| phylogenetic position of the menaquinone-containing acidophilic chemo-organotroph acidobacterium capsulatum. | the phylogenetic position of an acidophilic chemo-organotrophic menaquinone-containing bacterium, acidobacterium capsulatum, was studied on the basis of 16s rrna gene sequence information. a. capsulatum showed the highest level of sequence similarity to heliobacterium chlorum, a member of the gram-positive group, yet this level was only 81%. distance matrix tree analysis suggested that a. capsulatum belongs to a unique lineage deeply branching from the chlamydia-planctomyces group or from the gr ... | 1995 | 7590170 |
| transfer and expression of degradative and antibiotic resistance plasmids in acidophilic bacteria. | the genetic accessibility of selected acidophilic bacteria was investigated to evaluate their applicability to degrading pollutants in acidic environments. the incp1 antibiotic resistance plasmids rp4 and pvk101 and the phenol degradation-encoding plasmid ppgh11 were transferred from neutrophilic bacteria into the extreme acidophilic eubacterium acidiphilium cryptum at frequencies of 1.8 x 10(-2) to 9.8 x 10(-4) transconjugants per recipient cell. the incq antibiotic resistance plasmid psup106 w ... | 1994 | 8161188 |
| 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 |
| 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 |
| gene cloning and characterization of an acidic xylanase from acidobacterium capsulatum. | the gene xyna encoding an acid endo-beta-1,4-xylanase from an acidophilic bacterium, acidobacterium capsulatum 161, was cloned and expressed in eschrichia coli. the nucleotide sequence of the 1.6-kb dna fragment containing xyna was analyzed, revealing an open reading frame of 1,215 bp encoding a peptide of 405 amino acid residues. the deduced amino acid sequence of xyna was very similar to other xylanases that are from the glycosyl hydrolase family 10. xyna was purified to homogeneity by sds-pol ... | 1998 | 9692186 |
| wide distribution and diversity of members of the bacterial kingdom acidobacterium in the environment. | to assess the distribution and diversity of members of the recently identified bacterial kingdom acidobacterium, members of this kingdom present in 43 environmental samples were surveyed by pcr amplification. a primer designed to amplify rrna gene sequences (ribosomal dnas [rdnas]) from most known members of the kingdom was used to interrogate bulk dna extracted from the samples. positive pcr results were obtained with all temperate soil and sediment samples tested, as well as some hot spring sa ... | 1999 | 10103274 |
| 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 |
| stable-isotope probing as a tool in microbial ecology. | microorganisms are responsible for driving the biogeochemical cycling of elements on earth. despite their importance and vast diversity, the taxonomic identity of the microorganisms involved in any specific process has usually been confined to that small fraction of the microbiota that has been isolated and cultivated. the recent coupling of molecular biological methods with stable-isotope abundance in biomarkers has provided a cultivation-independent means of linking the identity of bacteria wi ... | 2000 | 10688198 |
| 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 |
| cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. | recent progress in molecular microbial ecology has revealed that traditional culturing methods fail to represent the scope of microbial diversity in nature, since only a small proportion of viable microorganisms in a sample are recovered by culturing techniques. to develop methods to investigate the full extent of microbial diversity, we used a bacterial artificial chromosome (bac) vector to construct libraries of genomic dna isolated directly from soil (termed metagenomic libraries). to date, w ... | 2000 | 10831436 |
| identification of 16s ribosomal dna-defined bacterial populations at a shallow submarine hydrothermal vent near milos island (greece). | in a recent publication (s. m. sievert, t. brinkhoff, g. muyzer, w. ziebis, and j. kuever, appl. environ. microbiol. 65:3834-3842, 1999) we described spatiotemporal changes in the bacterial community structure at a shallow-water hydrothermal vent in the aegean sea near the isle of milos (greece). here we describe identification and phylogenetic analysis of the predominant bacterial populations at the vent site and their distribution at the vent site as determined by sequencing of dna molecules ( ... | 2000 | 10877814 |
| 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 |
| response of a soil bacterial community to grassland succession as monitored by 16s rrna levels of the predominant ribotypes. | the composition of predominant soil bacteria during grassland succession was investigated in the dutch drentse a area. five meadows, taken out of agricultural production at different time points, and one currently fertilized plot represented different stages of grassland succession. since fertilization and agricultural production were stopped, the six plots showed a constant decline in the levels of nutrients and vegetation changes. the activity of the predominant bacteria was monitored by direc ... | 2000 | 10966420 |
| 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 |
| structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches. | until recently, our understanding of microbial community development in soil ecosystems exposed to different inorganic and organic pollutants has been limited to culturable microorganisms because of the techniques available. the discovery that most soil microorganisms are non-culturable but potentially viable and metabolically active accelerated the application of different culture-independent methods for structural diversity assessments of the microbial community. this review examines the resul ... | 2001 | 11118654 |
| 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 |
| bacterial populations colonizing and degrading rice straw in anoxic paddy soil. | rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. the bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. rice straw was incubated in paddy soil anaerobically for 71 days. denaturing gradient gel electrophoresis (dgge) of the amplified bacterial 16s rrna genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incub ... | 2001 | 11229927 |
| impact of cultivation on characterisation of species composition of soil bacterial communities. | the species composition of culturable bacteria in scottish grassland soils was investigated using a combination of biolog and 16s rdna analysis for characterisation of isolates. the inclusion of a molecular approach allowed direct comparison of sequences from culturable bacteria with sequences obtained during analysis of dna extracted directly from the same soil samples. bacterial strains were isolated on pseudomonas isolation agar (pia), a selective medium, and on tryptone soya agar (tsa), a ge ... | 2001 | 11248388 |
| diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. | there is a paucity of knowledge on microbial community diversity and naturally occurring seasonal variations in agricultural soil. for this purpose the soil microbial community of a wheat field on an experimental farm in the netherlands was studied by using both cultivation-based and molecule-based methods. samples were taken in the different seasons over a 1-year period. fatty acid-based typing of bacterial isolates obtained via plating revealed a diverse community of mainly gram-positive bacte ... | 2001 | 11319113 |
| 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 |
| altamira cave paleolithic paintings harbor partly unknown bacterial communities. | since it has been reported that microorganisms can affect painting pigments, paleolithic painting microbiology deserves attention. the present study is the first report on the bacterial colonization of the valuable paleolithic paintings in the famous altamira cave (spain). one sample taken from a painting area in the polychromes hall was analyzed culture-independently. this was the first time microbiologists were allowed to take sample material directly from altamira paintings. identification me ... | 2002 | 12052543 |
| phylogenetic 16s rrna analysis reveals the presence of complex and partly unknown bacterial communities in tito bustillo cave, spain, and on its palaeolithic paintings. | tito bustillo cave (ribadesella, spain) contains valuable palaeolithic paintings, which date back 15 000-20 000 years. since 1969, the cave has been open to the public. rock wall surfaces, spelaeothems and soils are covered by apparent biofilms of phototrophic microorganisms, which develop under artificial lighting. in addition, rock surfaces present conspicuous bacterial growth in the form of round colonies of different colours and about 1-2 mm in diameter. even the famous paintings panel shows ... | 2002 | 12123475 |
| biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. | isolated soil dna from an oak-hornbeam forest close to cologne, germany, was suitable for pcr amplification of gene segments coding for the 16s rrna and nitrogenase reductase (nifh), nitrous oxide reductase (nosz), cytochrome cd(1)-containing nitrite reductase (nirs), and cu-containing nitrite reductase (nirk) of denitrification. for each gene segment, diverse pcr products were characterized by cloning and sequencing. none of the 16s rrna gene sequences was identical to any deposited in the data ... | 2002 | 12147477 |
| molecular characterization of bacterial diversity from british columbia forest soils subjected to disturbance. | bacteria from forest soils were characterized by dna sequence analysis of cloned 16s rrna gene fragments (16s clones). surface organic matter and mineral soil samples from a british columbia ministry of forests long-term soil productivity (ltsp) installation were collected during winter and summer from two disturbance treatments: whole-tree harvesting with no soil compaction (plot n) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot s). phylo ... | 2002 | 12224564 |
| inducible aluminum resistance of acidiphilium cryptum and aluminum tolerance of other acidophilic bacteria. | aluminum ions are highly soluble in acidic environments. toxicity of aluminum ions for heterotrophic, facultatively and obligately chemolithoautotrophic acidophilic bacteria was examined. acidiphilium cryptum grew in glucose-mineral medium, ph 3, containing 300 mm aluminum sulfate [al(2)(so(4))(3)] after a lag phase of about 120 h with a doubling time of 7.6 h, as compared to 5.2 h of growth without aluminum. precultivation with 1 mm al(2)(so(4))(3) and transfer to a medium with 300 mm al(2)(so( ... | 2002 | 12420179 |
| recovery of novel bacterial diversity from a forested wetland impacted by reject coal. | sulphide mineral mining together with improperly contained sulphur-rich coal represents a significant environmental problem caused by leaching of toxic material. the savannah river site's d-area harbours a 22-year-old exposed reject coal pile (rcp) from which acidic, metal rich, saline runoff has impacted an adjacent forested wetland. in order to assess the bacterial community composition of this region, composite sediment samples were collected at three points along a contamination gradient (hi ... | 2002 | 12460285 |
| long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. | in this study, we examined the long-term development of the overall structural morphology and community composition of a biofilm formed in a model drinking water distribution system with biofilms from 1 day to 3 years old. visualization and subsequent quantification showed how the biofilm developed from an initial attachment of single cells through the formation of independent microcolonies reaching 30 micro m in thickness to a final looser structure with an average thickness of 14.1 micro m and ... | 2003 | 14602654 |
| 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 |
| 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 |
| 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 |
| purification and characterization of an acid trehalase from acidobacterium capsulatum. | we purified an acid trehalase (ec 3.2.1.28, alpha,alpha'-trehalose glucohydrolase) from an acidophilic bacterium, acidobacterium capsulatum. the enzyme was homogeneous based on polyacrylamide gel electrophoresis, and was composed of a single polypeptide chain with a molecular mass of 57 kda. maximum trehalase activity was observed at ph 2.5. the acid trehalase exhibited an apparent k(m) of 1.0 mm for trehalose at 30 degrees c and ph 3.0. the trehalase was located in the periplasmic space. the ac ... | 2001 | 16232965 |
| bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic "epsilonproteobacteria". | filamentous microbial mats from three aphotic sulfidic springs in lower kane cave, wyoming, were assessed with regard to bacterial diversity, community structure, and ecosystem function using a 16s rdna-based phylogenetic approach combined with elemental content and stable carbon isotope ratio analyses. the most prevalent mat morphotype consisted of white filament bundles, with low c:n ratios (3.5-5.4) and high sulfur content (16.1-51.2%). white filament bundles and two other mat morphotypes had ... | 2004 | 16329854 |
| hydrocarbon contamination changes the bacterial diversity of soil from around scott base, antarctica. | a combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from ross island, antarctica. while numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. members of the divisions fibrobacter/acidobacterium, cytophaga/flavobacterium/bacteroides, deinococcus/t ... | 2004 | 16329936 |
| bacterial diversity within the planktonic community of an artesian water supply. | culture and molecular methods were used to describe the planktonic bacterial diversity of an artesian water supply in rural latah county, idaho, within the drainage of a small perennial stream, thorn creek. the surrounding depth to groundwater at this location is thought to be significant (>100 m), and this transitional zone (basalt-granite) of the palouse aquifer system is little studied. the water produced by this artesian source is consistent even in years of drought and is of high quality, b ... | 2006 | 16604121 |
| identification and characterization of the gene encoding the acidobacterium capsulatum major sigma factor. | acidobacterium capsulatum is an acid-tolerant, encapsulated, gram-negative member of the ubiquitous, but poorly understood acidobacteria phylum. little is known about the genetics and regulatory mechanisms of a. capsulatum. to begin to address this gap, we identified the gene encoding the a. capsulatum major sigma factor, rpod, which encodes a 597-amino acid protein with a predicted sequence highly similar to the major sigma factors of solibacter usitatus ellin6076 and geobacter sulfurreducens p ... | 2006 | 16698197 |
| microbial communities in a porphyry copper tailings impoundment and their impact on the geochemical dynamics of the mine waste. | the distribution and diversity of acidophilic bacteria of a tailings impoundment at the la andina copper mine, chile, was examined. the tailings have low sulfide (1.7% pyrite equivalent) and carbonate (1.4% calcite equivalent) contents and are stratified into three distinct zones: a surface (0-70-80 cm) 'oxidation zone' characterized by low-ph (2.5-4), a 'neutralization zone' (70-80 to 300-400 cm) and an unaltered 'primary zone' below 400 cm. a combined cultivation-dependent and biomolecular app ... | 2007 | 17222129 |
| evidence that the potential for dissimilatory ferric iron reduction is widespread among acidophilic heterotrophic bacteria. | nineteen characterized strains and isolates of acidophilic heterotrophic bacteria were screened for their abilities to catalyse the reductive dissolution of the ferric iron mineral schwertmannite, under oxygen-limiting conditions. acidocella facilis, acidobacterium capsulatum, and all of the acidiphilium, acidocella and acidobacterium-like isolates that grew in liquid cultures were able to reduce iron. in contrast, neither acidisphaera rubrifaciens nor three acidisphaera-like isolates tested wer ... | 2008 | 18081844 |
| analysis of the bacterial community found in clay wall material used in the construction of traditional japanese buildings. | clay wall (also called mud wall in english and tsuchikabe in japanese) material is used in traditional japanese buildings. clay wall material is manufactured by fermenting a mixture of clay, sand, and rice straw. a culture-independent study based on 16s rrna sequences revealed that clostridiales of firmicutes, alpha-, gamma- and delta-proteobacteria of proteobacteria, and acidobacterium of acidobacteria exist in the clay wall material. of these, we focused on clostridium and geobacter and their ... | 2008 | 18256471 |
| [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 |
| molecular characterization of bacterial diversity in lodgepole pine (pinus contorta) rhizosphere soils from british columbia forest soils differing in disturbance and geographic source. | rhizosphere bacteria from lodgepole pine (pinus contorta) seedlings were characterized from forest soils which differed in disturbance and geographic source. soil disturbance treatments included whole-tree harvesting with and without heavy soil compaction and whole-tree harvesting with complete surface organic matter removal and heavy soil compaction from british columbia (bc) ministry of forests long-term soil productivity installations in three biogeoclimatic subzones in central bc, canada. ba ... | 2002 | 19709294 |
| phylogenetic diversity of bacteria associated with paleolithic paintings and surrounding rock walls in two spanish caves (llonín and la garma). | bacterial diversity in caves is still rarely investigated using culture-independent techniques. in the present study, bacterial communities on paleolithic paintings and surrounding rock walls in two spanish caves (llonín and la garma) were analyzed, using 16s rdna-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. results revealed complex bacterial communities consisting of a high number of novel 16s rdna sequence types and ... | 2004 | 19712338 |
| changes in developing plant microbial community structure as affected by contaminated water. | the effects of sand and clay soils and water contaminated by escherichia coli o157:h7 on the development of rhizosphere and phyllosphere microbial communities were analyzed to determine the influence of plant age on microbial community structure and composition. community bacterial nucleic acids were extracted from lettuce rhizosphere and phyllosphere samples at different stages of plant development after the soils were irrigated with water contaminated with e. coli o157:h7 at planting and 15 da ... | 2004 | 19712407 |
| isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a sphagnum peat bog. | two dense and highly enriched (up to 10(9) cells ml(-1), <10% of bacterial satellites) acido-tolerant (ph 4.0-6.5) methanogenic consortia, '26' and 'k', were isolated from the peat beneath a sphagnum-eriophorum-carex community in west siberia. both consortia produced methane from co2:h2 on chemically defined, diluted n-free media containing ti(iii)citrate as reducing agent. the phylogenetic analysis of 16s ribosomal dna revealed three archaeal and nine bacterial sequence types. consortium '26' c ... | 2003 | 19719599 |
| evaluation of nested pcr-dgge (denaturing gradient gel electrophoresis) with group-specific 16s rrna primers for the analysis of bacterial communities from different wastewater treatment plants. | the diversity of bacterial groups of activated sludge samples that received wastewater from four different types of industry was investigated by a nested pcr-dgge (denaturing gradient gel electrophoresis) approach. specific 16s rrna primers were chosen for large bacterial groups (bacteria and alpha-proteobacteria in particular), which dominate activated sludge communities, as well as for actinomycetes, ammonium oxidisers and methanotrophs (types i and ii). in addition primers for the new acidoba ... | 2002 | 19709189 |
| [influence of community structure of phosphorus removing bacteria under oxygen contain in processes for phosphorus removal]. | it was studied for community structure of microorganisms in the phosphorus removal processes under the circulating situation, and analyzed for microorganism's structure and behavior characteristics by the molecular biology technique with direct obtaining of dna from samples of activated sludge, and by nested pcr and dgge. it was also determined community structure of microorganisms. it was analyzed structures of proteobacteria and acidobacterium by 16s rdna v3 area gene fragments sequences in ac ... | 2008 | 18613523 |
| 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 |
| acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum acidobacteria. | two strains of aerobic acidophilic chemoorganotrophic bacteria designed strains ap8(t) and ap9 were isolated from acid mine drainage and acidic soil, respectively. these isolates were gram-negative, nonmotile cocci and coccobacilli measuring 0.5-0.8 μm in diameter. cells were capsulated. colonies on solid media were pink colored. the ph range for growth was 3.0-6.0 (optimum ph 4.5). sugars, gluconate, and some amino acids were good carbon and energy sources for growth. the main components of cel ... | 2011 | 21255071 |
| ph gradient-induced heterogeneity of fe(iii)-reducing microorganisms in coal mining-associated lake sediments. | lakes formed because of coal mining are characterized by low ph and high concentrations of fe(ii) and sulfate. the anoxic sediment is often separated into an upper acidic zone (ph 3; zone i) with large amounts of reactive iron and a deeper slightly acidic zone (ph 5.5; zone iii) with smaller amounts of iron. in this study, the impact of ph on the fe(iii)-reducing activities in both of these sediment zones was investigated, and molecular analyses that elucidated the sediment microbial diversity w ... | 2008 | 18083864 |
| geomicrobiology of la zarza-perrunal acid mine effluent (iberian pyritic belt, spain). | effluent from la zarza-perrunal, a mine on the iberian pyrite belt, was chosen to be geomicrobiologically characterized along a 1,200-m stream length. the ph at the origin was 3.1, which decreased to 1.9 at the final downstream sampling site. the total iron concentration showed variations along the effluent, resulting from (i) significant hydrolysis and precipitation of fe(iii) (especially along the first reach of the stream) and (ii) concentration induced by evaporation (mostly in the last reac ... | 2011 | 21357431 |
| telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the acidobacteria and emended description of acidobacterium capsulatum kishimoto et al. 1991. | a gram-negative, facultatively anaerobic, chemo-organotrophic, non-pigmented, slowly growing bacterium was isolated from acidic sphagnum peat and designated strain tpb6017t. cells of this strain are long rods that multiply by normal cell division and are motile by means of a single flagellum. they grow under reduced oxygen tension and under anoxic conditions and ferment sugars and several polysaccharides including amorphous and crystalline cellulose. strain tpb6017t is a psychrotolerant acidophi ... | 2011 | 21460138 |
| diversity and in situ quantification of acidobacteria subdivision 1 in an acidic mining lake. | analysis of 16s rrna gene clone libraries from acidic mining lake water and sediment, and from an enclosure to which organic carbon was added to stimulate microbial alkalinization processes of sulfate and iron reduction revealed the presence of diverse sequences affiliated with the acidobacteria subdivision 1. a novel oligonucleotide probe, acido228, was designed that covered most sequences of acidobacteria subdivision 1. the hybridization conditions were optimized using the type strain acidobac ... | 2008 | 18028401 |
| "bioshrouding": a novel approach for securing reactive mineral tailings. | a novel technique ("bioshrouding") for safeguarding highly reactive sulfidic mineral tailings deposits is proposed. in this, freshly milled wastes are colonised with ferric iron-reducing heterotrophic acidophilic bacteria that form biofilms on reactive mineral surfaces, thereby preventing or minimising colonisation by iron sulfide-oxidising chemolithotrophs such as acidithiobacillus ferrooxidans and leptospirillum spp. data from initial experiments showed that dissolution of pyrite could be redu ... | 2008 | 17975731 |
| microbial diversity in anaerobic sediments at rio tinto, a naturally acidic environment with a high heavy metal content. | the tinto river is an extreme environment located at the core of the iberian pyritic belt (ipb). it is an unusual ecosystem due to its size (100 km long), constant acidic ph (mean ph, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the tinto river basin comparable to acidic mine drainage (amd) systems. in this paper we present an extensive survey of the tinto river sediment microbiota using two culture-independent approaches: denaturing gr ... | 2011 | 21724883 |
| candidatus chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. | only five bacterial phyla with members capable of chlorophyll (chl)-based phototrophy are presently known. metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in yellowstone national park revealed the existence of a distinctive bacteriochlorophyll (bchl)-synthesizing, phototrophic bacterium. a highly enriched culture of this bacterium grew photoheterotrophically, synthesized bchls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. ... | 2007 | 17656724 |
| acidicapsa borealis gen. nov., sp. nov. and a. ligni sp. nov., two novel subdivision 1 acidobacteria from sphagnum peat and decaying wood. | two strains of subdivision 1 acidobacteria, namely the pink-pigmented bacterium ka1t and the colorless isolate wh120t, were obtained from acidic sphagnum peat and wood under decay by the white-rot fungus hyploma fasciculare, respectively. cells of these isolates are gram-negative, non-motile, short rods, which are covered by large polysaccharide capsules and occur singly, in pairs, or in short chains. strains ka1t and wh120t are strictly aerobic mesophiles that grow between 10 and 33єc, with an ... | 2011 | 21856984 |
| identification of the acidobacterium capsulatum lexa box reveals a lateral acquisition of the alphaproteobacteria lexa gene. | acidobacterium capsulatum is the most thoroughly studied species of a new bacterial phylogenetic group designated the phylum acidobacteria. through a tblastn search, the a. capsulatum lexa gene has been identified, and its product purified. electrophoretic mobility shift assays have shown that a. capsulatum lexa protein binds specifically to the direct repeat gttcn(7)gttc motif. strikingly, this is also the lexa box of the alphaproteobacteria, but had not previously been described outside this s ... | 2006 | 16549674 |
| 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 |
| 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 |
| molecular identification of bacteria and eukarya inhabiting an antarctic cryoconite hole. | inhabitants of a cryoconite hole formed in the canada glacier in the mcmurdo dry valley region of antarctica have been isolated and identified by small subunit (16s/18s) rdna amplification, cloning, and sequencing. the sequences obtained revealed the presence of members of eight bacterial lineages (acidobacterium, actinobacteria, cyanobacteria, cytophagales, gemmimonas, planctomycetes, proteobacteria, and verrucomicrobia) and metazoan (nematode, tardigrade, and rotifer), truffle (choiromyces), c ... | 2003 | 12768448 |
| a census of rrna genes and linked genomic sequences within a soil metagenomic library. | we have analyzed the diversity of microbial genomes represented in a library of metagenomic dna from soil. a total of 24,400 bacterial artificial chromosome (bac) clones were screened for 16s rrna genes. the sequences obtained from bac clones were compared with a collection generated by direct pcr amplification and cloning of 16s rrna genes from the same soil. the results indicated that the bac library had substantially lower representation of bacteria among the bacillus, alpha-proteobacteria, a ... | 2003 | 12732537 |
| soil microbial community structure across a thermal gradient following a geothermal heating event. | in this study microbial species diversity was assessed across a landscape in yellowstone national park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees c at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. changes in soil ... | 2002 | 12450855 |
| identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. | stable-isotope probing (sip) is a culture-independent technique that enables the isolation of dna from micro-organisms that are actively involved in a specific metabolic process. in this study, sip was used to characterize the active methylotroph populations in forest soil (ph 3.5) microcosms that were exposed to (13)ch(3)oh or (13)ch(4). distinct (13)c-labelled dna ((13)c-dna) fractions were resolved from total community dna by cscl density-gradient centrifugation. analysis of 16s rdna sequence ... | 2002 | 12177327 |
| 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 |
| comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. | soil bacteria are important contributors to primary productivity and nutrient cycling in arid land ecosystems, and their populations may be greatly affected by changes in environmental conditions. in parallel studies, the composition of the total bacterial community and of members of the acidobacterium division were assessed in arid grassland soils using terminal restriction fragment length polymorphism (trf, also known as t-rflp) analysis of 16s rrna genes amplified from soil dna. bacterial com ... | 2002 | 11916705 |
| 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 |
| the diversity of archaea and bacteria in association with the roots of zea mays l. | the diversity of bacteria and archaea associating on the surface and interior of maize roots (zea mays l.) was investigated. a bacterial 16s rdna primer was designed to amplify bacterial sequences directly from maize roots by pcr to the exclusion of eukaryotic and chloroplast dna. the mitochondrial sequence from maize was easily separated from the pcr-amplified bacterial sequences by size fractionation. the culturable component of the bacterial community was also assessed, reflecting a community ... | 2001 | 11391463 |
| ecophysiology of fe-cycling bacteria in acidic sediments. | using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. using six different media with ph values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. among the isolated strains, 22 st ... | 2010 | 20971876 |
| structural model and spectroscopic characteristics of the fmo antenna protein from the aerobic chlorophototroph, candidatus chloracidobacterium thermophilum. | the fenna-matthews-olson protein (fmo) binds seven or eight bacteriochlorophyll a (bchl a) molecules and is an important model antenna system for understanding pigment-protein interactions and mechanistic aspects of photosynthetic light harvesting. fmo proteins of green sulfur bacteria (chlorobiales) have been extensively studied using a wide range of spectroscopic and theoretical approaches because of their stability, the spectral resolution of their pigments, their water-soluble nature, and th ... | 2010 | 20875391 |
| environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria leptospirillum spp. in their natural microbial community. | extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). in the río tinto (spain), brown filaments develop under the water stream where the gram-negative iron-oxidizing bacteria leptospirillum spp. (l. ferrooxidans and l. ferriphilum) and acidithiobacillus ferrooxidans are abundant. these microorganisms play ... | 2010 | 20576116 |
| novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. | the remediation of benzene contaminated groundwater often involves biodegradation and although the mechanisms of aerobic benzene biodegradation in laboratory cultures have been well studied, less is known about the microorganisms responsible for benzene degradation in mixed culture samples or at contaminated sites. to address this knowledge gap, dna based stable isotope probing (sip) was utilized to identify active benzene degraders in microcosms constructed with soil from three sources (a conta ... | 2011 | 20549308 |
| molecular analyses of the microbial community composition of an anoxic basin of a municipal wastewater treatment plant reveal a novel lineage of proteobacteria. | a culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. two 16s rrna gene libraries were constructed using total genomic dna and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. phylogenetic analysis of 132 and 249 almost full-length 16s rrna genes for archaea and bacteria, respectively, was done using the arb software package. phylogene ... | 2010 | 20174790 |
| production of glycolic acid by chemolithotrophic iron- and sulfur-oxidizing bacteria and its role in delineating and sustaining acidophilic sulfide mineral-oxidizing consortia. | glycolic acid was detected as an exudate in actively growing cultures of three chemolithotrophic acidophiles that are important in biomining operations, leptospirillum ferriphilum, acidithiobacillus (at.) ferrooxidans, and at. caldus. although similar concentrations of glycolic acid were found in all cases, the concentrations corresponded to ca. 24% of the total dissolved organic carbon (doc) in cultures of l. ferriphilum but only ca. 5% of the total doc in cultures of the two acidithiobacillus ... | 2010 | 19933342 |
| effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil. | little is known about the chronic effect of herbicides on the soil microbial community, with most studies focusing on acute impacts. in this study, we investigated the effect of 20 years of atrazine and metolachlor application on the community structure, abundance and function of bacterial groups in the bulk soil of a maize monoculture. group-specific pcr-dgge (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16s rrna genes was used to characterize the composition of the mic ... | 2003 | 19719567 |
| terriglobus saanensis sp. nov., a novel acidobacterium isolated from tundra soil of northern finland. | two aerobic pink-pigmented bacteria, designated sp1pr4t and sp1pr5 were isolated from tundra soil samples collected from saana fjeld, north-western finland (69°01'n, 20°50'e). cells of both strains were gram-negative, non-motile rods. phylogenetic analysis indicated that the strains belong to the genus terriglobus in the subgroup 1 acidobacteria. the 16s rrna gene sequence similarity with terriglobus roseust was 97.2%. low dna-dna homology (3.1%) to t. roseus indicated that the tundra soil isola ... | 2010 | 21186292 |
| [spatial characteristics of microbial groups associated with the groundwater flow in a small watershed]. | few reports of microbial groups associated with the groundwater flow system are available in china. 16s rrna gene library was constructed by the cultured-independent approach to investigate gene sequences of microorganism in groundwater samples from the recharge (r), intermediate (m) and discharge (d) zones of an experimental watershed at zhuhai campus of sun yat-sen university. proteobacterium, candidate division opx, uncultured archaeon (uncultured crenarchaeote and euryarchaeote) and actinoba ... | 2010 | 21229735 |
| dynamic of active microorganisms inhabiting a bioleaching industrial heap of low-grade copper sulfide ore monitored by real-time pcr and oligonucleotide prokaryotic acidophile microarray. | the bioleaching of metal sulfide has developed into a very important industrial process and understanding the microbial dynamic is key to advancing commercial bioleaching operations. here we report the first quantitative description of the dynamic of active communities in an industrial bioleaching heap. acidithiobacillus ferrooxidans was the most abundant during the first part of the leaching cycle, while the abundance of leptospirillum ferriphilum and ferroplasma acidiphilum increased with age ... | 2009 | 21255296 |
| bryocella elongata gen. nov., sp. nov., a novel member of subdivision 1 of the acidobacteria isolated from a methanotrophic enrichment culture, and emended description of edaphobacter aggregans koch et al. 2008. | an aerobic, pink-pigmented, chemoorganotrophic bacterium, designated strain sn10t, was isolated from a methanotrophic enrichment culture obtained from an acidic sphagnum peat. this isolate was represented by gram-negative, non-motile rods that multiply by normal cell division and form rosettes. strain sn10t is obligately acidophilic, mesophilic bacterium capable of growth at ph values between 3.2 and 6.6 (with an optimum at ph 4.7-5.2) and at temperatures between 6 and 32°c (with an optimum at 2 ... | 2011 | 21551329 |
| petroleum-influenced beach sediments of the campeche bank, mexico: diversity and bacterial community structure assessment. | the bacterial diversity and community structure were surveyed in intertidal petroleum-influenced sediments of ~100 km of a beach, in the southern gulf of mexico. the beach was divided in twenty sampling sites according to high, moderate and low petroleum influence. densities of cultured heterotrophic (hab) and hydrocarbon degrading bacteria (hdb) were highly variable in sediments, with little morphological assortment in colonies. pcr-risa banding patterns differentiated distinct communities alon ... | 2011 | 21802196 |
| isolation and characterization of a homodimeric type-i reaction center complex from candidatus chloracidobacterium thermophilum, an aerobic chlorophototroph. | the recently discovered thermophilic acidobacterium candidatus chloracidobacterium thermophilum is the first aerobic chlorophototroph that has a type-i, homodimeric rc. this organism and its type-i rcs were initially detected by the occurrence of psca gene sequences, which encode the core subunit of the rc complex, in metagenomic sequence data derived from hot spring microbial mats. here, we report the isolation and initial biochemical characterization of the type-i rc from ca. c. thermophilum. ... | 2011 | 22184116 |
| Cloning and expression of a gene with phospholipase B activity from Pseudomonas fluorescens in Escherichia coli. | A gene from Pseudomonasfluorescens BIT-18 encoding a protein with phospholipase B activity (Pf-PLB) was cloned in E. coli BL21 (DE3). The open reading frame consists of 1272bp and potentially encodes a protein of 423 amino acid residues with a calculated molecular mass of 45.8kDa. The nucleotide sequence of Pf-PLB is 45%, 42%, 41%, 40%, 33%, and 31% identical to that of Bifidobacteriumanimals, Mycobacteriumparascrofulaceum, Acidobacteriumcapsulatum, Lactobacillusjohnsonii, Moraxellabovis, and Mo ... | 2012 | 22078969 |