Rhodobacter sediminis sp. nov., isolated from lagoon sediments

Abstract

Two Gram-stain-negative, rod-shaped phototrophic bacteria (designated strains N1 T and C7) were isolated from lagoon sediments. Both strains were positive for catalase and oxidase activity. Casein, starch, urea and Tween 20 were hydrolysed by both strains while chitin, gelatin and Tween 80 were not. In both strains, C 16 : 0 , C 18 : 0 ,C 16 : 1 !6c/C 16 : 1 !7c and C 18 : 1 !6c/ C 18 : 1 !7c were the predominant fatty acids, with minor amounts of C 8 : 0 3-OH, anteiso-C 14 : 0 , C 17 : 0 , C 14 : 1 !5c, C 17 : 1 10-methyl and C 18 : 1 !5c. Strains N1 T and C7 contained phosphatidylglycerol and phosphatidylethanolamine as major polar lipids with minor amounts of phosphatidylcholine, unidentified lipids and an unidentified phospholipid. The mean genomic DNA G+C content was 70.6±1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Strain N1 T has a 16S rRNA gene sequence similarity of 99.2 % with Rhodobacter capsulatus ATCC 11166 T , 99.1 % with Rhodobacter viridis JA737 T and <96.6 % with other members of the genus Rhodobacter. Strain N1 T and C7 shared 100 % 16S rRNA gene sequence similarity. DNA-DNA hybridization values between strain N1 T and the type strains of the nearest species were clearly below the 70 % threshold. On the basis of phenotypic and genotypic data, it is proposed that strain N1 T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter sediminis sp. nov. is proposed. The type strain is N1 T (=KEMB 563-471 T =JCM 31175 T ), and strain C7 is an additional strain of the species.

Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae

“…Differential characteristics of Rhodobacter tardus CYK-10 T and the type strains of related Rhodobacter species Strains: 1, CYK-10 T ; 2, Rhodobacter thermarum YIM 73036 T ; 3, Rhodobacter flagellatus SYSU G03088 T ; 4, Rhodobacter blasticus ATCC 33485 T ; 5, Rhodobacter capsulatus ATCC 11166 T . Data for R. thermarum YIM 73036 T from Khan et al [22], R. flagellatus SYSU G03088 T and R. blasticus ATCC 33485 T from Xian et al [23] and R. capsulatus ATCC 11166 T from Wang et al [12] and from Subhash and Lee [19]. +, Positive reaction; -, negative reaction.…”

“…The genus Rhodobacter comprises 13 species with validly published names so far stated on the List of Prokaryotic names with Standing in Nomenclature (https://lpsn.dsmz.de/genus/rhodobacter). Species of the genus Rhodobacter have been isolated from various environmental sources, including eutrophic freshwater, stagnant water, polluted water, alkaline water, hot spring, lagoon sediment, estuarine water and marine water [15–24]. Cells are Gram-stain-negative, motile or non-motile and ovoid to rod-shaped.…”

“…de/ genus/ rhodobacter). Species of the genus Rhodobacter have been isolated from various environmental sources, including eutrophic freshwater, stagnant water, polluted water, alkaline water, hot spring, lagoon sediment, estuarine water and marine water [15][16][17][18][19][20][21][22][23][24]. Cells are Gram-stain-negative, motile or non-motile and ovoid to rod-shaped.…”

Rhodobacter flagellatus sp. nov., a thermophilic bacterium isolated from a hot spring

“…The genus was created to move the species with vesicular intracytoplasmic membranes (ICM) from the genus Rhodopseudomonas [2]. Members of the genus Rhodobacter are widely distributed in oxic/anoxic niches of aquatic [3, 4], mud [5, 6], sediment [7, 8], agricultural field [9], estuarine [10, 11], sludge [12] and marine habitats [13]. At the time of writing, this genus comprises 16 species with validly published names, namely Rhodobacter aestuarii [11], Rhodobacter alkalitolerans [14], Rhodobacter azollae [4], Rhodobacter azotoformans [12], Rhodobacter blasticus [15], Rhodobacter capsulatus [2], Rhodobacter johrii [9], Rhodobacter lacus [4], Rhodobacter maris [10], Rhodobacter megalophilus [16], Rhodobacter ovatus [8], Rhodobacter sediminis [7], Rhodobacter sphaeroides [2], Rhodobacter veldkampii [3], Rhodobacter vinaykumarii [13] and Rhodobacter viridis [5].…”

Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter

“…lacus (Suresh et al, 2017) and Rba. sediminis (Subhash and Lee, 2016) are not available. A genomic summary of the twelve species (and some related strains) is presented in Figure 2 and Supplementary Table S3.…”