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

Abstract

The Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan A novel facultatively anaerobic bacterium, strain HC45 T , was isolated from sediment of a brackish meromictic lake in Japan, Lake Harutori. Cells were pleomorphic, and filamentous bodies were 5-100 mm in length. For growth, the optimum pH was 7.0 and the optimum temperature was 45-50 8C. The G+C content of the genomic DNA was 71 mol%. iso-C 15 : 0 and anteiso-C 15 : 0 were the major components in the cellular fatty acid profile. The predominant respiratory quinone was MK-7. Strain HC45 T shared very low 16S rRNA gene sequence similarity with cultivated strains (#85 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was distantly related to members of the family Symbiobacteriaceae and family XVII Incertae Sedis in the class Clostridia, and they formed a cluster separate from canonical species of the phylum Firmicutes. These results indicated that strain HC45 T should not be placed in any existing class of the phylum Firmicutes. On the basis of phylogenetic and phenotypic characterization, Limnochorda pilosa gen. nov., sp. nov. is proposed with HC45 T (5NBRC 110152 T 5DSM 28787 T ) as the type strain, as the first representative of novel taxa, Limnochordales ord. nov., Limnochordaceae fam. nov. in Limnochordia classis. nov.

Complete genome sequence and cell structure of Limnochorda pilosa, a Gram-negative spore-former within the phylum Firmicutes

“…Cell morphology and intracellular structures were observed by transmission electron microscopy (TEM). Cultivation and fixation of L. pilosa cells were performed as described previously (Watanabe et al, 2015). TEM was performed by postfixing cell samples with osmium tetroxide, followed by dehydration via a graded ethanol series (50-100 %).…”

“…T has a Gram-negative-type cell wall, on the basis of a Gram stain test and a trial to analyse amino acid components of the cell wall (Watanabe et al, 2015). Accordingly, the genome of L. pilosa HC45 T had characteristics that are specific to Gram-negative bacteria.…”

“…The phylum Firmicutes is also thought to be a possible ancestral lineage of the domain Bacteria (Ciccarelli et al, 2006;Koch, 2003). The phylum Firmicutes consists of bacteria with an enormous genetic range and contains six established classes (Bacilli, Clostridia, Negativicutes, Thermolithobacteria, Erysipelotrichia, 'Tissierellia' and Limnochordia) (Alauzet et al, 2014;Garrity et al, 2005;Ludwig et al, 2009;Marchandin et al, 2010;Sokolova et al, 2007;Watanabe et al, 2015). The class Negativicutes was defined as a class of Gram-negative, spore-forming organisms in this phylum (Marchandin et al, 2010), but phylogenetic analyses indicated that the class could be incorporated into the class Clostridia (Galperin, 2013;Yutin & Galperin, 2013).…”

“…The class Negativicutes was defined as a class of Gram-negative, spore-forming organisms in this phylum (Marchandin et al, 2010), but phylogenetic analyses indicated that the class could be incorporated into the class Clostridia (Galperin, 2013;Yutin & Galperin, 2013). The class Limnochordia was recently proposed to accommodate the strain Limnochorda pilosa HC45 T , which was isolated from the sediment of a meromictic lake in Japan (Watanabe et al, 2015).…”

“…These three genera are characterized by high DNA G+C content [except for sulfobacilli (46-62 mol%)], and their taxonomic affiliations are still controversial. L. pilosa HC45 T has some characteristics in common with these genera; the capability of facultative anaerobic growth and high DNA G+C content (71 mol%, as estimated by HPLC analysis), but it is Gram-stain-negative (Watanabe et al, 2015).…”