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Roseiflexus sp. strains were cultivated from a microbial mat of an alkaline siliceous hot spring in Yellowstone National Park. These strains are closely related to predominant filamentous anoxygenic phototrophs found in the mat, as judged by the similarity of small-subunit rRNA, lipid distributions, and genomic and metagenomic sequences. Like a Japanese isolate, R. castenholzii, the Yellowstone isolates contain bacteriochlorophyll a, but not bacteriochlorophyll c or chlorosomes, and grow photoheterotrophically or chemoheterotrophically under dark aerobic conditions. The genome of one isolate, Roseiflexus sp. strain RS1, contains genes necessary to support these metabolisms. This genome also contains genes encoding the 3-hydroxypropionate pathway for C[O.sub.2] fixation and a hydrogenase, which might enable photoautotrophic metabolism, even though neither isolate could be grown photoautotrophically with [H.sub.2] or [H.sub.2]S as a possible electron donor. The isolates exhibit temperature, pH, and sulfide preferences typical of their habitat. Lipids produced by these isolates matched much better with mat lipids than do lipids produced by R. castenholzii or Chloroflexus isolates. doi: 10.1128/JB.01610-09

The competitive fitness of three phenanthrene-mineralizing isolates is evaluated to find whether the contaminant availability determine the isolates competitive fitness. The results indicate that contaminant availability alone does not determine the isolates competitive fitness.

Research has been conducted on the filamentous Chloroflexaceae-related bacteria. The phenotypic and phylogenetic diversity of these bacteria have been investigated and the identification of the genus Chloroflexus and type C organisms has been carried out in analyzing their morphology and small-scale distribution in the microbial mats.

Research has been conducted on the filamentous bacteria containing bacteriochlorophylls c and a. The enrichment of these bacteria from the hypersaline microbial mats has been carried out and the results are described.

Research has been conducted on the hydrocarbon-degrading microbial population shifts in soil. The effect of surfactant addition on these shifts has been investigated.

Research has been conducted on the substrate bioavailability. The effect of the reduced substrate bioavailability on the contaminant degradation under enrichment culture conditions is discussed.

The cyanobacterium Synechococcus adopts a specific position in the mat depending on the time of day. Researchers discovered that the cells assume an upright position around noon, but were randomly oriented at other times.

Light-induced motility of two thermophilic Synechococcus isolates that are morphologically similar but that belong to different cyanobacterial lineages was observed. Both isolates migrated away from densely inoculated streaks to form fingerlike projections extending toward or away from the light source, depending on the light intensity. However, the two isolates appear to prefer widely different light conditions.

The mat cyanobacteria present in the hot springs in Yellowstone National Park produce mainly polysaccharide in the presence of light. The bacteria ferment polysaccharides during the night to produce acetate and propionate. Although the cyanobacteria are photosynthetically active, they show low synthesis of proteins and rRNA that are associated with growth. The mat cores mainly assimilate polyglucose during illumination periods. The rapidly growing Synechococcus sp. strain C1 partitions most of the incorporated 14CO2 into protein, low-molecular-weight metabolites and lipids.

Cloning and cultivation studies shows that the phenotypically diverse gram-positive bacterial isolates from a cyanobacterial mat from Octopus Spring, Yellowstone National Park, are genetically similar to Bacillus flavothermus. A comparison of cloning and cultivation methods shows that the cultivation methods fail to give the composition of the microbial community. The molecular retrieval technique is unable to describe the less abundant populations in microbial community.

The denaturing gradient gel electrophoresis separation of 16S rRNA gene fragment helps to study the effect of enrichment culture techniques on the composition of the aerobic chemoorganotrophic bacteria population in Octopus Spring, Yellowstone National Park. Variations in the enrichment conditions, degree of dilution of the inoculum and culture medium composition give 14 unique 16S rRNA sequences. The results reveal the diversity in bacterial populations obtained by enrichment methods in contrast to molecular retrieval and strain purification techniques.

A comparison of complex polar lipids in a hot spring cyanobacterial mat cultivated from various habitats helps examine microbial sources of major mat lipids. Fast atom bombardment mass spectrometry helps examine the masses in complex polar lipid components. Two-dimensional thin layer chromatography helps determine the chemistry of complex polar lipid components. Major lipids of mats are similar to those of cyanobacterial isolates.

Certain areas of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and chloroflexus-like bacteria, use oligodeoxynucleotide hybridization probes to measure light intensity at hot spring microbial mats. The probes used in the investigations revealed the variability of the effects of light intensity reduction on SSU rRNAs. SSU rRNA are used to identify genetically distinct members of microbial communities.

The derivation from the Octopus Spring cyanobacterial mat of 16S rRNA sequences as cDNA is discussed. The fragments were retieved from a cDNA library. Several previously uncharacterized communitymembers were recognized by the sequence information. It was found that size selection can cause a bias against the recovery of certain sequences as revealed in the analysis of shorter rcDNA products.

Chimeric small-subunit (SSU) rRNA sequences, obtained from a hot spring cyanobacterial mat, revealed genes of uncultivated species, when the short sequence domains were analyzed phylogenetically. PCR was used in the chimeric SSU rRNA genes recovery, which exhibited no secondary structural abnormality. PCR is used to retrieve SSU rRNA genes of distinct native microbial species from their natural environment.

The microbial mats and sediments from various hot springs in Yellowstone National Park were analyzed. Results concluded that the Glycerol dialkyl glycerol tetraethers (GDGTs) bacteria are developed from geothermally heated surrounding soils.

Seven crude oil contaminated soil types obtained from six geographically distinct areas of United States are used to examine soil bacterial population dynamics, identify the organisms associated with alkane degeneration and to assess patterns in microbial response. This study demonstrates that crude-oil contamination results in the selection of diverse microbial populations across geographically distinct soils.

The bacterial communities associated with natural hydrocarbon seeps in nonthermal soil at Rainbow Springs, Yellow Stone National Park was described. The soil chemical analysis revealed high sulphate concentrations and low pH value that are characteristic of acid-sulfate geothermal activity.

The differences in the carbon isotopic fractionation between inorganic carbon and lipid biomakers indicate photoautotrophic process in chloroflexus-like bacteria in sulfidic and nonsulfidic hotsprings. Research further shows that photoheterotrophy also exists in the hot-spring microbial mats when cyanobacteria cross-feed chloroflexus-like organisms.

Research has been conducted on the hypothesis that subsurface layer cells can represent low-light-adapted populations. The authors suggest the necessity of use of higher-resolution genetic markers in order to be able to observe vertical population structure at higher-temperature sites.

A shotgun metaproteomics approach was employed to identify proteins in a hot spring microbial mat community. We identified 202 proteins encompassing 19 known functions from 12 known phyla. Importantly, we identified two key enzymes involved in the 3-hydroxypropionate C02 fixation pathway in uncultivated Roseiflexus spp., which are known photoheterotrophs. [ABSTRACT FROM AUTHOR]