | | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Marios Drosos
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
| | - Rongjun Bian
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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35
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Bhattacharyya SS, Ros GH, Furtak K, Iqbal HMN, Parra-Saldívar R. Soil carbon sequestration - An interplay between soil microbial community and soil organic matter dynamics. Sci Total Environ 2022; 815:152928. [PMID: 34999062 DOI: 10.1016/j.scitotenv.2022.152928] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 02/08/2023]
Abstract
Soil carbon sequestration (SCS) refers to the uptake of carbon (C) containing substances from the atmosphere and its storage in soil C pools. Soil microbial community (SMC) play a major role in C cycling and their activity has been considered as the main driver of differences in the potential to store C in soils. The composition of the SMC is crucial for the maintenance of soil ecosystem services, as the structure and activity of SMC also regulates the turnover and delivery of nutrients, as well as the rate of decomposition of soil organic matter (SOM). Quantifying the impact of agricultural practices on both SMC and SCS is key to improve sustainability of soil management. Hence, we discuss the impact of farming practices improving SCS by altering SMC, SOM, and soil aggregates, unraveling their inter-and intra-relationships. Using quantitative and process driven insights from 197 peer-reviewed publications leads to the conclusion that the net benefits from agricultural management to improve SCS would not be sustainable if we overlook the role of soil microbial community. Reintroduction of the decayed microbial community to agricultural soils is crucial for enhancing long-term C storage potential of soils and stabilize them over time. The interactions among SMC, SOM, soil aggregates, and agricultural activities still require more knowledge and research to understand their full contribution to the SCS.
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Affiliation(s)
| | - Gerard H Ros
- Environmental Systems Analysis Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Karolina Furtak
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation - State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Science, Monterrey 64849, Mexico.
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36
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Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M. Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Front Microbiol 2022; 13:780346. [PMID: 35222325 PMCID: PMC8880816 DOI: 10.3389/fmicb.2022.780346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yihua Liu
- Department Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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37
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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: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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;
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38
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Adingo S, Yu JR, Xuelu L, Li X, Jing S, Xiaong Z. Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review. PeerJ 2021; 9:e12131. [PMID: 34721956 PMCID: PMC8522642 DOI: 10.7717/peerj.12131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/17/2021] [Indexed: 12/05/2022] Open
Abstract
Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.
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Affiliation(s)
- Samuel Adingo
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jie-Ru Yu
- College of Resources and Environment, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Liu Xuelu
- College of Resources and Environment, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaodan Li
- School of Management, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sun Jing
- College of Resources and Environment, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zhang Xiaong
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu, China
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Xiang S, Li Y, Wang W, Zhang B, Shi W, Zhang J, Huang F, Liu F, Guan X. Antibiotics adaptation costs alter carbon sequestration strategies of microorganisms in karst river. Environ Pollut 2021; 288:117819. [PMID: 34329060 DOI: 10.1016/j.envpol.2021.117819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 05/25/2023]
Abstract
Karst ecosystems make an important contribution to the global carbon cycle, in which carbon-fixing microorganisms play a vital role. However, the healthy functioning of karst ecosystems is threatened because pollutants easily diffuse and spread through them due to their strong hydraulic connectivity. The microbiome of a karst river contaminated with antibiotics was studied. Through co-occurrence network analysis, six ecological clusters (MOD 1-MOD 6) with different distribution characteristics were determined, of which four were significantly correlated with antibiotics. The carbon fixation pathways in different ecological clusters were varied, and the dominant hydroxypropionate-hydroxybutyrate cycle and reductive acetyl-CoA pathway were negatively and positively correlated with antibiotics, respectively. Long-term antibiotic contamination altered the selection of carbonic anhydrase (CA) encoding genes in some of the CA-producing mineralization microorganisms. The selection of different carbon fixation pathways is a possible strategy for the microbial community to compensate for the adaptation costs associated with the pressure of antibiotics contamination and emergence of antibiotics resistance. Bayesian network analysis revealed that some carbon sequestration functions (such as β-CA and reductive acetyl-CoA pathway) surpassed certain antibiotic resistance genes in the regulation of environmental factors and microbial networks. An ecological cluster (MOD5) that possibly homologous to antibiotic contamination was the final node of the microbial community in karst river, which indicated that ecological clusters were not only selected by antibiotics, but were also regulated by multiple environmental factors in the karst river system. The carbon sequestration pathway was more directly reflected in the abundance of ecological groups than in the influence of CA. This study provides new insights into the feedback effect of karst system on typical pollutants generated from human activities.
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Affiliation(s)
- Shizheng Xiang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Yiqiang Li
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Wanying Wang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Biao Zhang
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia Zhang
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Fuyang Huang
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China; Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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Wang Y, Brons JK, van Elsas JD. Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum-Proposal for a New Species, Sphingobacterium paramultivorum. Microorganisms 2021; 9:2057. [PMID: 34683378 DOI: 10.3390/microorganisms9102057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the ‘divergent’ 16S rRNA gene sequence of S. multivorum NCTC 11343T, yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum.
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Zhao J, Ma J, Yang Y, Yu H, Zhang S, Chen F. Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China. Front Microbiol 2021; 12:714967. [PMID: 34512593 PMCID: PMC8424123 DOI: 10.3389/fmicb.2021.714967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/30/2021] [Indexed: 11/25/2022] Open
Abstract
Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.
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Affiliation(s)
- Jiao Zhao
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China.,Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
| | - Jing Ma
- Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
| | - Yongjun Yang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Haochen Yu
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Shaoliang Zhang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Fu Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China.,Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
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Bei Q, Moser G, Müller C, Liesack W. Seasonality affects function and complexity but not diversity of the rhizosphere microbiome in European temperate grassland. Sci Total Environ 2021; 784:147036. [PMID: 33895508 DOI: 10.1016/j.scitotenv.2021.147036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Knowledge on how grassland microbiota responds on gene expression level to winter-summer change of seasons is poor. Here, we used a combination of quantitative PCR-based assays and metatranscriptomics to assess the impact of seasonality on the rhizospheric microbiota in temperate European grassland. Bacteria dominated, being at least one order of magnitude more abundant than fungi. Despite a fivefold summer increase in bacterial community size, season had nearly no effect on microbiome diversity. It, however, had a marked impact on taxon-specific gene expression, with 668 genes significantly differing in relative transcript abundance between winter and summer samples. Acidobacteria, Bacteroidetes, Planctomycetes, and Proteobacteria showed a greater relative gene expression activity in winter, while mRNA of Actinobacteria and Fungi was, relative to other taxa, significantly enriched in summer. On functional level, mRNA involved in protein turnover (e.g., transcription and translation) and cell maintenance (e.g., chaperones that protect against cell freezing damage such as GroEL and Hsp20) were highly enriched in winter. By contrast, mRNA involved in central carbon and amino acid metabolisms had a greater abundance in summer. Among carbohydrate-active enzymes, transcripts of GH36 family (hemicellulases) were highly enriched in winter, while those encoding GH3 family (cellulases) showed increased abundance in summer. The seasonal differences in plant polymer breakdown were linked to a significantly greater microbial network complexity in winter than in summer. Conceptually, the winter-summer change in microbiome functioning can be well explained by a shift from stress-tolerator to high-yield life history strategy.
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Affiliation(s)
- Qicheng Bei
- Research Group Methanotrophic Bacteria, and Environmental Genomics/Transcriptomics Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.
| | - Gerald Moser
- Department of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Christoph Müller
- Department of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; School of Biology and Environmental Science, University College Dublin, Ireland
| | - Werner Liesack
- Research Group Methanotrophic Bacteria, and Environmental Genomics/Transcriptomics Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.
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Liang Y, Lu Q, Liang Z, Liu X, Fang W, Liang D, Kuang J, Qiu R, He Z, Wang S. Substrate-dependent competition and cooperation relationships between Geobacter and Dehalococcoides for their organohalide respiration. ISME Commun 2021; 1:23. [PMID: 37938613 PMCID: PMC9723705 DOI: 10.1038/s43705-021-00025-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 05/19/2023]
Abstract
Obligate and non-obligate organohalide-respiring bacteria (OHRB) play central roles in the geochemical cycling and environmental bioremediation of organohalides. Their coexistence and interactions may provide functional redundancy and community stability to assure organohalide respiration efficiency but, at the same time, complicate isolation and characterization of specific OHRB. Here, we employed a growth rate/yield tradeoff strategy to enrich and isolate a rare non-obligate tetrachloroethene (PCE)-respiring Geobacter from a Dehalococcoides-predominant microcosm, providing experimental evidence for the rate/yield tradeoff theory in population selection. Surprisingly, further physiological and genomic characterizations, together with co-culture experiments, revealed three unique interactions (i.e., free competition, conditional competition and syntrophic cooperation) between Geobacter and Dehalococcoides for their respiration of PCE and polychlorinated biphenyls (PCBs), depending on both the feeding electron donors (acetate/H2 vs. propionate) and electron acceptors (PCE vs. PCBs). This study provides the first insight into substrate-dependent interactions between obligate and non-obligate OHRB, as well as a new strategy to isolate fastidious microorganisms, for better understanding of the geochemical cycling and bioremediation of organohalides.
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Affiliation(s)
- Yongyi Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Xiaokun Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Space & Environment, Beihang University, Beijing, China
| | - Jialiang Kuang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Rongliang Qiu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China.
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Finn DR, Bergk-Pinto B, Hazard C, Nicol GW, Tebbe CC, Vogel TM. Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. FEMS Microbiol Ecol 2021; 97:6271318. [PMID: 33960387 DOI: 10.1093/femsec/fiab068] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/05/2021] [Indexed: 01/13/2023] Open
Abstract
Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.
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Affiliation(s)
- Damien R Finn
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Brisbane 4072, Australia.,Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France.,Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Bundesallee 65 Braunschweig 38116, Germany
| | - Benoît Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
| | - Christoph C Tebbe
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Bundesallee 65 Braunschweig 38116, Germany
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Avenue Guy de Collongue 36 Écully 69134, France
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Müller AL, Gu W, Patsalo V, Deutzmann JS, Williamson JR, Spormann AM. An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 2021; 118:e2025854118. [PMID: 33879571 DOI: 10.1073/pnas.2025854118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most microorganisms in nature spend the majority of time in a state of slow or zero growth and slow metabolism under limited energy or nutrient flux rather than growing at maximum rates. Yet, most of our knowledge has been derived from studies on fast-growing bacteria. Here, we systematically characterized the physiology of the methanogenic archaeon Methanococcus maripaludis during slow growth. M. maripaludis was grown in continuous culture under energy (formate)-limiting conditions at different dilution rates ranging from 0.09 to 0.002 h-1, the latter corresponding to 1% of its maximum growth rate under laboratory conditions (0.23 h-1). While the specific rate of methanogenesis correlated with growth rate as expected, the fraction of cellular energy used for maintenance increased and the maintenance energy per biomass decreased at slower growth. Notably, proteome allocation between catabolic and anabolic pathways was invariant with growth rate. Unexpectedly, cells maintained their maximum methanogenesis capacity over a wide range of growth rates, except for the lowest rates tested. Cell size, cellular DNA, RNA, and protein content as well as ribosome numbers also were largely invariant with growth rate. A reduced protein synthesis rate during slow growth was achieved by a reduction in ribosome activity rather than via the number of cellular ribosomes. Our data revealed a resource allocation strategy of a methanogenic archaeon during energy limitation that is fundamentally different from commonly studied versatile chemoheterotrophic bacteria such as E. coli.
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Han Y, Jiao N, Zhang Y, Zhang F, He C, Liang X, Cai R, Shi Q, Tang K. Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms. Microbiome 2021; 9:71. [PMID: 33762013 PMCID: PMC7992965 DOI: 10.1186/s40168-021-01022-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how these opportunists are involved in the transformation of dissolved organic matter (DOM) when blooms occur and the subsequent impacts on biogeochemical cycles. RESULTS We used a combination of genomic, proteomic, and metabolomic approaches to study bacterial diversity, genome traits, and metabolic responses to assess the source and lability of DOM in a spring coastal bloom of Akashiwo sanguinea. We identified molecules that significantly increased during bloom development, predominantly belonging to amino acids, dipeptides, lipids, nucleotides, and nucleosides. The opportunistic members of the bacterial genera Polaribacter, Lentibacter, and Litoricola represented a significant proportion of the free-living and particle-associated bacterial assemblages during the stationary phase of the bloom. Polaribacter marinivivus, Lentibacter algarum, and Litoricola marina were isolated and their genomes exhibited streamlining characterized by small genome size and low GC content and non-coding densities, as well as a smaller number of transporters and peptidases compared to closely related species. However, the core proteomes identified house-keeping functions, such as various substrate transporters, peptidases, motility, chemotaxis, and antioxidants, in response to bloom-derived DOM. We observed a unique metabolic signature for the three species in the utilization of multiple dissolved organic nitrogen compounds. The metabolomic data showed that amino acids and dipeptides (such as isoleucine and proline) were preferentially taken up by P. marinivivus and L. algarum, whereas nucleotides and nucleosides (such as adenosine and purine) were preferentially selected by L. marina. CONCLUSIONS The results suggest that the enriched DOM in stationary phase of phytoplankton bloom is a result of ammonium depletion. This environment drives genomic streamlining of opportunistic bacteria to exploit their preferred nitrogen-containing compounds and maintain nutrient cycling. Video abstract.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Fan Zhang
- Department of Molecular Virology & Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Xuejiao Liang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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Zhang J, Feng Y, Wu M, Chen R, Li Z, Lin X, Zhu Y, Delgado-Baquerizo M. Evaluation of Microbe-Driven Soil Organic Matter Quantity and Quality by Thermodynamic Theory. mBio 2021; 12:e03252-20. [PMID: 33622716 DOI: 10.1128/mBio.03252-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microbial communities, coupled with substrate quality and availability, regulate the stock (formation versus mineralization) of soil organic matter (SOM) in terrestrial ecosystems. However, our understanding of how soil microbes interact with contrasting substrates influencing SOM quantity and quality is still very superficial. Here, we used thermodynamic theory principles and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to evaluate the linkages between dissolved organic matter (DOM [organic substrates in soil that are readily available]), thermodynamic quality, and microbial communities. We investigated soils from subtropical paddy ecosystems across a 1,000-km gradient and comprising contrasting levels of SOM content and nutrient availability. Our region-scale study suggested that soils with a larger abundance of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and higher SOM content. We further advocated a novel phylotype-level microbial classification based on their associations with OM quantities and qualities and identified two contrasting clusters of bacterial taxa: phylotypes that are highly positively correlated with thermodynamically favorable DOM and larger SOM content versus those which are associated with less-favorable DOM and lower SOM content. Both groups are expected to play critical roles in regulating SOM contents in the soil. By identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities and should be considered in models of soil organic matter preservation.IMPORTANCE Microbial communities are known to be important drivers of organic matter (OM) accumulation in terrestrial ecosystems. However, despite the importance of these soil microbes and processes, the mechanisms behind these microbial-SOM associations remain poorly understood. Here, we used the principles of thermodynamic theory and novel Fourier transform ion cyclotron resonance mass spectrometry techniques to investigate the links between microbial communities and dissolved OM (DOM) thermodynamic quality in soils across a 1,000-km gradient and comprising contrasting nutrient and C contents. Our region-scale study provided evidence that soils with a larger amount of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and larger SOM content. Moreover, we created a novel phylotype-level microbial classification based on the associations between microbial taxa and DOM quantities and qualities. We found two contrasting clusters of bacterial taxa based on their level of association with thermodynamically favorable DOM and SOM content. Our study advances our knowledge on the important links between microbial communities and SOM. Moreover, by identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities. Together, our findings support that the association between microbial species taxa and substrate thermodynamic quality constituted an important complement explanation for soil organic matter preservation.
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Cyle KT, Klein AR, Aristilde L, Martínez CE. Ecophysiological Study of Paraburkholderia sp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency. Appl Environ Microbiol 2020; 86:e01851-20. [PMID: 33008817 DOI: 10.1128/AEM.01851-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, Paraburkholderia sp. strain 1N. The growth of Paraburkholderia sp. 1N was monitored under aerobic conditions in a soil-extracted solubilized organic matter medium, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the medium and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the medium, and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as Paraburkholderia sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of Paraburkholderia sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression.IMPORTANCE Exometabolomic footprinting methods have the capability to provide time-resolved observations of the uptake and release of hundreds of compounds during microbial growth. Of particular interest is microbial phenotyping under environmentally relevant soil conditions, consisting of relatively low concentrations and modeling pulse input events. Here, we show that growth of a bacterial soil isolate, Paraburkholderia sp. 1N, on a dilute soil extract resulted in a multiauxic metabolic response, characterized by discrete temporal clusters of substrate depletion and metabolite production. Our data did not support the hypothesis that compounds with lower energy content are used preferentially, as each cluster contained compounds with a range of nominal oxidation states of carbon. These new findings with Paraburkholderia sp. 1N, which belongs to a metabolically diverse genus, provide insights on ecological strategies employed by aerobic heterotrophs competing for low-molecular-weight substrates in soil solution.
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Li Y, Wang ZB, Zhang XY, Dang YR, Sun LL, Zhang WP, Fu HH, Yang GP, Wang M, McMinn A, Chen XL, Chen Y, Wang S, Zhang YZ, Qin QL. Experimental evidence for long-term coexistence of copiotrophic and oligotrophic bacteria in pelagic surface seawater. Environ Microbiol 2020; 23:1162-1173. [PMID: 33185972 DOI: 10.1111/1462-2920.15321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022]
Abstract
Most marine copiotrophic bacteria can produce extracellular enzymes to degrade biopolymers into bio-available smaller solutes, while oligotrophic bacteria usually cannot. Bacterial extracellular enzymes and enzymatic products can be a common resource that could be utilized by both copiotrophs and oligotrophs; when present, oligotrophs may outcompete the enzyme-producing copiotrophs. However, copiotrophs and oligotrophs consistently coexist in the ocean. How they maintain coexistence has still not been experimentally studied. In this study, the interaction and coexistence of a copiotroph and an oligotroph, isolated from the same surface seawater sample and utilizing the same proteinaceous substrate, were experimentally investigated. The copiotroph could secrete extracellular proteases to degrade and then utilize the proteinaceous substrate. The oligotroph was unable to utilize the proteinaceous substrate by itself, but could grow by using the hydrolysate amino acids. The copiotroph outcompeted the oligotroph by adsorbing the amino acids quickly and having a higher growth rate in the rich medium. The oligotroph survived by adapting to low concentration of nutrients. The copiotroph and oligotroph were able to maintain long-term (up to 142 days) coexistence in the laboratory. This study indicates that differences in the utilization of different concentrations of nutrients can drive the coexistence of marine copiotrophs and oligotrophs.
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Affiliation(s)
- Yi Li
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Zhi-Bin Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Lin-Lin Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Wei-Peng Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Gui-Peng Yang
- Key Laboratory of Marine Chemistry Theory and Technology, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Shi Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Qi-Long Qin
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
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Doherty SJ, Barbato RA, Grandy AS, Thomas WK, Monteux S, Dorrepaal E, Johansson M, Ernakovich JG. The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession. Front Microbiol 2020; 11:596589. [PMID: 33281795 PMCID: PMC7691490 DOI: 10.3389/fmicb.2020.596589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 01/04/2023] Open
Abstract
The Northern high latitudes are warming twice as fast as the global average, and permafrost has become vulnerable to thaw. Changes to the environment during thaw leads to shifts in microbial communities and their associated functions, such as greenhouse gas emissions. Understanding the ecological processes that structure the identity and abundance (i.e., assembly) of pre- and post-thaw communities may improve predictions of the functional outcomes of permafrost thaw. We characterized microbial community assembly during permafrost thaw using in situ observations and a laboratory incubation of soils from the Storflaket Mire in Abisko, Sweden, where permafrost thaw has occurred over the past decade. In situ observations indicated that bacterial community assembly was driven by randomness (i.e., stochastic processes) immediately after thaw with drift and dispersal limitation being the dominant processes. As post-thaw succession progressed, environmentally driven (i.e., deterministic) processes became increasingly important in structuring microbial communities where homogenizing selection was the only process structuring upper active layer soils. Furthermore, laboratory-induced thaw reflected assembly dynamics immediately after thaw indicated by an increase in drift, but did not capture the long-term effects of permafrost thaw on microbial community dynamics. Our results did not reflect a link between assembly dynamics and carbon emissions, likely because respiration is the product of many processes in microbial communities. Identification of dominant microbial community assembly processes has the potential to improve our understanding of the ecological impact of permafrost thaw and the permafrost-climate feedback.
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Affiliation(s)
- Stacey Jarvis Doherty
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Cold Regions Research and Engineering Laboratory, Engineer Research Development Center, United States Army Corps of Engineers, Hanover, NH, United States
| | - Robyn A. Barbato
- Cold Regions Research and Engineering Laboratory, Engineer Research Development Center, United States Army Corps of Engineers, Hanover, NH, United States
| | - A. Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - W. Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Sylvain Monteux
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Department of Ecology and Environmental Sciences, Umeå University, Abisko, Sweden
| | - Margareta Johansson
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Jessica G. Ernakovich
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
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