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Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil. ISME JOURNAL 2018; 12:2532-2543. [PMID: 29950702 DOI: 10.1038/s41396-018-0190-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/16/2022]
Abstract
The Deepwater Horizon (DWH) blowout resulted in the deposition to the seafloor of up to 4.9% of 200 million gallons of oil released into the Gulf of Mexico. The petroleum hydrocarbon concentrations near the wellhead were high immediately after the spill, but returned to background levels a few years after the spill. Microbial communities in the seafloor are thought to be responsible for the degradation of hydrocarbons, however, our knowledge is primarily based upon gene diversity surveys and hydrocarbon concentration in field sediment samples. Here, we investigated the oil degradation potential and changes in bacterial community by amending seafloor sediment collected near the DWH site with crude oil and both oil and Corexit dispersant. Polycyclic aromatic hydrocarbons were rapidly degraded during the first 30 days of incubation, while alkanes were degraded more slowly. With the degradation of hydrocarbons, the relative abundances of Colwelliaceae, Alteromonadaceae, Methylococales, Alcanivorax, Bacteriovorax, and Phaeobacter increased remarkably. However, the abundances of oil-degrading bacteria changed with oil chemistry. Colwelliaceae decreased with increasing oil degradation, whereas Alcanivorax and Methylococcales increased considerably. We assembled seven genomes from the metagenome, including ones belonging to Colwellia, Alteromonadaceae, Rhodobacteraceae, the newly reported genus Woeseia, and candidate phylum NC10, all of which possess a repertoire of genes for hydrocarbon degradation. Moreover, genes related to hydrocarbon degradation were highly enriched in the oiled treatment, suggesting that the hydrocarbons were biodegraded, and that the indigenous microflora have a remarkable potential for the natural attenuation of spilled oil in the deep-sea surface sediment.
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52
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Zhu G, Wang S, Li Y, Zhuang L, Zhao S, Wang C, Kuypers MMM, Jetten MSM, Zhu Y. Microbial pathways for nitrogen loss in an upland soil. Environ Microbiol 2018. [PMID: 29528547 DOI: 10.1111/1462-2920.14098] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The distribution and importance of anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) have been identified in aquatic ecosystems; their role in agricultural upland soils however has not yet been well investigated. In this study, we examined spatio-temporal distributions of anammox and n-damo bacteria in soil profiles (300 cm depth) from an agricultural upland. Monitoring nitrogen (N) conversion activity using isotope-tracing techniques over the course of one year showed denitrification (99.0% N-loss in the winter and 85.0% N-loss in the summer) predominated over anammox (1.0% N-loss in the winter and 14.4% N-loss in the summer) and n-damo (0.6% N-loss in the winter) in surface soils (0-20 cm). While below 20 cm depth, N-loss was dominated by anammox (79.4 ± 14.3% in the winter and 65.4 ± 12.5% in the summer) and n-damo was not detected. Phylogenetic analysis showed that Candidatus Brocadia anammoxidans dominated the anammox community in the surface soil and Candidatus Brocadia fulgida dominated below 20 cm depth. Dissimilatory nitrate reduction to ammonium (DNRA), another nitrite reduction process, was found to play a limited role (4.9 ± 3.5%) in the surface soil compared with denitrification; below 80 cm DNRA rates were much higher than rates of anammox and denitrification. Ammonium oxidation was the main source of NO2- above 80 cm (70.9 ± 23.3%), the key influencing factor on anammox rates, and nitrate reduction (100%) was the main NO2- source below 80 cm. Considering the anammox, n-damo and denitrification rates as a whole in the sampled soil profile, denitrification is still the main N-loss process in upland soils.
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Affiliation(s)
- Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Yixiao Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Linjie Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Cheng Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, the Netherlands
| | - Yongguan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
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53
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Methane stimulates massive nitrogen loss from freshwater reservoirs in India. Nat Commun 2018; 9:1265. [PMID: 29593290 PMCID: PMC5871758 DOI: 10.1038/s41467-018-03607-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/28/2018] [Indexed: 11/08/2022] Open
Abstract
The fate of the enormous amount of reactive nitrogen released to the environment by human activities in India is unknown. Here we show occurrence of seasonal stratification and generally low concentrations of dissolved inorganic combined nitrogen, and high molecular nitrogen (N2) to argon ratio, thus suggesting seasonal loss to N2 in anoxic hypolimnia of several dam-reservoirs. However, 15N-experiments yielded low rates of denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium-except in the presence of methane (CH4) that caused ~12-fold increase in denitrification. While nitrite-dependent anaerobic methanotrophs belonging to the NC10 phylum were present, previously considered aerobic methanotrophs were far more abundant (up to 13.9%) in anoxic hypolimnion. Methane accumulation in anoxic freshwater systems seems to facilitate rapid loss of reactive nitrogen, with generally low production of nitrous oxide (N2O), through widespread coupling between methanotrophy and denitrification, potentially mitigating eutrophication and emissions of CH4 and N2O to the atmosphere.
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54
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Marlow JJ, Kumar A, Enalls BC, Reynard LM, Tuross N, Stephanopoulos G, Girguis P. Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas. Biotechnol Bioeng 2018; 115:1450-1464. [PMID: 29460958 PMCID: PMC5947824 DOI: 10.1002/bit.26576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023]
Abstract
Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy‐rich, yet the most efficient methane‐activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by‐products at a comparable rate and in near‐stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost‐effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep‐sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep‐sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full‐scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane‐oxidizing, sulfide‐generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane‐dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth‐based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane‐activating microbial communities using a low‐mass and sediment‐free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use.
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Affiliation(s)
- Jeffrey J Marlow
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Amit Kumar
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Brandon C Enalls
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Linda M Reynard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
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55
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Xu S, Lu W, Muhammad FM, Liu Y, Guo H, Meng R, Wang H. New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches. J Environ Sci (China) 2018; 65:367-374. [PMID: 29548408 DOI: 10.1016/j.jes.2017.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/22/2017] [Accepted: 04/19/2017] [Indexed: 06/08/2023]
Abstract
The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (p<0.05). The redundancy analysis further revealed that the pH, volatile solid and nitrite nitrogen were the most important factors in shaping the NC10 bacterial structure (p=0.01) based on the variation inflation factors selection and Monte Carlo test (999 times). Results of this study extended the existing molecular tools for studying the NC10 bacterial community structures and provided new information on the ecological distributions of NC10 bacteria.
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Affiliation(s)
- Sai Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China.
| | | | - Yanting Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanwen Guo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruihong Meng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongtao Wang
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China
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56
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Molecular and stable isotopic evidence for the occurrence of nitrite-dependent anaerobic methane-oxidizing bacteria in the mangrove sediment of Zhangjiang Estuary, China. Appl Microbiol Biotechnol 2018; 102:2441-2454. [DOI: 10.1007/s00253-017-8718-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/18/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
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57
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Martinez-Cruz K, Leewis MC, Herriott IC, Sepulveda-Jauregui A, Anthony KW, Thalasso F, Leigh MB. Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:23-31. [PMID: 28686892 DOI: 10.1016/j.scitotenv.2017.06.187] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 05/25/2023]
Abstract
Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH4 emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH4) emission, since CH4 production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH4 emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH4 cycling and ultimately to predicting future CH4 emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH4, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH4-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH4-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH4 oxidation in anaerobic lake sediments.
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Affiliation(s)
- Karla Martinez-Cruz
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Armando Sepulveda-Jauregui
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Katey Walter Anthony
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Frederic Thalasso
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
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58
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Shen LD, Wu HS, Liu X, Li J. Cooccurrence and potential role of nitrite- and nitrate-dependent methanotrophs in freshwater marsh sediments. WATER RESEARCH 2017; 123:162-172. [PMID: 28668629 DOI: 10.1016/j.watres.2017.06.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 05/31/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
Nitrite- and nitrate-dependent anaerobic methane oxidation are mediated by the NC10 bacteria closely related to "Candidatus Methylomirabilis oxyfera" (M. oxyfera) and the ANME-2d archaea closely related to "Candidatus Methanoperedens nitroreducens" (M. nitroreducens), respectively. Here, we investigated the occurrence and activity of both M. oxyfera-like bacteria and M. nitroreducens-like archaea in the sediment of freshwater marshes in Eastern China. The presence of diverse M. oxyfera-like bacteria (>87% identity to M. oxyfera) and M. nitroreducens-like archaea (>96% identity to M. nitroreducens) was confirmed by using Illumina-based total bacterial and archaeal 16S rRNA gene sequencing, respectively. The recovered M. oxyfera-like bacterial sequences accounted for 1.6-4.3% of the total bacterial 16S rRNA pool, and M. nitroreducens-like archaeal sequences accounted for 0.2-1.8% of the total archaeal 16S rRNA pool. The detected numbers of OTUs of the 16S rRNA genes of M. oxyfera-like bacteria and M. nitroreducens-like archaea were 78 and 72, respectively, based on 3% sequence difference. Quantitative PCR showed that the 16S rRNA gene abundance of M. oxyfera-like bacteria (6.1 × 106-3.2 × 107 copies g-1 sediment) was 2-4 orders of magnitude higher than that of M. nitroreducens-like archaea (1.4 × 103-3.2 × 104 copies g-1 sediment). Stable isotope experiments showed that the addition of both nitrite and nitrate stimulated the anaerobic methane oxidation, while the stimulation by nitrite is more significant than nitrate. Our results provide the first evidence that the M. oxyfera-like bacteria play a more important role than the M. nitroreducens-like archaea in methane cycling in wetland systems.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Hong-Sheng Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xu Liu
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ji Li
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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59
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Wang J, Shen L, He Z, Hu J, Cai Z, Zheng P, Hu B. Spatial and temporal distribution of nitrite-dependent anaerobic methane-oxidizing bacteria in an intertidal zone of the East China Sea. Appl Microbiol Biotechnol 2017; 101:8007-8014. [DOI: 10.1007/s00253-017-8521-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/21/2017] [Accepted: 09/06/2017] [Indexed: 12/18/2022]
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60
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Black EM, Chimenti MS, Just CL. Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment. PeerJ 2017; 5:e3536. [PMID: 28717594 PMCID: PMC5510576 DOI: 10.7717/peerj.3536] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/13/2017] [Indexed: 01/03/2023] Open
Abstract
Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.
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Affiliation(s)
- Ellen M Black
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States of America
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, United States of America
| | - Craig L Just
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States of America
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61
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Chronopoulou PM, Shelley F, Pritchard WJ, Maanoja ST, Trimmer M. Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone. THE ISME JOURNAL 2017; 11:1386-1399. [PMID: 28244978 PMCID: PMC5437358 DOI: 10.1038/ismej.2017.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/06/2016] [Accepted: 01/09/2017] [Indexed: 11/23/2022]
Abstract
Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (<15 m) water column profiles revealed a 300 m thick layer of elevated methane (20-105 nM) in the anoxic core of the largest OMZ, the Eastern Tropical North Pacific. Sediment core incubations identified a clear benthic methane source where the OMZ meets the continental shelf, between 350 and 650 m, with the flux reflecting the concentration of methane in the overlying anoxic water. Further incubations characterised a methanogenic potential in the presence of both porewater sulphate and nitrate of up to 88 nmol g-1day-1 in the sediment surface layer. In these methane-producing sediments, the majority (85%) of methyl coenzyme M reductase alpha subunit (mcrA) gene sequences clustered with Methanosarcinaceae (⩾96% similarity to Methanococcoides sp.), a family capable of performing non-competitive methanogenesis. Incubations with 13C-CH4 showed potential for both aerobic and anaerobic methane oxidation in the waters within and above the OMZ. Both aerobic and anaerobic methane oxidation is corroborated by the presence of particulate methane monooxygenase (pmoA) gene sequences, related to type I methanotrophs and the lineage of Candidatus Methylomirabilis oxyfera, known to perform nitrite-dependent anaerobic methane oxidation (N-DAMO), respectively.
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Affiliation(s)
| | - Felicity Shelley
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - William J Pritchard
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Susanna T Maanoja
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Mark Trimmer
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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62
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Long Y, Liu C, Lin H, Li N, Guo Q, Xie S. Vertical and horizontal distribution of sediment nitrite-dependent methane-oxidizing organisms in a mesotrophic freshwater reservoir. Can J Microbiol 2017; 63:525-534. [DOI: 10.1139/cjm-2016-0585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the present study, we investigated the spatial change of sediment nitrite-dependent anaerobic methane-oxidizing (n-damo) organisms in the mesotrophic freshwater Gaozhou Reservoir (6 different sampling locations and 2 sediment depths (0–5 cm, 5–10 cm)), one of the largest drinking water reservoirs in China. The abundance of sediment n-damo bacteria was quantified using quantitative polymerase chain reaction assay, while the richness, diversity, and composition of n-damo pmoA gene sequences were characterized using clone library analysis. Vertical and horizontal changes in sediment n-damo bacterial abundance occurred in Gaozhou Reservoir, with 1.37 × 105 to 8.24 × 105 n-damo 16S rRNA gene copies per gram of dry sediment. Considerable horizontal and vertical variations of n-damo pmoA gene diversity (Shannon index = 0.32–2.50) and composition also occurred in this reservoir. Various types of sediment n-damo pmoA genes existed in Gaozhou Reservoir. A small proportion of n-damo pmoA gene sequences (19.1%) were related to those recovered from “Candidatus Methylomirabilis oxyfera”. Our results suggested that sediment n-damo pmoA gene diversity might be regulated by nitrite, while n-damo pmoA gene richness might be governed by multiple environmental factors, including total organic carbon, total phosphorus, nitrite, and total nitrogen.
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Affiliation(s)
- Yan Long
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Changbao Liu
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Hengliang Lin
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Qingwei Guo
- South China Institute of Environmental Sciences, Ministry of Environment Protection, Guangzhou 510655, People’s Republic of China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, People’s Republic of China
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63
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Wang D, Wang Y, Liu Y, Ngo HH, Lian Y, Zhao J, Chen F, Yang Q, Zeng G, Li X. Is denitrifying anaerobic methane oxidation-centered technologies a solution for the sustainable operation of wastewater treatment Plants? BIORESOURCE TECHNOLOGY 2017; 234:456-465. [PMID: 28363395 DOI: 10.1016/j.biortech.2017.02.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 06/07/2023]
Abstract
With the world's increasing energy crisis, society is growingly considered that the operation of wastewater treatment plants (WWTPs) should be shifted in sustainable paradigms with low energy input, or energy-neutral, or even energy output. There is a lack of critical thinking on whether and how new paradigms can be implemented in WWTPs based on the conventional process. The denitrifying anaerobic methane oxidation (DAMO) process, which uses methane and nitrate (or nitrite) as electron donor and acceptor, respectively, has recently been discovered. Based on critical analyses of this process, DAMO-centered technologies can be considered as a solution for sustainable operation of WWTPs. In this review, a possible strategy with DAMO-centered technologies was outlined and illustrated how this applies for the existing WWTPs energy-saving and newly designed WWTPs energy-neutral (or even energy-producing) towards sustainable operations.
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Affiliation(s)
- Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China
| | - Yali Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
| | - Yu Lian
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China
| | - Jianwei Zhao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China
| | - Fei Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China
| | - Qi Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Xiaoming Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
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64
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Roland FAE, Darchambeau F, Morana C, Bouillon S, Borges AV. Emission and oxidation of methane in a meromictic, eutrophic and temperate lake (Dendre, Belgium). CHEMOSPHERE 2017; 168:756-764. [PMID: 27836279 DOI: 10.1016/j.chemosphere.2016.10.138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 10/13/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
We sampled the water column of the Dendre stone pit lake (Belgium) in spring, summer, autumn and winter. Depth profiles of several physico-chemical variables, nutrients, dissolved gases (CO2, CH4, N2O), sulfate, sulfide, iron and manganese concentrations and δ13C-CH4 were determined. We performed incubation experiments to quantify CH4 oxidation rates, with a focus on anaerobic CH4 oxidation (AOM), without and with an inhibitor of sulfate reduction (molybdate). The evolution of nitrate and sulfate concentrations during the incubations was monitored. The water column was anoxic below 20 m throughout the year, and was thermally stratified in summer and autumn. High partial pressure of CO2 and CH4 and high concentrations of ammonium and phosphate were observed in anoxic waters. Important nitrous oxide and nitrate concentration maxima were also observed (up to 440 nmol L-1 and 80 μmol L-1, respectively). Vertical profiles of δ13C-CH4 unambiguously showed the occurrence of AOM. Important AOM rates (up to 14 μmol L-1 d-1) were observed and often co-occurred with nitrate consumption peaks, suggesting the occurrence of AOM coupled with nitrate reduction. AOM coupled with sulfate reduction also occurred, since AOM rates tended to be lower when molybdate was added. CH4 oxidation was mostly aerobic (∼80% of total oxidation) in spring and winter, and almost exclusively anaerobic in summer and autumn. Despite important CH4 oxidation rates, the estimated CH4 fluxes from the water surface to the atmosphere were high (mean of 732 μmol m-2 d-1 in spring, summer and autumn, and up to 12,482 μmol m-2 d-1 in winter).
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Affiliation(s)
| | | | - Cédric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), Belgium
| | - Steven Bouillon
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), Belgium
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65
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Vaksmaa A, Jetten MSM, Ettwig KF, Lüke C. McrA primers for the detection and quantification of the anaerobic archaeal methanotroph 'Candidatus Methanoperedens nitroreducens'. Appl Microbiol Biotechnol 2017; 101:1631-1641. [PMID: 28084539 PMCID: PMC5266762 DOI: 10.1007/s00253-016-8065-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
The nitrogen and methane cycles are important biogeochemical processes. Recently, ‘Candidatus Methanoperedens nitroreducens,’ archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of ‘Candidatus M. nitroreducens’ are not yet available. Here, we report the design of two novel mcrA primer combinations that specifically target the alpha sub-unit of the methyl-coenzyme M reductase (mcrA) gene of ‘Candidatus M. nitroreducens’. The first primer pair produces a fragment of 186-bp that can be used to quantify ‘Candidatus M. nitroreducens’ cells, whereas the second primer pair yields an 1191-bp amplicon that is with sufficient length and well suited for more detailed phylogenetic analyses. Six different environmental samples were evaluated with the new qPCR primer pair, and the abundances were compared with those determined using primers for the 16S rRNA gene. The qPCR results indicated that the number of copies of the ‘Candidatus M. nitroreducens’ mcrA gene was highest in rice field soil, with 5.6 ± 0.8 × 106 copies g−1 wet weight, whereas Indonesian river sediment had only 4.6 ± 2.7 × 102 copies g−1 wet weight. In addition to freshwater environments, sequences were also detected in marine sediment of the North Sea, which contained approximately 2.5 ± 0.7 × 104 copies g−1 wet weight. Phylogenetic analysis revealed that the amplified 1191-bp mcrA gene sequences from the different environments all clustered together with available genome sequences of mcrA from known ‘Candidatus M. nitroreducens’ archaea. Taken together, these results demonstrate the validity and utility of the new primers for the quantitative and sensitive detection of the mcrA gene sequences of these important nitrate-dependent AOM archaea. Furthermore, the newly obtained mcrA sequences will contribute to greater phylogenetic resolution of ‘Candidatus M. nitroreducens’ sequences, which have been only poorly captured by general methanogenic mcrA primers.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, The Netherlands
| | - Katharina F Ettwig
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
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66
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Long Y, Guo Q, Li N, Li B, Tong T, Xie S. Spatial change of reservoir nitrite-dependent methane-oxidizing microorganisms. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1247-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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67
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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68
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Oswald K, Jegge C, Tischer J, Berg J, Brand A, Miracle MR, Soria X, Vicente E, Lehmann MF, Zopfi J, Schubert CJ. Methanotrophy under Versatile Conditions in the Water Column of the Ferruginous Meromictic Lake La Cruz (Spain). Front Microbiol 2016; 7:1762. [PMID: 27891115 PMCID: PMC5104750 DOI: 10.3389/fmicb.2016.01762] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/20/2016] [Indexed: 11/13/2022] Open
Abstract
Lakes represent a considerable natural source of methane to the atmosphere compared to their small global surface area. Methanotrophs in sediments and in the water column largely control methane fluxes from these systems, yet the diversity, electron accepting capacity, and nutrient requirements of these microorganisms have only been partially identified. Here, we investigated the role of electron acceptors alternative to oxygen and sulfate in microbial methane oxidation at the oxycline and in anoxic waters of the ferruginous meromictic Lake La Cruz, Spain. Active methane turnover in a zone extending well below the oxycline was evidenced by stable carbon isotope-based rate measurements. We observed a strong methane oxidation potential throughout the anoxic water column, which did not vary substantially from that at the oxic/anoxic interface. Both in the redox-transition and anoxic zones, only aerobic methane-oxidizing bacteria (MOB) were detected by fluorescence in situ hybridization and sequencing techniques, suggesting a close coupling of cryptic photosynthetic oxygen production and aerobic methane turnover. Additions of nitrate, nitrite and to a lesser degree iron and manganese oxides also stimulated bacterial methane consumption. We could not confirm a direct link between the reduction of these compounds and methane oxidation and we cannot exclude the contribution of unknown anaerobic methanotrophs. Nevertheless, our findings from Lake La Cruz support recent laboratory evidence that aerobic methanotrophs may be able to utilize alternative terminal electron acceptors under oxygen limitation.
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Affiliation(s)
- Kirsten Oswald
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of TechnologyZurich, Switzerland
| | - Corinne Jegge
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; School of Architecture, Civil and Environmental Engineering, EPFL, Swiss Federal Institute of TechnologyLausanne, Switzerland
| | - Jana Tischer
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Jasmine Berg
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Andreas Brand
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaum, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of TechnologyZurich, Switzerland
| | - María R Miracle
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Xavier Soria
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Eduardo Vicente
- Department of Microbiology and Ecology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia Burjassot, Spain
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Carsten J Schubert
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum, Switzerland
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69
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Chen J, Dick R, Lin JG, Gu JD. Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments. Appl Microbiol Biotechnol 2016; 100:9845-9860. [DOI: 10.1007/s00253-016-7853-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/11/2016] [Accepted: 09/13/2016] [Indexed: 11/29/2022]
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70
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Long Y, Jiang X, Guo Q, Li B, Xie S. Sediment nitrite-dependent methane-oxidizing microorganisms temporally and spatially shift in the Dongjiang River. Appl Microbiol Biotechnol 2016; 101:401-410. [DOI: 10.1007/s00253-016-7888-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 11/30/2022]
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71
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He Z, Cai C, Wang J, Xu X, Zheng P, Jetten MSM, Hu B. A novel denitrifying methanotroph of the NC10 phylum and its microcolony. Sci Rep 2016; 6:32241. [PMID: 27582299 PMCID: PMC5007514 DOI: 10.1038/srep32241] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/02/2016] [Indexed: 12/03/2022] Open
Abstract
The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.
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Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chaoyang Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xinhua Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
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72
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Vaksmaa A, Lüke C, van Alen T, Valè G, Lupotto E, Jetten MSM, Ettwig KF. Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil. FEMS Microbiol Ecol 2016; 92:fiw181. [PMID: 27562776 DOI: 10.1093/femsec/fiw181] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2016] [Indexed: 12/23/2022] Open
Abstract
In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g-1dw d-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 × 106 to 3.9 × 106 16S rRNA gene copies g-1dw in bulk soil and 0.27 × 106 to 2.8 × 106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy fields. Our data suggest an important role of AAA in methane cycling in paddy fields.
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Affiliation(s)
- A Vaksmaa
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - C Lüke
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - T van Alen
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - G Valè
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - E Lupotto
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - M S M Jetten
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - K F Ettwig
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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73
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Schütte UME, Cadieux SB, Hemmerich C, Pratt LM, White JR. Unanticipated Geochemical and Microbial Community Structure under Seasonal Ice Cover in a Dilute, Dimictic Arctic Lake. Front Microbiol 2016; 7:1035. [PMID: 27458438 PMCID: PMC4932660 DOI: 10.3389/fmicb.2016.01035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/20/2016] [Indexed: 11/13/2022] Open
Abstract
Despite most lakes in the Arctic being perennially or seasonally frozen for at least 40% of the year, little is known about microbial communities and nutrient cycling under ice cover. We assessed the vertical microbial community distribution and geochemical composition in early spring under ice in a seasonally ice-covered lake in southwest Greenland using amplicon-based sequencing that targeted 16S rRNA genes and using a combination of field and laboratory aqueous geochemical methods. Microbial communities changed consistently with changes in geochemistry. Composition of the abundant members responded strongly to redox conditions, shifting downward from a predominantly heterotrophic aerobic community in the suboxic waters to a heterotrophic anaerobic community in the anoxic waters. Operational taxonomic units (OTUs) of Sporichthyaceae, Comamonadaceae, and the SAR11 Clade had higher relative abundances above the oxycline and OTUs within the genus Methylobacter, the phylum Lentisphaerae, and purple sulfur bacteria (PSB) below the oxycline. Notably, a 13-fold increase in sulfide at the oxycline was reflected in an increase and change in community composition of potential sulfur oxidizers. Purple non-sulfur bacteria were present above the oxycline and green sulfur bacteria and PSB coexisted below the oxycline, however, PSB were most abundant. For the first time we show the importance of PSB as potential sulfur oxidizers in an Arctic dimictic lake.
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Affiliation(s)
- Ursel M E Schütte
- Integrated Program in the Environment, Indiana University, BloomingtonIN, USA; Institute of Arctic Biology, University of Alaska Fairbanks, FairbanksAK, USA
| | - Sarah B Cadieux
- Department of Geological Sciences, Indiana University, BloomingtonIN, USA; University of Illinois at Chicago, ChicagoIL, USA
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington IN, USA
| | - Lisa M Pratt
- Department of Geological Sciences, Indiana University, Bloomington IN, USA
| | - Jeffrey R White
- Integrated Program in the Environment, Indiana University, BloomingtonIN, USA; School of Public and Environmental Affairs, Indiana University, BloomingtonIN, USA
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74
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Bartosiewicz M, Laurion I, Clayer F, Maranger R. Heat-Wave Effects on Oxygen, Nutrients, and Phytoplankton Can Alter Global Warming Potential of Gases Emitted from a Small Shallow Lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6267-6275. [PMID: 27266257 DOI: 10.1021/acs.est.5b06312] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Increasing air temperatures may result in stronger lake stratification, potentially altering nutrient and biogenic gas cycling. We assessed the impact of climate forcing by comparing the influence of stratification on oxygen, nutrients, and global-warming potential (GWP) of greenhouse gases (the sum of CH4, CO2, and N2O in CO2 equivalents) emitted from a shallow productive lake during an average versus a heat-wave year. Strong stratification during the heat wave was accompanied by an algal bloom and chemically enhanced carbon uptake. Solar energy trapped at the surface created a colder, isolated hypolimnion, resulting in lower ebullition and overall lower GWP during the hotter-than-average year. Furthermore, the dominant CH4 emission pathway shifted from ebullition to diffusion, with CH4 being produced at surprisingly high rates from sediments (1.2-4.1 mmol m(-2) d(-1)). Accumulated gases trapped in the hypolimnion during the heat wave resulted in a peak efflux to the atmosphere during fall overturn when 70% of total emissions were released, with littoral zones acting as a hot spot. The impact of climate warming on the GWP of shallow lakes is a more complex interplay of phytoplankton dynamics, emission pathways, thermal structure, and chemical conditions, as well as seasonal and spatial variability, than previously reported.
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Affiliation(s)
- Maciej Bartosiewicz
- Centre Eau Terre Environnement, Institut national de la recherche scientifique , 490 de la Couronne, Québec G1K 9A9, Canada
- Groupe de Recherche Interuniversitaire en Limnologie et en environnement aquatique, Université de Montréal , C.P. 6128 Succ. Centre-Ville, Montréal, Québec H2V 2S9, Canada
| | - Isabelle Laurion
- Centre Eau Terre Environnement, Institut national de la recherche scientifique , 490 de la Couronne, Québec G1K 9A9, Canada
- Groupe de Recherche Interuniversitaire en Limnologie et en environnement aquatique, Université de Montréal , C.P. 6128 Succ. Centre-Ville, Montréal, Québec H2V 2S9, Canada
| | - François Clayer
- Centre Eau Terre Environnement, Institut national de la recherche scientifique , 490 de la Couronne, Québec G1K 9A9, Canada
| | - Roxane Maranger
- Groupe de Recherche Interuniversitaire en Limnologie et en environnement aquatique, Université de Montréal , C.P. 6128 Succ. Centre-Ville, Montréal, Québec H2V 2S9, Canada
- Département des Sciences Biologiques, Université de Montréal , C.P. 6128 Succ. Centre-Ville, Montréal H2V 2S9, Canada
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75
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Bornemann M, Bussmann I, Tichy L, Deutzmann J, Schink B, Pester M. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance. FEMS Microbiol Ecol 2016; 92:fiw123. [PMID: 27267930 DOI: 10.1093/femsec/fiw123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/14/2022] Open
Abstract
Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters.
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Affiliation(s)
- Maren Bornemann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Meeresstation Helgoland, Kurpromenade 201, D-27498 Helgoland, Germany
| | - Lucas Tichy
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Jörg Deutzmann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany Department of Civil and Environmental Engineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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76
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Shen LD, Hu BL, Liu S, Chai XP, He ZF, Ren HX, Liu Y, Geng S, Wang W, Tang JL, Wang YM, Lou LP, Xu XY, Zheng P. Anaerobic methane oxidation coupled to nitrite reduction can be a potential methane sink in coastal environments. Appl Microbiol Biotechnol 2016; 100:7171-80. [PMID: 27225473 DOI: 10.1007/s00253-016-7627-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/01/2016] [Accepted: 05/07/2016] [Indexed: 12/14/2022]
Abstract
In the current study, we investigated nitrite-dependent anaerobic methane oxidation (N-DAMO) as a potential methane sink in the Hangzhou Bay and the adjacent Zhoushan sea area. The potential activity of the N-DAMO process was primarily observed in Hangzhou Bay by means of (13)C-labeling experiments, whereas very low or no potential N-DAMO activity could be detected in the Zhoushan sea area. The measured potential N-DAMO rates ranged from 0.2 to 1.3 nmol (13)CO2 g(-1) (dry sediment) day(-1), and the N-DAMO potentially contributed 2.0-9.4 % to the total microbial methane oxidation in the examined sediments. This indicated that the N-DAMO process may be an alternative pathway in the coastal methane cycle. Phylogenetic analyses confirmed the presence of Candidatus Methylomirabilis oxyfera-like bacteria in all the examined sediments, while the group A members (the dominant bacteria responsible for N-DAMO) were found mainly in Hangzhou Bay. Quantitative PCR showed that the 16S rRNA gene abundance of Candidatus M. oxyfera-like bacteria varied from 5.4 × 10(6) to 5.0 × 10(7) copies g(-1) (dry sediment), with a higher abundance observed in Hangzhou Bay. In addition, the overlying water NO3 (-) concentration and salinity were identified as the most important factors influencing the abundance and potential activity of Candidatus M. oxyfera-like bacteria in the examined sediments. This study showed the evidence of N-DAMO in coastal environments and indicated the importance of N-DAMO as a potential methane sink in coastal environments.
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Affiliation(s)
- Li-Dong Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Bao-Lan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Ping Chai
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Zhan-Fei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Xing Ren
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Sha Geng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Wei Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jing-Liang Tang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Yi-Ming Wang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Li-Ping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiang-Yang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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77
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Shen LD, Wu HS, Gao ZQ, Liu X, Li J. Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats. Sci Rep 2016; 6:25647. [PMID: 27157928 PMCID: PMC4860643 DOI: 10.1038/srep25647] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/20/2016] [Indexed: 12/26/2022] Open
Abstract
Methane oxidation coupled to nitrite reduction is mediated by 'Candidatus Methylomirabilis oxyfera' (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4-2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 10(6) and 3.2 × 10(7) copies g(-1) sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.,Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Hong-Sheng Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.,Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhi-Qiu Gao
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Science, Beijing, China.,College of Geophysics and Remote Sensing, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xu Liu
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Ji Li
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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78
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Shen LD, Wu HS, Gao ZQ, Li J, Liu X. Presence of diverse Candidatus Methylomirabilis oxyfera
-like bacteria of NC10 phylum in agricultural soils. J Appl Microbiol 2016; 120:1552-60. [DOI: 10.1111/jam.13119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/02/2016] [Accepted: 02/23/2016] [Indexed: 12/26/2022]
Affiliation(s)
- L.-d. Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - H.-s. Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - Z.-q. Gao
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry; Institute of Atmospheric Physics; Chinese Academy of Science; Beijing China
- College of Geophysics and Remote Sensing; Nanjing University of Information Science and Technology; Nanjing China
| | - J. Li
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - X. Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
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79
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He Z, Wang J, Hu J, Zhang H, Cai C, Shen J, Xu X, Zheng P, Hu B. Improved PCR primers to amplify 16S rRNA genes from NC10 bacteria. Appl Microbiol Biotechnol 2016; 100:5099-108. [PMID: 27020287 DOI: 10.1007/s00253-016-7477-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Anaerobic oxidation of methane (AOM) coupled to nitrite reduction (AOM-NIR) is ecologically significant for mitigating the methane-induced greenhouse effect. The microbes responsible for this reaction, NC10 bacteria, have been widely detected in diverse ecosystems. However, some defects were discovered in the commonly used NC10-specific primers, 202F and qP1F. In the present work, the primers were redesigned and improved to overcome the defects found in the previous primers. A new nested PCR method was developed using the improved primers to amplify 16S ribosomal RNA (rRNA) genes from NC10 bacteria. In the new nested PCR method, the qP1mF/1492R and 1051F/qP2R primer sets were used in the first and second rounds, respectively. The PCR products were sequenced, and more operational taxonomic units (OTUs) of the NC10 phylum were obtained using the new primers compared to the previous primers. The sensitivity of the new nested PCR was tested by the serial dilution method, and the limit of detection was approximately 10(3) copies g(-1) dry sed. for the environmental samples compared to approximately 10(5) copies g(-1) dry sed. by the previous method. Finally, the improved primer, qP1mF, was used in quantitative PCR (qPCR) to determine the abundance of NC10 bacteria, and the results agreed well with the activity of AOM-NIR measured by isotope tracer experiments. The improved primers are able to amplify NC10 16S rRNA genes more efficiently than the previous primers and useful to explore the microbial community of the NC10 phylum in different systems.
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Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Chaoyang Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiaxian Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xinhua Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
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80
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Turner TE, Billett MF, Baird AJ, Chapman PJ, Dinsmore KJ, Holden J. Regional variation in the biogeochemical and physical characteristics of natural peatland pools. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 545-546:84-94. [PMID: 26745296 DOI: 10.1016/j.scitotenv.2015.12.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/30/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Natural open-water pools are a common feature of northern peatlands and are known to be an important source of atmospheric methane (CH4). Pool environmental variables, particularly water chemistry, vegetation community and physical characteristics, have the potential to exert strong controls on carbon cycling in pools. A total of 66 peatland pools were studied across three regions of the UK (northern Scotland, south-west Scotland, and Northern Ireland). We found that within-region variability of pool water chemistry was low; however, for many pool variables measured there were significant differences between regions. PCA analysis showed that pools in SW Scotland were strongly associated with greater vegetative cover and shallower water depth which is likely to increase dissolved organic carbon (DOC) mineralisation rates, whereas pools in N Scotland were more open and deeper. Pool water DOC, particulate organic carbon and dissolved CH4 concentrations were significantly different between regions. Pools in Northern Ireland had the highest concentrations of DOC (mean=14.5 mg L(-1)) and CH4 (mean=20.6 μg C L(-1)). Chloride and sulphate concentrations were significantly higher in the pools in N Scotland (mean values 26.3 and 2.40 mg L(-1), respectively) than elsewhere, due to a stronger marine influence. The ratio of UV absorbance at 465 nm to absorbance at 665 nm for pools in Northern Ireland indicated that DOC was sourced from poorly humified peat, potentially increasing the bioavailability and mineralisation of organic carbon in pools compared to the pools elsewhere. This study, which specifically aims to address a lack of basic biogeochemical knowledge about pool water chemistry, clearly shows that peatland pools are highly regionally variable. This is likely to be a reflection of significant regional-scale differences in peatland C cycling.
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Affiliation(s)
- T Edward Turner
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK.
| | - Michael F Billett
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, UK
| | - Andy J Baird
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK
| | - Pippa J Chapman
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK
| | | | - Joseph Holden
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK
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81
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Wang S, Wu Q, Lei T, Liang P, Huang X. Enrichment of denitrifying methanotrophic bacteria from Taihu sediments by a membrane biofilm bioreactor at ambient temperature. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5627-5634. [PMID: 26578374 DOI: 10.1007/s11356-015-5509-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/27/2015] [Indexed: 06/05/2023]
Abstract
Denitrification coupled to anaerobic methane oxidation is a recently discovered process performed by bacteria affiliated to the NC10 phylum. These microorganisms could play important roles in the energy-efficient way of anaerobic wastewater treatment where residual dissolved methane might be removed at the expense of nitrate or nitrite. The difficulty to enrich these microorganisms due to a slow growth rate, especially at low temperatures, limited its application in engineering field. In this study, an NC10 bacteria community was enriched from Taihu sediments by a membrane biofilm bioreactor at ambient temperature of 10-25 °C. After 13 months enrichment, the maximum denitrification rate of the enriched culture reached 0.54 mM day(-1) for nitrate and 1.06 mM day(-1) for nitrite. Anaerobic methane oxidation coupled denitrification was estimated from the (13)C-labeled CO2 ((13)CO2) production during batch incubations with (13)CH4. Furthermore, analysis of 16S rRNA genes clone library confirmed the presence of NC10 phylum bacteria and fluorescence in situ hybridization showed that NC10 bacteria dominated the reactor. All of the results indicated the NC10 bacteria community was competitive in terms of treating nitrate-contaminated water or wastewater under natural conditions.
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Affiliation(s)
- Shenghui Wang
- College of Life Science, Liaocheng University, Liaocheng, 252059, People's Republic of China
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Qing Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Ting Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China.
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82
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Fu L, Li SW, Ding ZW, Ding J, Lu YZ, Zeng RJ. Iron reduction in the DAMO/Shewanella oneidensis MR-1 coculture system and the fate of Fe(II). WATER RESEARCH 2016; 88:808-815. [PMID: 26599434 DOI: 10.1016/j.watres.2015.11.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/11/2015] [Accepted: 11/05/2015] [Indexed: 06/05/2023]
Abstract
Dissimilatory iron reduction and anaerobic methane oxidation processes play important roles in the global iron and carbon cycle, respectively. This study explored the ferrihydrite reduction process with methane as a carbon source in a coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes enriched in laboratory and Shewanella oneidensis MR-1, and then characterized the reduced products. Ferrihydrite reduction was also studied in the DAMO and Shewanella systems alone. The ferrihydrite was reduced slightly (<13.3%) in the separate systems, but greatly (42.0-88.3%) in the coculture system. Isotope experiment of (13)CH4 addition revealed that DAMO microbes coupled to S. oneidensis MR-1 in a ferric iron reduction process with (13)CH4 consumption and (13)CO2 production. Compared with ferrihydrite, the reduced products showed increased crystallinity (from amorphous state to crystallinity 77.1%) and magnetism (from paramagnetic to ferromagnetic). The produced ferrous iron was formed into minerals primarily composed of siderite with a small amount vivianite and magnetite. A portion of products covered the cell surface and hindered further reactions. The results presented herein widen the current understanding of iron metabolism and mineralization in the ocean, and show that the coculture systems of DAMO microbes and Shewanella have the potential to be globally important to iron reduction and methane oxidation.
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Affiliation(s)
- Liang Fu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Shan-Wei Li
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Zhao-Wei Ding
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Jing Ding
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China; Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, 215213, China
| | - Yong-Ze Lu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Raymond J Zeng
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China; Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, 215213, China.
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83
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Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source. ISME JOURNAL 2015; 10:1400-12. [PMID: 26636551 PMCID: PMC5029187 DOI: 10.1038/ismej.2015.213] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 12/18/2022]
Abstract
The occurrence of anaerobic oxidation of methane (AOM) and trace methane oxidation (TMO) was investigated in a freshwater natural gas source. Sediment samples were taken and analyzed for potential electron acceptors coupled to AOM. Long-term incubations with 13C-labeled CH4 (13CH4) and different electron acceptors showed that both AOM and TMO occurred. In most conditions, 13C-labeled CO2 (13CO2) simultaneously increased with methane formation, which is typical for TMO. In the presence of nitrate, neither methane formation nor methane oxidation occurred. Net AOM was measured only with sulfate as electron acceptor. Here, sulfide production occurred simultaneously with 13CO2 production and no methanogenesis occurred, excluding TMO as a possible source for 13CO2 production from 13CH4. Archaeal 16S rRNA gene analysis showed the highest presence of ANME-2a/b (ANaerobic MEthane oxidizing archaea) and AAA (AOM Associated Archaea) sequences in the incubations with methane and sulfate as compared with only methane addition. Higher abundance of ANME-2a/b in incubations with methane and sulfate as compared with only sulfate addition was shown by qPCR analysis. Bacterial 16S rRNA gene analysis showed the presence of sulfate-reducing bacteria belonging to SEEP-SRB1. This is the first report that explicitly shows that AOM is associated with sulfate reduction in an enrichment culture of ANME-2a/b and AAA methanotrophs and SEEP-SRB1 sulfate reducers from a low-saline environment.
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84
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Frindte K, Allgaier M, Grossart HP, Eckert W. Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface. PLoS One 2015; 10:e0143428. [PMID: 26599000 PMCID: PMC4657962 DOI: 10.1371/journal.pone.0143428] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/04/2015] [Indexed: 11/29/2022] Open
Abstract
The sediment–water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment–water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment–water interface.
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Affiliation(s)
- Katharina Frindte
- Department of Soil Science, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, Nußallee 13, Bonn, Germany
| | - Martin Allgaier
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, Potsdam, Germany
| | - Werner Eckert
- Israel Oceanographic and Limnological Research, The Yigal Allon Kinneret Limnological Laboratory, Migdal, Israel
- * E-mail:
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85
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Yan P, Li M, Wei G, Li H, Gao Z. Molecular Fingerprint and Dominant Environmental Factors of Nitrite-Dependent Anaerobic Methane-Oxidizing Bacteria in Sediments from the Yellow River Estuary, China. PLoS One 2015; 10:e0137996. [PMID: 26368535 PMCID: PMC4569144 DOI: 10.1371/journal.pone.0137996] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/25/2015] [Indexed: 11/18/2022] Open
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) is performed by “Candidatus Methylomirabilis oxyfera” (M. oxyfera), which connects the carbon and nitrogen global nutrient cycles. In the present study, M. oxyfera-like bacteria sequences were successfully recovered from Yellow River Estuary sediments using specific primers for 16S rRNA and pmoA genes. A M. oxyfera-like sequences analysis based on the 16S rRNA gene revealed greater diversity compared with the pmoA gene; the 16S rRNA gene sequences retrieved from the Yellow River Estuary sediments belong to groups A as well as B and were mainly found in freshwater habitats. Quantitative PCR showed that 16S rRNA gene abundance varied from 9.28±0.11×103 to 2.10±0.13×105 copies g-1 (dry weight), and the pmoA gene abundance ranged from 8.63±0.50×103 to 1.83±0.18×105 copies g-1 (dry weight). A correlation analysis showed that the total organic carbon (TOC) and ammonium (NH4+) as well as the ratio of total phosphorus to total nitrogen (TP/TN) influenced the M. oxyfera-like bacteria distribution in the Yellow River Estuary sediments. These findings will aid in understanding the n-damo bacterial distribution pattern as well as their correlation with surrounding environmental factors in temperate estuarine ecosystems.
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Affiliation(s)
- Pengze Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Guangshan Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
- * E-mail: (ZG); (HL)
| | - Zheng Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
- * E-mail: (ZG); (HL)
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86
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Oswald K, Milucka J, Brand A, Littmann S, Wehrli B, Kuypers MMM, Schubert CJ. Light-Dependent Aerobic Methane Oxidation Reduces Methane Emissions from Seasonally Stratified Lakes. PLoS One 2015; 10:e0132574. [PMID: 26193458 PMCID: PMC4508055 DOI: 10.1371/journal.pone.0132574] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/17/2015] [Indexed: 11/18/2022] Open
Abstract
Lakes are a natural source of methane to the atmosphere and contribute significantly to total emissions compared to the oceans. Controls on methane emissions from lake surfaces, particularly biotic processes within anoxic hypolimnia, are only partially understood. Here we investigated biological methane oxidation in the water column of the seasonally stratified Lake Rotsee. A zone of methane oxidation extending from the oxic/anoxic interface into anoxic waters was identified by chemical profiling of oxygen, methane and δ13C of methane. Incubation experiments with 13C-methane yielded highest oxidation rates within the oxycline, and comparable rates were measured in anoxic waters. Despite predominantly anoxic conditions within the zone of methane oxidation, known groups of anaerobic methanotrophic archaea were conspicuously absent. Instead, aerobic gammaproteobacterial methanotrophs were identified as the active methane oxidizers. In addition, continuous oxidation and maximum rates always occurred under light conditions. These findings, along with the detection of chlorophyll a, suggest that aerobic methane oxidation is tightly coupled to light-dependent photosynthetic oxygen production both at the oxycline and in the anoxic bottom layer. It is likely that this interaction between oxygenic phototrophs and aerobic methanotrophs represents a widespread mechanism by which methane is oxidized in lake water, thus diminishing its release into the atmosphere.
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Affiliation(s)
- Kirsten Oswald
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- * E-mail:
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Brand
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard Wehrli
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Marcel M. M. Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carsten J. Schubert
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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87
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Segarra KEA, Schubotz F, Samarkin V, Yoshinaga MY, Hinrichs KU, Joye SB. High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions. Nat Commun 2015; 6:7477. [DOI: 10.1038/ncomms8477] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 05/08/2015] [Indexed: 11/09/2022] Open
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88
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Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria. Appl Environ Microbiol 2015; 81:5538-45. [PMID: 26048927 DOI: 10.1128/aem.00984-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
Anaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA and pmoA gene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescence in situ hybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite.
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89
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Hanson BT, Madsen EL. In situ expression of nitrite-dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:252-264. [PMID: 25403415 DOI: 10.1111/1758-2229.12239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 06/04/2023]
Abstract
Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar-contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS-PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragment analysis using nano-liquid chromatography (LC)-mass spectrometry (MS)/MS of the three protein pools generated a total of 95,725 mass spectra. When analyzed using mascot v.2.3.02 and searched against the NCBInr bacterial database [confidence interval 99% (P < 0.01)], a total of 1,270 proteins had at least two peptide matches. Replication of identified proteins across the three libraries was low (3.3%); however, in each library, the most frequently identified protein host was Candidatus Methylomirabilis oxyfera (15, 12 and 62 proteins for each shotgun and the gel-slice library respectively). Remarkably, eight of the nine proteins in the nitrite-dependent anaerobic methane oxidation pathway were found. Additionally, 39 proteins were matched to known anammox bacteria including hydroxylamine and hydrazine oxidase. Metaproteomics thus revealed a microbial population, closely related to Ca. Methylomirabilis oxyfera, actively engaged in nitrite-dependent anaerobic methane oxidation and likely competing for nitrite with anammox bacteria.
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Affiliation(s)
- Buck T Hanson
- Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY, 14853, USA
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90
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Zhu G, Zhou L, Wang Y, Wang S, Guo J, Long XE, Sun X, Jiang B, Hou Q, Jetten MSM, Yin C. Biogeographical distribution of denitrifying anaerobic methane oxidizing bacteria in Chinese wetland ecosystems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:128-38. [PMID: 25223900 DOI: 10.1111/1758-2229.12214] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 08/31/2014] [Accepted: 09/04/2014] [Indexed: 05/26/2023]
Abstract
The discovery of denitrifying anaerobic methane oxidation with nitrite as electron acceptor mediated by 'Candidatus Methylomirabilis oxyfera' connected the biogeochemical carbon and nitrogen cycle in a new way. However, it is important to have a comprehensive understanding about the distribution of M. oxyfera-like bacteria in the terrestrial realm, especially the wetland ecosystems that are known as the largest natural source of atmospheric methane. Here, our molecular evidence demonstrated that a wide geographical distribution of M. oxyfera-like bacteria at oxic/anoxic interfaces of various wetlands (n = 91) over the Chinese territory. Intriguingly, the M. oxyfera-like bacteria were detected in some extreme environments, indicating that M. oxyfera-like bacteria occupied a wide range of habitats. Quantitative polymerase chain reaction estimated that the abundance of M. oxyfera-like bacteria ranged from 2.2 × 10(3) to 2.3 × 10(7) copies g(-1) dry soil, and up to around 0.62% of the total number of bacteria. Moreover, the M. oxyfera-like bacteria showed high biodiversity in wetland ecosystems based on the analysis of 462 pmoA and 287 16S rRNA gene sequences. The current study revealed the widespread distribution and biogeography of M. oxyfera-like bacteria in the terrestrial system.
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Affiliation(s)
- Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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91
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Cui M, Ma A, Qi H, Zhuang X, Zhuang G. Anaerobic oxidation of methane: an "active" microbial process. Microbiologyopen 2015; 4:1-11. [PMID: 25530008 PMCID: PMC4335971 DOI: 10.1002/mbo3.232] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/14/2014] [Accepted: 11/24/2014] [Indexed: 12/01/2022] Open
Abstract
The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. AOM was first found to be coupled with sulfate reduction and mediated by anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). ANME, often forming consortia with SRB, are phylogenetically related to methanogenic archaea. ANME-1 is even able to produce methane. Subsequently, it has been found that AOM can also be coupled with denitrification. The known microbes responsible for this process are Candidatus Methylomirabilis oxyfera (M. oxyfera) and Candidatus Methanoperedens nitroreducens (M. nitroreducens). Candidatus Methylomirabilis oxyfera belongs to the NC10 bacteria, can catalyze nitrite reduction through an "intra-aerobic" pathway, and may catalyze AOM through an aerobic methane oxidation pathway. However, M. nitroreducens, which is affiliated with ANME-2d archaea, may be able to catalyze AOM through the reverse methanogenesis pathway. Moreover, manganese (Mn(4+) ) and iron (Fe(3+) ) can also be used as electron acceptors of AOM. This review summarizes the mechanisms and associated microbes of AOM. It also discusses recent progress in some unclear key issues about AOM, including ANME-1 in hypersaline environments, the effect of oxygen on M. oxyfera, and the relationship of M. nitroreducens with ANME.
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Affiliation(s)
- Mengmeng Cui
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Anzhou Ma
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Hongyan Qi
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, 100085, China
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92
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Lofton DD, Whalen SC, Hershey AE. Vertical sediment distribution of methanogenic pathways in two shallow Arctic Alaskan lakes. Polar Biol 2015. [DOI: 10.1007/s00300-014-1641-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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93
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Vertical Profiles of Community Abundance and Diversity of Anaerobic Methanotrophic Archaea (ANME) and Bacteria in a Simple Waste Landfill in North China. Appl Biochem Biotechnol 2015; 175:2729-40. [DOI: 10.1007/s12010-014-1456-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
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94
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He Z, Geng S, Shen L, Lou L, Zheng P, Xu X, Hu B. The short- and long-term effects of environmental conditions on anaerobic methane oxidation coupled to nitrite reduction. WATER RESEARCH 2015; 68:554-562. [PMID: 25462761 DOI: 10.1016/j.watres.2014.09.055] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/24/2014] [Accepted: 09/28/2014] [Indexed: 06/04/2023]
Abstract
Anaerobic oxidation of methane coupled to nitrite reduction (n-damo) plays an important role in global carbon and nitrogen cycles and also is a potential bioprocess in wastewater treatment. In this work, the effects of environmental conditions – temperature, pH and salinity – on the metabolic activity and growth rate of n-damo bacteria were investigated by short-term batch test and long-term bacterial incubation. Quantitative PCR and 16S rRNA and pmoA gene sequencing were applied to detect the microbial community in the long-term incubation. The results indicated that all the three environmental factors significantly affected the metabolic activity and growth rate of n-damo bacteria and the optimum temperature, pH and salinity were 35 °C, 7.6 and 0 g NaCl L⁻¹, respectively. Notably, salinity adaption of n-damo bacteria was first observed under salinity stress of 20 g NaCl L⁻¹. It's predicted that n-damo process might occur in saline environments and future work could focus on this.
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Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
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95
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Shen LD, He ZF, Wu HS, Gao ZQ. Nitrite-Dependent Anaerobic Methane-Oxidising Bacteria: Unique Microorganisms with Special Properties. Curr Microbiol 2014; 70:562-70. [DOI: 10.1007/s00284-014-0762-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
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96
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Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake. Proc Natl Acad Sci U S A 2014; 111:18273-8. [PMID: 25472842 DOI: 10.1073/pnas.1411617111] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anaerobic methane oxidation coupled to denitrification, also known as "nitrate/nitrite-dependent anaerobic methane oxidation" (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660-4,890 µmol CH4⋅m(-2)⋅d(-1)) and actual rates calculated from microsensor profiles (31-437 µmol CH4⋅m(-2)⋅d(-1)) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones.
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97
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Shen LD, Wu HS, Gao ZQ. Distribution and environmental significance of nitrite-dependent anaerobic methane-oxidising bacteria in natural ecosystems. Appl Microbiol Biotechnol 2014; 99:133-42. [DOI: 10.1007/s00253-014-6200-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022]
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98
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Aerobic and nitrite-dependent methane-oxidizing microorganisms in sediments of freshwater lakes on the Yunnan Plateau. Appl Microbiol Biotechnol 2014; 99:2371-81. [PMID: 25698510 DOI: 10.1007/s00253-014-6141-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/24/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) bacteria can play an important role in mitigating the methane emission produced in anoxic sediment layers to the atmosphere. However, the environmental factors regulating the distribution of these methane-oxidizing microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the distribution of aerobic MOB and n-damo bacteria in sediments of various freshwater lakes on the Yunnan Plateau (China). Quantitative PCR assay and clone library analysis illustrated the spatial variations in the abundances and structures of aerobic MOB and n-damo bacterial communities. Type I MOB (Methylosoma and Methylobacter) and type II MOB (Methylocystis) were detected, while type I MOB was more abundant than type II MOB. Lake sediments n-damo bacterial communities were composed of novel Methylomirabilis oxyfera-like pmoA genes. Lake sediments in the same geographic region could share a relatively similar aerobic MOB community structure. Moreover, Pearson's correlation analysis indicated that n-damo pmoA gene diversity showed a positive correlation with the ratio of organic matter to total nitrogen in lake sediment.
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99
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Biological conversion of methane to liquid fuels: status and opportunities. Biotechnol Adv 2014; 32:1460-75. [PMID: 25281583 DOI: 10.1016/j.biotechadv.2014.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
Methane is the main component of natural gas and biogas. As an abundant energy source, methane is crucial not only to meet current energy needs but also to achieve a sustainable energy future. Conversion of methane to liquid fuels provides energy-dense products and therefore reduces costs for storage, transportation, and distribution. Compared to thermochemical processes, biological conversion has advantages such as high conversion efficiency and using environmentally friendly processes. This paper is a comprehensive review of studies on three promising groups of microorganisms (methanotrophs, ammonia-oxidizing bacteria, and acetogens) that hold potential in converting methane to liquid fuels; their habitats, biochemical conversion mechanisms, performance in liquid fuels production, and genetic modification to enhance the conversion are also discussed. To date, methane-to-methanol conversion efficiencies (moles of methanol produced per mole methane consumed) of up to 80% have been reported. A number of issues that impede scale-up of this technology, such as mass transfer limitations of methane, inhibitory effects of H2S in biogas, usage of expensive chemicals as electron donors, and lack of native strains capable of converting methane to liquid fuels other than methanol, are discussed. Future perspectives and strategies in addressing these challenges are also discussed.
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100
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Evidence for the cooccurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field. Appl Environ Microbiol 2014; 80:7611-9. [PMID: 25261523 DOI: 10.1128/aem.02379-14] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two of the most recent discoveries in the microbial nitrogen cycle. In the present study, we provide direct evidence for the cooccurrence of the anammox and n-damo processes in a flooded paddy field in southeastern China. Stable isotope experiments showed that the potential anammox rates ranged from 5.6 to 22.7 nmol N2 g(-1) (dry weight) day(-1) and the potential n-damo rates varied from 0.2 to 2.1 nmol CO2 g(-1) (dry weight) day(-1) in different layers of soil cores. Quantitative PCR showed that the abundance of anammox bacteria ranged from 1.0 × 10(5) to 2.0 × 10(6) copies g(-1) (dry weight) in different layers of soil cores and the abundance of n-damo bacteria varied from 3.8 × 10(5) to 6.1 × 10(6) copies g(-1) (dry weight). Phylogenetic analyses of the recovered 16S rRNA gene sequences showed that anammox bacteria affiliated with "Candidatus Brocadia" and "Candidatus Kuenenia" and n-damo bacteria related to "Candidatus Methylomirabilis oxyfera" were present in the soil cores. It is estimated that a total loss of 50.7 g N m(-2) per year could be linked to the anammox process, which is at intermediate levels for the nitrogen flux ranges of aerobic ammonium oxidation and denitrification reported in wetland soils. In addition, it is estimated that a total of 0.14 g CH4 m(-2) per year could be oxidized via the n-damo process, while this rate is at the lower end of the aerobic methane oxidation rates reported in wetland soils.
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