| molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations. | a 16s rdna based molecular ecological study was performed on a sample taken from a peat bog in germany. total dna was extracted by directly lysing micro-organisms in the peat matrix. the 5' 1400 nucleotides of the bacterial 16s rdna were amplified using conserved bacterial pcr primers. a clone library was generated by blunt-end cloning and 262 16s rdna clones were analysed. of these, 37 were located in the gram-positive phylum, as determined by hybridization to an oligonucleotide probe specific ... | 1996 | 8885402 |
| reduction of soluble iron and reductive dissolution of ferric iron-containing minerals by moderately thermophilic iron-oxidizing bacteria | five moderately thermophilic iron-oxidizing bacteria, including representative strains of the three classified species (sulfobacillus thermosulfidooxidans, sulfobacillus acidophilus, and acidimicrobium ferrooxidans), were shown to be capable of reducing ferric iron to ferrous iron when they were grown under oxygen limitation conditions. iron reduction was most readily observed when the isolates were grown as mixotrophs or heterotrophs with glycerol as an electron donor; in addition, some strains ... | 1998 | 9603832 |
| phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. | an unusually thick ( approximately 1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at iron mountain, near redding, calif. the slime was studied over the period of 1 year. the subaerial form of the slime distinguished it from more typical submerged streamers. phylogenetic analysis of 16s rrna genes revealed a diversity of sequences that were mostly novel. nearest relatives to the majority of sequences came from iron-oxidizing acidophile ... | 2000 | 10966399 |
| design and performance of rrna targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments. | at iron mountain, ca, there is an extreme occurrence of acid mine drainage (amd). this is a result of past mining activity that has exposed a sulfide ore body to weathering and microbial activity. this study presents seven new oligonucleotide probes for the detection of microorganisms at this amd site by fluorescent in situ hybridization. in the design of these probes we have accounted for a large body of 16s rrna sequence data recently compiled by us. this was obtained by pcr and cloning direct ... | 2001 | 12032620 |
| novel thermo-acidophilic bacteria isolated from geothermal sites in yellowstone national park: physiological and phylogenetic characteristics. | moderately thermophilic acidophilic bacteria were isolated from geothermal (30-83 degrees c) acidic (ph 2.7-3.7) sites in yellowstone national park. the temperature maxima and ph minima of the isolates ranged from 50 to 65 degrees c, and ph 1.0-1.9. eight of the bacteria were able to catalyze the dissimilatory oxidation of ferrous iron, and eleven could reduce ferric iron to ferrous iron in anaerobic cultures. several of the isolates could also oxidize tetrathionate. six of the iron-oxidizing is ... | 2003 | 12802481 |
| biooxidation of pyrite by defined mixed cultures of moderately thermophilic acidophiles in ph-controlled bioreactors: significance of microbial interactions. | the oxidative dissolution of pyrite (fes2) by pure and mixed cultures of moderately thermophilic acidophiles was studied in shake flask cultures and in ph-controlled bioreactors, incubated at 45 degrees c. various combinations of seven eubacteria (a leptospirillum sp. (mt6), acidimicrobium ferrooxidans, acidithiobacillus caldus, an alicyclobacillus sp. (y004), and three sulfobacillus spp.) and one archaeon (ferroplasma sp. mt17) were examined. pyrite dissolution was determined by measuring chang ... | 2004 | 15352055 |
| novel actinobacteria from marine sponges. | actinobacteria exclusively within the sub-class acidimicrobidae were shown by 16s rdna community analysis to be major components of the bacterial community associated with two sponge species in the genus xestospongia. four groups of actinobacteria were identified in xestospongia spp., with three of these four groups being found in both xestospongia muta from key largo, florida and xestospongia testudinaria from manado, indonesia. this suggests that these groups are true symbionts in these sponge ... | 2005 | 15726288 |
| anaerobic treatment of 2,4,6-trichlorophenol in an expanded granular sludge bed-anaerobic filter (egsb-af) bioreactor at 15 degrees c. | expanded granular sludge bed-anaerobic filter (egsb-af) bioreactors were operated at 15 degrees c for the treatment of 2,4,6-trichlorophenol (tcp)-containing volatile fatty acid (vfa)-based wastewaters. the seed sludge used as inoculum for the control (no tcp) and test reactor was unexposed to chlorophenols (cps) prior to the 425-day trial. tcp supplementation to the feed at 50 mg tcpl(-1) partially inhibited the anaerobic degradation of the vfa feed measured as cod removal efficiency. however, ... | 2004 | 16329938 |
| alignment-independent bilinear multivariate modelling (aibimm) for global analyses of 16s rrna gene phylogeny. | alignment-independent phylogenetic methods have interesting properties for global phylogenetic reconstructions, particularly with respect to speed and accuracy. here, we present a novel multimer-based alignment-independent bilinear mathematical modelling (aibimm) approach for global 16s rrna gene phylogenetic analyses. in aibimm, jackknife cross-validated principal component analyses (pca) are used to explain the variance in nucleotide n-mer frequency data. we compared aibimm with alignment-base ... | 2006 | 16825631 |
| a novel acidimicrobium species in continuous cultures of moderately thermophilic, mineral-sulfide-oxidizing acidophiles. | a novel species of acidimicrobium appeared to be the predominant ferrous iron oxidizer in a mixed culture that effected the continuous, efficient extraction of nickel from a mineral concentrate at 49 degrees c, but it was not isolated in pure culture. it outcompeted acidimicrobium ferrooxidans, which was expected to have a major role in iron oxidation in reactors gassed with air, and was outnumbered at 49 degrees c only by the sulfur-oxidizing acidithiobacillus caldus. sulfobacillus species were ... | 2007 | 17468267 |
| extremely acidic, pendulous cave wall biofilms from the frasassi cave system, italy. | the sulfide-rich frasassi cave system hosts an aphotic, subsurface microbial ecosystem including extremely acidic (ph 0-1), viscous biofilms (snottites) hanging from the cave walls. we investigated the diversity and population structure of snottites from three locations in the cave system using full cycle rrna methods and culturing. the snottites were composed primarily of bacteria related to acidithiobacillus species. other populations present in the snottites included thermoplasmata group arch ... | 2007 | 17504478 |
| microbiological and geochemical dynamics in simulated-heap leaching of a polymetallic sulfide ore. | the evolution of microbial populations involved in simulated-heap leaching of a polymetallic black schist sulfide ore (from the recently-commissioned talvivaara mine, finland) was monitored in aerated packed bed column reactors over a period of 40 weeks. the influence of ore particle size (2-6.5 mm and 6.5-12 mm) on changes in composition of the bioleaching microflora and mineral leaching dynamics in columns was investigated and compared to fine-grain (<2 microm) ore that was bioprocessed in sha ... | 2008 | 18496880 |
| culture-independent nested pcr method reveals high diversity of actinobacteria associated with the marine sponges hymeniacidon perleve and sponge sp. | a culture-independent nested polymerase chain reaction (pcr) technique was used to investigate the diversity of actinobacteria communities associated with the sponges hymeniacidon perleve and sponge sp. the phylogenetic affiliation of sponge-derived actinobacteria was then assessed by 16s rrna sequencing of cloned dna fragments. a total of 196 positive clones were screened by restriction fragment length polymorphism (rflp) analysis; 48 unique operational taxonomic units (otus) were selected for ... | 2008 | 18670903 |
| metals tolerance in moderately thermophilic isolates from a spent copper sulfide heap, closely related to acidithiobacillus caldus, acidimicrobium ferrooxidans and sulfobacillus thermosulfidooxidans. | selective enrichments enabled the recovery of moderately thermophilic isolates with copper bioleaching ability from a spent copper sulfide heap. phylogenetic and physiological characterization revealed that the isolates were closely related to sulfobacillus thermosulfidooxidans, acidithiobacillus caldus and acidimicrobium ferrooxidans. while isolates exhibited similar physiological characteristics to their corresponding type strains, in general they displayed similar or greater tolerance of high ... | 2009 | 19104861 |
| actinobacterial community dynamics in long term managed grasslands. | palace leas, a long-term experiment at cockle park farm, northumberland, uk was established in winter 1896-1897 since when the 13 plots have received regular and virtually unchanged mineral fertiliser and farm yard manure inputs. fertilisers have had a profound impact on soil ph with the organically fertilised plots showing a significantly higher ph than those receiving mineral fertiliser where ammonium sulphate has led to soil acidification. here, we investigate the impact of organic and minera ... | 2009 | 19247797 |
| iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber holothuria edulis, and proposal of iamiaceae fam. nov. | a novel, gram-positive bacterial strain, f12(t), was isolated from the abdominal epidermis of a sea cucumber, holothuria edulis, collected from seawater off the coast of japan. according to 16s rrna gene sequence analysis, this strain represents a novel, deep-rooting lineage within the class actinobacteria and clusters with uncultured bacteria and acidimicrobium ferrooxidans. compared to species with validly published names, the highest 16s rrna gene sequence similarity (89.8 %) was to acidimicr ... | 2009 | 19329622 |
| ferrimicrobium acidiphilum gen. nov., sp. nov. and ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria. | two novel extremely acidophilic, iron-oxidizing actinobacteria were isolated, one from a mine site in north wales, uk (isolate t23(t)), and the other from a geothermal site in yellowstone national park, wyoming, usa (y005(t)). these new actinobacteria belong to the subclass acidimicrobidae, and in contrast to the only other classified member of the subclass (acidimicrobium ferrooxidans), both isolates were obligate heterotrophs. the mine site isolate was mesophilic and grew as small rods, while ... | 2009 | 19406797 |
| ilumatobacter fluminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary. | bacterial strain ym22-133t was isolated from the sediment of an estuary and grew in media with an artificial seawater base. strain ym22-133t was gram-positive, aerobic, non-motile and rod shaped. the cell-wall peptidoglycan contained ll-dap, glycine, alanine and hydroxyglutamate. the predominant menaquinone was mk-9 (h8), with mk-9 (h0), mk-9 (h2), mk-9 (h4) and mk-9 (h6) present as minor menaquinones. the g+c content of the genomic dna from the strain was 68 mol%. phylogenetic analysis of the 1 ... | 2009 | 19590147 |
| bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil. | the microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. to assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. microbial activity was monitored continuously over 2 years throughou ... | 2010 | 21044099 |
| complete genome sequence of acidimicrobium ferrooxidans type strain (icp). | acidimicrobium ferrooxidans (clark and norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family acidimicrobiaceae and in the order acidomicrobiales. rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced co(2) concentration is characteristic for a. ferrooxidans. here we describe the features of this organism, together with the complete genome sequence, and annotation. this is the first comple ... | 2009 | 21304635 |
| autotrophic, sulfur-oxidizing actinobacteria in acidic environments. | some novel actinobacteria from geothermal environments were shown to grow autotrophically with sulfur as an energy source. these bacteria have not been formally named and are referred to here as "acidithiomicrobium" species, as the first of the acidophilic actinobacteria observed to grow on sulfur. they are related to acidimicrobium ferrooxidans with which they share a capacity for ferrous iron oxidation. ribulose bisphosphate carboxylase/oxygenase (rubisco) is active in co(2) fixation by acidim ... | 2011 | 21308384 |
| bioleaching in brackish waters-effect of chloride ions on the acidophile population and proteomes of model species. | high concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to western australian and chilean biomining operations. despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. this study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics t ... | 2011 | 22124722 |
| Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. | To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. | 2011 | 21912695 |