Mangrovivirga cuniculi gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family Mangrovivirgaceae fam. nov

Abstract

A strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain R1DC9^T, was isolated from sediments of a mangrove stand on the Red Sea coast of Saudi Arabia via diffusion chamber cultivation. Strain R1DC9^T grew at 20-40 °C (optimum, 37 °C), pH 6-10 (optimum, pH 8) and 3-11 % NaCl (optimum, 7-9 %) in the cultivation medium. The genome of R1DC9^T was 4 661 901 bp long and featured a G+C content of 63.1 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis using 120 concatenated single-copy genes revealed that R1DC9^T represents a distinct lineage in the order Cytophagales and the phylum Bacteroidetes separated from the Roseivirgaceae and Marivirgaceae families. R1DC9^T displayed 90 and 89 % 16S rRNA gene sequence identities with Marivirga sericea DSM 4125^T and Roseivirga ehrenbergii KMM 6017^T, respectively. The predominant quinone was MK7. The polar lipids were phosphatidylethanolamine, two unknown phospholipids and two unknown lipids. The predominant cellular fatty acids were the saturated branch chain fatty acids iso-C_{15 : 0}, iso-C_{17 : 0} 3-OH and iso-C_{17 : 0}, along with a low percentage of the monounsaturated fatty acid C_{16 : 1} ω5c. Based on differences in phenotypic, physiological and biochemical characteristics from known relatives, and the results of phylogenetic analyses, R1DC9^T (=KCTC 72349^T=JCM 33609^T=NCCB 100698^T) is proposed to represent a novel species in a new genus, and the name Mangrovivirga cuniculi gen. nov., sp. nov. is proposed. The distinct phylogenetic lineage among the families in the order Cytophagales indicates that R1DC9^T represents a new family for which the name Mangrovivirgaceae fam. nov. is proposed.

Keywords: Bacteroidetes; Mangrovivirga; Mangrovivirgaceae; cultivation; mangrove crabs; mangrove sediments.

Fig. 1.

(a) Sediments in the mangrove forest at KAUST bioturbated by Uca species crabs; crab barrows are indicated by yellow arrows. Leaves forming mangrove litter are also visible. Bar, 10 cm. (b) Aquarium filled with mangrove bioturbated sediments and FSW for the incubation of DCs; bar, 6 cm. (c) Aerial view of DCs placed on the surface of mangrove sediments and cover with FSW inside the aquarium; bar, 6 cm.

Fig. 2.

(a) Maximum-likelihood phylogenetic tree based on the 16S rRNA gene sequences presenting the position of Mangrovivirga cuniculi R1DC9^T (MT146883). Only bootstrap values (expressed as percentages of 1000 replications) exceeding 50 % are shown at branching points. Psychroflexus torquis ATCC 700755^T (GenBank accession no. U85881) was used as an outgroup. Bar, 0.040 substitutions per nucleotide position. Filled circles indicate branches that were also recovered using the neighbour-joining method. (b) Maximum-likelihood phylogenetic tree highlighting the position of R1DC9^T relative to the other type strains within the order Cytophagales, including members of the families Marivirgaceae, Roseivirgaceae, Reichenbachiellaceae, Fulvivirgaceae, Cesiribacteraceae and Flammeovirgaceae. The phylogenetic tree was built using 120 concatenated single-copy genes obtained using GTDB-Tk software [34]. Bootstrap values greater than 50 % based on 1000 replications are indicated at branching nodes. Bar, 0.2 substitutions per nucleotide position.

Fig. 3.

Scanning electron microscopy image of Mangrovivirga cuniculi R1DC9^T (bar, 1 µm).