Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)

Sikorski, Johannes; Tindall, Brian J.; Lowry, Stephen R.; Lucas, Susan; Nolan, Matt; Copeland, Alex; Rio, Tijana Glavina del; Tice, Hope; Cheng, Jan‐Fang; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia D.; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter; Lapidus, Alla

doi:10.4056/sigs.1042812

Cited by 21 publications

(8 citation statements)

References 37 publications

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“…In addition, a single set of ribulose-1,5-bisphosphate carboxylase (the key enzyme in the Calvin cycle) genes were identified at site 3 (BPEG3_14745 and BPEG3_14746). This sequence shares 89% amino acid identity with a predicted protein from Meiothermus silvanus DSM 9946 (YP_003686579) [57] , though Thermales are not known to be autotrophic. Malonate semialdehyde reductase, associated with the 3-hydroxypropionate cycle (3HP) was also found in the Chloroflexi consensus genome from sites 4 and 5, which was expected as this cycle is specific to the Chloroflexi [58] .…”

Section: Resultsmentioning

confidence: 93%

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

et al. 2012

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We have constructed a conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the “Bison Pool” (BP) Environmental Genome and a complementary contextual geochemical dataset of ∼75 geochemical parameters. 2,321 16S rRNA clones and 470 megabases of environmental sequence data were produced from biofilms at five sites along the outflow of BP, an alkaline hot spring in Sentinel Meadow (Lower Geyser Basin) of Yellowstone National Park. This channel acts as a >22 m gradient of decreasing temperature, increasing dissolved oxygen, and changing availability of biologically important chemical species, such as those containing nitrogen and sulfur. Microbial life at BP transitions from a 92°C chemotrophic streamer biofilm community in the BP source pool to a 56°C phototrophic mat community. We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering. We have also assigned environmental genome sequences to individual microbial community members by complementing traditional homology-based assignment with nucleotide word-usage algorithms, allowing more than 70% of all reads to be assigned to source organisms. This assignment yields high genome coverage in dominant community members, facilitating reconstruction of nearly complete metabolic profiles and in-depth analysis of the relation between geochemical and metabolic changes along the outflow. We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function. We have also identified an organism constituting a novel phylum in a metabolic “transition” community, located physically between the chemotroph- and phototroph-dominated sites. The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot spring, reconstructing whole metabolic networks in order to illuminate community roles in shaping and responding to geochemical variability.

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Section: Resultsmentioning

confidence: 93%

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

et al. 2012

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“…Two clones were classified as belonging to the phylum Deinococcus / Thermus . One of them close to Meiothermus silvanus , isolated from hot spring and whose optimal growth temperature ranges from 40°C to 60°C (Sikorski et al ., 2010). The presence of this type of bacteria was in agreement with the hydrothermal and volcanic history of the geological substrate that makes the Deception Island permafrost.…”

Section: Discussionmentioning

confidence: 99%

Prokaryotic communities and operating metabolisms in the surface and the permafrost of Deception Island (Antarctica)

Blanco¹,

Prieto-Ballesteros²,

Gómez³

et al. 2012

Environmental Microbiology

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In this study we examined the microbial community composition and operating metabolisms on the surface and in the permafrost of Deception Island, (Antarctica) with an on site antibody microarray biosensor. Samples (down to a depth of 4.2 m) were analysed with LDChip300 (Life Detector Chip), an immunosensor containing more than 300 antibodies targeted to bacterial and archaeal antigens. The immunograms showed positive antigen-antibody reactions in all surface samples (lichens, pyroclasts) and the top layer of the permafrost. The results indicated the presence of exopolysaccharides, bacteria belonging to the Alpha-, Delta- and Gammaproteobacteria, Bacteroidetes, Gram-positive Actinobacteria and Firmicutes, as well as archaeal species, most probably Methanobacterium spp. Positive reactions with antibodies to proteins and peptides revealed the presence of nitrogen fixation (NifHD, GlnB, HscA), methanogenic (McrB), iron homeostasis and iron scavenging (ferritins and DPS proteins) proteins, as well as ABC transporters, which indicated that these processes were operating at the time of sampling. These results were validated with other molecular ecology techniques such as oligonucleotide microarrays, 16S bacterial rRNA gene sequence analysis, aerobic viable counts and microscopy. Molecular ecology results showed a differentiated pattern along the depth of the drill, being the top active layer the most diverse, with Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes and the phototrophs Cyanobacteria and Chloroflexi as dominant groups. Actinobacteria and Firmicutes were dominant in depths from 0.5 to 2 m, and Betaproteobacteria from 3 to 4.2 m. The geochemical analysis revealed the presence of low molecular weight organic acids (acetate, formate) which could be used by microorganisms as energy sources for sulfate, nitrate and metal reduction under anaerobic conditions.

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“…Members of the genus Meiothermus have been isolated from natural hot springs and artificial thermal environments in many parts of the world including Russia, France, Portugal, China, Taiwan, Iceland and the Azores(Sikorski et al, 2010) in addition to South Africa (this study)where it made up 12.35% and 2.45% of bacterial sequences in the BV and CA mat samples, respectively. In another study,Spanevello and Patel (2004) successfully characterized some Meiothermus species from brown, green and red microbial mats of an Australian subsurface aquifer with temperatures ranging from 52°C to 66°C.…”

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confidence: 96%

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

2017

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Microbial mats are occasionally reported in thermal springs and information on such mats is very scarce. In this study, microbial mats were collected from two hot springs (Brandvlei (BV) and Calitzdorp (CA)), South Africa and subjected to scanning electron microscopy (SEM) and targeted 16S rRNA gene amplicon analysis using Next Generation Sequencing (NGS). Spring water temperature was 55°C for Brandvlei and 58°C for Calitzdorp while the pH of both springs was slightly acidic, with an almost identical pH range (6.2–6.3). NGS analysis resulted in a total of 4943 reads, 517 and 736 OTUs for BV and CA at, respectively, a combined total of 14 different phyla in both samples, 88 genera in CA compared to 45 in BV and 37.64% unclassified sequences in CA compared to 27.32% recorded in BV. Dominant bacterial genera in CA microbial mat were Proteobacteria (29.19%), Bacteroidetes (9.41%), Firmicutes (9.01%), Cyanobacteria (6.89%), Actinobacteria (2.65%), Deinococcus‐Thermus (2.57%), and Planctomycetes (1.94%) while the BV microbial mat was dominated by Bacteroidetes (47.3%), Deinococcus‐Thermus (12.35%), Proteobacteria (7.98%), and Planctomycetes (2.97%). Scanning electron microscopy results showed the presence of microbial filaments possibly resembling cyanobacteria, coccids, rod‐shaped bacteria and diatoms in both microbial mats. Dominant genera that were detected in this study have been linked to different biotechnological applications including hydrocarbon degradation, glycerol fermentation, anoxic‐fermentation, dehalogenation, and biomining processes. Overall, the results of this study exhibited thermophilic bacterial community structures with high diversity in microbial mats, which have a potential for biotechnological exploitation.

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Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)

Cited by 21 publications

References 37 publications

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem

Prokaryotic communities and operating metabolisms in the surface and the permafrost of Deception Island (Antarctica)

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

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