Intragenomic heterogeneity of the 16S rRNA gene in strain UFO1 caused by a 100-bp insertion in helix 6

Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI) T he throughput, depth, and reduced cost of second-generation DNA sequencing facilitate our ability to gain insight into a broad range of microbiological processes in the environment, and genome sequencing of prominent members of environmental microbial communities should contribute to the understanding of complex biogeochemical systems. Members of the Veillonellaceae, and particularly Pelosinus spp., have recently been reported to be among the more abundant bacterial taxa in chromate-reducing systems inoculated with material from the chromium-contaminated aquifer at the U.S. Department of Energy (DOE) Hanford 100H site in Washington State (1, 2) and in other contaminated aquifers (3-5). Chromate-reducing bacteria are of interest because in situ reductive immobilization is favored as one of the more cost-effective approaches to remediation of aquifers contaminated with Cr(VI), a potent toxicant, mutagen, and carcinogen (6, 7). Fermentative bacteria such as Pelosinus spp. may be of particular relevance to a common bioremediation scenario in which metabolism of organic electron donors (e.g., lactate-based polymers) injected into the subsurface readily consumes available electron acceptors (e.g., oxygen, nitrate, sulfate, and ferric iron) and drives the treated zone toward fermentative/methanogenic conditions.-In this article, we report on a variety of metabolic capabilities and their possible underlying genetic basis in a Pelosinus isolate that dominated a chromate-reducing community derived from aquifer sediment from the Hanford 100H site. The metabolic capabilities explored include lactate fermentation to propionate and acetate (related to the methylmalonyl-coenzyme A [CoA] pathway identified in the genome), Cr(VI) and Fe(III) reduction (both potentially related to identified flavoproteins), nitrate and nitrite reduction (potentially related to NrfH and NrfA as well as a membrane-bound, respiratory nitrate reductase), and H 2 metabolism (two [NiFe]-hydrogenases and four [FeFe]-hydrogenases were identified). We also report on focused transcriptional studies designed to more clearly associate certain genes with specific metabolic activities (namely, H 2 cycling and nitrate or nitrite reduction). Some metabolic activities and gene content reported here are unexpected for Pelosinus species and broaden our perspective on what metabolic and ecological roles this species might play in microbial communities in contaminated (and uncontaminated) environments. MATERIALS AND METHODSIsolation and cultivation of Pelosinus sp. strain HCF1. Pelosinus sp. strain HCF1 was isolated from the effluent of an anaerobic, chromatereducing, flowthrough column containing aquifer sediment from the DOE Hanford 100H site...

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“…UFO1 and Sporotalea sp. TM1 (29), suggesting that this is not an unusual phenomenon in the Pelosinus-Sporotalea group (Fig. 4).…”

Section: Resultsmentioning

confidence: 99%

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

Beller

Han

Karaöz

et al. 2013

Appl Environ Microbiol

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“…Such intervening sequences were also detected in the phylogenetically related strain UFO1 (Fig. 1), which was isolated from sediments at the Oak Ridge Integrated Field Research Challenge site in Tennessee, USA (Ray et al, 2010). Intervening sequences at variable region I are not uncommon in the class Clostridia and have been observed in Clostridium paradoxum (Rainey et al, 1996b) and the distantly related taxa Desulfotomaculum (Stackebrandt et al, 1997), Desulfitobacterium (Villemur et al, 2007) and Carboxydothermus hydrogenoformans (Wu et al, 2005).…”

mentioning

confidence: 86%

Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov.

Moe

Stebbing

Rao

et al. 2012

International Journal of Systematic and Evolutionary Microbiology

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Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov. , on the basis of their phenotypic and phylogenetic properties. The isolates were Gram-negative, spore-forming, motile rods with peritrichous flagella. Growth occurred at 10-42 6C and pH 5.5-8.5. Fermentative growth was observed on Casamino acids, fructose, fumarate, glucose, glycerol, pyruvate and yeast extract. The major organic acids produced from glucose and glycerol fermentation were propionate and acetate. The major organic acids produced from fermentation of fumarate were propionate, acetate and succinate. The major cellular fatty acids were summed feature 4 (consisting of C 15 : 1 v8c and/or C 15 : 2 ), summed feature 8 (consisting of C 17 : 1 v8c and/ or C 17 : 2 ) and C 14 : 0 dimethyl aldehyde. The polar lipids comprised aminophospholipids, including phosphatidylethanolamine and phosphatidylserine, and an unknown phospholipid. The genomic DNA G+C content was 39.2 mol%. We propose that strains SHI-1 T and SHI-2 are assigned to a novel species of the genus Pelosinus, with the name Pelosinus defluvii sp. nov. The genus Pelosinus was described by Shelobolina et al. (2007) to accommodate a bacterium belonging to the Sporomusa-Pectinatus-Selenomonas group of the phylum Firmicutes (Strömpl et al., 1999). This group is a heterogeneous assemblage of organisms with Gram-negative cell walls and is also referred to as clostridial cluster IX (Collins et al., 1994) and the family Veillonellaceae (Rogosa, 1971). At present, the genus Pelosinus is represented by a single species, Pelosinus fermentans, the type strain of which was first isolated from a subsurface kaolin deposit in Russia (Shelobolina et al., 2007). The genus Sporotalea contains the single species Sporotalea propionica and was described by Boga et al. (2007) to accommodate a propionigenic bacterium isolated from the intestinal tract of the soilfeeding termite Thoracotermes macrothorax. At the time of initial publication, the closest phylogenetic relative reported for both P. fermentans R7 T (Shelobolina et al., A supplementary figure is available with the online version of this paper.

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“…genomes have one copy of the 16S rRNA gene predicted on a single contig (3, 4), except strain A11, which has two copies predicted (870 and 1,315 bp), and strain HCF1, which has five sequences (34, 127, 172, 228, and 1,218 bp) on five individual contigs (2). Two different versions of the 16S rRNA gene have been identified in strain UFO1 using PCR, one of which contained a 100-bp insertion and was not expressed under the conditions assayed (8). …”

Section: Genome Announcementmentioning

confidence: 99%

Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology

et al. 2014

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Intragenomic heterogeneity of the 16S rRNA gene in strain UFO1 caused by a 100-bp insertion in helix 6

Cited by 13 publications

References 42 publications

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov.

Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology

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