| construction and use of an ipb dna module to generate pseudomonas strains with constitutive trichloroethene and isopropylbenzene oxidation activity. | pseudomonas sp. strain jr1 exhibits trichloroethene (tce) oxidation activity with isopropylbenzene (ipb) as the inducer substrate. we previously reported the genes encoding the first three enzymes of the ipb-degradative pathway (ipba1, ipba2, ipba3, ipba4, ipbb, and ipbc) and identified the initial ipb dioxygenase (ipba1 a2a3a4) as responsible for tce cooxidation (u. pflugmacher, b. averhoff, and g. gottschalk, appl. environ. microbiol. 62:3967-3977, 1996). primer extension analyses revealed mul ... | 1998 | 9647815 |
| distribution and life strategies of two bacterial populations in a eutrophic lake | monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified lake plusssee and characterize their life strategies. populations of comamonas acidovorans px54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas aeromonas hydrophila pu7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i. e., in the water layer with the h ... | 1998 | 9758799 |
| methanotrophs and methanogens in masonry | methanotrophs were present in 48 of 225 stone samples which were removed from 19 historical buildings in germany and italy. the average cell number of methanotrophs was 20 cfu per g of stone, and their activities ranged between 11 and 42 pmol of ch4 g of stone-1 day-1. twelve strains of methane-oxidizing bacteria were isolated. they belonged to the type ii methanotrophs of the genera methylocystis, methylosinus, and methylobacterium. in masonry, growth substrates like methane or methanol are ava ... | 1998 | 9797318 |
| assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. | biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. in this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. both 16s rrna and ammonia monooxygenase (amoa) genes were used to characterize the heterotrophi ... | 1998 | 9835577 |
| aerobic degradation of 1,1,1-trichloroethane by mycobacterium spp. isolated from soil. | two strains of 1,1,1-trichloroethane (tca)-degrading bacteria, ta5 and ta27, were isolated from soil and identified as mycobacterium spp. strains ta5 and ta27 could degrade 25 and 75 mg. liter of tca(-1) cometabolically in the presence of ethane as a carbon source, respectively. the compound 2,2,2-trichloroethanol was produced as a metabolite of the degradation process. | 1999 | 10508110 |
| 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 |
| 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 |
| bacillus subtilis yckg and yckf encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckh is required for their expression. | the ribulose monophosphate (rump) pathway is one of the metabolic pathways for the synthesis of compounds containing carbon-carbon bonds from one-carbon units and is found in many methane- and methanol-utilizing bacteria, which are known as methylotrophs. the characteristic enzymes of this pathway are 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexuloisomerase (phi), neither of which was thought to exist outside methylotrophs. however, the presumed yckg gene product (yckg) of bacillus ... | 1999 | 10572115 |
| soluble methane monooxygenase gene clusters from trichloroethylene-degrading methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. | the soluble mmo (smmo) gene clusters from group i methanotrophs were characterized. an 8.1-kb kpni fragment from methylomonas sp. strain kswiii and a 7.5-kb sali fragment from methylomonas sp. strain kspiii which contained the smmo gene clusters were cloned and sequenced. the sequences of these two fragments were almost identical. the smmo gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described smmo gene c ... | 1999 | 10583965 |
| 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 |
| polyclonal antibodies recognizing the amob protein of ammonia oxidizers of the beta-subclass of the class proteobacteria. | a 41-kda protein of nitrosomonas eutropha was purified, and the n-terminal amino acid sequence was found to be nearly identical with the sequence of amob, a subunit of ammonia monooxygenase. this protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the beta-subclass of proteobacteria (nitrosomonas, including nitrosococcus mobilis, which belongs phylogenetically to nitrosomonas; nitrosospira; nitrosolobus; and n ... | 2001 | 11133435 |
| enrichment of high-affinity co oxidizers in maine forest soil. | carboxydotrophic activity in forest soils was enriched by incubation in a flowthrough system with elevated concentrations of headspace co (40 to 400 ppm). co uptake increased substantially over time, while the apparent k(m) ((app)k(m)) for uptake remained similar to that of unenriched soils (<10 to 20 ppm). carboxydotrophic activity was transferred to and further enriched in sterile sand and forest soil. the (app)k(m)s for secondary and tertiary enrichments remained similar to values for unenric ... | 2001 | 11472946 |
| nifh sequences and nitrogen fixation in type i and type ii methanotrophs. | some methane-oxidizing bacteria (methanotrophs) are known to be capable of expressing nitrogenase and utilizing n2 as a nitrogen source. however, no sequences are available for nif genes in these strains, and the known nitrogen-fixing methanotrophs are confined mainly to a few genera. the purpose of this work was to assess the nitrogen-fixing capabilities of a variety of methanotroph strains. nifh gene fragments from four type i methanotrophs and seven type ii methanotrophs were pcr amplified an ... | 2001 | 11525998 |
| 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 |
| 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 |
| 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 |
| crystal structure of bacillus subtilis yckf: structural and functional evolution. | the crystal structure of the yckf protein from bacillus subtilis was determined with mad phasing and refined at 1.95a resolution. yckf forms a tight tetramer both in crystals and in solution. conservation of such oligomerization in other phosphate sugar isomerases indicates that the crystallographically observed tetramer is physiologically relevant. the structure of yckf was compared to with its ortholog from methanococcus jannaschii, mj1247. both of these proteins have phosphate hexulose isomer ... | 2004 | 15363790 |
| 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 |
| clonothrix fusca roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. | crenothrix polyspora cohn 1870 and clonothrix fusca roze 1896 are two filamentous, sheathed microorganisms exhibiting complex morphological differentiation, whose phylogeny and physiology have been obscure for a long time due to the inability to cultivate them. very recently, dna sequencing data from uncultured c. polyspora-enriched material have suggested that crenothrix is a methane-oxidizing gamma-proteobacterium (39). in contrast, the possible ecological function of c. fusca, originally cons ... | 2007 | 17416684 |
| planktonic and sediment-associated aerobic methanotrophs in two seep systems along the north american margin. | 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 v ... | 2008 | 18487407 |
| detection, isolation, and characterization of acidophilic methanotrophs from sphagnum mosses. | sphagnum peatlands are important ecosystems in the methane cycle. methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. yet little is known about the diversity and identity of the methanotrophs present in and on sphagnum mosses of peatlands, and only a few isolates are known. the methanotrophic community in sphagnum mosses, originating from a dutch peat bog, was investigated using a pmoa microarray. a high biodiversity of both gamma- and alphaprote ... | 2011 | 21724892 |
| complete genome sequence of the aerobic marine methanotroph methylomonas methanica mc09. | methylomonas methanica mc09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the gammaproteobacteria, isolated from coastal seawater. here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph. | 2011 | 22123758 |
| miniaturized extinction culturing is the preferred strategy for rapid isolation of fast-growing methane-oxidizing bacteria. | methane-oxidizing bacteria (mob) have a large potential as a microbial sink for the greenhouse gas methane as well as for biotechnological purposes. however, their application in biotechnology has so far been hampered, in part due to the relative slow growth rate of the available strains. to enable the availability of novel strains, this study compares the isolation of mob by conventional dilution plating with miniaturized extinction culturing, both performed after an initial enrichment step. th ... | 2011 | 22070783 |
| 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 |
| beating the acetyl coenzyme a-pathway to the origin of life. | attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. although we have no guarantee that life at its origin necessarily resembled biology in extant ... | 2013 | 23754811 |
| 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 |
| methods of combinatorial optimization to reveal factors affecting gene length. | in this paper we present a novel method for genome ranking according to gene lengths. the main outcomes described in this paper are the following: the formulation of the genome ranking problem, presentation of relevant approaches to solve it, and the demonstration of preliminary results from prokaryotic genomes ordering. using a subset of prokaryotic genomes, we attempted to uncover factors affecting gene length. we have demonstrated that hyperthermophilic species have shorter genes as compared ... | 2012 | 23300345 |
| lengths of orthologous prokaryotic proteins are affected by evolutionary factors. | proteins of the same functional family (for example, kinases) may have significantly different lengths. it is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. the main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. we believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome ... | 2015 | 26114113 |
| structural, bioinformatic, and in vivo analyses of two treponema pallidum lipoproteins reveal a unique trap transporter. | treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite atp-independent periplasmic transporter (trap-t). trap-ts typically employ a periplasmic substrate-binding protein (sbp) to deliver the cognate ligand to the transmembrane symporter. herein, we demonstrate that the genes encoding the putative trap-t components from t. pallidum, tp0957 (the sbp), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. we determined the cryst ... | 2012 | 22306465 |
| chaperone addiction of toxin-antitoxin systems. | bacterial toxin-antitoxin (ta) systems, in which a labile antitoxin binds and inhibits the toxin, can promote adaptation and persistence by modulating bacterial growth in response to stress. some atypical ta systems, known as tripartite toxin-antitoxin-chaperone (tac) modules, include a molecular chaperone that facilitates folding and protects the antitoxin from degradation. here we use a tac module from mycobacterium tuberculosis as a model to investigate the molecular mechanisms by which class ... | 2016 | 27827369 |
| iodide oxidation by a novel multicopper oxidase from the alphaproteobacterium strain q-1. | alphaproteobacterium strain q-1 is able to oxidize iodide (i(-)) to molecular iodine (i(2)) by an oxidase-like enzyme. one of the two isoforms of the iodide-oxidizing enzyme (ioe-ii) produced by this strain was excised from a native polyacrylamide gel, eluted, and purified. ioe-ii appeared as a single band (51 kda) and showed significant in-gel iodide-oxidizing activity in sodium dodecyl sulfate-polyacrylamide gel electrophoresis without heat treatment. however, at least two bands with much high ... | 2012 | 22447601 |
| 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 |
| 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 |
| members of the methanotrophic genus methylomarinum inhabit inland mud pots. | proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph methylomarinum va ... | 2016 | 27478692 |
| the expanding world of methylotrophic metabolism. | 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 disco ... | 2009 | 19514844 |
| the more, the merrier: heterotroph richness stimulates methanotrophic activity. | although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. we considered methane oxidation rate as a functional response variable. our results showed a significan ... | 2014 | 24785289 |
| quantitative and qualitative impact of hospital effluent on dissemination of the integron pool. | there is increasing evidence that human activity, and especially the resulting effluent, has a major role in the dissemination of bacterial antibiotic-resistance determinants in the environment. hospitals are the major antibiotic consumers and thus facilitate the spread of antibiotic resistance. questions are increasingly being raised about the management of hospital effluents, but their involvement in antibiotic-resistance dissemination has never been assessed. integrons are a paradigm of genet ... | 2013 | 24152716 |
| quantitative and qualitative impact of hospital effluent on dissemination of the integron pool. | there is increasing evidence that human activity, and especially the resulting effluent, has a major role in the dissemination of bacterial antibiotic-resistance determinants in the environment. hospitals are the major antibiotic consumers and thus facilitate the spread of antibiotic resistance. questions are increasingly being raised about the management of hospital effluents, but their involvement in antibiotic-resistance dissemination has never been assessed. integrons are a paradigm of genet ... | 2013 | 24152716 |
| the diversity of sulfide oxidation and sulfate reduction genes expressed by the bacterial communities of the cariaco basin, venezuela. | qualitative expression of dissimilative sulfite reductase (dsra), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. neither of the two could be amplified from mrna retrieved with niskin bottles but were amplified from mrna retrieved by the deep sid. the sqr and sqr-like genes retrieved from the cariaco basin were related to the sqr genes from a bradyrhizobium sp., methylomicrobium alcaliphilum, sulfurovum sp. nbc37-1, sul ... | 2016 | 27651847 |
| complete sequence analysis of two methanotroph-specific repabc-containing plasmids from methylocystis sp. strain sc2. | the complete nucleotide sequences of two large, low-copy-number plasmids of 229.6 kb (pbsc2-1) and 143.5 kb (pbsc2-2) were determined during assembly of the whole-genome shotgun sequences of the methane-oxidizing bacterium methylocystis sp. strain sc2. the physical existence of the two plasmids in strain sc2 was confirmed by pulsed-field gel electrophoresis followed by southern hybridization. both plasmids have a conserved replication module of the repabc system and carry genes involved in their ... | 2012 | 22504811 |
| interactions of methylotrophs with plants and other heterotrophic bacteria. | methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and co₂, the two most important greenhouse gases. this review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. methanol-utilizing methylotrophs ... | 2015 | 27682083 |
| facultative methanotrophs revisited. | | 2005 | 15968038 |
| functional gene analysis of freshwater iron-rich flocs at circumneutral ph and isolation of a stalk-forming microaerophilic iron-oxidizing bacterium. | iron-rich flocs often occur where anoxic water containing ferrous iron encounters oxygenated environments. culture-independent molecular analyses have revealed the presence of 16s rrna gene sequences related to diverse bacteria, including autotrophic iron oxidizers and methanotrophs in iron-rich flocs; however, the metabolic functions of the microbial communities remain poorly characterized, particularly regarding carbon cycling. in the present study, we cultivated iron-oxidizing bacteria (feob) ... | 2013 | 23811518 |
| microbial minorities modulate methane consumption through niche partitioning. | microbes catalyze all major geochemical cycles on earth. however, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. we show that the dynamics ... | 2013 | 23788331 |
| 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 |
| survival or revival: long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria. | knowledge on long-term preservation of micro-organisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. preservation of fastidious organisms such as methane-oxidizing bacteria (mob) has proven difficult. most mob do not survive lyophilization and only some can be cryopreserved successfully for short periods. a large-scale study was designed for a diverse set of mob applying fifteen cryopreservation or lyophilization ... | 2012 | 22539945 |
| characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. | the global methane cycle includes both terrestrial and atmospheric processes and may contribute to feedback regulation of the climate. most oxic soils are a net sink for methane, and these soils consume approximately 20 to 60 tg of methane per year. the soil sink for atmospheric methane is microbially mediated and sensitive to disturbance. a decrease in the capacity of this sink may have contributed to the approximately 1%. year(-1) increase in the atmospheric methane level in this century. the ... | 1999 | 10427012 |
| radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. | microorganisms that oxidize atmospheric methane in soils were characterized by radioactive labelling with (14)ch(4) followed by analysis of radiolabelled phospholipid ester-linked fatty acids ((14)c-plfas). the radioactive fingerprinting technique was used to compare active methanotrophs in soil samples from greenland, denmark, the united states, and brazil. the (14)c-plfa fingerprints indicated that closely related methanotrophic bacteria were responsible for the oxidation of atmospheric methan ... | 1999 | 10473417 |
| relevance of gc content to the conservation of dna polymerase iii/mismatch repair system in gram-positive bacteria. | the mechanism of dna replication is one of the driving forces of genome evolution. bacterial dna polymerase iii, the primary complex of dna replication, consists of polc and dnae. polc is conserved in gram-positive bacteria, especially in the firmicutes with low gc content, whereas dnae is widely conserved in most gram-negative and gram-positive bacteria. polc contains two domains, the 3'-5'exonuclease domain and the polymerase domain, while dnae only possesses the polymerase domain. accordingly ... | 2013 | 24062730 |
| methane and trichloroethylene degradation by methylosinus trichosporium ob3b expressing particulate methane monooxygenase. | whole-cell assays of methane and trichloroethylene (tce) consumption have been performed on methylosinus trichosporium ob3b expressing particulate methane monooxygenase (pmmo). from these assays it is apparent that varying the growth concentration of copper causes a change in the kinetics of methane and tce degradation. for m. trichosporium ob3b, increasing the copper growth concentration from 2.5 to 20 mum caused the maximal degradation rate of methane (v(max)) to decrease from 300 to 82 nmol o ... | 1998 | 16349516 |
| characterization of root-associated methanotrophs from three freshwater macrophytes: pontederia cordata, sparganium eurycarpum, and sagittaria latifolia. | root-associated methanotrophic bacteria were enriched from three common aquatic macrophytes: pontederia cordata, sparganium eurycarpum, and sagittaria latifolia. at least seven distinct taxa belonging to groups i and ii were identified and presumptively assigned to the genera methylosinus, methylocystis, methylomonas, and methylococcus. four of these strains appeared to be novel on the basis of partial 16s ribosomal dna sequence analysis. the root-methanotroph association did not appear to be hi ... | 1998 | 16349515 |
| haemolysin coregulated protein is an exported receptor and chaperone of type vi secretion substrates. | secretion systems require high-fidelity mechanisms to discriminate substrates among the vast cytoplasmic pool of proteins. factors mediating substrate recognition by the type vi secretion system (t6ss) of gram-negative bacteria, a widespread pathway that translocates effector proteins into target bacterial cells, have not been defined. we report that haemolysin coregulated protein (hcp), a ring-shaped hexamer secreted by all characterized t6sss, binds specifically to cognate effector molecules. ... | 2013 | 23954347 |
| seasonal methane oxidation potential in manure crusts. | organic crusts on liquid manure storage tanks harbor ammonia- and nitrite-resistant methane oxidizers and may significantly reduce methane emissions. methane oxidation potential (0.6 mol ch(4) m(-2) day(-1)) peaked during fall and winter, after 4 months of crust development. consequences for methane mitigation potential of crusts are discussed. | 2013 | 23104415 |
| trimethylamine and trimethylamine n-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling. | bacteria of the marine roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. trimethylamine (tma) and trimethylamine n-oxide (tmao) are methylated amines (ma) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after n2 gas, in the oceans. we investigated if the marine heterotrophic bacterium, ruegeria pomeroyi dss-3, could utilise tma and tmao as a supplementary energy source and ... | 2014 | 25148480 |
| trimethylamine and trimethylamine n-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling. | bacteria of the marine roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. trimethylamine (tma) and trimethylamine n-oxide (tmao) are methylated amines (ma) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after n2 gas, in the oceans. we investigated if the marine heterotrophic bacterium, ruegeria pomeroyi dss-3, could utilise tma and tmao as a supplementary energy source and ... | 2014 | 25148480 |
| cultivation and detection of endophytic aerobic methanotrophs isolated from sphagnum species as a perspective for environmental biotechnology. | enriched cultures of microorganisms are an essential step in the production of inoculum of these organisms for biotechnology and bioengineering. the potential application of methanotrophic microorganisms for removal of methane produced from landfills and coal mines as well as biodegradation of toxic compounds has been widely studied. therefore, searching for new sources of methanotrophs can contribute to increasing the possibilities of biotechnology and bioengineering. enrichment cultures of end ... | 2014 | 25401064 |
| niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit. | the currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. as a conseque ... | 2014 | 24708438 |
| soluble methane monooxygenase production and trichloroethylene degradation by a type i methanotroph, methylomonas methanica 68-1. | a methanotroph (strain 68-1), originally isolated from a trichloroethylene (tce)-contaminated aquifer, was identified as the type i methanotroph methylomonas methanica on the basis of intracytoplasmic membrane ultrastructure, phospholipid fatty acid profile, and 16s rrna signature probe hybridization. strain 68-1 was found to oxidize naphthalene and tce via a soluble methane monooxygenase (smmo) and thus becomes the first type i methanotroph known to be able to produce this enzyme. the specific ... | 1993 | 16348920 |
| the leeuwenhoek lecture 2000 the natural and unnatural history of methane-oxidizing bacteria. | methane gas is produced from many natural and anthropogenic sources. as such, methane gas plays a significant role in the earth's climate, being 25 times more effective as a greenhouse gas than carbon dioxide. as with nearly all other naturally produced organic molecules on earth, there are also micro-organisms capable of using methane as their sole source of carbon and energy. the microbes responsible (methanotrophs) are ubiquitous and, for the most part, aerobic. although anaerobic methanotrop ... | 2005 | 16147517 |
| 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 |
| worldwide distribution of nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by pcr and sequencing of 16s rrna and amoa genes. | diversity of cultured ammonia-oxidizing bacteria in the gamma-subdivision of the proteobacteria was investigated by using strains isolated from various parts of the world ocean. all the strains were very similar to each other on the basis of the sequences of both the 16s rrna and ammonia monooxygenase genes and could be characterized as a single species. sequences were also cloned directly from environmental dna from coastal pacific and atlantic sites, and these sequences represented the first n ... | 2002 | 12147525 |
| inferring phytoplankton, terrestrial plant and bacteria bulk δ¹³c values from compound specific analyses of lipids and fatty acids. | stable isotope mixing models in aquatic ecology require δ13c values for food web end members such as phytoplankton and bacteria, however it is rarely possible to measure these directly. hence there is a critical need for improved methods for estimating the δ13c ratios of phytoplankton, bacteria and terrestrial detritus from within mixed seston. we determined the δ13c values of lipids, phospholipids and biomarker fatty acids and used these to calculate isotopic differences compared to the whole-c ... | 2015 | 26208114 |
| molecular characterization of methanotrophic isolates from freshwater lake sediment. | profiles of dissolved o(2) and methane with increasing depth were generated for lake washington sediment, which suggested the zone of methane oxidation is limited to the top 0.8 cm of the sediment. methane oxidation potentials were measured for 0.5-cm layers down to 1.5 cm and found to be relatively constant at 270 to 350 micromol/liter of sediment/h. approximately 65% of the methane was oxidized to cell material or metabolites, a signature suggestive of type i methanotrophs. eleven methanotroph ... | 2000 | 11097900 |
| purification and characterization of the soluble methane monooxygenase of the type ii methanotrophic bacterium methylocystis sp. strain wi 14. | methane monooxygenase (mmo) catalyzes the oxidation of methane to methanol as the first step of methane degradation. a soluble nad(p)h-dependent methane monooxygenase (smmo) from the type ii methanotrophic bacterium wi 14 was purified to homogeneity. sequencing of the 16s rdna and comparison with that of other known methanotrophic bacteria confirmed that strain wi 14 is very close to the genus methylocystis. the smmo is expressed only during growth under copper limitation (<0.1 microm) and with ... | 1999 | 10473397 |
| isolation of copper biochelates from methylosinus trichosporium ob3b and soluble methane monooxygenase mutants. | methylosinus trichosporium ob3b produces an extracellular copper-binding ligand (cbl) with high affinity for copper. wild-type cells and mutants that express soluble methane monooxygenase (smmo) in the presence and absence of copper (smmoc) were used to obtain cell exudates that were separated and analyzed by size exclusion high-performance liquid chromatography. a single chromatographic peak, when present, contained most of the aqueous-phase cu(ii) present in the culture medium. in mutant cultu ... | 1998 | 9501450 |
| novel hopanoids from the methylotrophic bacteria methylococcus capsulatus and methylomonas methanica. (22s)-35-aminobacteriohopane-30,31,32,33,34-pentol and (22s)-35-amino-3 beta-methylbacteriohopane-30,31,32,33,34-pentol. | the major hopanoid of the methylotrophic bacteria methylococcus capsulatus and methylomonas methanica was identified by spectroscopic methods as (22s)-35-aminobacteriohopane-30,31,32,33,34-pentol. minor companions were, in both bacteria, 35-aminobacteriohopane-31,32,33,34-tetrol and in methylomonas methanica, 35-aminobacteriohopane-32,33,34-triol. in methylococcus capsulatus the aminopentol and the aminotetrol were accompanied by their homologues possessing an extra methyl group at c-3. bacteria ... | 1985 | 3935106 |
| architecture and active site of particulate methane monooxygenase. | particulate methane monooxygenase (pmmo) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. understanding pmmo function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. crystal structures of pmmos from three different methanotrophs reveal a trimeric architectu ... | 2012 | 22725967 |
| methanotrophic bacteria in oilsands tailings ponds of northern alberta. | we investigated methanotrophic bacteria in slightly alkaline surface water (ph 7.4-8.7) of oilsands tailings ponds in fort mcmurray, canada. these large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. they are primarily anoxic and produce methane but have an aerobic surface layer. aerobic methane oxidation was measured in the surface water at rates up to 152 nmol ch4 ml(-1) water d(-1). microbial diversity was investigated via ... | 2012 | 23254511 |
| methanotrophic bacteria in oilsands tailings ponds of northern alberta. | we investigated methanotrophic bacteria in slightly alkaline surface water (ph 7.4-8.7) of oilsands tailings ponds in fort mcmurray, canada. these large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. they are primarily anoxic and produce methane but have an aerobic surface layer. aerobic methane oxidation was measured in the surface water at rates up to 152 nmol ch4 ml(-1) water d(-1). microbial diversity was investigated via ... | 2012 | 23254511 |
| rapid consumption of low concentrations of methyl bromide by soil bacteria | a dynamic dilution system for producing low mixing ratios of methyl bromide (mebr) and a sensitive analytical technique were used to study the uptake of mebr by various soils. mebr was removed within minutes from vials incubated with soils and ~10 parts per billion by volume of mebr. killed controls did not consume mebr, and a mixture of the broad-spectrum antibiotics chloramphenicol and tetracycline inhibited mebr uptake by 98%, indicating that all of the uptake of mebr was biological and by ba ... | 1998 | 9572964 |
| a distinct pathway for tetrahymanol synthesis in bacteria. | tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. here we couple comparative genomics wi ... | 2015 | 26483502 |
| ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and dna-processing. | the mode of action of the bacterial ter cluster and tela genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages, has remained enigmatic for almost two decades. using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of b ... | 2012 | 23044854 |
| aerobic methanotrophic communities at the red sea brine-seawater interface. | the central rift of the red sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. three of these pools, the atlantis ii, kebrit and discovery deeps, are uniquely characterized by a high concentration of hydrocarbons. the brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. the current study analyz ... | 2014 | 25295031 |
| potential benefits of the application of yeast starters in table olive processing. | yeasts play an important role in the food and beverage industry, especially in products such as bread, wine, and beer, among many others. however, their use as a starter in table olive processing has not yet been studied in detail. the candidate yeast strains should be able to dominate fermentation, together with lactic acid bacteria, but should also provide a number of beneficial advantages. technologically, yeasts should resist low ph and high salt concentrations, produce desirable aromas, imp ... | 2014 | 22558000 |
| the bacteriohopanepolyol inventory of novel aerobic methane oxidising bacteria reveals new biomarker signatures of aerobic methanotrophy in marine systems. | aerobic methane oxidation (amo) is one of the primary biologic pathways regulating the amount of methane (ch4) released into the environment. amo acts as a sink of ch4, converting it into carbon dioxide before it reaches the atmosphere. it is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace amo events, especially at times when the role of methane in the carbon cycle was more pronounced than today. amo bacteria are known to synthesis ... | 2016 | 27824887 |
| acquisition of epibiotic bacteria along the life cycle of the hydrothermal shrimp rimicaris exoculata. | the caridean shrimp rimicaris exoculata dominates the fauna at several mid-atlantic ridge hydrothermal vent sites. this shrimp has an enlarged gill chamber, harboring a dense ectosymbiotic community of chemoautotrophic bacteria associated with mineral oxide deposits. until now, their acquisition is not fully understood. at three hydrothermal vent sites, we analyzed the epibionts diversity at different moult stages and also in the first stages of the shrimp life (eggs, hatched eggs (with larvae) ... | 2011 | 21993397 |
| mrna-based parallel detection of active methanotroph populations by use of a diagnostic microarray. | a method was developed for the mrna-based application of microbial diagnostic microarrays to detect active microbial populations. dna- and mrna-based analyses of environmental samples were compared and confirmed via quantitative pcr. results indicated that mrna-based microarray analyses may provide additional information on the composition and functioning of microbial communities. | 2006 | 16461725 |
| comparison of pmoa pcr primer sets as tools for investigating methanotroph diversity in three danish soils. | three particulate methane monooxygenase pcr primer sets (a189-a682, a189-a650, and a189-mb661) were investigated for their ability to assess methanotroph diversity in soils from three sites, i.e., heath, oak, and sitka, each of which was capable of oxidizing atmospheric concentrations of methane. each pcr primer set was used to construct a library containing 50 clones from each soil type. the clones from each library were grouped by restriction fragment length polymorphism, and representatives f ... | 2001 | 11525970 |
| acquisition of epibiotic bacteria along the life cycle of the hydrothermal shrimp rimicaris exoculata. | the caridean shrimp rimicaris exoculata dominates the fauna at several mid-atlantic ridge hydrothermal vent sites. this shrimp has an enlarged gill chamber, harboring a dense ectosymbiotic community of chemoautotrophic bacteria associated with mineral oxide deposits. until now, their acquisition is not fully understood. at three hydrothermal vent sites, we analyzed the epibionts diversity at different moult stages and also in the first stages of the shrimp life (eggs, hatched eggs (with larvae) ... | 2011 | 21993397 |
| metabolic regulation of "ca. methylacidiphilum fumariolicum" solv cells grown under different nitrogen and oxygen limitations. | aerobic methanotrophic bacteria can use methane as their sole energy source. the discovery of "ca. methylacidiphilum fumariolicum" strain solv and other verrucomicrobial methanotrophs has revealed that the ability of bacteria to oxidize ch(4) is much more diverse than has previously been assumed in terms of ecology, phylogeny, and physiology. a remarkable characteristic of the methane-oxidizing verrucomicrobia is their extremely acidophilic phenotype, growing even below ph 1. in this study we us ... | 2012 | 22848206 |
| map1b interaction with the fw domain of the autophagic receptor nbr1 facilitates its association to the microtubule network. | selective autophagy is a process whereby specific targeted cargo proteins, aggregates, or organelles are sequestered into double-membrane-bound phagophores before fusion with the lysosome for protein degradation. it has been demonstrated that the microtubule network is important for the formation and movement of autophagosomes. nbr1 is a selective cargo receptor that through its interaction with lc3 recruits ubiquitinated proteins for autophagic degradation. this study demonstrates an interactio ... | 2012 | 22654911 |
| microbial communities of deep-sea methane seeps at hikurangi continental margin (new zealand). | the methane-emitting cold seeps of hikurangi margin (new zealand) are among the few deep-sea chemosynthetic ecosystems of the southern hemisphere known to date. here we compared the biogeochemistry and microbial communities of a variety of hikurangi cold seep ecosystems. these included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. ... | 2013 | 24098632 |
| expanding the world of marine bacterial and archaeal clades. | determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. the importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the international census of marine microbes, ocean sampling day, or tara oceans. given decades of effort, we know that the large majority of marine bacteria and archaea belong to about a dozen phyla. in addition to the classically cul ... | 2015 | 26779174 |
| expanding the world of marine bacterial and archaeal clades. | determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. the importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the international census of marine microbes, ocean sampling day, or tara oceans. given decades of effort, we know that the large majority of marine bacteria and archaea belong to about a dozen phyla. in addition to the classically cul ... | 2015 | 26779174 |
| genome-scale metabolic reconstructions and theoretical investigation of methane conversion in methylomicrobium buryatense strain 5g(b1). | methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. however, the application of natural methanotrophic strains to large-scale production of value-added chemicals/biofuels requires a number of physiological and genetic alterations. an accurate metabolic model coupled with flux balance analysis can provide a solid interpretative framework for experimental data analyses and integration. | 2015 | 26607880 |
| conformational toggling controls target site choice for the heteromeric transposase element tn7. | the bacterial transposon tn7 facilitates horizontal transfer by directing transposition into actively replicating dna with the element-encoded protein tnse. structural analysis of the c-terminal domain of wild-type tnse identified a novel protein fold including a central v-shaped loop that toggles between two distinct conformations. the structure of a robust tnse gain-of-activity variant has this loop locked in a single conformation, suggesting that conformational flexibility regulates tnse acti ... | 2015 | 26384427 |
| draft genome sequences of gammaproteobacterial methanotrophs isolated from marine ecosystems. | the genome sequences of methylobacter marinus a45, methylobacter sp. strain bba5.1, and methylomarinum vadi it-4 were obtained. these aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems. | 2016 | 26798114 |
| metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. | metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). use of unbiased rna-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. however, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. systematic studies that compare data across microbiomes are needed to ... | 2016 | 26757703 |
| the origin, source, and cycling of methane in deep crystalline rock biosphere. | the emerging interest in using stable bedrock formations for industrial purposes, e.g., nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. considering the origin and evolution of life on earth, these environments may also serve as windows to the past. various geological, chemical, and biological processes can influence the deep carbon cycle. conditions of ch4 formation, avai ... | 2015 | 26236303 |
| rapid reactivation of deep subsurface microbes in the presence of c-1 compounds. | microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. however, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, here, we studied how microorganisms present in fracture fluid from a depth of 500 m in outokumpu, finland, respond ... | 2015 | 27682076 |
| draft genome sequences of eight obligate methane oxidizers occupying distinct niches based on their nitrogen metabolism. | the genome sequences of methylomonas methanica (ncimb 11130(t), r-45363, and r-45371), methylomonas koyamae (r-45378, r-45383, and r-49807), methylomonas lenta (r-45370), and methylosinus sp. (r-45379) were obtained. these aerobic methanotrophs were isolated from terrestrial ecosystems, and their distinct phenotypes related to nitrogen assimilation and dissimilation were previously reported. | 2016 | 27491982 |
| methylotroph [meth'il-o-trof"]. | | 2016 | 27326439 |
| a temperate river estuary is a sink for methanotrophs adapted to extremes of ph, temperature and salinity. | river tyne (uk) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (ph, salinity, temperature) that extended far beyond those found in situ. in aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoa). under near in situ conditions (4-30°c ... | 2016 | 26617278 |