251
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Conrad R. The global methane cycle: recent advances in understanding the microbial processes involved. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:285-292. [PMID: 23765881 DOI: 10.1111/j.1758-2229.2009.00038.x] [Citation(s) in RCA: 409] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The global budget of atmospheric CH4 , which is on the order of 500-600 Tg CH4 per year, is mainly the result of environmental microbial processes, such as archaeal methanogenesis in wetlands, rice fields, ruminant and termite digestive systems and of microbial methane oxidation under anoxic and oxic conditions. This review highlights recent progress in the research of anaerobic CH4 oxidation, of CH4 production in the plant rhizosphere, of CH4 serving as substrate for the aquatic trophic food chain and the discovery of novel aerobic methanotrophs. It also emphasizes progress and deficiencies in our knowledge of microbial utilization of low atmospheric CH4 concentrations in soil, CH4 production in the plant canopy, intestinal methanogenesis and CH4 production in pelagic water.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.8, 35043 Marburg, Germany
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252
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Kalyuhznaya MG, Martens-Habbena W, Wang T, Hackett M, Stolyar SM, Stahl DA, Lidstrom ME, Chistoserdova L. Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:385-392. [PMID: 23765891 DOI: 10.1111/j.1758-2229.2009.00046.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work we assessed the potential for the denitrification linked to methanol consumption in a microbial community inhabiting the top layer of the sediment of a pristine lake, Lake Washington in Seattle. Stable isotope probing with (13) C methanol was implemented in near in situ conditions and also in the presence of added nitrate. This revealed that the bacterial population involved in methanol uptake was dominated by species belonging to the Methylophilaceae, most prominently species belonging to the genus Methylotenera. Based on relative abundance of specific phylotypes in DNA clone libraries generated from (13) C labelled DNA, some of these species appear not to require nitrate to assimilate methanol while others assimilate methanol in a nitrate-dependent fashion. A pure culture of Methylotenera mobilis strain JLW8 previously isolated from the same study site was investigated for denitrification capability. This culture was demonstrated to be able to grow on methanol when nitrate was present, in aerobic conditions, while in media supplemented with ammonium it did not grow on methanol. The denitrifying capability of this strain was further demonstrated in defined laboratory conditions, by measuring accumulation of N2 O. This study provides new insights into the potential involvement of Methylophilaceae in global nitrogen cycling in natural environments and highlights the connection between global carbon and nitrogen cycles.
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Affiliation(s)
- Marina G Kalyuhznaya
- Departments of Microbiology, Civil and Environmental Engineering and Chemical Engineering, University of Washington, Seattle, WA 98195, USA
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253
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Vecherskaya M, Dijkema C, Saad HR, Stams AJM. Microaerobic and anaerobic metabolism of a Methylocystis parvus strain isolated from a denitrifying bioreactor. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:442-449. [PMID: 23765898 DOI: 10.1111/j.1758-2229.2009.00069.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
An obligate methanotrophic bacterium, strain MTS, was isolated from a methane-fed microaerobic denitrifying bioreactor. 16S rRNA and DNA-DNA hybridization analysis revealed that this organism was most closely related to Methylocystis parvus, a Type II methanotroph, belonging to the α-subclass of the Proteobacteria. The metabolism of the bacterium under microaerobic and anaerobic conditions was studied by (13) C-NMR. (13) C-labelled poly-β-hydroxybutyrate (PHB) formation occurred in cell suspensions incubated with (13) C-labelled methane at low (5-10%) oxygen concentration. Under these conditions low levels of succinate, acetate and 2,3-butanediol were formed and excreted into the culture medium. Intracellular PHB degradation was observed in intact cells under anaerobic conditions in the absence of an exogenous carbon source during a long-term incubation of 90 days. Multiple (13) C-labelled β-hydroxybutyrate, butyrate, acetate, acetone, isopropanol, 2,3-butanediol and succinate were identified as products in in vivo(13) C-NMR spectra and in the spectra of culture medium during the dynamic PHB degradation. The isolated obligate methanotroph clearly shows a fermentative metabolism of PHB under anaerobic conditions. The excreted products may serve as substrates for denitrifying bacteria.
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Affiliation(s)
- Margarita Vecherskaya
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands. Laboratory of Biophysics, Wageningen University, Dreijenplein 3, 6703 HA, Wageningen, the Netherlands. Department of Biological Systems, Universidad Autónoma Metropolitana, 06960 Mexico City, Mexico
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254
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Hu S, Zeng RJ, Burow LC, Lant P, Keller J, Yuan Z. Enrichment of denitrifying anaerobic methane oxidizing microorganisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:377-384. [PMID: 23765890 DOI: 10.1111/j.1758-2229.2009.00083.x] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The microorganisms responsible for anaerobic oxidation of methane (AOM) coupled to denitrification have not been clearly elucidated. Three recent publications suggested it can be achieved by a denitrifying bacterium with or without the involvement of anaerobic methanotrophic archaea. A key factor limiting the progress in this research field is the shortage of enrichment cultures performing denitrifying anaerobic methane oxidation (DAMO). In this study, DAMO cultures were enriched from mixed inoculum including sediment from a freshwater lake, anaerobic digester sludge and return activated sludge from a sewage treatment plant. Two reactors, operated at 35°C and at 22°C, respectively, showed simultaneous methane oxidation and nitrate reduction after several months of operation. Analysis of 16S rRNA gene clone libraries from the 35°C enrichment showed the presence of an archaeon closely related to other DAMO archaea and a dominated bacterium belonging to the yet uncultivated NC10 phylum. This culture preferred nitrite to nitrate as the electron acceptor. The present study suggests that the archaea are rather methanotrophs than methanogens. The highest denitrification rate achieved was 2.35 mmol NO3 (-) -N gVSS(-1) day(-1) . The culture enriched at 22°C contained the same NC10 bacterium observed in the culture enriched at 35°C but no archaea.
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Affiliation(s)
- Shihu Hu
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld 4072, Australia
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255
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Molecular characterization of potential nitrogen fixation by anaerobic methane-oxidizing archaea in the methane seep sediments at the number 8 Kumano Knoll in the Kumano Basin, offshore of Japan. Appl Environ Microbiol 2009; 75:7153-62. [PMID: 19783748 DOI: 10.1128/aem.01184-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential for microbial nitrogen fixation in the anoxic methane seep sediments in a mud volcano, the number 8 Kumano Knoll, was characterized by molecular phylogenetic analyses. A total of 111 of the nifH (a gene coding a nitrogen fixation enzyme, Fe protein) clones were obtained from different depths of the core sediments, and the phylogenetic analysis of the clones indicated the genetic diversity of nifH genes. The predominant group detected (methane seep group 2), representing 74% of clonal abundance, was phylogenetically related to the nifH sequences obtained from the Methanosarcina species but was most closely related to the nifH sequences potentially derived from the anoxic methanotrophic archaea (ANME-2 archaea). The recovery of the nif gene clusters including the nifH sequences of the methane seep group 2 and the subsequent reverse transcription-PCR detection of the nifD and nifH genes strongly suggested that the genetic components of the gene clusters would be operative for the in situ assimilation of molecular nitrogen (N(2)) by the host microorganisms. DNA-based quantitative PCR of the archaeal 16S rRNA gene, the group-specific mcrA (a gene encoding the methyl-coenzyme M reductase alpha subunit) gene, and the nifD and nifH genes demonstrated the similar distribution patterns of the archaeal 16S rRNA gene, the mcrA groups c-d and e, and the nifD and nifH genes through the core sediments. These results supported the idea that the anoxic methanotrophic archaea ANME-2c could be the microorganisms hosting the nif gene clusters and could play an important role in not only the in situ carbon (methane) cycle but also the nitrogen cycle in subseafloor sediments.
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256
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Zaikova E, Walsh DA, Stilwell CP, Mohn WW, Tortell PD, Hallam SJ. Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ Microbiol 2009; 12:172-91. [PMID: 19788414 DOI: 10.1111/j.1462-2920.2009.02058.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Dissolved oxygen concentration plays a major role in shaping biotic interactions and nutrient flows within marine ecosystems. Throughout the global ocean, regions of low dissolved oxygen concentration (hypoxia) are a common and expanding feature of the water column, with major feedback on productivity and greenhouse gas cycling. To better understand microbial diversity underlying biogeochemical transformations within oxygen-deficient oceanic waters, we monitored and quantified bacterial and archaeal community dynamics in relation to dissolved gases and nutrients during a seasonal stratification and deep water renewal cycle in Saanich Inlet, British Columbia, a seasonally anoxic fjord. A number of microbial groups partitioned within oxygen-deficient waters including Nitrospina and SAR324 affiliated with the delta-proteobacteria, SAR406 and gamma-proteobacteria related to thiotrophic gill symbionts of deep-sea clams and mussels. Microbial diversity was highest within the hypoxic transition zone decreasing dramatically within anoxic basin waters and temporal patterns of niche partitioning were observed along defined gradients of oxygen and phosphate. These results provide a robust comparative phylogenetic framework for inferring systems metabolism of nitrogen, carbon and sulfur cycling within oxygen-deficient oceanic waters and establish Saanich Inlet as a tractable model for studying the response of microbial communities to changing levels of water column hypoxia.
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Affiliation(s)
- Elena Zaikova
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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257
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Jagersma GC, Meulepas RJW, Heikamp-de Jong I, Gieteling J, Klimiuk A, Schouten S, Damsté JSS, Lens PNL, Stams AJM. Microbial diversity and community structure of a highly active anaerobic methane-oxidizing sulfate-reducing enrichment. Environ Microbiol 2009; 11:3223-32. [PMID: 19703218 DOI: 10.1111/j.1462-2920.2009.02036.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Anaerobic oxidation of methane (AOM) is an important methane sink in the ocean but the microbes responsible for AOM are as yet resilient to cultivation. Here we describe the microbial analysis of an enrichment obtained in a novel submerged-membrane bioreactor system and capable of high-rate AOM (286 mumol g(dry weight)(-1) day(-1)) coupled to sulfate reduction. By constructing a clone library with subsequent sequencing and fluorescent in situ hybridization, we showed that the responsible methanotrophs belong to the ANME-2a subgroup of anaerobic methanotrophic archaea, and that sulfate reduction is most likely performed by sulfate-reducing bacteria commonly found in association with other ANME-related archaea in marine sediments. Another relevant portion of the bacterial sequences can be clustered within the order of Flavobacteriales but their role remains to be elucidated. Fluorescent in situ hybridization analyses showed that the ANME-2a cells occur as single cells without close contact to the bacterial syntrophic partner. Incubation with (13)C-labelled methane showed substantial incorporation of (13)C label in the bacterial C(16) fatty acids (bacterial; 20%, 44% and 49%) and in archaeal lipids, archaeol and hydroxyl-archaeol (21% and 20% respectively). The obtained data confirm that both archaea and bacteria are responsible for the anaerobic methane oxidation in a bioreactor enrichment inoculated with Eckernförde bay sediment.
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Affiliation(s)
- G Christian Jagersma
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
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258
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Stams AJM, Plugge CM. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 2009; 7:568-77. [PMID: 19609258 DOI: 10.1038/nrmicro2166] [Citation(s) in RCA: 701] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.
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Affiliation(s)
- Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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259
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Nitrogen removal by co-occurring methane oxidation, denitrification, aerobic ammonium oxidation, and anammox. Appl Microbiol Biotechnol 2009; 84:977-85. [DOI: 10.1007/s00253-009-2112-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 06/06/2009] [Accepted: 06/24/2009] [Indexed: 11/30/2022]
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260
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Affiliation(s)
- Emily J Beal
- Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA.
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261
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Dutilh BE, Huynen MA, Strous M. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. ACTA ACUST UNITED AC 2009; 25:2878-81. [PMID: 19542148 PMCID: PMC2781756 DOI: 10.1093/bioinformatics/btp377] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Motivation: Most microbial species can not be cultured in the laboratory. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold. Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population. Contact:dutilh@cmbi.ru.nl Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bas E Dutilh
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands, Germany.
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262
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Jetten MSM, Niftrik LV, Strous M, Kartal B, Keltjens JT, Op den Camp HJM. Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 2009; 44:65-84. [DOI: 10.1080/10409230902722783] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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263
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Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum. Appl Environ Microbiol 2009; 75:3656-62. [PMID: 19329658 DOI: 10.1128/aem.00067-09] [Citation(s) in RCA: 330] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic methane oxidation coupled to denitrification was recently assigned to bacteria belonging to the uncultured phylum NC10. In this study, we incubated sediment from a eutrophic ditch harboring a diverse community of NC10 bacteria in a bioreactor with a constant supply of methane and nitrite. After 6 months, fluorescence in situ hybridization showed that NC10 bacteria dominated the resulting population. The enrichment culture oxidized methane and reduced nitrite to dinitrogen gas. We assessed NC10 phylum diversity in the inoculum and the enrichment culture, compiled the sequences currently available for this bacterial phylum, and showed that of the initial diversity, only members of one subgroup had been enriched. The growth of this subgroup was monitored by quantitative PCR and correlated to nitrite-reducing activity and the total biomass of the culture. Together, the results indicate that the enriched subgroup of NC10 bacteria is responsible for anaerobic methane oxidation coupled to nitrite reduction. Due to methodological limitations (a strong bias against NC10 bacteria in 16S rRNA gene clone libraries and inhibition by commonly used stopper material) the environmental distribution and importance of these bacteria could be largely underestimated at present.
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264
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Abstract
This special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen-fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite-dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.
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