Complete Genome Sequence of Geobacillus strain Y4.1MC1, a Novel CO-Utilizing Geobacillus thermoglucosidasius Strain Isolated from Bath Hot Spring in Yellowstone National Park

Brumm, Phillip J.; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Chang, Yen‐Hsiang; Mead, David A.

doi:10.1007/s12155-015-9585-2

Cited by 19 publications

(16 citation statements)

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“…In contrast to the typical single CRISPR locus in most bacterial genomes, Y51MC23 contains 7 definite CRISPR loci ( Table 5 ), similar to the hyperthermophile Sulfolobus solfataricus , which contains 6 CRISPR loci [ 73 ]. Similar numbers of CRISPR loci were found in organisms isolated from Yellowstone hot springs and sequenced by our group, including Geobacillus thermoglucosidasius Y41MC1 (Bath hot spring, 6 CRISPRs) [ 41 ], Geobacillus thermocatenulatus strains Y412MC52 and Y41MC61(Obsidian Pool, 6 CRISPRs each), and Geobacillus thermoglucosidasius C56-YS93 (Obsidian Pool, 6 CRISPRs). Features of the definite CRISPR loci and flanking ORFs (arrows indicate reading frame orientation) are listed below.…”

Section: Resultssupporting

confidence: 65%

“…Thermus aquaticus Y51MC23 is one of a number of novel thermophilic species isolated from 88°C water in the northern outflow channel of Bath hot spring in the Lower Geyser Basin of Yellowstone National Park [ 41 ]. The general features of the organism are summarized in Table 1 .…”

Section: Resultsmentioning

confidence: 99%

“…The thirteen Y51MC23 tryptophan biosynthesis genes are scattered throughout the genome (genes 520, 521, 522, 1058, 1353, 1354, 1447, 1733, 1734, 2080, 2187, 2188, and 2189), unlike the tryptophan operon in E . coli [ 55 ] or thirteen-gene operon (GY4MC1_1353 through GY4MC1_1364) for tryptophan biosynthesis present in Geobacillus thermoglucosidasius Y4.1MC1, a Gram-positive organism isolated from the same hot spring as Y51MC23 [ 41 ].…”

Section: Resultsmentioning

confidence: 99%

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Complete Genome Sequence of Thermus aquaticus Y51MC23

et al. 2015

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Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser Basin of Yellowstone National Park. Remarkably, this T. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. Y51MC23 is a Gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C. Growth studies suggest that Y51MC23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular proteases and peptidases as well as transporter systems for amino acids and peptides. The genome was assembled de novo using a 350 bp fragment library (paired end sequencing) and an 8 kb long span mate pair library. A closed and finished genome was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on megaplasmids were identified on the chromosome. The Y51MC23 genome contains two full and two partial prophage as well as numerous CRISPR loci. The high identity and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is interesting, given the 8,800 km separation of the two hot springs from which they were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple morphologies present in cultures. The use of fluorescence microscopy reveals new details about these unusual morphological features, including the presence of multiple types of large and small spheres, often forming a confluent layer of spheres. Many of the spheres appear to be formed not from cell envelope or outer membrane components as previously believed, but from a remodeled peptidoglycan cell wall. These complex morphological forms may serve multiple functions in the survival of the organism, including food and nucleic acid storage as well as colony attachment and organization.

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Section: Resultssupporting

confidence: 65%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Complete Genome Sequence of Thermus aquaticus Y51MC23

et al. 2015

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“…can grow anaerobically, where they produce lactate, formate, acetate, ethanol and succinate using mixed acid fermentation pathways [ 7 ]. Recently, we showed that the type strain of Parageobacillus thermoglucosidasius is also able to produce hydrogen gas (H 2 ) in the anaerobic phase following aerobic growth, concomitant with the consumption of carbon monoxide (CO) [ 11 ]. Genomic analysis linked this capacity to a genetic locus comprising of three genes coding for a carbon monoxide dehydrogenase (CODH) and 12 genes coding for a NiFe group 4a hydrogenase.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

et al. 2018

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BackgroundThe facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase–hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source.ResultsThe WGS-catalyzed H2 production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542T, DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H2 production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype.ConclusionsDisparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5302-9) contains supplementary material, which is available to authorized users.

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“…Geobacillus species have been isolated from a number of extreme environments including high-temperature oilfields [ 10 ], a corroded pipeline in an extremely deep well [ 11 ], African [ 12 ] and Russian [ 13 ] hot springs, marine vents [ 14 ], and the Mariana Trench [ 15 ], yet they can also be found in garden soils [ 16 ] and hay composts [ 17 ]., The ability of Geobacillus species to thrive in these varied and often hostile environments suggests that these species possess enzymes suitable for applications in challenging industrial environments. We therefore sequenced a number of these Geobacillus isolates including strains Y41MC52, Y41MC61, C56-T3, and Y4.1MC1 [ 18 ] to identify new enzymes suitable for use in biomass conversion into fuels and chemicals.…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park

Brumm

Land

Hauser

et al. 2015

Stand in Genomic Sci

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Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes and average nucleotide identity, Geobacillus sp. Y412MC52 and the related Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus. The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of 3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057 bp and an average G + C content of 45 %. Y412MC52 possesses arabinan, arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of hemicellulose from biomass. Transport and utilization clusters are also present for other carbohydrates including starch, cellobiose, and α- and β-galactooligosaccharides.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-015-0075-0) contains supplementary material, which is available to authorized users.

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Complete Genome Sequence of Geobacillus strain Y4.1MC1, a Novel CO-Utilizing Geobacillus thermoglucosidasius Strain Isolated from Bath Hot Spring in Yellowstone National Park

Cited by 19 publications

References 36 publications

Complete Genome Sequence of Thermus aquaticus Y51MC23

Complete Genome Sequence of Thermus aquaticus Y51MC23

Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park

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