Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae

Abstract

Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae A Gram-negative, aerobic, neutrophilic, coccoid bacterium, strain E4A9 T , was isolated from a deep-sea sediment sample collected from the East Pacific polymetallic nodule region. 16S rRNA gene sequence analysis showed that the isolate was related to the type strain of Altererythrobacter epoxidivorans (96.0 % sequence similarity). Lower 16S rRNA gene sequence similarities were observed with other members of the genera Altererythrobacter (94.7 %), Erythrobacter (94.0-95.4 %), Erythromicrobium (94.8 %) and Porphyrobacter (94.6-95.1 %) of the family Erythrobacteraceae. Phylogenetic analysis including all described species of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a distinct phylogenetic lineage with the family Erythrobacteraceae. Chemotaxonomic analysis revealed ubiquinone-10 as the predominant respiratory quinone, anteiso-C 15 : 0 , iso-C 14 : 0 and iso-C 15 : 0 as major fatty acids, and phosphatidylglycerol as the major polar lipid. The DNA G+C content was 71.5 mol%. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic and genotypic data presented in this study, strain E4A9 T represents a novel species in a new genus in the family Erythrobacteraceae for which the name Croceicoccus marinus gen. nov., sp. nov. is proposed; the type strain is E4A9 T (5CGMCC 1.6776 T 5JCM 14846 T ).The family Erythrobacteraceae (order Sphingomonadales, class Alphaproteobacteria) was proposed by Lee et al. (2005) based on a comprehensive phylogenetic analysis and, at present, it comprises four recognized genera: Altererythrobacter (Kwon et al., 2007), Erythrobacter (Shiba & Simidu, 1982), Erythromicrobium (Yurkov et al., 1994) and Porphyrobacter (Fuerst et al., 1993).Members of the family Erythrobacteraceae are aerobic and produce pink, orange or yellow pigments. Ubiquinone-10 is the major respiratory quinone. Most species in the family have been isolated from various aquatic environments such as freshwater, seawater, marine mats or sediment, a hot spring, seaweed, a starfish and coral (Shiba & Simidu, 1982; Fuerst et al., 1993;Yurkov et al., 1994; Hanada et al., 1997; Denner et al., 2002; Hiraishi et al., 2002;Rainey et al., 2003;Yoon et al., 2003Yoon et al., , 2004a Yoon et al., , b, 2005a Yoon et al., , b, 2006Ivanova et al., 2005;Kwon et al., 2007). This study focuses on the description of strain E4A9 T , isolated from a deep-sea sediment sample. Based on the taxonomic data, it is proposed that this strain be included in a new genus within the family Erythrobacteraceae.The deep-sea sediment samples were collected by a multicorer from the East Pacific polymetallic nodule region (8 u 229 380 N 145 u 239 560 W) at a depth of Abbreviation: BChl a, bacteriochlorophyll a.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain E4A9 T is EF62399...

Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next‐generation sequencing

“…Also, Enterobacter , Escherichia , Klebsiella , Serratia , Bacteroides , Bacillus and Propionibacterium , which are not considered as pathogens, were also found in whitefish kidney and previously reported in freshwater fish digestive tracts in general (Austin, ). Most of the other bacteria that we found in our study are ubiquitous and can be present in soil, water or plants, for instance Methylobacterium , Paracoccus , Stenotrophomonas, Bradyrhizobium , Altererythrobacter, Croceicoccus , Kocuria or Burkholderia (Kaneko et al ., ; Lidstrom & Chistoserdova, ; Kelly et al ., ; Kwon et al ., ; Ryan et al ., ; Xu et al ., ; Bontemps et al ., ; Savini et al ., ).…”

Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

“…The culturing also recovered some rare genera from the waters deeper than 6000 m, including Lysinibacillus, Citreicella, Altererythrobacter, Croceicoccus, Luteimonas and Winogradskyella. These genera have been previously found in deep-sea environments (Fan et al 2014;Lai et al 2009Lai et al , 2011Xu et al 2009) and some have been shown to have the ability to degrade (e.g., Lysinibacillus can degrade xylan, fomesafen and ethanethiol) (Lee et al 2010;Liang et al 2009;Wan et al 2010), indicating that they may have evolved specific strategies to survive in deep-sea environments such as the Mariana Trench. Some of the abundant groups in other culture-independent study, e.g., Epsilonproteobacteria and Cytophagia (Liu et al 2019c;Tarn et al 2016), were rare in the cultivation study reported here, indicating that the culture conditions still have many limitations.…”

Structural and Functional Insights Into CmGH1, a Novel GH39 Family β-Glucosidase From Deep-Sea Bacterium

“…The catalytic activity of Q157E was 15 times higher than that of wild type CmGH1, most probably because that Gln157 acted as an auxiliary catalytic proton donor and glutamine had a weaker proton donating ability than glutamic acid (Brooks et al, 2001;Vocadlo et al, 2002). The bacteria C. marinus E4A9 T might prefer a weaker acid/base residue to keep an insufficient catalytic activity, which was related to the evolution divergence and was an adaptive selection for the extreme environment in deep sea (Xu et al, 2009).…”

“…Croceicoccus marinus E4A9 T , a member of Erythrobacteraceae family, was isolated from a deep-sea sediment sample that was collected from the East pacific polymetallic nodule region, and was cultivated in 2216 marine broth (BD, United States) at 30 • C (Xu et al, 2009). Plasmid pSMT3 was stored in our lab and used as the vector for gene cloning and expression.…”

“…Croceicoccus marinus E4A9 T , the type species of the genus Croceicoccus, was isolated from deep-sea sediment at the East Pacific polymetallic nodule region (5,280 m depth, 2 • C, 34 salinity) (Xu et al, 2009). The enzymes from marine bacteria might have good stress tolerance (Jiang et al, 2012;De Santi et al, 2016;Huang et al, 2016).…”