Publications

sterol synthesis in diverse bacteria.	sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. however, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. phylogenomic studies have identified g ...	2016	27446030
draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.	genome sequences of methylobacter luteus, methylobacter whittenburyi, methylosarcina fibrata, methylomicrobium agile, and methylovulum miyakonense were generated. the strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.	2015	26044417
diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoa as molecular marker.	methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. in particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoa) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences rep ...	2015	26696968
characterization of anode and anolyte community growth and the impact of impedance in a microbial fuel cell.	a laboratory-scale two-chamber microbial fuel cell employing an aerated cathode with no catalyst was inoculated with mixed inoculum and acetate as the carbon source. electrochemical impedance spectroscopy (eis) was used to study the behavior of the mfc during initial biofilm (week 1) and maximum power density (week 20). eis were performed on the anode chamber, biofilm (without anolyte) and anolyte (without biofilm). nyquist plots of the eis data were fitted with two equivalent electrical circuit ...	2014	25487741
genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in methylocystis sp. strain sc2.	methylocystis sp. strain sc2 can adapt to a wide range of methane concentrations. this is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. to gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 mb chromosome and two large plasmids.	2013	24130670
the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments.	the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ...	2013	23451130
structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils.	climate change will lead to more extreme precipitation and associated increase of flooding events of soils. this can turn these soils from a sink into a source of atmospheric methane. the latter will depend on the balance of microbial methane production and oxidation. in the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. four sites differing in flooding frequency were sampled and soil-physico-chem ...	2012	22408730
diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (fish).	the diversity of cultivable methane-oxidizing bacteria (mob) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (fish) techniques. seven microsites of a japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. based on pmoa gene analysis and transmission electron microscopy (tem), four type i, and nine type ...	2012	22446309
detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing.	genomic analysis of the methanotrophic verrucomicrobium "methylacidiphilum infernorum" strain v4 has shown that most pathways conferring its methanotrophic lifestyle are similar to those found in proteobacterial methanotrophs. however, due to the large sequence divergence of its methane monooxygenase-encoding genes (pmo), "universal" pmoa polymerase chain reaction (pcr) primers do not target these bacteria. unlike proteobacterial methanotrophs, "methylacidiphilum" fixes carbon autotrophically, a ...	2012	22912630
corals form characteristic associations with symbiotic nitrogen-fixing bacteria.	the complex symbiotic relationship between corals and their dinoflagellate partner symbiodinium is believed to be sustained through close associations with mutualistic bacterial communities, though little is known about coral associations with bacterial groups able to fix nitrogen (diazotrophs). in this study, we investigated the diversity of diazotrophic bacterial communities associated with three common coral species (acropora millepora, acropora muricata, and pocillopora damicormis) from thre ...	2012	22344646
Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia.	Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest so ...	2011	21984248
identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing.	marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. we used stable isotope probing (sip) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the coal oil point seep field located offshore of santa barbara, california. after incubating sediment with (13)c-labeled methane, ethane, or propane, we confirmed the incorporation of (13)c into fatty acids and dna. terminal restriction fragment length polymorphism (t-rflp) analys ...	2010	20675448
stable isotope probing analysis of the diversity and activity of methanotrophic bacteria in soils from the canadian high arctic.	the melting of permafrost and its potential impact on ch(4) emissions are major concerns in the context of global warming. methanotrophic bacteria have the capacity to mitigate ch(4) emissions from melting permafrost. here, we used quantitative pcr (qpcr), stable isotope probing (sip) of dna, denaturing gradient gel electrophoresis (dgge) fingerprinting, and sequencing of the 16s rrna and pmoa genes to study the activity and diversity of methanotrophic bacteria in active-layer soils from ellesme ...	2010	20622133
two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in methylocystis sp. strain sc2.	methane-oxidizing bacteria (methanotrophs) attenuate methane emission from major sources, such as wetlands, rice paddies, and landfills, and constitute the only biological sink for atmospheric methane in upland soils. their key enzyme is particulate methane monooxygenase (pmmo), which converts methane to methanol. it has long been believed that methane at the trace atmospheric mixing ratio of 1.75 parts per million by volume (ppmv) is not oxidized by the methanotrophs cultured to date, but rathe ...	2008	18632585
differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils.	the impact of environmental perturbation (e.g., nitrogenous fertilizers) on the dynamics of methane fluxes from soils and wetland systems is poorly understood. results of fertilizer studies are often contradictory, even within similar ecosystems. in the present study the hypothesis of whether these contradictory results may be explained by the composition of the methane-consuming microbial community and hence whether methanotrophic diversity affects methane fluxes was investigated. to this end, ...	2006	16461686
sensing of gram-positive bacteria in drosophila: gnbp1 is needed to process and present peptidoglycan to pgrp-sa.	genetic evidence indicates that drosophila defense against gram-positive bacteria is mediated by two putative pattern recognition receptors acting upstream of toll, namely gram-negative binding protein 1 (gnbp1) and peptidoglycan recognition protein sa (pgrp-sa). until now however, the molecular recognition proceedings for sensing of gram-positive pathogens were not known. in the present, we report the physical interaction between gnbp1 and pgrp-sa using recombinant proteins. gnbp1 was able to h ...	2006	17024181
nutrient amendments in soil dna stable isotope probing experiments reduce the observed methanotroph diversity.	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 activi ...	2006	17122398
nutrient amendments in soil dna stable isotope probing experiments reduce the observed methanotroph diversity.	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 activi ...	2006	17122398
characterization of c1-metabolizing prokaryotic communities in methane seep habitats at the kuroshima knoll, southern ryukyu arc, by analyzing pmoa, mmox, mxaf, mcra, and 16s rrna genes.	samples from three submerged sites (mc, a core obtained in the methane seep area; mr, a reference core obtained at a distance from the methane seep; and hc, a gas-bubbling carbonate sample) at the kuroshima knoll in the southern ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16s rrna gene analyses by quantitative real-time pcr and clone library sequencing revealed that the mc core sediments contained abu ...	2004	15574947
wide distribution of a novel pmoa-like gene copy among type ii methanotrophs, and its expression in methylocystis strain sc2.	experiments were conducted to determine if a novel pmoa-like gene (pmoa2) recently discovered in the methane-oxidizing bacterium methylocystis strain sc2 (p. f. dunfield, m. tchawa yimga, s. d. dedysh, u. berger, w. liesack, and j. heyer, fems microbiol. ecol. 41:17-26, 2002) is present in other methane-oxidizing bacteria (mob), and if it is expressed. a newly developed primer combination (pmoa206f-pmoa703b) allowed a differential detection of pmoa1 and pmoa2. by using this primer combination, w ...	2003	12957949
quantitative detection of methanotrophs in soil by novel pmoa-targeted real-time pcr assays.	methane oxidation in soils is mostly accomplished by methanotrophic bacteria. little is known about the abundance of methanotrophs in soils, since quantification by cultivation and microscopic techniques is cumbersome. comparison of 16s ribosomal dna and pmoa (alpha subunit of the particulate methane monooxygenase) phylogenetic trees showed good correlation and revealed five distinct groups of methanotrophs within the alpha and gamma subclasses of proteobacteria: the methylococcus group, the met ...	2003	12732507
detection and enumeration of methanotrophs in acidic sphagnum peat by 16s rrna fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for methylocella palustris.	two 16s rrna-targeted oligonucleotide probes, mcell-1026 and mcell-181, were developed for specific detection of the acidophilic methanotroph methylocella palustris using fluorescence in situ hybridization (fish). the fluorescence signal of probe mcell-181 was enhanced by its combined application with the oligonucleotide helper probe h158. mcell-1026 and mcell-181, as well as 16s rrna oligonucleotide probes with reported group specificity for either type i methanotrophs (probes m-84 and m-705) o ...	2001	11571193
family- and genus-level 16s rrna-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria.	methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. to facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16s rrna from environmental samples. two probes target methanotrophs in the family methylocystaceae (type ii methanotrophs) as a group. no oligonucleotide signatures t ...	2001	11571178
comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments.	the oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. in this study, we compared results of rrna gene (rdna) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the californian continental margin. two distinct archaeal lineages (anme-1 and anme-2), peripherally related to the order methanosarcinales, were consistently associated ...	2001	11282650
detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoa, mmox, mxaf, and 16s rrna and ribosomal dna, including pmoa-based terminal restriction fragment length polymorphism profiling.	the diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. the research focused mainly on the retrieval of pmoa, which encodes the alpha subunit of the particulate methane monooxygenase. a novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (t-rflp) technique. the t-rflp profiles clearly revealed a more complex root-associated methanot ...	2001	11526021
comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria.	in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ...	2000	11055963
production and consumption of nitric oxide by three methanotrophic bacteria.	we studied nitrogen oxide production and consumption by methanotrophs methylobacter luteus (group i), methylosinus trichosporium ob3b (group ii), and an isolate from a hardwood swamp soil, here identified by 16s ribosomal dna sequencing as methylobacter sp. strain t20 (group i). all could consume nitric oxide (nitrogen monoxide, no), and produce small amounts of nitrous oxide (n(2)o). only methylobacter strain t20 produced large amounts of no (>250 parts per million by volume [ppmv] in the heads ...	2000	10966405
molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments.	the 16s rrna and pmoa genes from natural populations of methane-oxidizing bacteria (methanotrophs) were pcr amplified from total community dna extracted from lake washington sediments obtained from the area where peak methane oxidation occurred. clone libraries were constructed for each of the genes, and approximately 200 clones from each library were analyzed by using restriction fragment length polymorphism (rflp) and the tetrameric restriction enzymes mspi, haeiii, and hhai. the pcr products ...	1999	10543824
methanotroph diversity in landfill soil: isolation of novel type i and type ii methanotrophs whose presence was suggested by culture-independent 16s ribosomal dna analysis.	the diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. for the first of the molecular studies, two primer pairs specific for the 16s rrna gene of validly published type i (including the former type x) and type ii methanotrophs were identified and tested. these primers were used to amplify directly extracted soil dna, and the products were used to const ...	1999	10543800
effect of selected monoterpenes on methane oxidation, denitrification, and aerobic metabolism by bacteria in pure culture.	selected monoterpenes inhibited methane oxidation by methanotrophs (methylosinus trichosporium ob3b, methylobacter luteus), denitrification by environmental isolates, and aerobic metabolism by several heterotrophic pure cultures. inhibition occurred to various extents and was transient. complete inhibition of methane oxidation by methylosinus trichosporium ob3b with 1.1 mm (-)-alpha-pinene lasted for more than 2 days with a culture of optical density of 0.05 before activity resumed. inhibition w ...	1998	9464387
atmospheric methane consumption by forest soils and extracted bacteria at different ph values.	the effect of ph on atmospheric methane (ch4) consumption was studied with slurries of forest soils and with bacteria extracted from the same soils. soil samples were collected from a mixed hardwood stand in new hampshire, from jackpine and aspen stands at the boreas (boreal ecosystem atmosphere study) site near thompson, northern manitoba, from sites in southern québec, including a beech stand and a meadow, and from a site in ontario (cultivated humisol). consumption of atmospheric ch4 (concent ...	1998	9647806