| 5s rrna sequences from nitrobacter winogradskyi, caulobacter crescentus, stella humosa and verrucomicrobium spinosum. | | 1987 | 3684605 |
| phylogeny of prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the bacteria. | prosthecobacter fusiformis is morphologically similar to caulobacters; however, it lacks a dimorphic life cycle. to determine the relatedness of the genus prosthecobacter to dimorphic caulobacters and other prosthecate members of the alpha subgroup of the proteobacteria (alpha-proteobacteria), we isolated and sequenced 16s rrna genes from four prosthecobacter strains. surprisingly, the results of phylogenetic analyses placed the fusiform caulobacters in a deeply rooted division of the bacteria t ... | 1996 | 8863424 |
| bacterial diversity of a carolina bay as determined by 16s rrna gene analysis: confirmation of novel taxa. | carolina bays are naturally occurring shallow elliptical depressions largely fed by rain and shallow ground water. to identify members of the domain bacteria which inhibit such an environment, we used pcr to construct a library of 16s rrna genes (16s rdnas) cloned from dna extracted from the sediments of rainbow bay, located on the savannah river site, near aiken, s.c. oligonucleotides complementary to conserved regions of 16s rdna were used as primers for pcr, and gel-purified pcr products were ... | 1997 | 9097448 |
| verrucomicrobia div. nov., a new division of the bacteria containing three new species of prosthecobacter. | four strains of nonmotile, prosthecate bacteria were isolated in the 1970s and assigned to the genus prosthecobacter. these strains were compared genotypically by dna/dna reassociation and 16s rdna based phylogenetic analyses. genotypic comparisons were complemented with phenotypic characterizations. together, these studies clearly indicate each prosthecobacter strain represents a novel species of bacteria. we propose three new species of prosthecobacter, p. dejongeii strain fc1, p. vanneervenii ... | 1997 | 9296261 |
| the presence of a dnak (hsp70) multigene family in members of the orders planctomycetales and verrucomicrobiales. | sequences of the dnak gene, coding for the 70-kda heat shock protein (hsp70), were determined for six members of the order planctomycetales, including representatives of three genera, and for the only cultivated member of the order verrucomicrobiales, verrucomicrobium spinosum. a fragment of the dnak gene was amplified from these strains by pcr with oligonucleotide primers targeting regions of the dnak gene that are conserved at the amino acid level, and the resulting pcr products were cloned in ... | 1997 | 9335284 |
| phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. | the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ... | 1999 | 10388721 |
| novel bacterial diversity recovered from the rhizosphere of oilseed rape (brassica napus) determined by the analysis of 16s ribosomal dna. | soil was sampled to a distance of 2.5 mm beneath a root mat of oilseed rape (brassica napus) in a model rhizosphere system. dna was extracted and the 16s rdna amplified, cloned and sequenced. phylogenetic analysis of these sequences with those held on-line, revealed that 37% of the clones fell within the holophaga /acidobacterium phylum, 17% were within the proteobacteria, 14% of the clones were close relatives of bacillus megaterium and 5% were related to verrucomicrobium spinosum. an additiona ... | 2000 | 11016691 |
| comparative phylogenetic analyses of members of the order planctomycetales and the division verrucomicrobia: 23s rrna gene sequence analysis supports the 16s rrna gene sequence-derived phylogeny. | almost complete 23s rrna gene sequences were obtained from 13 planctomycete strains, the fimbriated, prosthecate bacterium verrucomicrobium spinosum and two strains of the genus prosthecobacter. the 23s rrna genes were amplified by the pcr, using modified primers. the majority of the planctomycete strains investigated were shown to have 23s rrna genes that were not linked to the 16s rrna genes. amplification of the 5'-termini of these genes was achieved using a novel primer-design strategy. comp ... | 2000 | 11155969 |
| phylogenetic composition of bacterioplankton assemblages from the arctic ocean. | we analyzed the phylogenetic composition of bacterioplankton assemblages in 11 arctic ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16s rrna genes. the sequencing effort was directed by denaturing gradient gel electrophoresis (dgge) screening of samples and the clone libraries. sequences of 88 clones fell into seven major lineages of the domain bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-p ... | 2002 | 11823184 |
| use of the verrucomicrobia-specific probe eub338-iii and fluorescent in situ hybridization for detection of "candidatus xiphinematobacter" cells in nematode hosts. | fluorescent in situ hybridization with a 16s rrna probe specific for verrucomicrobia was used to (i) confirm the division-level identity of and (ii) study the behavior of the obligate intracellular verrucomicrobium "candidatus xiphinematobacter" in its nematode hosts. endosymbionts in the egg move to the pole where the gut primordium arises; hence, they populate the intestinal epithelia of juvenile worms. during the host's molt to adult female, the endosymbionts concentrate around the developing ... | 2002 | 12039775 |
| analysis of 16s libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. | total genomic dna from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for pcr amplification of 16s rrna gene sequences with conserved bacterial primers. phylogenetic analysis of the amplification products revealed 40 unique 16s rdna sequences. of these sequences, 25% (10/40) corresponded to described intestinal organisms of the mouse, including lactobacillus spp., helicobacter spp., segmented filamentous bacteria and members of the altered schaed ... | 2002 | 12427955 |
| seasonal changes in an alpine soil bacterial community in the colorado rocky mountains. | the period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. the large winter microbial community begins to turn over rapidly, releasing nutrients to plants. past studies have shown that the soil microbial community in alpine dry meadows of the colorado rocky mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. however, little specific information exists on the diversity of the alpine bacterial communit ... | 2004 | 15128545 |
| akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. | the diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16s rrna-dependent approaches. a dominant bacterium, strain muct, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. a pure culture was obtained using the anaerobic soft agar technique. strain muct was a gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow si ... | 2004 | 15388697 |
| the nomenclatural types of the orders acholeplasmatales, halanaerobiales, halobacteriales, methanobacteriales, methanococcales, methanomicrobiales, planctomycetales, prochlorales, sulfolobales, thermococcales, thermoproteales and verrucomicrobiales are the genera acholeplasma, halanaerobium, halobacterium, methanobacterium, methanococcus, methanomicrobium, planctomyces, prochloron, sulfolobus, thermococcus, thermoproteus and verrucomicrobium, respectively. opinion 79. | the judicial commission of the international committee on systematics of prokaryotes has corrected the nomenclatural types of 12 orders: acholeplasmatales, halanaerobiales, halobacteriales, methanobacteriales, methanococcales, methanomicrobiales, planctomycetales, prochlorales, sulfolobales, thermococcales, thermoproteales and verrucomicrobiales. | 2005 | 15653928 |
| bioinformatics, genomics and evolution of non-flagellar type-iii secretion systems: a darwinian perspective. | we review the biology of non-flagellar type-iii secretion systems from a darwinian perspective, highlighting the themes of evolution, conservation, variation and decay. the presence of these systems in environmental organisms such as myxococcus, desulfovibrio and verrucomicrobium hints at roles beyond virulence. we review newly discovered sequence homologies (e.g., yopn/tyea and sepl). we discuss synapomorphies that might be useful in formulating a taxonomy of type-iii secretion. the problem of ... | 2005 | 15808742 |
| exopolysaccharide-associated protein sorting in environmental organisms: the pep-cterm/epsh system. application of a novel phylogenetic profiling heuristic. | protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families. | 2006 | 16930487 |
| a canonical ftsz protein in verrucomicrobium spinosum, a member of the bacterial phylum verrucomicrobia that also includes tubulin-producing prosthecobacter species. | the origin and evolution of the homologous gtp-binding cytoskeletal proteins ftsz typical of bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. both ftsz and tubulin are central to key cell biology processes--bacterial septation and cell division in the case of ftsz and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in eukaryotes. the origin of tubulin in particular is ... | 2007 | 17349062 |
| phylogeny and shared conserved inserts in proteins provide evidence that verrucomicrobia are the closest known free-living relatives of chlamydiae. | the evolutionary relationships of chlamydiales, verrucomicrobia and planctomycetes were studied based on phylogenetic trees for a concatenated dataset of 11 widely distributed proteins, as well as conserved inserts in several proteins. in phylogenetic trees, a close relationship of chlamydiae to verrucomicrobium was supported by different phylogenetic methods. although the planctomycetes branched close to the chlamydiae-verrucomicrobia clade, their specific affiliation to these groups was genera ... | 2007 | 17660429 |
| characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla verrucomicrobia, lentisphaerae, chlamydiae, and planctomycetes and phylogenetic comparison with rrna genes. | in the past, studies on the relationships of the bacterial phyla planctomycetes, chlamydiae, lentisphaerae, and verrucomicrobia using different phylogenetic markers have been controversial. investigations based on 16s rrna sequence analyses suggested a relationship of the four phyla, showing the branching order planctomycetes, chlamydiae, verrucomicrobia/lentisphaerae. phylogenetic analyses of 23s rrna genes in this study also support a monophyletic grouping and their branching order--this group ... | 2008 | 18310338 |
| metagenomic analysis of a freshwater toxic cyanobacteria bloom. | high molecular weight (hmw) dna prepared from a toxic freshwater cyanobacterial bloom sample was used to construct a pcr-generated 75-clone, 16s rrna gene library and a 2850-clone bacterial artificial chromosome (bac) library. phylogenetic analysis of the 16s rrna gene library demonstrated that members of eight phyla of domain bacteria, which included cyanobacteria, actinobacteria, verrucomicrobium, bacteriodetes, planctomycetes, chloroflexi, candidate division op10 and alpha-, beta- and gammapr ... | 2008 | 18328084 |
| structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment. | the bacterial diversity of a chronically oil-polluted retention basin sediment located in the berre lagoon (etang-de-berre, france) was investigated. this study combines chemical and molecular approaches in order to define how the in situ petroleum hydrocarbon contamination level affects the bacterial community structure of a subsurface sediment. hydrocarbon content analysis clearly revealed a gradient of hydrocarbon contamination in both the water and the sediment following the basin periphery ... | 2008 | 18803671 |
| influence of support material on the immobilization of biomass for the degradation of linear alkylbenzene sulfonate in anaerobic reactors. | two horizontal-flow anaerobic immobilized biomass reactors (haib) were used to study the degradation of the las surfactant: one filled with charcoal (haib1) and the other with a mixed bed of expanded clay and polyurethane foam (haib2). the reactors were fed with synthetic substrate supplemented with 14 mg l(-1)of las, kept at 30+/-2 degrees c and operated with a hydraulic retention time (hrt) of 12h. the surfactant was quantified by hplc. spatial variation analyses were done to quantify organic ... | 2009 | 18814953 |
| phylum verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum planctomycetes. | the phylum verrucomicrobia is a divergent phylum within domain bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. at least one genus, prosthecobacter, includes species with genes homologous to those encoding eukaryotic tubulins. a significant superphylum relationship of verrucomicrobia with members of phylum planctomycetes possessing a unique compartmentalized cel ... | 2009 | 19133117 |
| [bacterial diversity of disused thermal vents in tibetan yangbajing region]. | to study the bacterial diversity in sediment and water from two disused thermal vents in yangbajing, tibet, china. | 2009 | 19445178 |
| xanthan and gellan degradation by bacteria of activated sludge. | owing to increasing amounts of xanthan and gellan in food, cosmetics and pharmaceuticals, as well as in some technical spheres, studies were carried out on the xanthan and gellan degrading bacteria present in activated sludge. the activated sludge used in the study was able to degrade both carbohydrates over 7 days, with levels of xanthan and gellan utilizing microbes estimated at 10(5) cells/g of dry sludge weight. isolating key degrading bacteria revealed the important role of genus paenibacil ... | 2009 | 19700835 |
| bacterial community composition in the rhizosphere of a transgenic, herbicide-resistant maize (zea mays) and comparison to its non-transgenic cultivar bosphore. | bacterial communities in rhizospheres of transgenic maize (zea mays, with the pat-gene conferring resistance to the herbicide glufosinate; syn. l-phosphinothricin) were compared to its isogenic, non-transgenic cultivar. total dna was extracted from bacterial cell consortia collected from rhizospheres of plants grown in an agricultural field. with the use of three different primer pairs binding to evolutionarily conserved regions of the bacterial 16s rrna gene, partial sequences were amplified by ... | 2002 | 19709208 |
| molecular inventory of faecal microflora in patients with crohn's disease. | intestinal microbial community is involved in the pathogenesis of crohn's disease, but knowledge of its potential abnormalities has been limited by the impossibility to grow many dominant intestinal bacteria. using sequence analysis of randomly cloned bacterial 16s ribosomal dna, the dominant faecal species from four crohn's disease patients and four controls were compared. whereas marked inter-individual differences were observed in the faecal microflora of patients, three remained distantly re ... | 2004 | 19712374 |
| role of the c-terminal extension in a bacterial tyrosinase. | the well studied bacterial tyrosinases from the streptomyces sp. bacteria are distinguishable from their eukaryotic counterparts by the absence of a c-terminal extension. in the present study, we report that the tyrosinase from the bacterium verrucomicrobium spinosum also has such a c-terminal extension, thus making it distinct from the streptomyces enzymes. the entire tyrosinase gene from v. spinosum codes for a 57 kda protein (full-length unprocessed form), which has a twin arginine translocas ... | 2010 | 20345903 |
| the effect of resource quantity and resource stoichiometry on microbial carbon-use-efficiency. | the carbon-use-efficiency (cue) of microorganisms is an important parameter in determining ecosystem-level carbon (c) cycling; however, little is known about how variance in resources affects microbial cue. to elucidate how resource quantity and resource stoichiometry affect microbial cue, we cultured four microorganisms - two fungi (aspergillus nidulans and trichoderma harzianum) and two bacteria (pectobacterium carotovorum and verrucomicrobium spinosum) - under 12 unique c, nitrogen (n) and ph ... | 2010 | 20550579 |
| [influence of low frequency magnetic field on characteristic of pseudomonas aeruginosa]. | to assess the level of bacteriostatic effect of low frequency magnetic field (lfmf) on gram-negative bacteria able to form biofilms (pseudomonas aeruginosa) compared to able to aggregation oligotrophes caulobactor crescentus, arcicella aquatica and verrucomicrobium spinosum. | 2010 | 20795390 |
| cross-linking and immobilisation of different proteins with recombinant verrucomicrobium spinosum tyrosinase. | this paper reports on the cross-linking and immobilisation of various proteins by the recombinant tyrosinase from verrucomicrobium spinosum (vs-tyrosinase). in general it is found that vs-tyrosinase can readily cross-link proteins with a low degree of complexity, such as casein, but that the enzyme cannot readily cross-link well folded protein substrates such as lysozyme, myoglobin, cytochrome c or candida antarctica lipase b (calb). however, the inclusion of phenolic compounds (phenol or caffei ... | 2010 | 20969899 |
| random transposon mutagenesis of verrucomicrobium spinosum dsm 4136(t). | the verrucomicrobia are a bacterial group of growing interest due to their environmental ubiquity as free-living and host-associated microbes. they also exhibit an unusual compartmentalized cell plan, shared with members of neighboring phyla that include the planctomycete bacteria. however, verrucomicrobia are currently difficult to study, due to a lack of available genetic tools that would permit robust testing of hypotheses formulated from ecological and genomic data. to our knowledge, there a ... | 2010 | 21184215 |
| genome sequence of the verrucomicrobium opitutus terrae pb90-1, an abundant inhabitant of rice paddy soil ecosystems. | bacteria of the deeply branching phylum verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. we have sequenced the genome of opitutus terrae pb90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides. | 2011 | 21398538 |
| Genomic and Experimental Evidence Suggests that Verrucomicrobium spinosum Interacts with Eukaryotes. | Our knowledge of pathogens and symbionts is heavily biased toward phyla containing species that are straightforward to isolate in pure culture. Novel bacterial phyla are often represented by a handful of strains, and the number of species interacting with eukaryotes is likely underestimated. Identification of predicted pathogenesis and symbiosis determinants such as the Type III Secretion System (T3SS) in the genomes of "free-living" bacteria suggests that these microbes participate in uncharact ... | 2011 | 22022322 |