A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera

Yoneda, Yasuko; Yoshida, Takashi; Yasuda, Hisato; Imada, Chiaki; Sako, Yoshihiko

doi:10.1099/ijs.0.050468-0

Cited by 43 publications

(31 citation statements)

References 38 publications

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“…As reported previously, the C. maritimus KKC1 is most closely related to Moorella species on the basis of 16S rRNA phylogenetic analysis (23) (Fig. 1A).…”

Section: Resultssupporting

confidence: 53%

“…maritimus KKC1 can grow heterotrophically on pyruvate, lactate, fumarate, glucose, fructose, and mannose with thiosulfate as an electron acceptor under an N 2 atmosphere (23). Metabolic pathways predicted by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the C. maritimus KKC1 genome encoded a complete glycolytic pathway and an incomplete tricarboxylic acid (TCA) cycle that lacked citrate synthase (present in Moorella species) and malate dehydrogenase (see Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The frameshift mutation in cooS within cooS-ACS, which has been reported in C. hydrogenoformans (9), was also found in C. maritimus KKC1. Even so, C. maritimus KKC1 is known to produce a small amount of acetate during hydrogenogenic growth under a CO atmosphere (23). According to a study by Svetlitchnyi and colleagues (6) which suggests that CooS may be unnecessary for operation of the Wood-Ljungdahl pathway, the frameshift mutation in cooS (KKC1_09930-40) within the cooS-ACS gene cluster might not affect pathway function.…”

Section: Discussionmentioning

confidence: 99%

“…S2). Unlike for Moorella species, no HydABC and NfnAB homologs were found in the C. maritimus KKC1 genome, consistent with its failure of acetogenic growth on H 2 and CO 2 (23). The authentic PFOR of M. thermoacetica is encoded in Moth_0064 and contains three domains, the ␣, ␥, and ␤ subunits, annotated as COG0674, COG1014, and COG1013, respectively (31).…”

Section: Caldanaerobius Polysaccharolyticus Dsm 13641mentioning

confidence: 99%

“…to the family Thermoanaerobacteraceae and the phylum Firmicutes and is most closely related to members of the genus Moorella (23). Although Moorella stamsii and Moorella thermoacetica strain AMP are reported to be hydrogenogenic carboxydotrophs like C. maritimus KKC1 (24,25), most Moorella strains are known homoacetogens.…”

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confidence: 99%

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Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment

Omae

Yoneda

Fukuyama

et al. 2017

Appl Environ Microbiol

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Calderihabitans maritimus KKC1 is a thermophilic, hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe the de novo sequencing and feature analysis of the C. maritimus KKC1 genome. Genomebased phylogenetic analysis confirmed that C. maritimus KKC1 was most closely related to the genus Moorella, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella, C. maritimus KKC1 retained both the CO 2 -reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but it lacked the HydABC and NfnAB electron-bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction for acetogenic growth. Furthermore, C. maritimus KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas Moorella possessed only two CooS genes. Our analysis revealed that three cooS genes formed known gene clusters in other microorganisms, i.e., cooS-acetyl coenzyme A (acetylCoA) synthase (which contained a frameshift mutation), cooS-energy-converting hydrogenase, and cooF-cooS-FAD-NAD oxidoreductase, while the other three had novel genomic contexts. Sequence composition analysis indicated that these cooS genes likely evolved from a common ancestor. Collectively, these data suggest that C. maritimus KKC1 may be highly dependent on CO as a low-potential electron donor to directly reduce ferredoxin and may be more suited to carboxydotrophic growth compared to the acetogenic growth observed in Moorella, which show adaptation at a thermodynamic limit.IMPORTANCE Calderihabitans maritimus KKC1 and members of the genus Moorella are phylogenetically related but physiologically distinct. The former is a hydrogenogenic carboxydotroph that can grow on carbon monoxide (CO) with H 2 production, whereas the latter include acetogenic bacteria that grow on H 2 plus CO 2 with acetate production. Both species may require reduced ferredoxin as an actual "energy equivalent," but ferredoxin is a low-potential electron carrier and requires a highenergy substrate as an electron donor for reduction. Comparative genomic analysis revealed that C. maritimus KKC1 lacked specific electron-bifurcating enzymes and possessed six CO dehydrogenases, unlike Moorella species. This suggests that C. maritimus KKC1 may be more dependent on CO, a strong electron donor that can directly reduce ferredoxin via CO dehydrogenase, and may exhibit a survival strategy different from that of acetogenic Moorella, which solves the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen.

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“…As reported previously, the C. maritimus KKC1 is most closely related to Moorella species on the basis of 16S rRNA phylogenetic analysis (23) (Fig. 1A).…”

Section: Resultssupporting

confidence: 53%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Caldanaerobius Polysaccharolyticus Dsm 13641mentioning

confidence: 99%

mentioning

confidence: 99%

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Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment

Omae

Yoneda

Fukuyama

et al. 2017

Appl Environ Microbiol

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C alderihabitans

Yoneda¹,

Yoshida²,

Sako³

2019

Bergey's Manual of Systematics of Archaea and Bacteria

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Cal.de.ri.ha′bi.tans. N.L. fem. n. caldera from the Portuguese n. caldera cauldron; ‐i‐ connecting vowel; L. masc. n. habitans dweller, inhabitant; N.L. masc. n. Calderihabitans inhabitant of a caldera, referring to the isolation source of the type strain. Firmicutes / Clostridia / Thermoanaerobacterales / Thermoanaerobacteraceae / Calderihabitans The genus comprises a single species and single strain C. maritimus KKC1 T . C. maritimus KKC1 T is non‐motile, Gram‐negative staining, straight rods which forms round endospores. Thermophilic, strictly anaerobic, and hydrogenogenic carboxydotroph capable to grow chemolithotrophically on carbon monoxide with production of molecular hydrogen as a main product. If present, electron acceptors such as ferric iron and thiosulfate are coupled to carbon monoxide oxidation. Grows heterotrophically on organic substrates such as pyruvate, fumarate, and glucose in presence of electron acceptors. Grows under conditions of 55–68°C, pH 5.2–9.2, and 0.8–14% (w/v) salinity (optimum at 65°C, pH 7.0–7.5, and 2.46% salinity). Major fatty acid is C 16:0 . Most closely related to the members of the genera Moorella , in the family Thermoanaerobacteraceae ; however, assignment of higher taxa is under discussion. The DNA G + C content of the type strain KKC1 T is 50.6 mol% measured by HPLC and 47 mol% in draft genome sequence. The genome of the type strain KKC1 T harbors six carbon monoxide dehydrogenase (CODH) genes, all of them in different genomic context that each may have unique physiological role. The type strain KKC1 T was isolated from an inaccessible environment, that is sediment of undersea caldera and there has been no natural habitat revealed from metagenome database. DNA G + C content (mol%) : 50.6. Type species : Calderihabitans maritimus Yoneda et al. 2013 VP .

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T hermodesulfitimonas

Slobodkina¹

2019

Bergey's Manual of Systematics of Archaea and Bacteria

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Ther.mo.de.sul.fi.ti.mo'nas. Gr. adj. thermos , warm, hot; L. pref. de from, off, away; N.L. n. sulfis ‐itis sulfite; L. fem. n. monas , a unit, monad; N.L. fem. n. Thermodesulfitimonas , thermophilic sulfite‐reducing body. Firmicutes / Clostridia / Thermoanaerobacterales / Thermoanaerobacteraceae / Thermodesulfitimonas Gram‐positive straight rods with rounded ends. Cells are motile due to lateral flagellation. Spores are not produced. Strictly anaerobic. Thermophilic . Neutrophilic. Chemolithoautotrophic. Growth with molecular hydrogen as electron donor, sodium sulfite or SO 2 gas as electron acceptor, and bicarbonate/CO 2 as a carbon source. The major fatty acids are C 16:0 , C 18:0 , iso‐C 16:0 , and anteiso‐C 15:0 . Member of the family Thermoanaerobacteraceae, class Clostridia . The closest relatives are species of the genus Ammonifex . The type species , Thermodesulfitimonas autotrophica SF97 T , was isolated from a terrestrial hot spring (Kuril Islands, Russia). DNA G+C content (mol%) : 55.8 ( T m ). Type species : Thermodesulfitimonas autotrophica , Slobodkina, Baslerov, Novikov, Bonch‐Osmolovskaya and Slobodkin 2017, 305 VP .

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A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera

Cited by 43 publications

References 38 publications

Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment

Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment

C alderihabitans

T hermodesulfitimonas

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