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Xu J, Ming H, Ren K, Li D, Huang H, Li J, Shao K, Li H, Fan J. Spatial heterogeneity plays a vital role in shaping the structure and function of estuarine carbon-fixing bacterial communities. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106544. [PMID: 38795574 DOI: 10.1016/j.marenvres.2024.106544] [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: 11/09/2023] [Revised: 04/18/2024] [Accepted: 05/05/2024] [Indexed: 05/28/2024]
Abstract
Carbon-fixing bacterial communities are essential drivers of carbon fixation in estuarine ecosystems that critically affect the global carbon cycle. This study compared the abundances of the Calvin cycle functional genes cbbL and cbbM and Reductive tricarboxylic acid cycle gene aclB, as well as compared carbon-fixing bacterial community features in the two estuaries, predicted potential ecological functions of carbon-fixation bacteria, and analyzed their symbiosis strategies in two estuaries having different geographical distributions. Gammaproteobacteria was the dominant carbon-fixing bacterial community in the two estuaries. However, a higher number of Alphaproteobacteria were noted in the Liaohe Estuary, and a higher number of Betaproteobacteria were found in the Yalujiang Estuary. The carbon-fixing functional gene levels exhibited the order of aclB > cbbL > cbbM, and significant effects of Cu, Pb, and petroleum were observed (p < 0.05). Nitrogen-associated nutrient levels are major environmental factors that affect carbon-fixing bacterial community distribution patterns. Spatial factors significantly affected cbbL carbon-fixing functional bacterial community structure more than environmental factors. With the increase in offshore distance, the microbial-led processes of methylotrophy and nitrogen fixation gradually weakened, but a gradual strengthening of methanotrophy and nitrification was observed. Symbiotic network analysis of the microorganisms mediating these ecological processes revealed that the carbon-fixing bacterial community in these two estuaries had a non-random symbiotic pattern, and microbial communities from the same module were strongly linked among the carbon, nitrogen, and sulfur cycle. These findings could advance the understanding of carbon fixation in estuarine ecosystems.
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Affiliation(s)
- Jianrong Xu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hongxia Ming
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Kaijia Ren
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Dongwei Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; College of Environmental Sciences and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Huiling Huang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jiajie Li
- Faculty of Science, The University of Sydney, Sydney, 2007, Australia
| | - Kuishuang Shao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jingfeng Fan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China.
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2
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Yang M, Zhang X, Ma S, Zhang Q, Peng C, Fan H, Dai L, Li J, Cheng L. Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis. Antonie Van Leeuwenhoek 2023; 116:1359-1374. [PMID: 37843737 DOI: 10.1007/s10482-023-01878-1] [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: 10/13/2022] [Accepted: 09/03/2023] [Indexed: 10/17/2023]
Abstract
A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0 µm in length and 0.4-0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).
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Affiliation(s)
- Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China
| | - Qiumei Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China.
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China.
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China.
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3
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Lu M, Schneider D, Daniel R. Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. Front Microbiol 2022; 13:851969. [PMID: 35756004 PMCID: PMC9226776 DOI: 10.3389/fmicb.2022.851969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
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Affiliation(s)
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
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Lee YY, Seo Y, Ha M, Lee J, Yang H, Cho KS. Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea). ENVIRONMENTAL RESEARCH 2021; 194:110606. [PMID: 33345896 DOI: 10.1016/j.envres.2020.110606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/24/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Rhizoremediation, CH4 emission, and bacterial community dynamics were evaluated in diesel-contaminated soil cultivated with tall fescue via a pot experiment. At the beginning of the experiment, total petroleum hydrocarbons (TPHs) removal efficiency was 30.2% in tall fescue-cultivated soil, which was significantly higher than that of unplanted soil (19.4%). However, when compost was added as a soil amendment, TPHs removal efficiency increased to 39.2% in tall fescue-cultivated soil. Interestingly, potential CH4 emissions were more affected by the initial diesel concentration than by compost addition or tall fescue planting. Specifically, the potential CH4 emission was approximately 3.8 times higher in the treatment with the highest initial diesel concentration (T-WC38) than that of the treatment with the lowest initial diesel concentration (T-WC5). Functional gene analysis revealed that TPHs removal had a linear correlation with the alkB/16S gene ratio, whereas potential CH4 emission had a linear correlation with pmoA gene copy numbers. Initial diesel concentrations in soil also affected bacterial community structures and the genera Rhizobium, Halothiobacillus, and Geobacter were found to be positively linked to diesel-contaminated soil rhizoremediation. Therefore, this study provides useful insights into the development of strategies to enhance rhizoremediation efficiency and CH4 emission mitigation in diesel-contaminated soils.
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Affiliation(s)
- Yun-Yeong Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yoonjoo Seo
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Minyoung Ha
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jiho Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyoju Yang
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.
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5
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Shelton JL, Andrews RS, Akob DM, DeVera CA, Mumford A, McCray JE, McIntosh JC. Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood. FEMS Microbiol Ecol 2018; 94:5067868. [PMID: 30101289 PMCID: PMC6108538 DOI: 10.1093/femsec/fiy153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
Injecting CO2 into depleted oil reservoirs to extract additional crude oil is a common enhanced oil recovery (CO2-EOR) technique. However, little is known about how in situ microbial communities may be impacted by CO2 flooding, or if any permanent microbiological changes occur after flooding has ceased. Formation water was collected from an oil field that was flooded for CO2-EOR in the 1980s, including samples from areas affected by or outside of the flood region, to determine the impacts of CO2-EOR on reservoir microbial communities. Archaea, specifically methanogens, were more abundant than bacteria in all samples, while identified bacteria exhibited much greater diversity than the archaea. Microbial communities in CO2-impacted and non-impacted samples did not significantly differ (ANOSIM: Statistic R = -0.2597, significance = 0.769). However, several low abundance bacteria were found to be significantly associated with the CO2-affected group; very few of these species are known to metabolize CO2 or are associated with CO2-rich habitats. Although this study had limitations, on a broad scale, either the CO2 flood did not impact the microbial community composition of the target formation, or microbial communities in affected wells may have reverted back to pre-injection conditions over the ca. 40 years since the CO2-EOR.
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Affiliation(s)
- Jenna Lk Shelton
- Eastern Energy Resources Science Center, U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA, 20192 USA
| | - Robert S Andrews
- Water Mission Area, U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA, 20192 USA
| | - Denise M Akob
- Water Mission Area, U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA, 20192 USA
| | - Christina A DeVera
- Eastern Energy Resources Science Center, U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA, 20192 USA
| | - Adam Mumford
- Water Mission Area, U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA, 20192 USA
| | - John E McCray
- Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illisnois Street, Golden, CO, 80401 USA.,Hydrologic Science and Engineering Program, Colorado School of Mines, 1500 Illinois Street, Golden, CO, 80401 USA
| | - Jennifer C McIntosh
- Department of Hydrology and Atmospheric Sciences, University of Arizona, 1133 E. James E. Rogers Way, Tucson, AZ, 85721 USA
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6
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Im CH, Kim C, Song YE, Oh SE, Jeon BH, Kim JR. Electrochemically enhanced microbial CO conversion to volatile fatty acids using neutral red as an electron mediator. CHEMOSPHERE 2018; 191:166-173. [PMID: 29032261 DOI: 10.1016/j.chemosphere.2017.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 09/30/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
Conversion of C1 gas feedstock, including carbon monoxide (CO), into useful platform chemicals has attracted considerable interest in industrial biotechnology. Nevertheless, the low conversion yield and/or growth rate of CO-utilizing microbes make it difficult to develop a C1 gas biorefinery process. The Wood-Ljungdahl pathway which utilize CO is a pathway suffered from insufficient electron supply, in which the conversion can be increased further when an additional electron source like carbohydrate or hydrogen is provided. In this study, electrode-based electron transference using a bioelectrochemical system (BES) was examined to compensate for the insufficient reducing equivalent and increase the production of volatile fatty acids. The BES including neutral red (BES-NR), which facilitated electron transfer between bacteria and electrode, was compared with BES without neutral red and open circuit control. The coulombic efficiency based on the current input to the system and the electrons recovered into VFAs, was significantly higher in BES-NR than the control. These results suggest that the carbon electrode provides a platform to regulate the redox balance for improving the bioconversion of CO, and amending the conventional C1 gas fermentation.
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Affiliation(s)
- Chae Ho Im
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Changman Kim
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Young Eun Song
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Sang-Eun Oh
- Department of Biological Environment, Kangwon National University, 192-1, Hyoja 2-dong, Chuncheon, Kangwon-do 200-701, Republic of Korea
| | - Byong-Hun Jeon
- Department of Natural Resources and Environmental Engineering, Hanyang University, Seoul 133- 791, Republic of Korea.
| | - Jung Rae Kim
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Republic of Korea.
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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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8
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Using Prokaryotes for Carbon Capture Storage. Trends Biotechnol 2017; 35:22-32. [DOI: 10.1016/j.tibtech.2016.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 11/20/2022]
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9
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Mei N, Postec A, Monnin C, Pelletier B, Payri CE, Ménez B, Frouin E, Ollivier B, Erauso G, Quéméneur M. Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia. Front Microbiol 2016; 7:1301. [PMID: 27625634 PMCID: PMC5003875 DOI: 10.3389/fmicb.2016.01301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/08/2016] [Indexed: 12/01/2022] Open
Abstract
High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.
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Affiliation(s)
- Nan Mei
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Anne Postec
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Christophe Monnin
- GET UMR5563 (Centre National de la Recherche Scientifique/UPS/IRD/CNES), Géosciences Environnement ToulouseToulouse, France
| | - Bernard Pelletier
- Institut pour la Recherche et le Développement (IRD) Centre de Nouméa, MIO UM 110Nouméa, Nouvelle-Calédonie
| | - Claude E. Payri
- Institut pour la Recherche et le Développement (IRD) Centre de Nouméa, MIO UM 110Nouméa, Nouvelle-Calédonie
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche ScientifiqueParis, France
| | - Eléonore Frouin
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Gaël Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Marianne Quéméneur
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
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10
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Nie Y, Zhao JY, Tang YQ, Guo P, Yang Y, Wu XL, Zhao F. Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly. Front Microbiol 2016; 7:1254. [PMID: 27570522 PMCID: PMC4981601 DOI: 10.3389/fmicb.2016.01254] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/28/2016] [Indexed: 12/17/2022] Open
Abstract
Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013). Although the dominant bacteria and the proportion of hydrogenotrophic and acetoclastic methanogens were different among oil metagenomes, compared with the metagenomes from other environments, all the oil metagenomes contained higher abundances of genes involved in methanogenic hydrocarbon degradation and stress response systems. In addition, a "shape-sorting" manner was proposed for the assembly of microbial communities in oil reservoirs, with the oil reservoir acting as a function sorter to select microbes with special functions from its endemic pool of microorganisms. At the functional level, we found that environmental metagenomes were generally clustered according to their isolation environments but not their geographical locations, suggesting selective processes to be involved in the assembly of microbial communities based on functional gene composition.
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Affiliation(s)
- Yong Nie
- College of Engineering, Peking University, Beijing China
| | - Jie-Yu Zhao
- College of Engineering, Peking University, Beijing China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu China
| | - Peng Guo
- College of Engineering, Peking University, Beijing China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, BeijingChina; Institute of Engineering (Baotou), College of Engineering, Peking University, BaotouChina
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing China
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11
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Yang GC, Zhou L, Mbadinga SM, Liu JF, Yang SZ, Gu JD, Mu BZ. Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate. Front Microbiol 2016; 7:365. [PMID: 27047478 PMCID: PMC4801891 DOI: 10.3389/fmicb.2016.00365] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/07/2016] [Indexed: 11/13/2022] Open
Abstract
CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs.
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Affiliation(s)
- Guang-Chao Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China; Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China; Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China
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12
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The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil. Curr Microbiol 2016; 72:663-70. [PMID: 26858133 DOI: 10.1007/s00284-016-1001-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/27/2015] [Indexed: 10/22/2022]
Abstract
Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites.
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13
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Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China. Sci Rep 2016; 6:20174. [PMID: 26838035 PMCID: PMC4738313 DOI: 10.1038/srep20174] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/22/2015] [Indexed: 02/01/2023] Open
Abstract
To investigate the spatial distribution of microbial communities and their drivers in petroleum reservoir environments, we performed pyrosequencing of microbial partial 16S rRNA, derived from 20 geographically separated water-flooding reservoirs, and two reservoirs that had not been flooded, in China. The results indicated that distinct underground microbial communities inhabited the different reservoirs. Compared with the bacteria, archaeal alpha-diversity was not strongly correlated with the environmental variables. The variation of the bacterial and archaeal community compositions was affected synthetically, by the mining patterns, spatial isolation, reservoir temperature, salinity and pH of the formation brine. The environmental factors explained 64.22% and 78.26% of the total variance for the bacterial and archaeal communities, respectively. Despite the diverse community compositions, shared populations (48 bacterial and 18 archaeal genera) were found and were dominant in most of the oilfields. Potential indigenous microorganisms, including Carboxydibrachium, Thermosinus, and Neptunomonas, were only detected in a reservoir that had not been flooded with water. This study indicates that: 1) the environmental variation drives distinct microbial communities in different reservoirs; 2) compared with the archaea, the bacterial communities were highly heterogeneous within and among the reservoirs; and 3) despite the community variation, some microorganisms are dominant in multiple petroleum reservoirs.
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14
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Gu JD, Wang YS. Coastal and marine pollution and ecotoxicology. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1407-1410. [PMID: 26391368 DOI: 10.1007/s10646-015-1528-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China.
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, People's Republic of China.
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