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Li F, Chen L, Jia Z, Zhang J, Zhao Z, Han Y, Wang Y. Core microbial taxonomies that maintain high organic carbon content in upland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173300. [PMID: 38810757 DOI: 10.1016/j.scitotenv.2024.173300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
The accumulation of soil carbon (C) is crucial for the productivity and ecological function of farmland ecosystems. The balance between microbial carbon dioxide (CO2) emission and fixation determines the sustained accumulation potential of C in soil. Microorganisms involved in this process are highly obscure, thus hindering identification and further application of microorganisms with fertile soil function. In this study, a series of typical upland farmland soils were collected from 29 regions and their microbial community structure and soil C fractions were analyzed. Additionally, the rates of CO2 emission and fixation in each soil were measured. The results showed that the correlation between soil CO2 emissions and the SOC concentration was logarithmic, while that between CO2 fixation and SOC was linear. Bacterial and fungal diversity showed an upward trend with increasing soil C, and their α diversity was significantly correlated with CO2 fixation, but not correlated with CO2 emission. Fungi were more associated with soil C than bacteria, and the strength of linkage with soil C varied among the different phyla of microorganisms. Furthermore, the core microbial taxa in soils with low, medium and high SOC levels were identified by discarding redundant amplicon sequence variants, and their community differentiation was significantly driven by soil CO2 emission and fixation based on Mantel analysis. The high abundance of Chloroflexi, Nitrospirota, Actinobacteria, and Mortierellomycota in core taxa might indicate a high level of SOC level. This study highlights that SOC fluctuations are mainly driven by the core microbial taxa, rather than all microbial taxa in the agricultural system. Our research sheds light on the targeted regulation of the soil microbial community structure in upland farmland for soil fertility enhancement.
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Affiliation(s)
- Fang Li
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Lin Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhongjun Jia
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhanhui Zhao
- School of Survey and Urban Spatial Information, Henan University of Urban Construction, Pingdingshan 467021, China
| | - Yanlai Han
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China; Co-construction State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yi Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China; Co-construction State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
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2
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Mendonca CM, Zhang L, Waldbauer JR, Aristilde L. Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38860668 DOI: 10.1021/acs.est.4c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.
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Affiliation(s)
- Caroll M Mendonca
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637, United States
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637, United States
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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3
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Dang C, Morrissey EM. The size and diversity of microbes determine carbon use efficiency in soil. Environ Microbiol 2024; 26:e16633. [PMID: 38733078 DOI: 10.1111/1462-2920.16633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.
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Affiliation(s)
- Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
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4
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Xu Q, Li L, Guo J, Guo H, Liu M, Guo S, Kuzyakov Y, Ling N, Shen Q. Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils. mBio 2024; 15:e0017724. [PMID: 38376207 PMCID: PMC10936188 DOI: 10.1128/mbio.00177-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ling Li
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Junjie Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hanyue Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Manqiang Liu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shiwei Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Gottingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Gottingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ning Ling
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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Qu R, Chen S, Wang K, Liu Q, Yang B, Yue M, Peng C. Potential future changes in soil carbon dynamics in the Ziwuling Forest, China under different climate change scenarios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169008. [PMID: 38040362 DOI: 10.1016/j.scitotenv.2023.169008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
Soil carbon (C) cycling processes in terrestrial ecosystems are significantly influenced by global changes, and soil microorganisms play a crucial role in soil organic carbon (SOC) and its feedbacks to climate change. To investigate the potential future changes in soil C dynamics under different scenarios in the Ziwuling Forest region, China, we conducted a soil observation and sampling experiment from April 2021 to July 2022. By utilizing a microbial ecological model (MEND), we aimed to predict the future dynamics of soil C under different scenarios in the area. Our results demonstrate that under the RCP2.6 (Representative Concentration Pathway) scenario, SOC showed a rapid increase, SOC under the RCP2.6 scenario will be significantly higher than those under the RCP4.5 scenario and RCP8.5 scenario in the topsoil and whole soil. Furthermore, the positive correlation between total litter carbon (LC) and SOC under the RCP2.6 scenario highlights the potential role of total litter carbon in driving SOC dynamics. Our study also revealed that the low greenhouse gas (GHG) emission scenario favors the accumulation of SOC in the study area, while the high GHG emission scenario leads to greater soil carbon loss. Overall, these results underscore the importance of considering the impact of climate change, especially global warming, on soil ecosystems in the future. Protecting the soil ecosystem of the Loess Plateau is critical for maintaining soil carbon sinks, preventing soil erosion, and improving and regulating the surrounding environmental climate.
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Affiliation(s)
- Ruosong Qu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Northwest University, Xi'an 710069, China; Northwest Electric Power Design Institute Co., Ltd. of China Power Engineering Consulting Group, China
| | - Shiyi Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Northwest University, Xi'an 710069, China; College of Life Science, Northwest University, Xi'an 710069, China
| | - Kefeng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Northwest University, Xi'an 710069, China; College of Life Science, Northwest University, Xi'an 710069, China.
| | - Qiuyu Liu
- School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an 710049, China
| | - Bin Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ming Yue
- Xi'an Botanical Garden of Shaanxi Province, China; College of Life Science, Northwest University, Xi'an 710069, China
| | - Changhui Peng
- Department of Biology Sciences, Institute of Environment Sciences, University of Quebec at Montreal, C.P. 8888, Succ. Centre-Ville, Montreal H3C 3P8, Canada
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6
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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] [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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7
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Liu X, Lai Q, Yin S, Bao Y, Tong S, Adiya Z, Sanjjav A, Gao R. Spatio-temporal patterns and control mechanism of the ecosystem carbon use efficiency across the Mongolian Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167883. [PMID: 37863235 DOI: 10.1016/j.scitotenv.2023.167883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/10/2023] [Accepted: 10/14/2023] [Indexed: 10/22/2023]
Abstract
Carbon use efficiency (CUE) is a crucial parameter that reflects the carbon storage within ecosystems, providing insight into the potential for carbon sequestration at the ecosystem scale and its feedback on climate change. The Mongolian Plateau exemplifies an arid and semi-arid region with a delicate ecological environment that displays heightened sensitivity to global climate change. Understanding the variation and control of CUE is critical for assessing regional carbon. However, few studies have focused on the interaction of factors influencing CUE; furthermore, how CUE responds to climate change and anthropogenic activities remains unclear. Here, we aimed to investigate spatiotemporal patterns and their control mechanisms by generating CUE data based on multi-source remote sensing data. CUE demonstrated a slow downward trend from 2000 to 2018, with higher values in relatively dry-cool regions and lower values in relatively humid-warm regions. Furthermore, CUE values were ranked by biome as follows: grassland > sandy vegetation > cropland > shrubs > forest, driven by climate characteristics, vegetation coverage, water stress, stand age, and management practices. Additionally, climatic factors affected CUE more than the soil variables, except for alpine meadows. The climate factors of precipitation (PPT), index of water availability (IWA) (QPPT = 0.487, QIWA = 0.444), and soil factors, e.g., pH and soil organic content (SOC) (QPH = 0.397, QSOC = 0.372), had the greatest influence on CUE. Finally, most two explanatory factors interacted to effectively enhance the explanation of CUE; the synergy of the IWA and PPT contributed the most to CUE (QIWA∩PPT = 0.604). Moreover, the joint effect of climate change and anthropogenic activities was identified as the major contributor (68 %) to the decline in CUE within this region. This study presents compelling evidence highlighting the importance of considering climate change and anthropogenic disturbances in ecosystem management and conservation efforts in arid and semi-arid regions.
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Affiliation(s)
- Xinyi Liu
- College of Geographical Science, Inner Mongolia Normal University, Hohhot 010022, China
| | - Quan Lai
- College of Geographical Science, Inner Mongolia Normal University, Hohhot 010022, China; Inner Mongolia Key Laboratory of Remote Sensing and Geographic Information Systems, Inner Mongolia, Normal University, Hohhot 010022, China.
| | - Shan Yin
- College of Geographical Science, Inner Mongolia Normal University, Hohhot 010022, China; Inner Mongolia Key Laboratory of Remote Sensing and Geographic Information Systems, Inner Mongolia, Normal University, Hohhot 010022, China
| | - Yuhai Bao
- College of Geographical Science, Inner Mongolia Normal University, Hohhot 010022, China; Inner Mongolia Key Laboratory of Remote Sensing and Geographic Information Systems, Inner Mongolia, Normal University, Hohhot 010022, China
| | - Siqin Tong
- College of Geographical Science, Inner Mongolia Normal University, Hohhot 010022, China; Inner Mongolia Key Laboratory of Remote Sensing and Geographic Information Systems, Inner Mongolia, Normal University, Hohhot 010022, China
| | - Zolzaya Adiya
- Institute of Geography and Geoecology, Mongolian Academy of Sciences, Ulaanbaatar 14201, Mongolia
| | - Amarjargal Sanjjav
- Institute of Geography and Geoecology, Mongolian Academy of Sciences, Ulaanbaatar 14201, Mongolia
| | - Rihe Gao
- College of Geography and Environmental Sciences, Tianjin Normal University, Tianjin 300382, China
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8
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Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Microbiol Mol Biol Rev 2023; 87:e0004823. [PMID: 37914532 PMCID: PMC10732025 DOI: 10.1128/mmbr.00048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
SUMMARY Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.
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Affiliation(s)
- Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Dana Z. Tribbia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
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9
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Mahmoudi N, Wilhelm RC. Can we manage microbial systems to enhance carbon storage? Environ Microbiol 2023; 25:3011-3018. [PMID: 37431673 DOI: 10.1111/1462-2920.16462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.
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Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montréal, Quebec, Canada
| | - Roland C Wilhelm
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana, USA
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10
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Liu M, Wei Y, Lian L, Wei B, Bi Y, Liu N, Yang G, Zhang Y. Macrofungi promote SOC decomposition and weaken sequestration by modulating soil microbial function in temperate steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165556. [PMID: 37459997 DOI: 10.1016/j.scitotenv.2023.165556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
Soil organic carbon (SOC) sequestration is a key grassland ecosystem function, and the magnitude of SOC reservoirs depends on microbial involvement, especially that of fungi. Mycelia developed by macrofungi potentially influence carbon (C) fixation and decomposition; however, the mechanisms underlying their effects on SOC storage in grassland ecosystems remain poorly understood. The fairy rings formed by macrofungi in grasslands are natural platform for exploring macrofungal effects on SOC. In this study, we collected topsoil (0-10 cm) from four different fairy ring zones in a temperate steppe to reveal the macrofungal effects on SOC fractions, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the SOC storage microbial mechanism using metagenomic sequencing technology. Both POC and MAOC decreased after macrofungal passage, resulting in a 7.37 % reduction in SOC. Macrofungal presence reduced microbial biomass carbon (MBC), but significantly enhanced the β-1,4-glucosidase (BG) activity, which increased dissolved organic carbon (DOC). In addition, the abundance of copiotrophs (Proteobacteria and Bacteroidetes) with lower C metabolic rates increased, and that of oligotrophs (Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia) with higher substrate utilization efficiency decreased in the presence of macrofungi. This may further promote SOC decomposition. Correspondingly, there was a lower abundance of C-fixation genes but more C-degradation genes (especially hemicellulosic degradation genes) during macrofungal passage. Our results indicate that the presence of macrofungi can modulate the soil microbial community and functional genes to reduce SOC storage by inhibiting microbial C sequestration while promoting C decomposition in grassland ecosystems. These findings refine our mechanistic understanding of SOC persistence through the interactions between macrofungi and other microbes.
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Affiliation(s)
- Mohan Liu
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China
| | - Yuqi Wei
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China
| | - Lu Lian
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China
| | - Bin Wei
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China
| | - Yixian Bi
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China
| | - Nan Liu
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China; Key Laboratory of Grassland Management and Rational Utilization, Ministry of Agriculture, Beijing 100193, China
| | - Gaowen Yang
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China
| | - Yingjun Zhang
- College of Grassland Science and Technology, China Agricultural University, 2 Yuan Ming Yuan West Road, Haidian District, Beijing 100193, China; Key Laboratory of Grassland Management and Rational Utilization, Ministry of Agriculture, Beijing 100193, China.
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11
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Zhang Q, Qin W, Feng J, Li X, Zhang Z, He JS, Schimel JP, Zhu B. Whole-soil-profile warming does not change microbial carbon use efficiency in surface and deep soils. Proc Natl Acad Sci U S A 2023; 120:e2302190120. [PMID: 37523548 PMCID: PMC10410710 DOI: 10.1073/pnas.2302190120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023] Open
Abstract
The paucity of investigations of carbon (C) dynamics through the soil profile with warming makes it challenging to evaluate the terrestrial C feedback to climate change. Soil microbes are important engines driving terrestrial biogeochemical cycles; their carbon use efficiency (CUE), defined as the proportion of metabolized organic C allocated to microbial biomass, is a key regulator controlling the fate of soil C. It has been theorized that microbial CUE should decline with warming; however, empirical evidence for this response is scarce, and data from deeper soils are particularly scarce. Here, based on soil samples from a whole-soil-profile warming experiment (0 to 1 m, +4 °C) and 18O tracing approach, we examined the vertical variation of microbial CUE and its response to ~3.3-y experimental warming in an alpine grassland on the Qinghai-Tibetan Plateau. Microbial CUE decreased with soil depth, a trend that was primarily controlled by soil C availability. However, warming had limited effects on microbial CUE regardless of soil depth. Similarly, warming had no significant effect on soil C availability, as characterized by extractable organic C, enzyme-based lignocellulose index, and lignin phenol-based ratios of vanillyls, syringyls, and cinnamyls. Collectively, our work suggests that short-term warming does not alter microbial CUE in either surface or deep soils, and emphasizes the regulatory role of soil C availability on microbial CUE.
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Affiliation(s)
- Qiufang Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing100871, China
- School of Geographical Sciences, Fujian Normal University, Fuzhou350117, China
| | - Wenkuan Qin
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing100871, China
| | - Jiguang Feng
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing100871, China
| | - Xiaojie Li
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing100871, China
| | - Zhenhua Zhang
- Qinghai Haibei National Field Research Station of Alpine Grassland Ecosystem, and Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008China
| | - Jin-Sheng He
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing100871, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730000, China
| | - Joshua P. Schimel
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing100871, China
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12
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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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13
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Mao Z, Zhao Z, Da J, Tao Y, Li H, Zhao B, Xing P, Wu Q. The selection of copiotrophs may complicate biodiversity-ecosystem functioning relationships in microbial dilution-to-extinction experiments. ENVIRONMENTAL MICROBIOME 2023; 18:19. [PMID: 36932455 PMCID: PMC10024408 DOI: 10.1186/s40793-023-00478-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
The relationships between biodiversity-ecosystem functioning (BEF) for microbial communities are poorly understood despite the important roles of microbes acting in natural ecosystems. Dilution-to-extinction (DTE), a method to manipulate microbial diversity, helps to fill the knowledge gap of microbial BEF relationships and has recently become more popular with the development of high-throughput sequencing techniques. However, the pattern of community assembly processes in DTE experiments is less explored and blocks our further understanding of BEF relationships in DTE studies. Here, a microcosm study and a meta-analysis of DTE studies were carried out to explore the dominant community assembly processes and their potential effect on exploring BEF relationships. While stochastic processes were dominant at low dilution levels due to the high number of rare species, the deterministic processes became stronger at a higher dilution level because the microbial copiotrophs were selected during the regrowth phase and rare species were lost. From the view of microbial functional performances, specialized functions, commonly carried by rare species, are more likely to be impaired in DTE experiments while the broad functions seem to be less impacted due to the good performance of copiotrophs. Our study indicated that shifts in the prokaryotic community and its assembly processes induced by dilutions result in more complex BEF relationships in DTE experiments. Specialized microbial functions could be better used for defining BEF. Our findings may be helpful for future studies to design, explore, and interpret microbial BEF relationships using DTE.
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Affiliation(s)
- Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zifan Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jun Da
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- College of Life Science, Anhui Normal University, Wuhu, 241002, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Biying Zhao
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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14
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Smith TP, Mombrikotb S, Ransome E, Kontopoulos DG, Pawar S, Bell T. Latent functional diversity may accelerate microbial community responses to temperature fluctuations. eLife 2022; 11:80867. [DOI: 10.7554/elife.80867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically and functionally distinct communities emerge at each of these temperatures, with K-strategist taxa favored under cooler conditions and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation) is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to ‘switch on’ at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.
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Affiliation(s)
- Thomas P Smith
- The Georgina Mace Centre for the Living Planet, Imperial College London
| | - Shorok Mombrikotb
- The Georgina Mace Centre for the Living Planet, Imperial College London
| | - Emma Ransome
- The Georgina Mace Centre for the Living Planet, Imperial College London
| | | | - Samraat Pawar
- The Georgina Mace Centre for the Living Planet, Imperial College London
| | - Thomas Bell
- The Georgina Mace Centre for the Living Planet, Imperial College London
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15
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Zhao F, He L, Bond-Lamberty B, Janssens IA, Wang J, Pang G, Wu Y, Xu X. Latitudinal shifts of soil microbial biomass seasonality. PNAS NEXUS 2022; 1:pgac254. [PMID: 36712352 PMCID: PMC9802431 DOI: 10.1093/pnasnexus/pgac254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/26/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Soil microbes ultimately drive the mineralization of soil organic carbon and thus ecosystem functions. We compiled a dataset of the seasonality of microbial biomass carbon (MBC) and developed a semi-mechanistic model to map monthly MBC across the globe. MBC exhibits an equatorially symmetric seasonality between the Northern and Southern Hemispheres. In the Northern Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes (<25°N), peaks in the spring and is minimal in autumn at mid-latitudes (25°N to 50°N), while peaks in autumn and is minimal in spring at high latitudes (>50°N). This latitudinal shift of MBC seasonality is attributed to an interaction of soil temperature, soil moisture, and substrate availability. The MBC seasonality is inconsistent with patterns of heterotrophic respiration, indicating that MBC as a proxy for microbial activity is inappropriate at this resolution. This study highlights the need to explicitly represent microbial physiology in microbial models. The interactive controls of environments and substrate on microbial seasonality provide insights for better representing microbial mechanisms in simulating ecosystem functions at the seasonal scale.
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Affiliation(s)
| | - Liyuan He
- To whom correspondence should be addressed:
| | - Ben Bond-Lamberty
- Pacific Northwest National Laboratory, Joint Global Change Research Institute at the University of Maryland–College Park, College Park, MD 20740, USA
| | - Ivan A Janssens
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jieying Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an 710127, China
| | - Guowei Pang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an 710127, China
| | - Yuwei Wu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an 710127, China
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16
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Rijkers R, Rousk J, Aerts R, Sigurdsson BD, Weedon JT. Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming. GLOBAL CHANGE BIOLOGY 2022; 28:6050-6064. [PMID: 35838347 PMCID: PMC9546092 DOI: 10.1111/gcb.16342] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature-growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (Topt ) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0-30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.
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Affiliation(s)
- Ruud Rijkers
- Amsterdam Institute for Life and Environment, Section of Systems EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Johannes Rousk
- Microbial Ecology, Department of BiologyLund UniversityLundSweden
| | - Rien Aerts
- Amsterdam Institute for Life and Environment, Section of Systems EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest SciencesAgricultural University of IcelandBorgarnesIceland
| | - James T. Weedon
- Amsterdam Institute for Life and Environment, Section of Systems EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
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17
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Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations. mSystems 2022; 7:e0058822. [PMID: 35950761 PMCID: PMC9426432 DOI: 10.1128/msystems.00588-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG'), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism's ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.
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18
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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] [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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19
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Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. THE ISME JOURNAL 2022; 16:1327-1336. [PMID: 35001085 PMCID: PMC9038731 DOI: 10.1038/s41396-021-01159-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 11/08/2022]
Abstract
Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.
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20
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Pold G, Baillargeon N, Lepe A, Rastetter EB, Sistla SA. Warming effects on arctic tundra biogeochemistry are limited but habitat‐dependent: a meta‐analysis. Ecosphere 2021. [DOI: 10.1002/ecs2.3777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Grace Pold
- Natural Resources Management & Environmental Sciences College of Agriculture, Food & Environmental Sciences California Polytechnic State University San Luis Obispo California USA
| | - Natalie Baillargeon
- Smith College Northampton Massachusetts USA
- Woodwell Climate Research Center Woods Hole Massachusetts USA
| | - Adan Lepe
- Amherst College Amherst Massachusetts USA
| | - Edward B. Rastetter
- Marine Biological Laboratories The Ecosystems Center Woods Hole Massachusetts USA
| | - Seeta A. Sistla
- Natural Resources Management & Environmental Sciences College of Agriculture, Food & Environmental Sciences California Polytechnic State University San Luis Obispo California USA
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21
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Roy Chowdhury P, Golas SM, Alteio LV, Stevens JTE, Billings AF, Blanchard JL, Melillo JM, DeAngelis KM. The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest. Front Microbiol 2021; 12:666558. [PMID: 34512564 PMCID: PMC8429792 DOI: 10.3389/fmicb.2021.666558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.
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Affiliation(s)
| | - Stefan M. Golas
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren V. Alteio
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Joshua T. E. Stevens
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Andrew F. Billings
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jeffrey L. Blanchard
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jerry M. Melillo
- The Ecosystems Center, Marine Biological Laboratories, Woods Hole, MA, United States
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
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22
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Smith TP, Clegg T, Bell T, Pawar S. Systematic variation in the temperature dependence of bacterial carbon use efficiency. Ecol Lett 2021; 24:2123-2133. [PMID: 34240797 DOI: 10.1111/ele.13840] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022]
Abstract
Carbon use efficiency (CUE) is a key characteristic of microbial physiology and underlies community-level responses to changing environments. Yet, we currently lack general empirical insights into variation in microbial CUE at the level of individual taxa. Here, through experiments with 29 strains of environmentally isolated bacteria, we find that bacterial CUE typically responds either positively to temperature, or has no discernible response, within biologically meaningful temperature ranges. Using a global data synthesis, we show that these results are generalisable across most culturable groups of bacteria. This variation in the thermal responses of bacterial CUE is taxonomically structured, and stems from the fact that relative to respiration rates, bacterial population growth rates typically respond more strongly to temperature, and are also subject to weaker evolutionary constraints. Our results provide new insights into microbial physiology, and a basis for more accurately modelling the effects of thermal fluctuations on complex microbial communities.
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Affiliation(s)
- Thomas P Smith
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Tom Clegg
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Samrāt Pawar
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
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23
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Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile. Nat Commun 2021; 12:2089. [PMID: 33828081 PMCID: PMC8027381 DOI: 10.1038/s41467-021-22408-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.
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25
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Wan W, Liu S, Li X, Xing Y, Chen W, Huang Q. Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation. mSystems 2021; 6:e01221-20. [PMID: 33785569 PMCID: PMC8547000 DOI: 10.1128/msystems.01221-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/03/2021] [Indexed: 01/09/2023] Open
Abstract
Bacterial diversity and ecosystem multifunctionality (EMF) vary along environmental gradients. However, little is known about interconnections between EMF and taxonomic and phylogenetic diversities of rare and abundant bacteria. Using MiSeq sequencing and multiple statistical analyses, we evaluated the maintenance of taxonomic and phylogenetic diversities of rare and abundant bacteria and their contributions to EMF in salinized agricultural soils (0.09 to 19.91 dS/m). Rare bacteria exhibited closer phylogenetic clustering and broader environmental breadths than abundant ones, while abundant bacteria showed higher functional redundancies and stronger phylogenetic signals of ecological preferences than rare ones. Variable selection (86.7%) dominated rare bacterial community assembly, and dispersal limitation (54.7%) and variable selection (24.5%) determined abundant bacterial community assembly. Salinity played a decisive role in mediating the balance between stochastic and deterministic processes and showed significant effects on functions and diversities of both rare and abundant bacteria. Rare bacterial taxonomic α-diversity and abundant bacterial phylogenetic α-diversity contributed significantly to EMF, while abundant bacterial taxonomic α-diversity and rare bacterial phylogenetic α-diversity did not. Additionally, abundant rather than rare bacterial community function had a significant effect on soil EMF. These findings extend our knowledge of environmental adaptation of rare and abundant bacteria and highlight different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF.IMPORTANCE Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality. Our sequence-based data showed differences in environmental adaptations of rare and abundant bacteria at taxonomic and phylogenetic levels, which led to different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. Studying the diversity of rare and abundant bacteria and their contributions to EMF in salinized soils is critical for guiding soil restoration.
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Affiliation(s)
- Wenjie Wan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yonghui Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, People's Republic of China
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26
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Effect of Cover Crop Type and Application Rate on Soil Nitrogen Mineralization and Availability in Organic Rice Production. SUSTAINABILITY 2021. [DOI: 10.3390/su13052866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In drill-seeded, delay-flooded organic rice production, reliable predictions of N supply from cover crop (CC) residues to subsequent rice are still a challenge. An incubation was conducted to determine the effects of CC types (clover, ryegrass, clover and ryegrass mixtures, and fallow), residue application rates (0, 0.6, 1.2, 1.8, and 2.4%) and incubation time on soil CO2 evolution and N mineralization and availability. The cumulative CO2 evolution linearly increased with increasing residue rate. Compared to the control, adding CCs residue significantly increased the cumulative CO2 emission, which was greatest in soils with clover or mixtures of clover and ryegrass, followed by fallow, and lowest in soils with ryegrass. The modeling results indicated clover had the greatest initial C and N mineralization rates and the shortest half-lives. A temporary decrease in soil mineral N caused by immobilization occurred at the initial incubation stage in all treatments. However, the trend reversed progressively, with the clover treatment requiring the shortest time to meet the crossover point. The results suggested clover was the optimal CC type, 0.6% was the optimal residue rate, and a minimum of 27 days between CC termination and rice planting was required to maximize mineral N supply for organic rice.
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27
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Domeignoz-Horta LA, Pold G, Liu XJA, Frey SD, Melillo JM, DeAngelis KM. Microbial diversity drives carbon use efficiency in a model soil. Nat Commun 2020; 11:3684. [PMID: 32703952 PMCID: PMC7378083 DOI: 10.1038/s41467-020-17502-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/19/2020] [Indexed: 02/01/2023] Open
Abstract
Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.
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Affiliation(s)
| | - Grace Pold
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Xiao-Jun Allen Liu
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Serita D Frey
- School of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
| | - Jerry M Melillo
- The Ecosystems Center, Marine Biological Laboratories, Woods Hole, MA, 02543, USA
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA.
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28
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Muscarella ME, Howey XM, Lennon JT. Trait-based approach to bacterial growth efficiency. Environ Microbiol 2020; 22:3494-3504. [PMID: 32510726 DOI: 10.1111/1462-2920.15120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022]
Abstract
Bacterial growth efficiency (BGE) is the proportion of assimilated carbon that is converted into biomass and reflects the balance between growth and energetic demands. Often measured as an aggregate property of the community, BGE is highly variable within and across ecosystems. To understand this variation, we first identified how species identity and resource type affect BGE using 20 bacterial isolates belonging to the phylum Proteobacteria that were enriched from north temperate lakes. Using a trait-based approach that incorporated genomic and phenotypic information, we characterized the metabolism of each isolate and tested for predicted trade-offs between growth rate and efficiency. A substantial amount of variation in BGE could be explained at broad (i.e., order, 20%) and fine (i.e., strain, 58%) taxonomic levels. While resource type was a relatively weak predictor across species, it explained >60% of the variation in BGE within a given species. A metabolic trade-off (between maximum growth rate and efficiency) and genomic features revealed that BGE may be a species-specific metabolic property. Our study suggests that genomic and phylogenetic information may help predict aggregate microbial community functions like BGE and the fate of carbon in ecosystems.
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Affiliation(s)
- Mario E Muscarella
- Department of Biology, Indiana University, Bloomington, IN, USA.,Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Xia Meng Howey
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
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29
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Distinct Assembly Processes and Microbial Communities Constrain Soil Organic Carbon Formation. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.oneear.2020.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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