301
|
Al Hasin A, Gurman SJ, Murphy LM, Perry A, Smith TJ, Gardiner PHE. Remediation of chromium(VI) by a methane-oxidizing bacterium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:400-5. [PMID: 20039753 DOI: 10.1021/es901723c] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Methane-oxidizing bacteria are ubiquitous in the environment and are globally important in oxidizing the potent greenhouse gas methane. It is also well recognized that they have wide potential for bioremediation of organic and chlorinated organic pollutants, thanks to the wide substrate ranges of the methane monooxygenase enzymes that they produce. Here we have demonstrated that the well characterized model methanotroph Methylococcus capsulatus (Bath) is able to bioremediate chromium(VI) pollution over a wide range of concentrations (1.4-1000 mg L(-1) of Cr(6+)), thus extending the bioremediation potential of this major group of microorganisms to include an important heavy-metal pollutant. The chromium(VI) reduction reaction was dependent on the availability of reducing equivalents from the growth substrate methane and was partially inhibited by the metabolic poison sodium azide. X-ray spectroscopy showed that the cell-associated chromium was predominantly in the +3 oxidation state and associated with cell- or medium-derived moieties that were most likely phosphate groups. The genome sequence of Mc. capsulatus (Bath) suggests at least five candidate genes for the chromium(VI) reductase activity in this organism.
Collapse
Affiliation(s)
- Abubakr Al Hasin
- Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | | | | | | | | | | |
Collapse
|
302
|
Steenbergh AK, Meima MM, Kamst M, Bodelier PL. Biphasic kinetics of âa methanotrophic community is a combination of growth and increased activity per cell. FEMS Microbiol Ecol 2010; 71:12-22. [DOI: 10.1111/j.1574-6941.2009.00782.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
303
|
Kielak A, Rodrigues JL, Kuramae EE, Chain PS, Van Veen JA, Kowalchuk GA. Phylogenetic and metagenomic analysis of Verrucomicrobiaâin former âagricultural grassland soil. FEMS Microbiol Ecol 2010; 71:23-33. [DOI: 10.1111/j.1574-6941.2009.00785.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
304
|
Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P. Biogeography of wetland rice methanotrophs. Environ Microbiol 2009; 12:862-72. [DOI: 10.1111/j.1462-2920.2009.02131.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
305
|
Han B, Chen Y, Abell G, Jiang H, Bodrossy L, Zhao J, Murrell JC, Xing XH. Diversity and activity of methanotrophs in alkaline soil from a Chinese coal mine. FEMS Microbiol Ecol 2009; 70:40-51. [DOI: 10.1111/j.1574-6941.2009.00707.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
306
|
Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME. The expanding world of methylotrophic metabolism. Annu Rev Microbiol 2009; 63:477-99. [PMID: 19514844 DOI: 10.1146/annurev.micro.091208.073600] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the past few years, the field of methylotrophy has undergone a significant transformation in terms of discovery of novel types of methylotrophs, novel modes of methylotrophy, and novel metabolic pathways. This time has also been marked by the resolution of long-standing questions regarding methylotrophy and the challenge of long-standing dogmas. This chapter is not intended to provide a comprehensive review of metabolism of methylotrophic bacteria. Instead we focus on significant recent discoveries that are both refining and transforming the current understanding of methylotrophy as a metabolic phenomenon. We also review new directions in methylotroph ecology that improve our understanding of the role of methylotrophy in global biogeochemical processes, along with an outlook for the future challenges in the field.
Collapse
Affiliation(s)
- Ludmila Chistoserdova
- Departments of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | | | | |
Collapse
|
307
|
Abstract
This special issue highlights several recent discoveries in the microbial methane cycle, including the diversity and activity of methanotrophic bacteria in special habitats, distribution and contribution of the newly discovered Verrucomicrobia, metabolism of methane and related one-carbon compounds such as methanol and methylamine in freshwater and marine environments, methanol and methane-dependent nitrate reduction, the relationships of methane cycle microorganisms with plants and animals, and the environmental factors that regulate microbial processes of the methane cycle. These articles also highlight the plethora of new organisms and metabolism relating to the methane cycle that have been discovered in recent years and outline the many questions in the methane cycle that still need to be addressed. It is clear that despite a tremendous amount of research on the biology of the methane cycle, the microbes involved in catalysing methane production and consumption harbour many secrets that need to be disclosed in order for us to fully understand how the biogeochemical methane cycle is regulated in the environment, and for us to make future predictions about the global sources and sinks of methane and how anthropogenic changes impact on the cycling of this important greenhouse gas.
Collapse
Affiliation(s)
- J Colin Murrell
- Department of Microbiology, Warwick University, Warwick, UK. Department of Microbiology, IWWR Radboud University, Nijmegen, The Netherlands. Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | |
Collapse
|
308
|
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: 406] [Impact Index Per Article: 27.1] [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.
Collapse
Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.8, 35043 Marburg, Germany
| |
Collapse
|
309
|
Abell GCJ, Stralis-Pavese N, Sessitsch A, Bodrossy L. Grazing affects methanotroph activity and diversity in an alpine meadow soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:457-465. [PMID: 23765900 DOI: 10.1111/j.1758-2229.2009.00078.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
The role of methane-oxidizing bacteria (MOB) in alpine environments is poorly understood, but is of importance given the abundance of alpine environments and the role of MOB in the global carbon cycle. Using a combination of approaches we examined both seasonal and land usage effects on the ecology of microbial methane oxidation in an alpine meadow soil. Analysis of the abundance and diversity of MOB demonstrated that the abundance and diversity of the dominant type II MOB, predominantly Metylocystis and relatives, was only influenced by season. Conversely type Ia MOB abundance was significantly affected by season and land usage, while diversity changes were effected predominantly by land use. Assessment of methane oxidation potential and soil physical properties demonstrated a strong link between type Ia MOB abundance and methane oxidation potential as well as a complex series of relationships between soil moisture, pH and MOB abundance, changing with season. The results of this study suggest that, while type II MOB, unaffected by land use, represent the dominant MOB, Methylobacter-related type Ia MOB appear to be responsible for the majority of methane oxidation and are strongly affected by the grazing of cattle.
Collapse
Affiliation(s)
- Guy C J Abell
- Austrian Research Centers, Department of Bioresources, A-2444 Seibersdorf, Austria
| | | | | | | |
Collapse
|
310
|
Petersen JM, Dubilier N. Methanotrophic symbioses in marine invertebrates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:319-335. [PMID: 23765884 DOI: 10.1111/j.1758-2229.2009.00081.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Symbioses between marine animals and aerobic methane-oxidizing bacteria are found at hydrothermal vents and cold seeps in the deep sea where reduced, methane-rich fluids mix with the surrounding oxidized seawater. These habitats are 'oases' in the otherwise nutrient-poor deep sea, where entire ecosystems are fueled by microbial chemosynthesis. By associating with bacteria that gain energy from the oxidation of CH4 with O2 , the animal host is indirectly able to gain nutrition from methane, an energy source that is otherwise only available to methanotrophic microorganisms. The host, in turn, provides its symbionts with continuous access to both electron acceptors and donors that are only available at a narrow oxic - anoxic interface for free-living methanotrophs. Symbiotic methane oxidizers have resisted all attempts at cultivation, so that all evidence for these symbiotic associations comes from ultrastructural, enzymatic, physiological, stable isotope and molecular biological studies of the symbiotic host tissues. In this review, we present an overview of the habitats and invertebrate hosts in which symbiotic methane oxidizers have been found, and the methods used to investigate these symbioses, focusing on the symbioses of bathymodiolin mussels that have received the most attention among methanotrophic associations.
Collapse
Affiliation(s)
- Jillian M Petersen
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | | |
Collapse
|
311
|
Op den Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A, Dunfield PF. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:293-306. [PMID: 23765882 DOI: 10.1111/j.1758-2229.2009.00022.x] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Aerobic methanotrophic bacteria are capable of utilizing methane as their sole energy source. They are commonly found at the oxic/anoxic interfaces of environments such as wetlands, aquatic sediments, and landfills, where they feed on methane produced in anoxic zones of these environments. Until recently, all known species of aerobic methanotrophs belonged to the phylum Proteobacteria, in the classes Gammaproteobacteria and Alphaproteobacteria. However, in 2007-2008 three research groups independently described the isolation of thermoacidophilic methanotrophs that represented a distinct lineage within the bacterial phylum Verrucomicrobia. Isolates were obtained from geothermal areas in Italy, New Zealand and Russia. They are by far the most acidophilic methanotrophs known, with a lower growth limit below pH 1. Here we summarize the properties of these novel methanotrophic Verrucomicrobia, compare them with the proteobacterial methanotrophs, propose a unified taxonomic framework for them and speculate on their potential environmental significance. New genomic and physiological data are combined with existing information to allow detailed comparison of the three strains. We propose the new genus Methylacidiphilum to encompass all three newly discovered bacteria.
Collapse
Affiliation(s)
- Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands. Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7800, N-5020 Bergen, Norway. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand. Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada, T2N 1N4. NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
312
|
Kolb S. The quest for atmospheric methane oxidizers in forest soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:336-46. [PMID: 23765885 DOI: 10.1111/j.1758-2229.2009.00047.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Aerobic methanotrophs in forest soils are the largest biological sink for atmospheric methane (CH4 ). Community structures in 53 soils from Europe, Russia, North and South America, Asia and New Zealand located in boreal, temperate and tropical forests were analysed and maximal abundances of 2.1 × 10(7) methanotrophs g(-1) DW were measured. In acidic soils, the most frequently detected pmoA genotypes were Upland Soil Cluster α (USCα) and Methylocystis spp. Phospholipid fatty acids that were labelled by consumption of (14/13) CH4 suggested the activity of type II methanotrophs. Cluster 1 (Methylocystaceae), USCγ and Methylocystis spp. were frequently detected genotypes in pH-neutral soils. Genotypes with ambiguous functional affiliation were co-detected (Clusters MR1, RA21, 2) and may represent aerobic methanotrophs, ammonia oxidizers or enzymes with an unknown function. The physiological traits of atmospheric CH4 oxidizers are largely unknown because organisms possessing the key forest soil pmoA genotypes (USCα, USCγ, Cluster 1) have not been cultivated. Some methanotrophic strains belonging to the family Methylocystaceae have been shown to oxidize CH4 at atmospheric mixing ratios. Methylocystis strain SC2 was found to have an alternative particulate CH4 monooxygenase responsible for CH4 oxidation at atmospheric mixing ratios. pH, forest type and temperature might be environmental factors that shape methanotrophic communities in forest soils. However, specific effects on individual species are largely unknown, and only a limited number of studies have addressed environmental controls of methanotrophic diversity, pointing to the need for future research in this area.
Collapse
Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
313
|
Kumaresan D, Abell GCJ, Bodrossy L, Stralis-Pavese N, Murrell JC. Spatial and temporal diversity of methanotrophs in a landfill cover soil are differentially related to soil abiotic factors. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:398-407. [PMID: 23765893 DOI: 10.1111/j.1758-2229.2009.00059.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Methanotrophs present in landfill cover soil can limit methane emissions from landfill sites by oxidizing methane produced in landfill. Understanding the spatial and temporal distribution of populations of methanotrophs and the factors influencing their activity and diversity in landfill cover soil is critical to devise better landfill cover soil management strategies. pmoA-based microarray analyses of methanotroph community structure revealed a temporal shift in methanotroph populations across different seasons. Type II methanotrophs (particularly Methylocystis sp.) were found to be present across all seasons. Minor shifts in type I methanotroph populations were observed. In the case of spatial distribution, only minor differences in methanotroph community structure were observed with no recognizable patterns (both vertical and horizontal) at a 5 m scale. Correlation analysis between soil abiotic parameters (total C, N, NH4 (+) , NO3 (-) and water content) and distribution of methanotrophs revealed a lack of conclusive evidence for any distinct correlation pattern between measured abiotic parameters and methanotroph community structure, suggesting that complex interactions of several physico-chemical parameters shape methanotroph diversity and activity in landfill cover soils.
Collapse
Affiliation(s)
- Deepak Kumaresan
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK. Department of Bioresources, A-2444 Seibersdorf, Austria
| | | | | | | | | |
Collapse
|
314
|
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.
Collapse
Affiliation(s)
- Elena Zaikova
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | | | | |
Collapse
|
315
|
Tuomivirta TT, Yrjälä K, Fritze H. Quantitative PCR of pmoA using a novel reverse primer correlates with potential methane oxidation in Finnish fen. Res Microbiol 2009; 160:751-6. [PMID: 19781637 DOI: 10.1016/j.resmic.2009.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/02/2009] [Accepted: 09/03/2009] [Indexed: 11/28/2022]
Abstract
We report a new reverse primer (A621r) for use with A189f in PCR amplification of pmoA alleles in type II methanotrophs. The new primer combination was used to successfully amplify pmoA in peat monolith samples of various depths taken from fen-type peatlands in Finland. In quantitative PCR, pmoA amplicons produced from two sets of three replicate monoliths showed a significant Pearson correlation coefficient (r=0.77 and 0.61) with methane oxidation potential. The maximum methane oxidation potential and number of pmoA amplicons ranged between 8.8-40.5 micromol g (dry weight)(-1) d(-1) and 5.5 x 10(7)-18.7 x 10(7) g (wet weight)(-1), respectively, occurring in depths between 10 and 30 cm beneath the surface in the seven individual monoliths used in this study.
Collapse
Affiliation(s)
- Tero T Tuomivirta
- Finnish Forest Research Institute, Vantaa Research Unit, Box 18, FI-01301 Vantaa, Finland.
| | | | | |
Collapse
|
316
|
Bengtson P, Basiliko N, Dumont MG, Hills M, Murrell JC, Roy R, Grayston SJ. Links between methanotroph community composition and CH oxidation in a pine forest soil. FEMS Microbiol Ecol 2009; 70:356-66. [PMID: 19811539 DOI: 10.1111/j.1574-6941.2009.00751.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The main gap in our knowledge about what determines the rate of CH(4) oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following (13)CH(4) incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH(4) oxidation rates. The rates of (13)C incorporation into PLFAs differed between horizons, with low (13)C incorporation in the organic soil and relatively high (13)C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the (13)C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH(4) oxidation rates. Both PLFA and pmoA-based data indicated that CH(4) oxidizers in this soil belong to the uncultivated 'upland soil cluster alpha'. CH(4) oxidation potential exhibited the opposite pattern to (13)C incorporation, suggesting that CH(4) oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient (13)C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.
Collapse
Affiliation(s)
- Per Bengtson
- Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada.
| | | | | | | | | | | | | |
Collapse
|
317
|
Ait-Benichou S, Jugnia LB, Greer CW, Cabral AR. Methanotrophs and methanotrophic activity in engineered landfill biocovers. WASTE MANAGEMENT (NEW YORK, N.Y.) 2009; 29:2509-2517. [PMID: 19477627 DOI: 10.1016/j.wasman.2009.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 05/01/2009] [Accepted: 05/05/2009] [Indexed: 05/27/2023]
Abstract
The dynamics and changes in the potential activity and community structure of methanotrophs in landfill covers, as a function of time and depth were investigated. A passive methane oxidation biocover (PMOB-1) was constructed in St-Nicéphore MSW Landfill (Quebec, Canada). The most probable number (MPN) method was used for methanotroph counts, methanotrophic diversity was assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting of the pmoA gene and the potential CH(4) oxidation rate was determined using soil microcosms. Results of the PMOB-1 were compared with those obtained for the existing landfill cover (silty clay) or a reference soil (RS). During the monitoring period, changes in the number of methanotrophic bacteria in the PMOB-1 exhibited different developmental phases and significant variations with depth. In comparison, no observable changes over time occurred in the number of methanotrophs in the RS. The maximum counts measured in the uppermost layer was 1.5x10(9) cells g dw(-1) for the PMOB-1 and 1.6x10(8) cells g dw(-1) for the RS. No distinct difference was observed in the methanotroph diversity in the PMOB-1 or RS. As expected, the potential methane oxidation rate was higher in the PMOB-1 than in the RS. The maximum potential rates were 441.1 and 76.0 microg CH(4) h(-1) g dw(-1) in the PMOB and RS, respectively. From these results, the PMOB was found to be a good technology to enhance methane oxidation, as its performance was clearly better than the starting soil that was present in the landfill site.
Collapse
Affiliation(s)
- S Ait-Benichou
- Faculty of Engineering, Civil Engineering Department, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, Québec, Canada J1K 2R1
| | | | | | | |
Collapse
|
318
|
Trotsenko YA, Medvedkova KA, Khmelenina VN, Eshinimayev BT. Thermophilic and thermotolerant aerobic methanotrophs. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709040018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
319
|
Angel R, Conrad R. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils. Environ Microbiol 2009; 11:2598-610. [PMID: 19601957 DOI: 10.1111/j.1462-2920.2009.01984.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aerated soils are a biological sink for atmospheric methane. However, the activity of desert soils and the presence of methanotrophs in these soils have hardly been studied. We studied on-site atmospheric methane consumption rates as well as the diversity and expression of the pmoA gene, coding for a subunit of the particulate methane monooxygenase, in arid and hyperarid soils in the Negev Desert, Israel. Methane uptake was only detected in undisturbed soils in the arid region (approximately 90 mm year(-1)) and vertical methane profiles in soil showed the active layer to be at 0-20 cm depth. No methane uptake was detected in the hyperarid soils (approximately 20 mm year(-1)) as well as in disturbed soils in the arid region (i.e. agricultural field and a mini-catchment). Molecular analysis of the methanotrophic community using terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene detected methanotrophs in the active soils, whereas the inactive ones were dominated by sequences of the homologous gene amoA, coding for a subunit of the ammonia monooxygenase. Even in the active soils, methanotrophs (as well as in situ activity) could not be detected in the soil crust, which is the biologically most important layer in desert soils. All pmoA sequences belonged to yet uncultured strains. Transcript analysis showed dominance of sequences clustering within the JR3, formerly identified in Californian grassland soils. Our results show that although active methanotrophs are prevalent in arid soils they seem to be absent or inactive in hyperarid and disturbed arid soils. Furthermore, we postulate that methanotrophs of the yet uncultured JR3 cluster are the dominant atmospheric methane oxidizers in this ecosystem.
Collapse
Affiliation(s)
- Roey Angel
- Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.
| | | |
Collapse
|
320
|
Abstract
Methanol is an atmospheric compound that is primarily released from plant polymers and impacts ozone formation. The global methanol emission rate from terrestrial ecosystems is of the same order of magnitude (4.9 x 10(12) mol year(-1)) as that of methane (10 x 10(12) mol year(-1)). The major proportion of the annual plant-released methanol does not enter the atmosphere, but may be reoxidized by biological methanol oxidation, which is catalyzed by methanol-oxidizing prokaryotes. Fifty-six aerobic methanol-oxidizing species have been isolated from soils. These methylotrophs belong to the Alpha-, Beta-, and Gammaproteobacteria, Verrucomicrobia, Firmicutes, and Actinobacteria. Their ecological niches are determined by oxygen and methanol concentration, temperature, pH, the capability to utilize nitrate as an electron acceptor, and the spectrum of nitrogen sources and utilizable multicarbon substrates. Recently discovered interactions with eukaryotes indicate that their ecological niches may not solely be defined by physicochemical parameters. Nonetheless, there are still gaps in knowledge; based on global methanol budgets, methanol oxidation in soil is important, but has not been addressed adequately by biogeochemical studies. Ratios of above-ground and soil-internal methanol oxidation are not known. The contribution to methanol-oxidation by aerobic and anaerobic methylotrophs in situ also needs further research.
Collapse
Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany.
| |
Collapse
|
321
|
Nyerges G, Stein LY. Ammonia cometabolism and product inhibition vary considerably among species of methanotrophic bacteria. FEMS Microbiol Lett 2009; 297:131-6. [PMID: 19566684 DOI: 10.1111/j.1574-6968.2009.01674.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ecological studies have indicated that relative abundances of Gammaproteobacteria methanotrophs (Gamma-MOB) vs. Alphaproteobacteria methanotrophs (Alpha-MOB) in nitrogen (N) impacted soils are dictated in part by their abilities to tolerate inhibitory effects of ammonium and nitrite. In particular, ammonia is a cometabolic substrate and competitive inhibitor of methane monooxygenase. The rates of ammonia and hydroxylamine oxidation and inhibition of methane-oxidizing activity by ammonium and nitrite were compared among two Gamma-MOB and two Alpha-MOB to determine whether methanotrophs of the same class shared similar physiological profiles. Each isolate exhibited unique K(m(app)) for ammonia and V(max) for nitrite production with or without reductant (methane or sodium formate). The rates of nitrite production from hydroxylamine followed similar trends to rates of ammonia oxidation, indicating that hydroxylamine-oxidizing enzymes were central participants in the ammonia-oxidizing pathway. Methylomonas methanica was incapable of either ammonia or hydroxylamine oxidation. A broad range of sensitivities to ammonium and nitrite inhibition were measured with little consistency between isolates of the same class. The results indicate that physiological responses, and perhaps environmental adaptations, to N compounds are organism specific for methanotrophs.
Collapse
Affiliation(s)
- Györgyi Nyerges
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | | |
Collapse
|
322
|
Zhao C, Zheng J, Li H, Wen G, He Y, Yang S, Dong C, Choi M. Characterization of a methane-utilizing strain and its application for monitoring methane. J Appl Microbiol 2009; 106:2024-30. [DOI: 10.1111/j.1365-2672.2009.04169.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
323
|
Bodelier PLE, Gillisen MJB, Hordijk K, Damsté JSS, Rijpstra WIC, Geenevasen JAJ, Dunfield PF. A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME JOURNAL 2009; 3:606-17. [PMID: 19194481 DOI: 10.1038/ismej.2009.6] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope ((13)C) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (omega 7c,12c and omega 6c,12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible.
Collapse
Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Wetland Ecology, Centre for Limnology, Netherlands Institute of Ecology (NIOO-KNAW), Maarssen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
324
|
Research progress in genomics of environmental and industrial microorganisms. ACTA ACUST UNITED AC 2009; 52:64-73. [DOI: 10.1007/s11427-009-0013-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 10/08/2008] [Indexed: 11/26/2022]
|
325
|
Lee KC, Webb RI, Janssen PH, Sangwan P, Romeo T, Staley JT, Fuerst JA. Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes. BMC Microbiol 2009; 9:5. [PMID: 19133117 PMCID: PMC2647929 DOI: 10.1186/1471-2180-9-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 01/08/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The phylum Verrucomicrobia is a divergent phylum within domain Bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. At least one genus, Prosthecobacter, includes species with genes homologous to those encoding eukaryotic tubulins. A significant superphylum relationship of Verrucomicrobia with members of phylum Planctomycetes possessing a unique compartmentalized cell plan, and members of the phylum Chlamydiae including human pathogens with a complex intracellular life cycle, has been proposed. Based on the postulated superphylum relationship, we hypothesized that members of the two separate phyla Planctomycetes and Verrucomicrobia might share a similar ultrastructure plan differing from classical prokaryote organization. RESULTS The ultrastructure of cells of four members of phylum Verrucomicrobia - Verrucomicrobium spinosum, Prosthecobacter dejongeii, Chthoniobacter flavus, and strain Ellin514 - was examined using electron microscopy incorporating high-pressure freezing and cryosubstitution. These four members of phylum Verrucomicrobia, representing 3 class-level subdivisions within the phylum, were found to possess a compartmentalized cell plan analogous to that found in phylum Planctomycetes. Like all planctomycetes investigated, they possess a major pirellulosome compartment containing a condensed nucleoid and ribosomes surrounded by an intracytoplasmic membrane (ICM), as well as a ribosome-free paryphoplasm compartment between the ICM and cytoplasmic membrane. CONCLUSION A unique compartmentalized cell plan so far found among Domain Bacteria only within phylum Planctomycetes, and challenging our concept of prokaryote cell plans, has now been found in a second phylum of the Domain Bacteria, in members of phylum Verrucomicrobia. The planctomycete cell plan thus occurs in at least two distinct phyla of the Bacteria, phyla which have been suggested from other evidence to be related phylogenetically in the proposed PVC (Planctomycetes-Verrucomicrobia-Chlamydiae) superphylum. This planctomycete cell plan is present in at least 3 of 6 subdivisions of Verrucomicrobia, suggesting that the common ancestor of the verrucomicrobial phylum was also compartmentalized and possessed such a plan. The presence of this compartmentalized cell plan in both phylum Planctomycetes and phylum Verrucomicrobia suggest that the last common ancestor of these phyla was also compartmentalized.
Collapse
Affiliation(s)
- Kuo-Chang Lee
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Richard I Webb
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Parveen Sangwan
- CSIRO Manufacturing and Materials Technology, Private Bag 33, Clayton South Victoria 3169, Australia
| | - Tony Romeo
- University of Sydney, Sydney, New South Wales, Australia
| | - James T Staley
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|
326
|
Ferrando L, Tarlera S. Activity and diversity of methanotrophs in the soil-water interface and rhizospheric soil from a flooded temperate rice field. J Appl Microbiol 2009; 106:306-16. [DOI: 10.1111/j.1365-2672.2008.04004.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
327
|
Schmid MC, Hooper AB, Klotz MG, Woebken D, Lam P, Kuypers MMM, Pommerening-Roeser A, Op den Camp HJM, Jetten MSM. Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ Microbiol 2008; 10:3140-9. [PMID: 18973625 DOI: 10.1111/j.1462-2920.2008.01732.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Bacterial aerobic ammonium oxidation and anaerobic ammonium oxidation (anammox) are important processes in the global nitrogen cycle. Key enzymes in both processes are the octahaem cytochrome c (OCC) proteins, hydroxylamine oxidoreductase (HAO) of aerobic ammonium-oxidizing bacteria (AOB), which catalyses the oxidation of hydroxylamine to nitrite, and hydrazine oxidoreductase (HZO) of anammox bacteria, which converts hydrazine to N(2). While the genomes of AOB encode up to three nearly identical copies of hao operons, genome analysis of Candidatus'Kuenenia stuttgartiensis' showed eight highly divergent octahaem protein coding regions as possible candidates for the HZO. Based on their phylogenetic relationship and biochemical characteristics, the sequences of these eight gene products grouped in three clusters. Degenerate primers were designed on the basis of available gene sequences with the aim to detect hao and hzo genes in various ecosystems. The hao primer pairs amplified gene fragments from 738 to 1172 bp and the hzo primer pairs amplified gene fragments from 289 to 876 bp in length, when tested on genomic DNA isolated from a variety of AOB and anammox bacteria. A selection of these primer pairs was also used successfully to amplify and analyse the hao and hzo genes in community DNA isolated from different ecosystems harbouring both AOB and anammox bacteria. We propose that OCC protein-encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium-oxidizing bacteria.
Collapse
Affiliation(s)
- Markus C Schmid
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | | | | | | | | | | | | | | | | |
Collapse
|
328
|
High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 2008; 26:1029-34. [PMID: 18711340 DOI: 10.1038/nbt.1488] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 07/21/2008] [Indexed: 11/08/2022]
Abstract
Most microbes in the biosphere remain unculturable. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities. However, in communities of high complexity, metagenomics fails to link specific microbes to specific ecological functions. To overcome this limitation, we developed a method to target microbial subpopulations by labeling DNA through stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis of microbes from Lake Washington in Seattle that oxidize single-carbon (C1) compounds shows specific sequence enrichments in response to different C1 substrates, revealing the ecological roles of individual phylotypes. We also demonstrate the utility of our approach by extracting a nearly complete genome of a novel methylotroph, Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems.
Collapse
|
329
|
Nemergut DR, Townsend AR, Sattin SR, Freeman KR, Fierer N, Neff JC, Bowman WD, Schadt CW, Weintraub MN, Schmidt SK. The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environ Microbiol 2008; 10:3093-105. [PMID: 18764871 DOI: 10.1111/j.1462-2920.2008.01735.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diana R Nemergut
- Institute of Arctic and Alpine Research, Environmental Studies Program, University of Colorado, Boulder, Colorado, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
330
|
Jensen S, Neufeld JD, Birkeland NK, Hovland M, Murrell JC. Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway. FEMS Microbiol Ecol 2008; 66:320-30. [PMID: 18811651 DOI: 10.1111/j.1574-6941.2008.00575.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 micromol 13CH4 g(-1) wet weight occurred. Extracted DNA was separated into 'light' and 'heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs.
Collapse
Affiliation(s)
- Sigmund Jensen
- Department of Biology, University of Bergen, Bergen, Norway.
| | | | | | | | | |
Collapse
|
331
|
Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou S, Alam M, Dunfield PF. Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 2008; 10:2030-41. [DOI: 10.1111/j.1462-2920.2008.01621.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
332
|
Chen Y, Dumont MG, Neufeld JD, Bodrossy L, Stralis-Pavese N, McNamara NP, Ostle N, Briones MJI, Murrell JC. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands. Environ Microbiol 2008; 10:2609-22. [PMID: 18631364 DOI: 10.1111/j.1462-2920.2008.01683.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.
Collapse
Affiliation(s)
- Yin Chen
- Department of Biological Sciences, the University of Warwick, Coventry, CV4 7AL, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
333
|
Hou S, Makarova KS, Saw JHW, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 2008; 3:26. [PMID: 18593465 PMCID: PMC2474590 DOI: 10.1186/1745-6150-3-26] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 07/01/2008] [Indexed: 12/31/2022] Open
Abstract
Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins. Conclusion The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria. Reviewers This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.
Collapse
Affiliation(s)
- Shaobin Hou
- Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall #319, Honolulu, Hawaii, 96822, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
334
|
Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. ADVANCES IN APPLIED MICROBIOLOGY 2008; 63:183-229. [PMID: 18395128 DOI: 10.1016/s0065-2164(07)00005-6] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yuri A Trotsenko
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
| | | |
Collapse
|
335
|
Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. Appl Environ Microbiol 2008; 74:3985-95. [PMID: 18487407 DOI: 10.1128/aem.00069-08] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane vents are of significant geochemical and ecological importance. Notable progress has been made toward understanding anaerobic methane oxidation in marine sediments; however, the diversity and distribution of aerobic methanotrophs in the water column are poorly characterized. Both environments play an essential role in regulating methane release from the oceans to the atmosphere. In this study, the diversity of particulate methane monooxygenase (pmoA) and 16S rRNA genes from two methane vent environments along the California continental margin was characterized. The pmoA phylotypes recovered from methane-rich sediments and the overlying water column differed. Sediments harbored the greatest number of unique pmoA phylotypes broadly affiliated with the Methylococcaceae family, whereas planktonic pmoA phylotypes formed three clades that were distinct from the sediment-hosted methanotrophs and distantly related to established methanotrophic clades. Water column-associated phylotypes were highly similar between field sites, suggesting that planktonic methanotroph diversity is controlled primarily by environmental factors rather than geographical proximity. Analysis of 16S rRNA genes from methane-rich waters did not readily recover known methanotrophic lineages, with only a few phylotypes demonstrating distant relatedness to Methylococcus. The development of new pmo primers increased the recovery of monooxygenase genes from the water column and led to the discovery of a highly diverged monooxygenase sequence which is phylogenetically intermediate to Amo and pMMO. This sequence potentiates insight into the amo/pmo superfamily. Together, these findings lend perspective into the diversity and segregation of aerobic methanotrophs within different methane-rich habitats in the marine environment.
Collapse
|
336
|
Life in the extreme: thermoacidophilic methanotrophy. Trends Microbiol 2008; 16:190-3. [PMID: 18420412 DOI: 10.1016/j.tim.2008.02.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 02/13/2008] [Accepted: 02/20/2008] [Indexed: 11/23/2022]
Abstract
Aerobic methane-oxidizing bacteria (methanotrophs) have a key role in the global carbon cycle, converting methane to biomass and carbon dioxide. Although these bacteria have been isolated from many environments, until recently, it was not known if they survived, much less thrived in thermoacidic environments, that is, locations with pH values of approximately 1 and temperatures greater than 50 degrees C. Recently, three independent studies have isolated unusual methanotrophs from such extreme environments, expanding the known functional and phylogenetic diversity of methanotrophs.
Collapse
|
337
|
Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. J Bacteriol 2008; 190:3817-23. [PMID: 18390659 DOI: 10.1128/jb.00180-08] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some members of Burkholderiales are able to grow on methanol but lack the genes (mxaFI) responsible for the well-characterized two-subunit pyrroloquinoline quinone-dependent quinoprotein methanol dehydrogenase that is widespread in methylotrophic Proteobacteria. Here, we characterized novel, mono-subunit enzymes responsible for methanol oxidation in four strains, Methyloversatilis universalis FAM5, Methylibium petroleiphilum PM1, and unclassified Burkholderiales strains RZ18-153 and FAM1. The enzyme from M. universalis FAM5 was partially purified and subjected to matrix-assisted laser desorption ionization-time of fight peptide mass fingerprinting. The resulting peptide spectrum was used to identify a gene candidate in the genome of M. petroleiphilum PM1 (mdh2) predicted to encode a type I alcohol dehydrogenase related to the characterized methanol dehydrogenase large subunits but at less than 35% amino acid identity. Homologs of mdh2 were amplified from M. universalis FAM5 and strains RZ18-153 and FAM1, and mutants lacking mdh2 were generated in three of the organisms. These mutants lost their ability to grow on methanol and ethanol, demonstrating that mdh2 is responsible for oxidation of both substrates. Our findings have implications for environmental detection of methylotrophy and indicate that this ability is widespread beyond populations possessing mxaF, the gene traditionally used as a genetic marker for environmental detection of methanol-oxidizing capability. Our findings also have implications for understanding the evolution of methanol oxidation, suggesting a convergence toward the enzymatic function for methanol oxidation in MxaF and Mdh2-type proteins.
Collapse
|
338
|
Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ. ISME JOURNAL 2008; 2:602-14. [DOI: 10.1038/ismej.2008.34] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
339
|
Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
340
|
Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington. ISME JOURNAL 2008; 2:696-706. [PMID: 18607374 DOI: 10.1038/ismej.2008.32] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Redox sensor green (RSG), a novel fluorescent dye from Invitrogen was employed as a tool for real-time detection of microbes metabolically active in situ, in combination with flow cytometry and cell sorting. Lake Washington sediment, an environment known for high rates of methane oxidation, was used as a model, and methylotrophs were targeted as a functional group. We first tested and optimized the performance of the dye with pure methylotroph cultures. Most cells in actively growing cultures were positive for staining, whereas in starved cultures, few cells fluoresced. However, starved cells could be activated by addition of substrate. High numbers of fluorescing cells were observed in a Lake Washington sediment sample, and activation of subpopulations of cells was demonstrated in response to methane, methanol, methylamine and formaldehyde. The fraction of the population activated by methane was investigated in more detail, by phylogenetic profiling. This approach showed that the major responding species were the Methylomonas species, previously isolated from the site, and Methylobacter species that have not yet been cultivated from Lake Washington. In addition, from the methane-stimulated fraction, uncultivated bacterial sequences were obtained that belonged to unclassified Deltaproteobacteria, unclassified Verrucomicrobiles and unclassified Acidobacteria, suggesting that these microbes may also be involved in methane metabolism. The approach was further tested for its utility in facilitating enrichment for functional types that possess specific metabolic activities but resist cultivation. It was demonstrated that in enrichment cultures inoculated with cells that were sorted after stimulation with methane, Methylobacter sequences could be detected, whereas in enrichment cultures inoculated by randomly sorted cells, Methylomonas species quickly outcompeted all other types.
Collapse
|
341
|
Methane oxidation at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci U S A 2008; 105:300-4. [PMID: 18172218 DOI: 10.1073/pnas.0704162105] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. These bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. Phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the Proteobacteria. Here, we report the isolation and initial characterization of a nonproteobacterial obligately methanotrophic bacterium. The isolate, designated Kam1, was recovered from an acidic hot spring in Kamchatka, Russia, and is more thermoacidophilic than any other known methanotroph, with optimal growth at approximately 55 degrees C and pH 3.5. Kam1 is only distantly related to all previously known methanotrophs and belongs to the Verrucomicrobia lineage of evolution. Genes for methane monooxygenases, essential for initiation of methane oxidation, could not be detected by using standard primers in PCR amplification and Southern blot analysis, suggesting the presence of a different methane oxidation enzyme. Kam1 also lacks the well developed intracellular membrane systems typical for other methanotrophs. The isolate represents a previously unrecognized biological methane sink, and, due to its unusual phylogenetic affiliation, it will shed important light on the origin, evolution, and diversity of biological methane oxidation and on the adaptation of this process to extreme habitats. Furthermore, Kam1 will add to our knowledge of the metabolic traits and biogeochemical roles of the widespread but poorly understood Verrucomicrobia phylum.
Collapse
|
342
|
Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 2007; 74:1305-15. [PMID: 18165358 DOI: 10.1128/aem.02233-07] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|