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Colin J Murrell - One of the best experts on this subject based on the ideXlab platform.
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draft genome sequence of methyloferula stellata ar4 an obligate Methanotroph possessing only a soluble methane monooxygenase
Genome Announcements, 2015Co-Authors: Svetlana N Dedysh, Colin J Murrell, Marina G Kalyuzhnaya, Alexey Vorobev, D G Naumoff, Nikos C Kyrpides, Tanja Woyke, Nicole Shapiro, Andrew T Crombie, Angela V SmirnovaAbstract:Methyloferula stellata AR4 is an aerobic acidophilic Methanotroph, which, in contrast to most known Methanotrophs but similar to Methylocella spp., possesses only a soluble methane monooxygenase. However, it differs from Methylocella spp. by its inability to grow on multicarbon substrates. Here, we report the draft genome sequence of this bacterium.
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trace gas metabolic versatility of the facultative Methanotroph methylocella silvestris
Nature, 2014Co-Authors: Andrew T Crombie, Colin J MurrellAbstract:The climate-active gas methane is generated both by biological processes and by thermogenic decomposition of fossil organic material, which forms methane and short-chain alkanes, principally ethane, propane and butane1, 2. In addition to natural sources, environments are exposed to anthropogenic inputs of all these gases from oil and gas extraction and distribution. The gases provide carbon and/or energy for a diverse range of microorganisms that can metabolize them in both anoxic3 and oxic zones. Aerobic Methanotrophs, which can assimilate methane, have been considered to be entirely distinct from utilizers of short-chain alkanes, and studies of environments exposed to mixtures of methane and multi-carbon alkanes have assumed that disparate groups of microorganisms are responsible for the metabolism of these gases. Here we describe the mechanism by which a single bacterial strain, Methylocella silvestris, can use methane or propane as a carbon and energy source, documenting a Methanotroph that can utilize a short-chain alkane as an alternative to methane. Furthermore, during growth on a mixture of these gases, efficient consumption of both gases occurred at the same time. Two soluble di-iron centre monooxygenase (SDIMO) gene clusters were identified and were found to be differentially expressed during bacterial growth on these gases, although both were required for efficient propane utilization. This report of a Methanotroph expressing an additional SDIMO that seems to be uniquely involved in short-chain alkane metabolism suggests that such metabolic flexibility may be important in many environments where methane and short-chain alkanes co-occur.
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soil methane oxidation and Methanotroph responses to afforestation of pastures with pinus radiata stands
Soil Biology & Biochemistry, 2009Co-Authors: Brajesh K Singh, K R Tate, D J Ross, Jagrati Singh, John Dando, Nadine Thomas, Peter Millard, Colin J MurrellAbstract:Abstract Afforestation of pastures in New Zealand reduces methane (CH4) production from soil, while also stimulating oxidation of atmospheric CH4 by soil Methanotrophs. However, neither the mechanisms by which soil CH4 oxidation is enhanced by afforestation, nor how long after forest planting tree-dependent responses in CH4 oxidation become detectable are fully known. Here, we investigated the effects of different-aged stands (5–20 y) of the exotic pine (Pinus radiata (D. Don)) on CH4 oxidation and Methanotrophic community structure in soils, compared with adjacent, long-established pastures. Two of the pastures were on volcanic soils and two were on non-volcanic soils. Although the CH4 fluxes in soils from these young stands were not significantly different from those in the associated pastures, the rate of oxidation of added 13CH4 was higher in the pine soils. Both fluxes and 13CH4 oxidation rates were higher in the volcanic than the non-volcanic soils. Combined phospholipid fatty acid (PLFA) and stable isotope probe (SIP) analyses suggested that type II Methanotrophs (PLFA C18:1ω7) were most active in all soils followed by uncultivable bacteria (C17:0ai). Molecular analysis of the Methanotrophic community structure using pmoA (particulate methane monooxygenase) genes suggested that a particular type II Methanotroph (TRF 35) was dominant in all soils, but more so in the pine than in pasture soils. A type I Methanotroph (TRF 245) was more prevalent in the pasture than in associated pine soils, whereas TRF 128 (a type II Methanotroph) was slightly more dominant in soils under pine. Cloning and sequencing data suggest TRFs 35 and 128, which differ from one another, belong to distant relatives of Methylocapsa sp; TRF 245 is related to Methylococcus capsulatus. Land-use change resulted in changes in soil bulk density, porosity, moisture contents and in Methanotrophic community structure. Methane oxidation rates were most closely related to soil moisture, as well as to the Methanotrophic community structure, and nitrate-N, extractable C and total C concentrations. Stepwise multiple regression also suggested a weak effect (P = 0.06) of stand age on CH4 oxidation rate. By contrast, the responses of the Methanotrophic community structure to this land-use change were more readily detected by the specific molecular analyses, and indicated a predominance of type II Methanotrophs in pine soils.
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paraffin oil as a methane vector for rapid and high cell density cultivation of methylosinus trichosporium ob3b
Applied Microbiology and Biotechnology, 2009Co-Authors: Tao Su, Hao Jiang, Xinhui Xing, Hao Wu, Yin Chen, Xin Li, Colin J MurrellAbstract:Slow growth and relatively low cell densities of Methanotrophs have limited their uses in industrial applications. In this study, a novel method for rapid cultivation of Methylosinus trichosporium OB3b was studied by adding a water-immiscible organic solvent in the medium. Paraffin oil was the most effective at enhancing cell growth and final cell density. This is at least partially due to the increase of methane gas transfer between gas and medium phases since methane solubility is higher in paraffin than in water/nitrate minimal salt medium. During cultivation with paraffin oil at 5% (v/v) in the medium, M. trichosporium OB3b cells also showed higher concentrations of the intermediary metabolites, such as formic acid and pyruvic acid, and consumed more methane compared with the control. Paraffin as methane vector to improve Methanotroph growth was further studied in a 5-L fermentor at three concentrations (i.e., 2.5%, 5%, and 10%). Cell density reached about 14 g dry weight per liter with 5% paraffin, around seven times higher than that of the control (without paraffin). Cells cultivated with paraffin tended to accumulate around the interface between oil droplets and the water phase and could exist in oil phase in the case of 10% (v/v) paraffin. These results indicated that paraffin could enhance Methanotroph growth, which is potentially useful in cultivation of Methanotrophs in large scale in industry.
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analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in Methanotroph community structure
Applied and Environmental Microbiology, 2005Co-Authors: Samantha B Joye, Johannes C M Scholten, Hendrik Schafer, Ian R Mcdonald, Colin J MurrellAbstract:Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved pmoA sequences showed a broad diversity of aerobic methane oxidizers including the type I Methanotrophs Methylobacter (the dominant genus), Methylomicrobium, and Methylothermus, and the type II Methanotroph Methylocystis. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of pmoA using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in Methanotroph community composition.
Mary E Lidstrom - One of the best experts on this subject based on the ideXlab platform.
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oxygen limited metabolism in the Methanotroph methylomicrobium buryatense 5gb1c
PeerJ, 2017Co-Authors: Alexey Gilman, David A C Beck, Yanfen Fu, Melissa C Hendershott, Aaron W Puri, Amanda L Smith, Mitchell W Pesesky, Rose Lieberman, Mary E LidstromAbstract:The bacteria that grow on methane aerobically (Methanotrophs) support populations of non-Methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation. We examined this O2-starvation condition in the Methanotroph Methylomicrobium buryatense 5GB1. The M. buryatense 5GB1 genome contains homologs for all enzymes necessary for a fermentative metabolism, and we hypothesize that a metabolic switch to fermentation can be induced by low-O2 conditions. Under prolonged O2-starvation in a closed vial, this Methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1, formate and acetate are excreted in response to redox imbalance. Our results indicate that even under O2-starvation conditions, M. buryatense 5GB1 maintains a metabolic state representing a combination of fermentation and respiration metabolism.
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the oxidative tca cycle operates during Methanotrophic growth of the type i Methanotroph methylomicrobium buryatense 5gb1
Metabolic Engineering, 2017Co-Authors: Yanfen Fu, Yi Li, Mary E LidstromAbstract:Abstract Methanotrophs are a group of bacteria that use methane as sole carbon and energy source. Type I Methanotrophs are gamma-proteobacterial Methanotrophs using the ribulose monophosphate cycle (RuMP) cycle for methane assimilation. In order to facilitate metabolic engineering in the industrially promising Type I Methanotroph Methylomicrobium buryatense 5GB1, flux analysis of cellular metabolism is needed and 13 C tracer analysis is a foundational tool for such work. This biological system has a single-carbon input and a special network topology that together pose challenges to the current well-established methodology for 13 C tracer analysis using a multi-carbon input such as glucose, and to date, no 13 C tracer analysis of flux in a Type I Methanotroph has been reported. In this study, we showed that by monitoring labeling patterns of several key intermediate metabolites in core metabolism, it is possible to quantitate the relative flux ratios for important branch points, such as the malate node. In addition, it is possible to assess the operation of the TCA cycle, which has been thought to be incomplete in Type I Methanotrophs. Surprisingly, our analysis provides direct evidence of a complete, oxidative TCA cycle operating in M. buryatense 5GB1 using methane as sole carbon and energy substrate, contributing about 45% of the total flux for de novo malate production. Combined with mutant analysis, this method was able to identify fumA (METBUDRAFT_1453/MBURv2__60244) as the primary fumarase involved in the oxidative TCA cycle, among 2 predicted fumarases, supported by 13 C tracer analysis on both fumA and fumC single knockouts. Interrupting the oxidative TCA cycle leads to a severe growth defect, suggesting that the oxidative TCA cycle functions to not only provide precursors for de novo biomass synthesis, but also to provide reducing power to the system. This information provides new opportunities for metabolic engineering of M. buryatense for the production of industrially relevant products.
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xoxf acts as the predominant methanol dehydrogenase in the type i Methanotroph methylomicrobium buryatense
Journal of Bacteriology, 2016Co-Authors: Mary E LidstromAbstract:ABSTRACT Many methylotrophic taxa harbor two distinct methanol dehydrogenase (MDH) systems for oxidizing methanol to formaldehyde: the well-studied calcium-dependent MxaFI type and the more recently discovered lanthanide-containing XoxF type. MxaFI has traditionally been accepted as the major functional MDH in bacteria that contain both enzymes. However, in this study, we present evidence that, in a type I Methanotroph, Methylomicrobium buryatense, XoxF is likely the primary functional MDH in the environment. The addition of lanthanides increases xoxF expression and greatly reduces mxa expression, even under conditions in which calcium concentrations are almost 100-fold higher than lanthanide concentrations. Mutations in genes encoding the MDH enzymes validate our finding that XoxF is the major functional MDH, as XoxF mutants grow more poorly than MxaFI mutants under unfavorable culturing conditions. In addition, mutant and transcriptional analyses demonstrate that the lanthanide-dependent MDH switch operating in Methanotrophs is mediated in part by the orphan response regulator MxaB, whose gene transcription is itself lanthanide responsive. IMPORTANCE Aerobic Methanotrophs, bacteria that oxidize methane for carbon and energy, require a methanol dehydrogenase enzyme to convert methanol into formaldehyde. The calcium-dependent enzyme MxaFI has been thought to primarily carry out methanol oxidation in Methanotrophs. Recently, it was discovered that XoxF, a lanthanide-containing enzyme present in most Methanotrophs, can also oxidize methanol. In a Methanotroph with both MxaFI and XoxF, we demonstrate that lanthanides transcriptionally control genes encoding the two methanol dehydrogenases, in part by controlling expression of the response regulator MxaB. Lanthanides are abundant in the Earth9s crust, and we demonstrate that micromolar amounts of lanthanides are sufficient to suppress MxaFI expression. Thus, we present evidence that XoxF acts as the predominant methanol dehydrogenase in a Methanotroph.
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Electroporation-Based Genetic Manipulation in Type I Methanotrophs
Applied and Environmental Microbiology, 2016Co-Authors: Aaron W Puri, Yanfen Fu, Mary E LidstromAbstract:ABSTRACT Methane is becoming a major candidate for a prominent carbon feedstock in the future, and the bioconversion of methane into valuable products has drawn increasing attention. To facilitate the use of Methanotrophic organisms as industrial strains and accelerate our ability to metabolically engineer Methanotrophs, simple and rapid genetic tools are needed. Electroporation is one such enabling tool, but to date it has not been successful in a group of Methanotrophs of interest for the production of chemicals and fuels, the gammaproteobacterial (type I) Methanotrophs. In this study, we developed electroporation techniques with a high transformation efficiency for three different type I Methanotrophs: Methylomicrobium buryatense 5GB1C, Methylomonas sp. strain LW13, and Methylobactertundripaludum 21/22. We further developed this technique in M. buryatense, a haloalkaliphilic aerobic Methanotroph that demonstrates robust growth with a high carbon conversion efficiency and is well suited for industrial use for the bioconversion of methane. On the basis of the high transformation efficiency of M. buryatense, gene knockouts or integration of a foreign fragment into the chromosome can be easily achieved by direct electroporation of PCR-generated deletion or integration constructs. Moreover, site-specific recombination (FLP-FRT [FLP recombination target] recombination) and sacB counterselection systems were employed to perform marker-free manipulation, and two new antibiotics, zeocin and hygromycin, were validated to be antibiotic markers in this strain. Together, these tools facilitate the rapid genetic manipulation of M. buryatense and other type I Methanotrophs, promoting the ability to perform fundamental research and industrial process development with these strains.
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genetic tools for the industrially promising Methanotroph methylomicrobium buryatense
Applied and Environmental Microbiology, 2015Co-Authors: Aaron W Puri, Marina G Kalyuzhnaya, David A C Beck, Sarah Owen, Theodore A Chavkin, Mary E LidstromAbstract:Aerobic Methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for Methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type I) Methanotroph. M. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other Methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in M. buryatense by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractable variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make M. buryatense a promising model system for studying aerobic Methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane.
Jizheng He - One of the best experts on this subject based on the ideXlab platform.
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effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on Methanotroph abundance and methane uptake in a grazed pasture soil
Environmental Science and Pollution Research, 2013Co-Authors: Hong J Di, K C Cameron, Jizheng HeAbstract:Methane-oxidizing bacteria (Methanotrophs) in the soil are a unique group of methylotrophic bacteria that utilize methane (CH4) as their sole source of carbon and energy which limit the flux of methane to the atmosphere from soils and consume atmospheric methane. A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of Methanotrophs and on methane flux in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha(-1) and animal urine at 300 and 600 kg N ha(-1). DCD was applied at 10 kg ha(-1). The results showed that both the DNA and selected mRNA copy numbers of the Methanotroph pmoA gene were not affected by the application of urea, urine or DCD. The Methanotroph DNA and mRNA pmoA gene copy numbers were low in this soil, below 7.13 x 10(3) g(-1) soil and 3.75 x 10(3) mu g(-1) RNA, respectively. Daily CH4 flux varied slightly among different treatments during the experimental period, ranging from -12.89 g CH4 ha(-1) day(-1) to -0.83 g CH4 ha(-1) day(-1), but no significant treatment effect was found. This study suggests that the application of urea fertilizer, animal urine returns and the use of the nitrification inhibitor DCD do not significantly affect soil Methanotroph abundance or daily CH4 fluxes in grazed grassland soils.
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Methanotroph abundance not affected by applications of animal urine and a nitrification inhibitor dicyandiamide in six grazed grassland soils
Journal of Soils and Sediments, 2011Co-Authors: Hong J Di, K C Cameron, Jupei Shen, Chris S Winefield, Maureen Ocallaghan, Saman Bowatte, Jizheng HeAbstract:Methanotrophs are an important group of methane (CH(4))-oxidizing bacteria in the soil, which act as a major sink for the greenhouse gas, CH(4). In grazed grassland, one of the ecologically most sensitive areas is the animal urine patch soil, which is a major source of both nitrate (NO(3) (-)) leaching and nitrous oxide (N(2)O) emissions. Nitrification inhibitors, such as dicyandiamide (DCD), have been used to mitigate NO(3) (-) leaching and N(2)O emissions in grazed pastures. However, it is not clear if the high nitrogen loading rate in the animal urine patch soil and the use of nitrification inhibitors would have an impact on the abundance of Methanotrophs in grazed grassland soils. The purpose of this study was to determine the effect of animal urine and DCD on Methanotroph abundance in grazed grassland soils. A laboratory incubation study was conducted to determine the effect of urine and DCD applications on the abundance of Methanotrophs in six grazed grassland soils sampled from across New Zealand, using real-time PCR targeting the functional pmoA gene. Results showed that the pmoA gene copy numbers were low in these soils, mostly below 2.36 x 10(4) g(-1) soil except in the West Coast soil where pmoA gene copy number reached 8.95 x 10(5) g(-1) soil. Most of the clones identified were aligned to the type II Methanotrophs. There was no significant effect (P l 0.05) on the abundance of Methanotrophs by the applications of urine at 1,000 kg N ha(-1) or DCD at 10 kg ha(-1). These results suggest that the abundance of Methanotrophs is not affected by urine deposition or the application of DCD to mitigate NO(3) (-) leaching and N(2)O emissions in grazed grassland soils.
J C Murrell - One of the best experts on this subject based on the ideXlab platform.
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nutrient amendments in soil dna stable isotope probing experiments reduce the observed Methanotroph diversity
Applied and Environmental Microbiology, 2007Co-Authors: Aurelie Cebron, Nancy Stralispavese, Levente Bodrossy, Andrew C Singer, Ian P Thompson, James I Prosser, J C MurrellAbstract:Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating 13C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient 13C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, Methanotroph activity and diversity in soil was examined during the consumption of 13CH4 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most Methanotroph diversity (type I and type II Methanotrophs) was observed in nonamended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of 13CH4 was slow and some cross-feeding of 13C occurred, thereby leading to labeling of nonMethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of 13CH4, resulting in the labeling of a less diverse population of only type I Methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of 13C into active Methanotrophs while avoiding the cross-feeding of 13C.
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molecular analysis of the pmo particulate methane monooxygenase operons from two type ii Methanotrophs
Applied and Environmental Microbiology, 2000Co-Authors: Bettina Gilbert, Ian R Mcdonald, R Finch, Graham P Stafford, A K Nielsen, J C MurrellAbstract:The particulate methane monooxygenase gene clusters, pmoCAB, from two representative type II Methanotrophs of the a-Proteobacteria, Methylosinus trichosporium OB3b and Methylocystis sp. strain M, have been cloned and sequenced. Primer extension experiments revealed that the pmo cluster is probably transcribed from a single transcriptional start site located 300 bp upstream of the start of the first gene, pmoC, for Methylocystis sp. strain M. Immediately upstream of the putative start site, consensus sequences for s 70 promoters were identified, suggesting that these pmo genes are recognized by s 70 and negatively regulated under low-copper conditions. The pmo genes were cloned in several overlapping fragments, since parts of these genes appeared to be toxic to the Escherichia coli host. Methanotrophs contain two virtually identical copies of pmo genes, and it was necessary to use Southern blotting and probing with pmo gene fragments in order to differentiate between the two pmoCAB clusters in both Methanotrophs. The complete DNA sequence of one copy of pmo genes from each organism is reported here. The gene sequences are 84% similar to each other and 75% similar to that of a type I Methanotroph of the g-Proteobacteria, Methylococcus capsulatus Bath. The derived proteins PmoC and PmoA are predicted to be highly hydrophobic and consist mainly of transmembranespanning regions, whereas PmoB has only two putative transmembrane-spanning helices. Hybridization experiments showed that there are two copies of pmoC in both M. trichosporium OB3b and Methylocystis sp. strain M, and not three copies as found in M. capsulatus Bath.
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Detection of methanogens and Methanotrophs in natural environments
Global Change Biology, 1997Co-Authors: Donald A. Ritchie, Ian R Mcdonald, Clive Edwards, J C MurrellAbstract:The role of methane as a greenhouse gas and the contribution of bacteria to the production (methanogenesis) and destruction (methane oxidation) of methane is described. Using experimental approaches based on DNA sequences identifying either methanogen-specific or Methanotroph-specific gene sequences methods were developed to broaden the detection and identification of methane metabolizing bacteria in natural environments. These methods were focused on blanket bog peat but are suitable for other environments. In addition to group specific 16S rRNA DNA sequences, specific functional gene probes based on methane coenzyme reductase sequences for methanogens and methane monooxygenase sequences for Methanotrophs, were developed. These sequences were used in PCR-based protocols to detect and amplify specific gene sequences from the total DNA isolated from transverse sections of blanket bog peat. This permitted the analysis of the vertical distribution of methanogen and Methanotroph populations, discrimination between different sub-sets of these populations, and the identification of novel organisms not previously detected by culture-based methods.
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the soluble methane monooxygenase gene cluster of the trichloroethylene degrading Methanotroph methylocystis sp strain m
Applied and Environmental Microbiology, 1997Co-Authors: I R Mcdonald, H Uchiyama, S Kambe, O Yagi, J C MurrellAbstract:In Methanotrophic bacteria, methane is oxidized to methanol by the enzyme methane monooxygenase (MMO). The soluble MMO enzyme complex from Methylocystis sp. strain M also oxidizes a wide range of aliphatic and aromatic compounds, including trichloroethylene. In this study, heterologous DNA probes from the type II Methanotroph Methylosinus trichosporium OB3b were used to isolate souble MMO (sMMO) genes from the type II Methanotroph Methylocystis sp. strain M. sMMO genes from strain M are clustered on the chromosome and show a high degree of identity with the corresponding genes from Methylosinus trichosporium OB3b. Sequencing and phylogenetic analysis of the 16S rRNA gene from Methylocystis sp. strain M have confirmed that it is most closely related to the type II Methanotroph Methylocystis parvus OBBP, which, unlike Methylocystis sp. strain M, does not possess an sMMO. A similar phylogenetic analysis using the pmoA gene, which encodes the 27-kDa polypeptide of the particulate MMO, also places Methylocystis sp. strain M firmly in the genus Methylocystis. This is the first report of isolation and characterization of methane oxidation genes from Methanotrophs of the genus Methylocystis.
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detection of novel marine Methanotrophs using phylogenetic and functional gene probes after methane enrichment
Microbiology, 1995Co-Authors: Andrew J Holmes, N J P Owens, J C MurrellAbstract:A major limitation of rRNA-targeted group-specific probes is that they may cross-react with organisms of other physiological, or even phylogenetic groups when applied to environmental samples containing unknown sequences. We have exploited the restricted physiology of methane-oxidizing bacteria to assess the specificity and efficiency of probes for this physiological type which target the 16S rRNA or genes involved in Methanotroph physiology. Seawater samples were enriched for Methanotrophs by addition of methane and essential nutrients. The changes in composition of the bacterial population were monitored by analysis of 16S rRNA gene libraries. Methanotroph group-specific probes failed to give a signal with samples from these enrichments even though a methanol dehydrogenase structural gene was detected. A 16S rDNA sequence that was abundant only after methane addition was recovered and found to show a close phylogenetic relationship to Methylomonas. Organisms containing this sequence were observed in enrichments by in situ hybridization. The combination of enrichment on methane and screening with the broad specificity methanol dehydrogenase probe allowed detection of novel Methanotrophs that were not detected with the original suite of Methanotroph group-specific probes.
Adrian Ho - One of the best experts on this subject based on the ideXlab platform.
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Succession of bacterial community and Methanotrophy during lake shrinkage
Journal of Soils and Sediments, 2019Co-Authors: Yongliang Mo, Taogetao Baoyin, Adrian Ho, Feng Jin, Yan Zheng, Zhongjun JiaAbstract:PurposeThe shrinkage of vast inland lakes affects microbially mediated soil biogeochemical processes, which are critical for maintaining ecosystem sustainability, such as microbial diversity and a balanced CH_4 budget. Here we aimed to elucidate shifts in the bacterial community and Methanotrophy during the shrinkage of a saline lake.Materials and methodsSediments and soils along a gradient transecting a saline lake, saline riparian land, and grassland were collected. The succession of microbial communities was characterized by high-throughput sequencing of the V4-V5 region of 16S rRNA genes coupled to non-metric multidimensional scaling (NMDS), linear discriminant effect size (LEfSe), community assembly, and co-occurrence network analyses. We further incubated these samples under a 10% CH_4 ( v / v ) atmospheric condition to determine the response of methane oxidation potentials and of Methanotrophs to lake shrinkage by using pmoA -based qPCR and amplicon sequencing.Results and discussionLEfSe and NMDS analyses showed significant differences in bacterial communities among 3 stages of lake shrinkage. The microbial taxa with the highest increase were phylogenetically affiliated with unclassified Rhizobiales, Panacagrimonas , and Pseudomonas in saline and grassland soils when compared with sediments. Microbial community assembly was largely determined by deterministic rather than stochastic processes (NTI > 2). The drastic increase of Methylocystis -like (type II) Methanotrophs was observed during lake shrinkage, while type I Methanotrophs showed a decreasing trend. However, upon consuming high-concentration methane of about 10%, type I Methanotrophs dominated methane-oxidizing communities in lake sediment ( Methylomonas ), riparian saline soil ( Methylomicrobium ), and grassland soil ( Methylobacter ). Structural equation model identified soil pH, C/N ratio, and soil texture as key factors affecting methane oxidation rates and the Methanotrophic community.ConclusionsLake shrinkage showed profound impacts on the overall bacterial communities and methane oxidizers. Soil physico-chemical properties likely shaped the bacterial community and phylogenetically distinct Methanotrophs during lake shrinkage.
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Environmental Applications of Methanotrophs
Methanotrophs, 2019Co-Authors: Adrian Ho, Miye Kwon, Marcus A. Horn, Sukhwan YoonAbstract:Methanotrophs are microorganisms that are able to utilize methane as the electron donor and carbon source. For long, Methanotrophs have been widely studied for their application in environmental biotechnology, due mainly to the exclusive ownership of the unique enzymes that mediate oxidation of methane to methanol, namely the particulate methane monooxygenases (pMMO) and soluble methane monooxygenases (sMMO). Utilizing these methane monooxygenases, Methanotrophs are capable of co-oxidizing a broad range of organic pollutants including chlorinated ethenes. Thus, Methanotrophs have long been studied and utilized as biocatalysts for in situ bioremediation of soil and aquatic environments contaminated with these xenobiotic compounds. Due to the growing concerns in anthropogenically induced climate change and global warming, Methanotrophs have increasingly gained attention also for greenhouse gas mitigation purposes. Active methane removal using Methanotrophic biofilters of diverse configurations have proven to be effective for treatments of gases with relatively high methane concentrations, e.g., landfill gases and animal husbandry tank exhausts. Furthermore, improving the atmospheric methane sink capability of agricultural soils has been one of the foremost foci of climate-smart soil research. This chapter provides an extensive overview of scientific and engineering breakthroughs geared towards practical applications of Methanotroph biotechnology in managing impending environmental problems.
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Novel approaches and reasons to isolate Methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives
Applied Microbiology and Biotechnology, 2018Co-Authors: Miye Kwon, Adrian Ho, Sukhwan YoonAbstract:The recent drop in the price of natural gas has rekindled the interests in Methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in Methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse Methanotrophs with relatively high growth rates. For long, isolation of Methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted Methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive Methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing Methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable Methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.
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Termites facilitate methane oxidation and shape the Methanotrophic community
Applied and Environmental Microbiology, 2013Co-Authors: Adrian Ho, H. Erens, B. B. Mujinya, Bellinda Schneider, Geert Baert, Peter Frenzel, Pascal Boeckx, Nico Boon, Eric V. Van RanstAbstract:Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (Methanotrophs). However, a considerable fraction of the methane produced can be consumed by Methanotrophs that inhabit the mound material, yet the Methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and in situ (∼0.004%) methane concentrations through a vertical profile of a termite (Macrotermes falciger) mound and a reference soil. Interestingly, the mound material showed higher Methanotrophic activity. The Methanotroph community structure was determined by means of a pmoA-based diagnostic microarray. Although the Methanotrophs in the mound were derived from populations in the reference soil, it appears that termite activity selected for a distinct community. Applying an indicator species analysis revealed that putative atmospheric methane oxidizers (high-indicator-value probes specific for the JR3 cluster) were indicative of the active nest area, whereas Methanotrophs belonging to both type I and type II were indicative of the reference soil. We conclude that termites modify their environment, resulting in higher methane oxidation and selecting and/or enriching for a distinct Methanotroph population.
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Heat stress and methane-oxidizing bacteria: Effects on activity and population dynamics
Soil Biology and Biochemistry, 2012Co-Authors: Adrian Ho, Peter FrenzelAbstract:We studied the effects of an acute temperature increase (heat stress) on methane oxidation and Methanotroph community structure in a laboratory-scale experiment with paddy soil. Methane oxidation was resilient, recovering already six days after heat stress, and later on even reached higher values than in the control. It was consistently shown by qPCR and by terminal restriction length polymorphism (T-RFLP) that type II Methanotrophs increased over time. While this was a general trend, the initial increase of type II was much more pronounced after heat stress at 45 °C. Type I Methanotrophs were inversely correlated to type II and temperature. Overall, heat stress is a potential factor shifting the community towards a dominance of type II Methanotrophs. © 2012 Elsevier Ltd.