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.

Abstract

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.

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

“…4 and Additional file 1 : Figure S6). Members of this family have been detected in paddy soils [ 51 ] and shown to be capable of producing propionate [ 52 ]. Most likely, Peptococcaceae were the major players in syntrophic propionate oxidation (Additional file 1 : Figure S6).…”

Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes

“…According to Da Costa et al (2009), the genera Thermaerobacter and Sulfobacillus are classified within the family XVII Incertae Sedis within the class Clostridia . The genus Symbiobacterium is placed in the family XVIII Incertae Sedis within the same class, but the family Symbiobacteriaceae was recently proposed (Beppu & Ueda, 2009; Shiratori-Takano et al , 2014). 16S rRNA gene phylogeny showed that the genus Symbiobacterium is related to the phylum ‘ Actinobacteria ’ rather than members of the phylum Firmicutes (Ohno et al , 2000; Ludwig et al , 2009b), but relatedness among the class Clostridia was also shown by genome-based analyses (Ueda et al , 2004; Nishida et al , 2009).…”

Interactions between the calcium scaling inhibitor NC47.1 B, geothermal fluids, and microorganisms – results of in situ monitoring in the Bavarian Molasse Basin (Germany) and accompanying laboratory experiments

“…An isomer of fumaric acid is maleic acid, which is copolymerized with acrylic acid to form the side chains of the inhibitor. Representatives of Symbiobacterium reduce nitrate (Shiratori-Takano et al, 2014), however the genus identified in the batch experiments is only distantly related to Symbiobacterium (identity 85 %-87 %). Relatives of Thermincola were represented by up to 10 %.…”

“…The scaling inhibitor NC47.1 B is a comb polymer with polycarboxylate side chains. It prevents the formation of crystal nuclei mainly via a threshold effect (Sieben and Niederrhein Chemie GmbH, 2016). The spine structure consists of a polysaccharide, which makes the molecule accessible for biodegradation.…”

“…In addition, sulfate reducers can also use hydrogen to reduce sulfate (Cypionka, 2010). If sulfate availability is limited, methanogenic archaea utilize products of fermentation such as acetate to produce methane and carbon dioxide (acetoclastic methanogenesis) or form methane from hydrogen and carbon dioxide (Schink, 1997). Methanogenesis and the relative abundance of methanogenic archaea were observed to sharply increase once sulfate is depleted below a threshold of 3 mg/L (Winfrey and Ward, 1983;Flynn et al, 2013).…”