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He H, Zhou J, Wang Y, Jiao S, Qian X, Liu Y, Liu J, Chen J, Delgado-Baquerizo M, Brangarí AC, Chen L, Cui Y, Pan H, Tian R, Liang Y, Tan W, Ochoa-Hueso R, Fang L. Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers. GLOBAL CHANGE BIOLOGY 2024; 30:e17028. [PMID: 37955302 DOI: 10.1111/gcb.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
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Affiliation(s)
- Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxiong Zhou
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an, 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
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Albert C Brangarí
- Institute for Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Haibo Pan
- 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
| | - Renmao Tian
- Institute for Food Safety and Health (IFSH), Illinois Institute of Technology, Bedford Park, Illinois, USA
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, Cádiz, Spain
| | - Linchuan Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
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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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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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Haoyu L, Karimi R. Investigating a promising iron-doped graphene sensor for SO2 gas: DFT calculations and QTAIM analysis. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-210153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Examination of a promising iron-doped graphene (FG) sensor for the sulfur oxide (SO2) toxic gas was done in this work at the molecular and atomic scales of density functional theory (DFT). The models were stabilized by performing optimization calculations and their electronic features were evaluated. Two models were obtained by relaxing each of the O or S atoms towards the Fe-doped region of surface. Energy values indicated higher strength for formation of the O@FG model in comparison with the S@FG model. The evaluated quantities and qualities of electronic molecular orbitals indicated the effects of occurrence of adsorption processes on the electronic conductivity property of FG as a required feature of a sensor material. As a consequence, the idea of proposing the investigated FG as a promising sensor of the hazardous SO2 gas was affirmed in this work based on the obtained structural and electronic features.
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Affiliation(s)
- Li Haoyu
- School of Materials Science and Engineering, North China University of Science and Technology, Tangshan Province, China
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Bay SK, Waite DW, Dong X, Gillor O, Chown SL, Hugenholtz P, Greening C. Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. THE ISME JOURNAL 2021; 15:3339-3356. [PMID: 34035443 PMCID: PMC8528921 DOI: 10.1038/s41396-021-01001-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H2 oxidation, chemosynthetic CO2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.
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Affiliation(s)
- Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
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Greening C, Islam ZF, Bay SK. Hydrogen is a major lifeline for aerobic bacteria. Trends Microbiol 2021; 30:330-337. [PMID: 34462186 DOI: 10.1016/j.tim.2021.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022]
Abstract
Molecular hydrogen (H2) is available in trace amounts in most ecosystems through atmospheric, biological, geochemical, and anthropogenic sources. Aerobic bacteria use this energy-dense gas, including at atmospheric concentrations, to support respiration and carbon fixation. While it was thought that aerobic H2 consumers are rare community members, here we summarize evidence suggesting that they are dominant throughout soils and other aerated ecosystems. Bacterial cultures from at least eight major phyla can consume atmospheric H2. At the ecosystem scale, H2 consumers are abundant, diverse, and active across diverse soils and are key primary producers in extreme environments such as hyper-arid deserts. On this basis, we propose that H2 is a universally available energy source for the survival of aerobic bacteria.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
| | - Zahra F Islam
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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