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Shoemaker A, Maritan A, Cosar S, Nupp S, Menchaca A, Jackson T, Dang A, Baxter BK, Colman DR, Dunham EC, Boyd ES. Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah. FEMS Microbiol Ecol 2024; 100:fiae105. [PMID: 39054286 PMCID: PMC11287216 DOI: 10.1093/femsec/fiae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/03/2024] [Accepted: 07/24/2024] [Indexed: 07/27/2024] Open
Abstract
Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.
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Affiliation(s)
- Anna Shoemaker
- Department of Earth Sciences, Montana State University, P.O. Box 173480, Bozeman, MT 59717, United States
| | - Andrew Maritan
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Su Cosar
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Sylvia Nupp
- Department of Chemistry and Biochemistry, Montana State University, P.O. Box 173400, Bozeman, MT 59717, United States
| | - Ana Menchaca
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Thomas Jackson
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Aria Dang
- Department of Chemistry and Biochemistry, Montana State University, P.O. Box 173400, Bozeman, MT 59717, United States
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster University, 1840 South 1300 East, Salt Lake City, UT 84105, United States
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Eric C Dunham
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
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Liu Z, Gu H, Yao Q, Jiao F, Hu X, Liu J, Jin J, Liu X, Wang G. Soil pH and carbon quality index regulate the biogeochemical cycle couplings of carbon, nitrogen and phosphorus in the profiles of Isohumosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171269. [PMID: 38423323 DOI: 10.1016/j.scitotenv.2024.171269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
Soil biogeochemical cycles are essential for regulating ecosystem functions and services. However, little knowledge has been revealed on microbe-driven biogeochemical processes and their coupling mechanisms in soil profiles. This study investigated the vertical distribution of soil functional composition and their contribution to carbon (C), nitrogen (N) and phosphorus (P) cycling in the humus horizons (A-horizons) and parent material horizons (C-horizons) in Udic and Ustic Isohumosols using shotgun sequencing. Results showed that the diversity and relative abundance of microbial functional genes was influenced by soil horizons and soil types. In A-horizons, the relative abundances of N mineralization and liable C decomposition genes were significantly greater, but the P cycle-related genes, recalcitrant C decomposition and denitrification genes were lower compared to C-horizons. While, Ustic Isohumosols had lower relative abundances of C decomposition genes but higher relative abundances of N mineralization and P cycling-related pathways compared to Udic Isohumosols. The network analysis revealed that C-horizons had more interactions and stronger stability of functional gene networks than in A-horizons. Importantly, our results provide new insights into the potential mechanisms for the coupling processes of soil biogeochemical cycles among C, N and P, which is mediated by specific microbial taxa. Soil pH and carbon quality index (CQI) were two sensitive indicators for regulating the relative abundances and the relationships of functional genes in biogeochemical cycles. This study contributes to a deeper understanding of the ecological functions of soil microorganisms, thus providing a theoretical basis for the exploration and utilization of soil microbial resources and the development of soil ecological control strategies.
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Affiliation(s)
- Zhuxiu Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Yao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Feng Jiao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiaobing Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
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Odisi EJ, de Freitas RC, do Amaral DS, da Silva SB, da Silva MAC, de Oliveira Sant Ana W, de Souza Lima AO, Rörig LR. Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil). Extremophiles 2023; 28:8. [PMID: 38133826 DOI: 10.1007/s00792-023-01324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.
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Affiliation(s)
- Estácio Jussie Odisi
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil
- Biome4All, São Paulo, SP, 01419-909, Brazil
| | | | - Diego Serrasol do Amaral
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil
| | | | - Marcus Adonai Castro da Silva
- Center for Earth and Sea Technological Sciences, University of Vale Do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, 88302-202, Brazil
| | - William de Oliveira Sant Ana
- SATC Technological Center, Beneficent Association of the Santa Catarina Coal Industry (SATC), Pascoal Meller St. 73, Criciúma, SC, Brazil
| | - André Oliveira de Souza Lima
- Center for Earth and Sea Technological Sciences, University of Vale Do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, 88302-202, Brazil
| | - Leonardo Rubi Rörig
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil.
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Irazoqui JM, Eberhardt MF, Adjad MM, Amadio AF. Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PeerJ 2022; 10:e12772. [PMID: 35310160 PMCID: PMC8929167 DOI: 10.7717/peerj.12772] [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: 07/13/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023] Open
Abstract
Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.
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Affiliation(s)
- Jose M. Irazoqui
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria F. Eberhardt
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria M. Adjad
- Estacion Experimental Rafaela (INTA), Rafaela, Santa Fe, Argentina
| | - Ariel F. Amadio
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
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5
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Zhang Y, Hua ZS, Lu H, Oehmen A, Guo J. Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics. WATER RESEARCH 2019; 148:219-230. [PMID: 30388523 DOI: 10.1016/j.watres.2018.10.061] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/11/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.
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Affiliation(s)
- Yan Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; School of Environmental and Chemical Engineering, Foshan University, Foshan, 528000, PR China
| | - Zheng-Shuang Hua
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China.
| | - Adrian Oehmen
- School of Chemical Engineering, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, 4072, Australia.
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Harrison JP, Dobinson L, Freeman K, McKenzie R, Wyllie D, Nixon SL, Cockell CS. Aerobically respiring prokaryotic strains exhibit a broader temperature-pH-salinity space for cell division than anaerobically respiring and fermentative strains. J R Soc Interface 2016; 12:0658. [PMID: 26354829 DOI: 10.1098/rsif.2015.0658] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biological processes on the Earth operate within a parameter space that is constrained by physical and chemical extremes. Aerobic respiration can result in adenosine triphosphate yields up to over an order of magnitude higher than those attained anaerobically and, under certain conditions, may enable microbial multiplication over a broader range of extremes than other modes of catabolism. We employed growth data published for 241 prokaryotic strains to compare temperature, pH and salinity values for cell division between aerobically and anaerobically metabolizing taxa. Isolates employing oxygen as the terminal electron acceptor exhibited a considerably more extensive three-dimensional phase space for cell division (90% of the total volume) than taxa using other inorganic substrates or organic compounds as the electron acceptor (15% and 28% of the total volume, respectively), with all groups differing in their growth characteristics. Understanding the mechanistic basis of these differences will require integration of research into microbial ecology, physiology and energetics, with a focus on global-scale processes. Critical knowledge gaps include the combined impacts of diverse stress parameters on Gibbs energy yields and rates of microbial activity, interactions between cellular energetics and adaptations to extremes, and relating laboratory-based data to in situ limits for cell division.
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Affiliation(s)
- Jesse P Harrison
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Luke Dobinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Kenneth Freeman
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Ross McKenzie
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Dale Wyllie
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Sophie L Nixon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
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Abstract
The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana 59717-2900;
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