Distribution of<i>Symbiobacterium thermophilum</i>and Related Bacteria in the Marine Environment

Sugihara, Takafumi; Watsuji, Tomo‐o; Kubota, Shin; Yamada, Kazune; Oka, Kaori; Watanabe, Kiyoshi; Meguro, Michiko; Sawada, Emi; Yoshihara, Kiyoshi; Uéda, Kenji; Beppu, Teruhiko

doi:10.1271/bbb.70619

Cited by 9 publications

(5 citation statements)

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“…Considering that CO 2 is the major growth factor of Symbiobacterium , its symbiotic partners may not be limited to Geobacillus . Symbiobacterium is widespread in different natural environments [ 26 , 27 ]. The difference in the genome base compositions between Symbiobacterium and its symbiotic partners may lead to a decrease in the frequency of a homologous recombination between the 2 genomes.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

Nishida

Yun

2011

International Journal of Evolutionary Biology

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Although the bacterium Symbiobacterium thermophilum has a genome with a high guanine-cytosine (GC) content (69%), it belongs to a low GC content bacterial group. We detected only 18 low GC content regions with 5 or more consecutive genes whose GC contents were below 65% in the genome of this organism. S. thermophilum has 66 transposase genes, which are markers of transposable genetic elements, and 38 (58%) of them were located in the low GC content regions, suggesting that Symbiobacterium has a similar gene silencing system as Salmonella. The top hit (best match) analyses for each Symbiobacterium protein showed that putative horizontally transferred genes and vertically inherited genes are scattered across the genome. Approximately 25% of the 3338 Symbiobacterium proteins have the highest similarity with the protein of a phylogenetically distant organism. The putative horizontally transferred genes also have a high GC content, suggesting that Symbiobacterium has gained many DNA fragments from phylogenetically distant organisms during the early stage of Firmicutes evolution. After acquiring genes, Symbiobacterium increased the GC content of the horizontally transferred genes and thereby maintained a genome with a high GC content.

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Section: Resultsmentioning

confidence: 99%

Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

Nishida

Yun

2011

International Journal of Evolutionary Biology

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“…The 16S rRNA gene sequences of the novel strains were related to those of the uncultured clones KW19 and KW186, obtained previously from the seaweeds Meristotheca papulosa and Ulva conglobata, respectively (Sugihara et al, 2008), with sequence identities of 90-93 %. The phylogenetic tree (Fig.…”

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confidence: 94%

“…On the other hand, detailed taxonomic characterization of these organisms has not yet been performed, mostly owing to difficulties in their isolation. However, we subsequently discovered that efficient isolation and cultivation of members of the genus Symbiobacterium can be carried out using conditioned media (complex media supplied with culture supernatant of G. stearothermophilus strain S) solidified by gellan gum in an anaerobic atmosphere containing CO 2 (Sugihara et al, 2008). Furthermore, the use of a specific PCR has allowed the effective selection of cultures containing phylogenetically distinctive strains of the genus Symbiobacterium (Sugihara et al, 2008).…”

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confidence: 99%

“…Strains KY38 T , KY46 T and KA13 T were isolated from oyster shell, a horned turban (Turbo cornutus) and a barnacle (Terraclita japonica), respectively, that were collected on the Pacific coastline of Enoshima, Kanagawa prefecture, Japan. The procedures used for their isolation have been described previously (Sugihara et al, 2008). Routine cultivation of the isolates was performed using Sym I medium (KY38 T ) or Sym II medium (KY46 T and KA13 T ).…”

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confidence: 99%

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Description of Symbiobacterium ostreiconchae sp. nov., Symbiobacterium turbinis sp. nov. and Symbiobacterium terraclitae sp. nov., isolated from shellfish, emended description of the genus Symbiobacterium and proposal of Symbiobacteriaceae fam. nov.

Shiratori-Takano

Akita

Yamada

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Three novel moderately anaerobic, thermophilic, rod-shaped bacterial strains, KY38T, KY46T and KA13T, were isolated from shellfish collected on the Pacific coastline of Enoshima, Japan. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these bacteria belong to the genus Symbiobacterium , sharing sequence similarities of 97.8 % (KY38T), 96.4 % (KY46T) and 93.3 % (KA13T) with the type strain of Symbiobacterium thermophilum , the only species of the genus with a validly published name. These isolates reduced nitrate and grew optimally at 55–60 °C. Strains KY38T and KA13T formed endospore-like structures in the terminal or subterminal part of their cells at low frequencies. Genomic DNA G+C contents were 68.8 (KY38T), 67.2 (KY46T) and 67.1 (KA13T) mol%. The isolates all presented the predominant menaquinone MK-6, major fatty acids iso-C15 : 0, C16 : 0 and iso-C17 : 0 and the major polar lipids phosphatidylglycerol, phosphatidylethanolamine and unknown glycol-containing phospholipids. On the basis of their morphological, physiological and phylogenetic properties, strains KY38T, KY46T and KA13T represent three novel species, for which the names Symbiobacterium ostreiconchae sp. nov. (type strain KY38T = DSM 27624T = KCTC 4567T = JCM 15048T), Symbiobacterium turbinis sp. nov. (type strain KY46T = DSM 27625T = KCTC 4568T = JCM 15996T) and Symbiobacterium terraclitae sp. nov. (type strain KA13T = DSM 27138T = KCTC 4569T = JCM 15997T) are proposed. An emended description of the genus Symbiobacterium is also presented. The phylogenetic distinctiveness of the genus Symbiobacterium indicates its affiliation with a novel family, for which the name Symbiobacteriaceae fam. nov. is proposed.

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“…Symbiobacterium thermophilum , a Gram-negative syntrophic bacterium, was first obtained at 60 °C with a thermophilic Bacillus strain S, which was identified two decades later as Geobacillus stearothermophilus through phylogenetic analysis [ 21 , 22 ]. Despite having a syntrophic property proposed to be caused by the genetic defect of carbonic anhydrase [ 23 ], the bacterium showed a wide occurrence in the environment throughout soils and fertilizers.…”

Section: Introductionmentioning

confidence: 99%

MazEF Homologs in Symbiobacterium thermophilum Exhibit Cross-Neutralization with Non-Cognate MazEFs

Jiang,

Tamiya-Ishitsuka,

Aoi

et al. 2024

Toxins

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Toxin–antitoxin systems are preserved by nearly every prokaryote. The type II toxin MazF acts as a sequence-specific endoribonuclease, cleaving ribonucleotides at specific sequences that vary from three to seven bases, as has been reported in different host organisms to date. The present study characterized the MazEF module (MazEF-sth) conserved in the Symbiobacterium thermophilum IAM14863 strain, a Gram-negative syntrophic bacterium that can be supported by co-culture with multiple bacteria, including Bacillus subtilis. Based on a method combining massive parallel sequencing and the fluorometric assay, MazF-sth was determined to cleave ribonucleotides at the UACAUA motif, which is markedly similar to the motifs recognized by MazF from B. subtilis (MazF-bs), and by several MazFs from Gram-positive bacteria. MazF-sth, with mutations at conserved amino acid residues Arg29 and Thr52, lost most ribonuclease activity, indicating that these residues that are crucial for MazF-bs also play significant roles in MazF-sth catalysis. Further, cross-neutralization between MazF-sth and the non-cognate MazE-bs was discovered, and herein, the neutralization mechanism is discussed based on a protein-structure simulation via AlphaFold2 and multiple sequence alignment. The conflict between the high homology shared by these MazF amino acid sequences and the few genetic correlations among their host organisms may provide evidence of horizontal gene transfer.

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Distribution ofSymbiobacterium thermophilumand Related Bacteria in the Marine Environment

Cited by 9 publications

References 14 publications

Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

Description of Symbiobacterium ostreiconchae sp. nov., Symbiobacterium turbinis sp. nov. and Symbiobacterium terraclitae sp. nov., isolated from shellfish, emended description of the genus Symbiobacterium and proposal of Symbiobacteriaceae fam. nov.

MazEF Homologs in Symbiobacterium thermophilum Exhibit Cross-Neutralization with Non-Cognate MazEFs

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