| o-demethylation by the homoacetogenic anaerobe holophaga foetida studied by a new photometric methylation assay using electrochemically produced cob(i)alamin. | the previously studied complete methyl transfer sequence of tetrahydrofolate-dependent o-demethylation catalyzed by holophaga foetida strain tmbs4 extracts was separated into two steps using cobalamins as non-physiological substrates: electrochemically produced cob(i) alamin served as methyl acceptor for phenyl methyl ether demethylation, yielding methylcob(iii)alamin (reaction i), and methylcob(iii)alamin served as donor for tetrahydrofolate methylation, yielding 5-methyl tetrahydrofolate (reac ... | 1994 | 7813485 |
| holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. | a polyphasic approach was used in which genotypic and phenotypic properties of a gram-negative, obligately anaerobic, rod-shaped bacterium isolated from a black anoxic freshwater mud sample were determined. based on these results, the name holophaga foetida gen. nov., sp. nov. is proposed. this microorganism produced dimethylsulfide and methanethiol during growth on trimethoxybenzoate or syringate. the only other compounds utilized were pyruvate and trihydroxybenzenes such as gallate, phlorogluc ... | 1994 | 8085918 |
| detection and in situ identification of representatives of a widely distributed new bacterial phylum. | 16s rrna gene libraries were prepared by polymerase chain reaction amplification and cloning from soil samples taken periodically from a field with genetically modified plants. sequence analyses of the cloned rdnas indicated that 140 of them clustered apart from known bacterial phyla. based on 31 full sequences a new phylum could be defined. it includes holophaga foetida, 'geothrix fermentans' and acidobacterium capsulatum as the only cultured species so far. therefore, this line of descent was ... | 1997 | 9252585 |
| geothrix fermentans gen. nov., sp. nov., a novel fe(iii)-reducing bacterium from a hydrocarbon-contaminated aquifer. | in an attempt to understand better the micro-organisms involved in anaerobic degradation of aromatic hydrocarbons in the fe(iii)-reducing zone of petroleum-contaminated aquifers, fe(iii)-reducing micro-organisms were isolated from contaminated aquifer material that had been adapted for rapid oxidation of toluene coupled to fe(iii) reduction. one of these organisms, strain h-5t, was enriched and isolated on acetate/fe(iii) medium. strain h-5t is a gram-negative strict anaerobe that grows with var ... | 1999 | 10555343 |
| phylogenetic analysis of bacterial communities associated with leaves of the seagrass halophila stipulacea by a culture-independent small-subunit rrna gene approach. | the phylogenetic diversity of the bacterial community associated with leaves of the marine plant halophila stipulacea in the northern gulf of elat was examined by 16s rrna gene (rdna) sequence analyses of a clone library. for 59 clones corresponding to 51 ardra (amplified rdna restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ardra groups of the leaf library was calculated. the class proteobacteria was represented by 62.6% of t ... | 2000 | 10790514 |
| phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. | the phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. these reactors were operated at both mesophilic (28 to 32 degrees c) and thermophilic (50 to 58 degrees c) temperatures. community fingerprint analysis by denaturing gradient gel electrophoresis (dgge) of the pcr-amplified v3 region of the 16s rrna gene from the domain bacteria revealed that these seven reactors supported three distinct microbial commu ... | 2000 | 10966414 |
| 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 |
| identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. | the presumptive metabolically active members of a bacterial community in a moorland soil in germany, highly polluted with polychlorinated biphenyls (pcbs), were identified by sequencing of cloned reverse transcription-polymerase chain reaction (rt-pcr) amplification products of 16s rrna generated from total rna extracts. analysis of the 16s rrna clone library revealed a considerable diversity of metabolically active bacteria in the soil, despite the acidic ph and high concentrations of pcbs. clo ... | 1999 | 11207739 |
| microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. | soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. in this study, topsoil samples of different fertilizer treat ... | 2001 | 11526026 |
| microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. | we studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (wadi gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. phormidium- and oscillatoria-like cyanobacterial morphotypes were dominant in the field. bacteria belonging to different groups, mainly the cytophaga-flavobacterium-bacteriodes group, the gamma and beta subclasses of the class p ... | 2002 | 11916684 |
| origin and phylogeny of microbes living in permanent antarctic lake ice. | a bstractthe phylogenetic diversity of bacteria and cyanobacteria colonizing sediment particles in the permanent ice cover of an antarctic lake was characterized by analyses of 16s rrna genes amplified from environmental dna. samples of mineral particles were collected from a depth of 2.5 m in the 4-m-thick ice cover of lake bonney, mcmurdo dry valleys, antarctica. a rrna gene clone library of 198 clones was made and characterized by sequencing and oligonucleotide probe hybridization. the librar ... | 2000 | 12035096 |
| bacterial communities associated with flowering plants of the ni hyperaccumulator thlaspi goesingense. | thlaspi goesingense is able to hyperaccumulate extremely high concentrations of ni when grown in ultramafic soils. recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. in this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing t. goesingense were characterized in detail by using both cultivation and cultivation-independent te ... | 2004 | 15128517 |
| bacterial diversity in marine hydrocarbon seep sediments. | marine seeps introduce significant amounts of hydrocarbons into oceans and create unusual habitats for microfauna and -flora. in the vicinity of chronic seeps, microbes likely exert control on carbon quality entering the marine food chain and, in turn, hydrocarbons could influence microbial community composition and diversity. to determine the effects of seep oil on marine sediment bacterial communities, we collected sediment piston cores within an active marine hydrocarbon seep zone in the coal ... | 2004 | 15250882 |
| comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. | the diversity and composition of soil bacterial communities were compared among six austrian natural forests, including oak-hornbeam, spruce-fir-beech, and austrian pine forests, using terminal restriction fragment length polymorphism (t-rflp, or trf) analysis and sequence analysis of 16s rrna genes. the forests studied differ greatly in soil chemical characteristics, microbial biomass, and nutrient turnover rates. the aim of this study was to relate these differences to the composition of the b ... | 2004 | 15345382 |
| a survey of the composition and diversity of bacterial populations in bleached kraft pulp-mill wastewater secondary treatment systems. | bacterial community compositions from 10 pulp- and paper-mill treatment systems were compared using both traditional and molecular techniques. 16s-rflp (random fragment length polymorphisms) analysis was used to examine the genotypic profiles of the whole bacterial community of each treatment system. although all the communities shared approximately 60% of their dna band pattern, as determined by computer-assisted cluster analysis, each community displayed a unique profile that was stable over t ... | 2004 | 15467789 |
| influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm. | we characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the pensacola bay estuary using two complementary cultivation-independent molecular techniques. biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. this study assessed wheth ... | 2004 | 15528551 |
| biological soil crusts of sand dunes in cape cod national seashore, massachusetts, usa. | biological soil crusts cover hundreds of hectares of sand dunes at the northern tip of cape cod national seashore (massachusetts, usa). although the presence of crusts in this habitat has long been recognized, neither the organisms nor their ecological roles have been described. in this study, we report on the microbial community composition of crusts from this region and describe several of their physical and chemical attributes that bear on their environmental role. microscopic and molecular a ... | 2004 | 15546040 |
| bacterial community composition in different sediments from the eastern mediterranean sea: a comparison of four 16s ribosomal dna clone libraries. | the regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16s ribosomal dna (rdna) clone libraries from sediments in different regions of the eastern mediterranean sea (thermaikos gulf, cretan sea, and south lonian sea). amplified rdna restriction analysis of 664 clones from the libraries indicate that the rdna richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique ... | 2005 | 16328662 |
| microbial diversity in sediments of saline qinghai lake, china: linking geochemical controls to microbial ecology. | saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. the objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from qinghai lake. the lake is saline (12.5 g/l salinity) and alkaline (ph 9.4) and is located on the qinghai-tibetan plateau at an altitude of 3196 m above sea level. pore water chemistry of the cor ... | 2006 | 16400537 |
| edaphobacter modestus gen. nov., sp. nov., and edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. | the phylum acidobacteria is currently represented mostly by environmental 16s rrna gene sequences, and the phylum so far contains only four species with validly published names, holophaga foetida, geothrix fermentans, acidobacterium capsulatum and terriglobus roseus. in the present study, two novel strains of acidobacteria were isolated. high-throughput enrichments were set up with the microdrop technique using an alpine calcareous soil sample and a mixture of polymeric carbon compounds suppleme ... | 2008 | 18450699 |
| [effects of 2-chlorophenol-acclimation on microbial community structure in anaerobic granular sludge]. | the microbial community structure in 2-chlorophenol-acclimated anaerobic granular sludge and inoculating sludge were analyzed by 16s rdna-based approach. total dna was extracted directly from the inoculating sludge and 2-cp-acclimated anaerobic sludge, and then amplified by polymerase chain reaction (pcr) technique with the specific primer pair arc21f/arc958r for archaea and 31f/907r for acidobacteria respectively. the positive pcr products were cloned and sequenced. the sequences analysis shows ... | 2008 | 18649544 |
| 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 |
| acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of acanthopleuribacteraceae fam. nov., acanthopleuribacterales ord. nov., holophagaceae fam. nov., holophagales ord. nov. and holophagae classis nov. in the phylum 'acidobacteria'. | strain fyk2218(t) was isolated from a specimen of the chiton acanthopleura japonica, which had been collected from a beach on the boso peninsula in japan. phylogenetic analyses based on 16s rrna gene sequences revealed that the strain belonged to the phylum 'acidobacteria'. the most closely related type strains to strain fyk2218(t) were holophaga foetida tmbs4(t) (83.6 % 16s rrna gene sequence similarity) and geothrix fermentans h-5(t) (83.6 %) in subdivision 8 of the 'acidobacteria'. cells of f ... | 2008 | 18984699 |
| 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 |