Grimontia sedimenti sp. nov., isolated from benthic sediments near coral reefs south of Kuwait

Abstract

A Gram-stain-negative, rod and rod-curved shaped motile bacterium designated strain S25T was obtained from benthic sediment collected near the Kubbar Island coral reefs south of Kuwait. Phenotypic analysis revealed that strain S25T was slightly halophilic, mesophilic and facultative anaerobic, fermenting d-glucose, d-ribose, d-mannose, d-mannitol, maltose, fructose, gentiobiose, cellobiose, melibiose, trehalose and sucrose. It was positive for oxidase and indole production and negative for arginine dihydrolase and lysine and ornithine decarboxylases. It contained C16 : 1 ω7c/C16 : 1 ω6c (summed feature 3), C18 : 1 ω7c (summed feature 8) and C16 : 0 as the major fatty acids. Strain S25T grew optimally at 30 °C and pH 8 in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA sequences revealed that strain S25T is related to species of the genus Grimontia , having 99.15 % similarity to ‘Grimontia indica’ AK16T, 99.08 % to Grimontia celer 96-237T and 98.66 % to Grimontia marina IMCC 5001T. The DNA G+C content was 48.8 mol% and the full genome analysis for the strain S25T showed that the bacterium has a genome size of 5 158 621 bp and contains 4730 predicted protein-encoding genes. The average nucleotide identity values between the S25T genome and the genomes of its nearest matches ranged between 81.39 and 94.16 %. The strain was distinguishable from the phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strain S25T represents a novel species in the genus Grimontia , for which the name Grimontia sedimenti sp. nov. is proposed. The type strain of Grimontia sedimenti is S25T (=DSM 28878T=LMG 28315T).

Description of Jidongwangia harbinensis gen. nov. sp. nov

“…A distance matrix was generated using Kimura’s two-parameter model [14] for the neighbour-joining method and the Tamura–Nei 1993 3-parameter model [15] with proportional discrete Gamma distribution and a fraction of invariant sites sites (TN93+G+I) for maximum-likelihood method. For the maximum-parsimony tree, 1000 bootstrapping replicates were used in conjunction with tree-bisection-and-reconnection branch swapping and 10 random sequence addition replicates [16]. All positions containing gaps and missing data were eliminated from the dataset (complete deletion option).…”

Grimontia kaedaensis sp. nov., isolated from the estuary of Kaeda river in Miyazaki, Japan

“…The key phenotypic characteristics of strain 020920N T have been compared to those in Grimontia celer [18], G. sedimenti [19] and ‘ G. indica ’ [16] (). Three of the four species were identified as sharing a recent common ancestor with strain 020920N T ().…”

“…The key phenotypic characteristics of strain 020920N T have been compared to those in Grimontia celer [18], G. sedimenti [19] and 'G. indica' [16] (Table 1).…”

Nucisporomicrobium flavum gen. nov., sp. nov., a new member of the family Micromonosporaceae isolated from saline-alkali soil

“…A distance matrix was generated using Kimura’s two-parameter model [36] for the neighbour-joining method and the Tamura three-parameter model [37] with invariant sites (T92) for the maximum-likelihood method. For the maximum-parsimony tree, 1000 bootstrapping replicates were used in conjunction with tree-bisection-and-reconnection branch swapping and 10 random sequence addition replicates [38]. All positions containing gaps and missing data were eliminated from the dataset (complete deletion option).…”