Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia

Abstract

The King Abdullah University of Science and Technology, Thuwal, Saudi Arabia A slow-growing, strictly aerobic, Gram-negative, coccus bacterial strain, designated KAUST100406-0324 T , was isolated from sea-floor sediment collected from the Red Sea, Saudi Arabia. The catalase-and oxidase-positive strain was non-sporulating and only slightly halophilic. Optimum growth occurred at 20-25 6C and at pH values ranging from 7.0 to 8.0. The major cellular fatty acids of the strain were unsaturated C 18 : 1 v6c and/or C 18 : 1 v7c, C 18 : 1 v7c 11-methyl and C 16 : 1 v7c and/or C 16 : 1 v6c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. Ubiquinone 10 was the predominant lipoquinone. The DNA G+C content of strain KAUST100406-0324 T was 64.0 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that the novel strain belonged to the family Rhodobacteraceae of the class Alphaproteobacteria but formed a distinct evolutionary lineage from other bacterial species with validly published names. The 16S rRNA gene sequence of the novel strain was distantly related, but formed a monophyletic cluster with, those of bacteria from two moderately halophilic genera, Hwanghaeicola and Maribius. The similarity of the sequence between the novel strain KAUST100406-0324 T and the type strains Hwanghaeicola aestuarii Y26 T (accession number FJ230842), Maribius pelagius B5-6 T (DQ514326) and Maribius salinus CL-SP27 T (AY906863) were 94.5 %, 95.2 % and 95.3 %, respectively. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we propose that this strain represents a novel species of a new genus in the family Rhodobacteraceae, for which the name of Profundibacterium mesophilum gen. nov., sp. nov. was proposed, with KAUST100406-0324 T (5JCM 17872 T 5NRRL B-59665 T ) as the type strain.The family Rhodobacteraceae (Garrity et al., 2005), which belongs to the class Alphaproteobacteria, contains approximately 90 recognized genera (type genus, Rhodobacter) at the time of writing. Most of the species within the family originated from marine environments. Members of the family Rhodobacteraceae are metabolically and physiologically diverse and occupy a wide range of niches in various habitats, such as seawater, saline, sediments, sea ice, microbial mats, seaweeds and marine animal tissues. Several genera, including Maribius (Choi et al., 2007), Marivita (Hwang et al., 2009), Mameliella (Wang et al., 2010, Roseovarius (Zheng et al., 2010) and Hwanglaeicola (Kim et al., 2010), have been described in the last 4 years. In this study, a novel and slightly halophilic strain, designated KAUST-100406-0324 T , was isolated from the sediment near a deep-sea brine pool in the Red Sea and characterized using a polyphasic approach. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain KAUST100406-0324 T is JF776971.

Boseongicola aestuarii gen. nov., sp. nov., isolated from a tidal flat sediment

“…Comparative 16S rRNA gene sequence analysis indicated that the novel strain has the closest phylogenetic affiliation to the genus Profundibacterium. The genus Profundibacterium was recently proposed by Lai et al (2013) with the description of a single novel species, Profundibacterium mesophilum, isolated from deep-sea sediment. The aim of the present work was to determine the exact taxonomic position of strain BS-W15 T from its polyphasic characterization, which included determination of its chemotaxonomic and other phenotypic properties as well as detailed phylogenetic investigations based on 16S rRNA gene sequences.…”

Indications for algae-degrading benthic microbial communities in deep-sea sediments along the Antarctic Polar Front

“…Rhodobacteraceae include many strictly aerobic and often pelagic clades, such as Roseobacter (Buchan et al, 2005;Choi et al, 2007), but they are increasingly found and isolated from coastal (Tian et al, 2009) and deep-sea sediments (Lai et al, 2013;Wang et al, 2009), suggesting that this family is important in many oxic marine realms. However, the Rhodobacteraceae-affiliated organisms that were most abundant in our sequencing dataset could not be classified, indicating that they belonged to novel clades.…”

Physiological and genomic features of Paraoceanicella profunda gen. nov., sp. nov., a novel piezophile isolated from deep seawater of the Mariana Trench

“…The family Rhodobacteraceae (type genus, Rhodobacter ) contains more than 130 genera (http://www.bacterio.net/), many members of which have been isolated from the marine environment (Albuquerque, Rainey, Nobre, & da Costa, ; Chang et al, ; Chang, Meng, Du, & Du, ). Additionally, some members have been isolated from deep‐sea environment, such as members belonging to the genera Acidimangrovimonas (Jiang, Xu, Shao, & Long, ), Brevirhabdus (Wu et al, ), Celeribacter (Lai, Cao, Yuan, Li, & Shao, ), Citreicella (Lai et al, ), Marinibacterium (Li, Lai, et al, ), Meridianimarinicoccus (Ren et al, ), Pararhodobacter (Lai, Liu, Yuan, Xie, & Shao, ), Profundibacterium (Lai et al, ), and Thiobacimonas (Li, Tang, Liu, & Jiao, ). In this study, the marine bacterial strain D4M1 T was characterized using a polyphasic approach, along with the genome sequence analysis and high‐pressure adaptation.…”