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Gao N, Wen H, Shang Z, Zou Y, Zhao W, He Y, Yang S, Zhang H, Qin J, Zhu S, Wang W. Macrogenomics reveal the effects of inter-cropping perilla on kiwifruit: impact on inter-root soil microbiota and gene expression of carbon, nitrogen, and phosphorus cycles in kiwifruit. Front Microbiol 2024; 15:1349305. [PMID: 38887707 PMCID: PMC11180754 DOI: 10.3389/fmicb.2024.1349305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Intercropping systems can improve soil fertility and health, however, soil microbial communities and functional genes related to carbon, nitrogen and phosphorus cycling under the intercropping system of mesquite and perilla have not been studied. Therefore, in the present study, different planting densities and varieties of Perilla frutescens (L.) Britt and kiwifruit were used for intercropping, and changes in soil microbial communities and carbon, nitrogen, and phosphorus cycling genes in kiwifruit inter-roots under inter-cropping conditions were investigated by macro-genome sequencing technology. The results showed that intercropping with Perill caused a decrease in most soil nutrients, soil enzyme activities, and had a significant impact on the microbial (bacteria and fungi) diversity. Inter-cropping increased the relative abundance of the dominant bacterial phylum "Proteobacteria" and "Actinobacteria" by 47 and 57%, respectively, but decreased the relative abundance of the dominant fungal phylum "Chordata" and "Streptophyta" by 11 and 20%, respectively, in the inter-root soil of kiwifruit, and had a significant impact on the microbial (bacteria and fungi) diversity. In addition, inter-cropping could greatly increase the inter-root soil carbon sequestration (PccA, korA/B/C/D, fhs, and rbcl/s), carbon degradation (abfD), organic nitrogen mineralization (GDH2), denitrification (napA/B, nirB, norB), organic phosphorus mineralization (phop, phn), and inorganic phosphorus solubilization (gcd, ppk) gene abundance. The gene co-occurrence network indicated that soil korB, nirB, and gnd key functional genes for carbon, nitrogen, and phosphorus cycling in kiwifruit inter-root soils and their expression was up-regulated in the inter-cropping group. Structural equation (SEM) further showed that soil total nitrogen, organic matter, total carbon and acid phosphatase had significant effects on microbial diversity (p < 0.05) and soil carbon cycling gene korB and phosphorus cycling gene purH (p < 0.001), while korB and purH had positive effects on kiwifruit quality. In conclusion, intercropping perilla in kiwifruit orchards changed the structure of bacterial and fungal communities in the inter-root soil of kiwifruit, but I believe that intercropping perilla stimulates carbon degradation, leading to carbon emission and serious loss of soil nutrients, and that prolonged intercropping may adversely affect the quality of kiwifruit, and thus its limitations should be noted in future studies.
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Affiliation(s)
- Ning Gao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guizhou Minzu University, Guizhou, China
| | - He Wen
- Guizhou Minzu University, Guizhou, China
| | | | - Yifei Zou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wei Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yun He
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Sen Yang
- Guizhou Minzu University, Guizhou, China
| | - Heng Zhang
- Guizhou Minzu University, Guizhou, China
| | - Jiahao Qin
- Guizhou Minzu University, Guizhou, China
| | - Sixi Zhu
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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Zhang RY, Wang YR, Liu RL, Rhee SK, Zhao GP, Quan ZX. Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment. MICROBIOME 2024; 12:7. [PMID: 38191433 PMCID: PMC10773090 DOI: 10.1186/s40168-023-01728-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. RESULTS In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. CONCLUSIONS One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.
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Affiliation(s)
- Ru-Yi Zhang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan-Ren Wang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Ru-Long Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Guo-Ping Zhao
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhe-Xue Quan
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
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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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Hameed A, Suchithra KV, Lin SY, Stothard P, Young CC. Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-E T affiliated to family Paracoccaceae. Antonie Van Leeuwenhoek 2023; 116:1247-1259. [PMID: 37740842 DOI: 10.1007/s10482-023-01881-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023]
Abstract
Ecological studies on marine microbial communities largely focus on fundamental biogeochemical processes or the most abundant constituents, while minor biological fractions are frequently neglected. Youngimonas vesicularis CC-AMW-ET, isolated from coastal surface seawater in Taiwan, is an under-represented marine Paracoccaceae (earlier Rhodobacteraceae) member. The CC-AMW-ET genome was sequenced to gain deeper insights into its role in marine carbon and sulfur cycles. The draft genome (3.7 Mb) contained 63.6% GC, 3773 coding sequences and 51 RNAs, and displayed maximum relatedness (79.06%) to Thalassobius litoralis KU5D5T, a Roseobacteraceae member. While phototrophic genes were absent, genes encoding two distinct subunits of carbon monoxide dehydrogenases (CoxL, BMS/Form II and a novel form III; CoxM and CoxS), and proteins involved in HCO3- uptake and interconversion, and anaplerotic HCO3- fixation were found. In addition, a gene coding for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, form II), which fixes atmospheric CO2 was found in CC-AMW-ET. Genes for complete assimilatory sulfate reduction, sulfide oxidation (sulfide:quinone oxidoreductase, SqrA type) and dimethylsulfoniopropionate (DMSP) cleavage (DMSP lyase, DddL) were also identified. Furthermore, genes that degrade aromatic hydrocarbons such as quinate, salicylate, salicylate ester, p-hydroxybenzoate, catechol, gentisate, homogentisate, protocatechuate, 4-hydroxyphenylacetic acid, N-heterocyclic aromatic compounds and aromatic amines were present. Thus, Youngimonas vesicularis CC-AMW-ET is a potential chemolithoautotroph equipped with genetic machinery for the metabolism of aromatics, and predicted to play crucial roles in the biogeochemical cycling of marine carbon and sulfur.
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Affiliation(s)
- Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India.
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Kokkarambath Vannadil Suchithra
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 402, Taiwan.
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Chen L, Shi Y, Wang S, Sun M, Wang M, Ren X, Gao Z, Zhou Y, Zhang J, Zhuang W, Su X, Fu Y, Wu M. Temperature and phosphorus: the main environmental factors affecting the seasonal variation of soil bacterial diversity in Nansi Lake Wetland. Front Microbiol 2023; 14:1169444. [PMID: 37455734 PMCID: PMC10348425 DOI: 10.3389/fmicb.2023.1169444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The soil bacteria promote the circulation conversion of lake nutrients and play an important role in maintaining the balance of the lake ecosystem. Few studies have investigated the association of seasonal variation in bacteria and environmental factors in inland freshwater lake wetlands. Nansi Lake is a large shallow freshwater lake in northern China. It is an important hub of the eastern route of the South-to-North Water Diversion Project. Methods In this study, bacterial 16S rRNA genes were used to analyze the variation of soil bacterial community diversity in Nansi Lake Wetland and its influencing factors in different seasons. Results It is showed that the phylum, family, and genus with the largest relative abundance in the soil of Nansi Lake Wetland are Proteobacteria, Nitrosomonadaceae, and MND1, respectively. There were significant seasonal differences in soil bacterial diversity in Nansi Lake Wetland, which was significantly higher in summer than in winter. Seasonal variation in environmental factors was significantly correlated with the variation in bacterial communities. Temperature and the content of available phosphorus may be the key factors influencing seasonal variation in bacterial diversity. Discussion The results of this study further enhance our understanding of the relationship between bacterial community diversity and environmental factors in the lake wetland ecosystem, which can provide scientific data for the conservation of Nansi Lake Wetland.
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Affiliation(s)
- Lei Chen
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yuying Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Shen Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Mengyao Sun
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Meng Wang
- Lunan Geo-Engineering Exploration Institute of Shandong Province, Yanzhou, Shandong, China
| | - Xiaoyue Ren
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Zenghao Gao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yiping Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Jie Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Weijing Zhuang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xinyue Su
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yongchao Fu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Mengmeng Wu
- Shandong Freshwater Fisheries Research Institute, Jinan, Shandong, 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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Kuhl T, Chowdhury SP, Uhl J, Rothballer M. Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits. Front Microbiol 2021; 12:708605. [PMID: 34489897 PMCID: PMC8416521 DOI: 10.3389/fmicb.2021.708605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/26/2021] [Indexed: 11/24/2022] Open
Abstract
Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.
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Affiliation(s)
- Theresa Kuhl
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jenny Uhl
- Research Unit Analytical Biogeochemistry, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Rothballer
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
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Matheus Carnevali PB, Lavy A, Thomas AD, Crits-Christoph A, Diamond S, Méheust R, Olm MR, Sharrar A, Lei S, Dong W, Falco N, Bouskill N, Newcomer ME, Nico P, Wainwright H, Dwivedi D, Williams KH, Hubbard S, Banfield JF. Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. MICROBIOME 2021; 9:121. [PMID: 34022966 PMCID: PMC8141241 DOI: 10.1186/s40168-020-00957-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor. RESULTS We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor. CONCLUSIONS The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change. Video abstract.
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Affiliation(s)
| | - Adi Lavy
- Department of Earth and Planetary Science, University of California, Berkeley, USA
| | - Alex D. Thomas
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
| | | | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, USA
| | - Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, USA
- Innovative Genomics Institute, Berkley, CA USA
| | - Matthew R. Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
- Current affiliation: Department of Microbiology and Immunology, Stanford University, Palo Alto, CA USA
| | - Allison Sharrar
- Department of Earth and Planetary Science, University of California, Berkeley, USA
| | - Shufei Lei
- Department of Earth and Planetary Science, University of California, Berkeley, USA
| | - Wenming Dong
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Nicola Falco
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Nicholas Bouskill
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michelle E. Newcomer
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Peter Nico
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Haruko Wainwright
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Dipankar Dwivedi
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Susan Hubbard
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
- Innovative Genomics Institute, Berkley, CA USA
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA USA
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Wu F, Jiao S, Hu J, Wu X, Wang B, Shen G, Yang Y, Tao S, Wang X. Stronger impacts of long-term relative to short-term exposure to carbon nanomaterials on soil bacterial communities. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124550. [PMID: 33223310 DOI: 10.1016/j.jhazmat.2020.124550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/27/2020] [Accepted: 11/10/2020] [Indexed: 06/11/2023]
Abstract
Environmental impacts of carbon nanomaterials (CNMs) have been attracting increasing concerns in recent years. Knowledge on how short-term exposure to CNMs influences soil microbial communities is available. However, little is known about the possible difference in effects of long-term versus short-term exposure of CNMs on soil microbial communities. In this study, we systematically compared effects of fullerene (C60), single-walled carbon nanotubes (SW), and graphene (GR) on soil bacterial communities over short (30 d) and long (360 d) term exposure durations. Our findings revealed that short-term exposure to all CNMs significantly increased the alpha diversity of soil bacterial communities. SW and GR exposure for 360 d relative to that for 30 d more significantly decreased their alpha diversity. Compared to short-term exposure, a long term exposure to CNMs more strongly altered the beta diversity of soil bacterial communities. LEfSe analysis showed that, GR relative to C60 and SW exposure more strongly altered soil bacterial community composition especially for long-term duration at various taxonomic levels; more taxa were also identified by LEfSe analysis as biomarkers upon long-term GR exposure. More OTUs were affected by long-term GR exposure. These differences resulted from both distinct physicochemical properties of various CNMs and their exposure durations.
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Affiliation(s)
- Fan Wu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shuo Jiao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jing Hu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xinyi Wu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Bin Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Guofeng Shen
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada, Reno, NV 89557, USA
| | - Shu Tao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xilong Wang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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10
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Trace gas oxidizers are widespread and active members of soil microbial communities. Nat Microbiol 2021; 6:246-256. [PMID: 33398096 DOI: 10.1038/s41564-020-00811-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/08/2020] [Indexed: 01/24/2023]
Abstract
Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.
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11
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Shang Y, Wu X, Wei Q, Dou H, Wang X, Chen J, Zhang H, Ma S, Zhang H. Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China. Front Microbiol 2020; 11:548607. [PMID: 33072010 PMCID: PMC7541820 DOI: 10.3389/fmicb.2020.548607] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/24/2020] [Indexed: 01/29/2023] Open
Abstract
Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO4 2-)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.
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Affiliation(s)
- Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shengchao Ma
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, China
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12
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Saavedra-Lavoie J, de la Porte A, Piché-Choquette S, Guertin C, Constant P. Biological H 2 and CO oxidation activities are sensitive to compositional change of soil microbial communities. Can J Microbiol 2020; 66:263-273. [PMID: 31999470 DOI: 10.1139/cjm-2019-0412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%-98% less H2 oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.
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Affiliation(s)
- Julien Saavedra-Lavoie
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Anne de la Porte
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Sarah Piché-Choquette
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Claude Guertin
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.,Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
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13
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Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF. Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nat Microbiol 2019; 4:1356-1367. [PMID: 31110364 PMCID: PMC6784897 DOI: 10.1038/s41564-019-0449-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/03/2019] [Indexed: 12/15/2022]
Abstract
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.
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Affiliation(s)
- Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhou Li
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Katherine R Lane
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
- School of Computer Science and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
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14
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Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME JOURNAL 2019; 13:2868-2881. [PMID: 31358912 PMCID: PMC6794299 DOI: 10.1038/s41396-019-0479-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/22/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022]
Abstract
Carbon monoxide (CO) is a ubiquitous atmospheric trace gas produced by natural and anthropogenic sources. Some aerobic bacteria can oxidize atmospheric CO and, collectively, they account for the net loss of ~250 teragrams of CO from the atmosphere each year. However, the physiological role, genetic basis, and ecological distribution of this process remain incompletely resolved. In this work, we addressed these knowledge gaps through culture-based and culture-independent work. We confirmed through shotgun proteomic and transcriptional analysis that the genetically tractable aerobic soil actinobacterium Mycobacterium smegmatis upregulates expression of a form I molydenum-copper carbon monoxide dehydrogenase by 50-fold when exhausted for organic carbon substrates. Whole-cell biochemical assays in wild-type and mutant backgrounds confirmed that this organism aerobically respires CO, including at sub-atmospheric concentrations, using the enzyme. Contrary to current paradigms on CO oxidation, the enzyme did not support chemolithoautotrophic growth and was dispensable for CO detoxification. However, it significantly enhanced long-term survival, suggesting that atmospheric CO serves a supplemental energy source during organic carbon starvation. Phylogenetic analysis indicated that atmospheric CO oxidation is widespread and an ancestral trait of CO dehydrogenases. Homologous enzymes are encoded by 685 sequenced species of bacteria and archaea, including from seven dominant soil phyla, and we confirmed genes encoding this enzyme are abundant and expressed in terrestrial and marine environments. On this basis, we propose a new survival-centric model for the evolution of aerobic CO oxidation and conclude that, like atmospheric H2, atmospheric CO is a major energy source supporting persistence of aerobic heterotrophic bacteria in deprived or changeable environments.
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15
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Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide. ISME JOURNAL 2019; 13:1801-1813. [PMID: 30872805 PMCID: PMC6776052 DOI: 10.1038/s41396-019-0393-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/21/2019] [Accepted: 02/20/2019] [Indexed: 11/29/2022]
Abstract
Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H2), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments showed that T. roseum aerobically respires H2 and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the hydrogenases and carbon monoxide dehydrogenases mediating these processes are widely distributed in Chloroflexi genomes and have probably been horizontally acquired on more than one occasion. Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 (class Ktedonobacteria) also oxidises atmospheric H2 and CO during persistence, though further studies are required to determine if these findings extend to mesophilic strains. This study provides axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum, following Actinobacteria and Acidobacteria, to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H2 oxidation. This adds to the growing body of evidence that atmospheric trace gases are dependable energy sources for bacterial persistence.
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16
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Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature 2017; 552:400-403. [DOI: 10.1038/nature25014] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/09/2017] [Indexed: 12/19/2022]
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17
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Truu M, Ostonen I, Preem JK, Lõhmus K, Nõlvak H, Ligi T, Rosenvald K, Parts K, Kupper P, Truu J. Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand. Front Microbiol 2017; 8:557. [PMID: 28421053 PMCID: PMC5376589 DOI: 10.3389/fmicb.2017.00557] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/16/2017] [Indexed: 01/05/2023] Open
Abstract
Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N2O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity.
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Affiliation(s)
- Marika Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Jens-Konrad Preem
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Krista Lõhmus
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Hiie Nõlvak
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Teele Ligi
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Katrin Rosenvald
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Kaarin Parts
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Priit Kupper
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Jaak Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
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18
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Lynn TM, Ge T, Yuan H, Wei X, Wu X, Xiao K, Kumaresan D, Yu SS, Wu J, Whiteley AS. Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems. MICROBIAL ECOLOGY 2017; 73:645-657. [PMID: 27838764 DOI: 10.1007/s00248-016-0890-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/27/2016] [Indexed: 05/03/2023]
Abstract
CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of 14C (14C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of 14C-labeled soil organic carbon (14C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, 14C-SOC level, and 14C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO2-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.
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Affiliation(s)
- Tin Mar Lynn
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
- Biotechnology Research Department, Ministry of Education, Kyaukse, Myanmar
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China.
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China.
| | - Hongzhao Yuan
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
| | - Xiaomeng Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
| | - Xiaohong Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
| | - Keqing Xiao
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, NyMunkegade 114, 8000, Aarhus C, Denmark
| | - Deepak Kumaresan
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China
- School of Earth and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - San San Yu
- Biotechnology Research Department, Ministry of Education, Kyaukse, Myanmar
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China
| | - Andrew S Whiteley
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China
- School of Earth and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
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19
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Weber CF, King GM. Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex. Front Microbiol 2017; 8:207. [PMID: 28270796 PMCID: PMC5318905 DOI: 10.3389/fmicb.2017.00207] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/30/2017] [Indexed: 11/16/2022] Open
Abstract
Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai‘i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia, respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia: Paraburkholderia hiiakae sp. nov. (type strain I2T = DSM 28029T = LMG 27952T); Paraburkholderia paradisi sp. nov. (type strain WAT = DSM 28027T = LMG 27949T); Paraburkholderia peleae sp. nov. (type strain PP52-1T = DSM 28028T = LMG 27950T); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1T = DSM 28030T = LMG 28140T). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38T = DSM 28031T = LMG 28138T).
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Affiliation(s)
- Carolyn F Weber
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA; College of Health Sciences, Des Moines UniversityDes Moines, IA, USA
| | - Gary M King
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
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Peck V, Quiza L, Buffet JP, Khdhiri M, Durand AA, Paquette A, Thiffault N, Messier C, Beaulieu N, Guertin C, Constant P. Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices. Microb Biotechnol 2016; 9:316-29. [PMID: 26853704 PMCID: PMC4835570 DOI: 10.1111/1751-7915.12348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/15/2015] [Indexed: 11/30/2022] Open
Abstract
The impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high‐throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment.
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Affiliation(s)
- Vincent Peck
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Liliana Quiza
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Jean-Philippe Buffet
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Mondher Khdhiri
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Audrey-Anne Durand
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Alain Paquette
- Centre d'étude de la forêt, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, Canada, H3C 3P8
| | - Nelson Thiffault
- Centre d'étude de la forêt, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, Canada, H3C 3P8.,Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs, 2700 Einstein, Québec, Québec, Canada, G1P 3W8
| | - Christian Messier
- Centre d'étude de la forêt, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, Canada, H3C 3P8.,Institut des Sciences de la Forêt Tempérée (ISFORT), Université du Québec en Outaouais (UQO), 58 rue Principale, Ripon, Québec, Canada, J0V 1V0
| | - Nadyre Beaulieu
- Produits Forestiers Résolu, 2419 Route 155 sud, La Tuque, Québec, Canada, G9X 3N8
| | - Claude Guertin
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Philippe Constant
- INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
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Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms. Appl Environ Microbiol 2015; 82:1324-1333. [PMID: 26682854 DOI: 10.1128/aem.03595-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/12/2015] [Indexed: 12/25/2022] Open
Abstract
Surveys of the coxL gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of coxL sequences encompassing the atypical genotype coxL type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available coxL reference genome sequences, this unusual genotype was assigned to an unknown member of the Deltaproteobacteria, with the coxL sequence from Haliangium ochraceum being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the coxL group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of Deltaproteobacteria was too small to account for the abundance of the coxL group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of coxL genotypes and CO uptake activity in soil. We found that most of the coxL genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to Actinobacteria and Alphaproteobacteria. Our analysis did not provide any evidence that coxL group x genotypes belonged to Deltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical coxL group x genotype are mixotrophic K-strategists.
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Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging. Proc Natl Acad Sci U S A 2015; 112:10497-502. [PMID: 26240343 DOI: 10.1073/pnas.1508385112] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence.
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Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK. Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. Front Microbiol 2014; 5:698. [PMID: 25566214 PMCID: PMC4269115 DOI: 10.3389/fmicb.2014.00698] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022] Open
Abstract
Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75-78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56-72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.
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Affiliation(s)
- Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - John L. Darcy
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Diana R. Nemergut
- Environmental Studies Program, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
- Department of Biology, Duke UniversityDurham, NC, USA
| | - Steve K. Schmidt
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
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