Characterization of Kordiimonas marina sp. nov. and Kordiimonas laminariae sp. nov. and Comparative Genomic Analysis of the Genus Kordiimonas, A Marine-Adapted Taxon

Abstract

Two novel rod-shaped and Gram-negative bacterial strains, designated A6E486T and 5E331T, were isolated from a coastal sediment sample taken from Xiaoshi Island, Weihai, China, and a fresh kelp sample collected from a kelp culture area, Rongcheng, China, respectively. Growth of strain A6E486T occurred at 20°C–43°C (optimum, 33°C–35°C) at pH 5.5–7.5 (optimum, 6.5) and in the presence of 1.0%–5.5% (w/v) NaCl (optimum, 2.5%–3.0%). Strain 5E331T grew with 1.5%–5.0% (w/v) NaCl (optimum, 3.0%) at 15°C–40°C (optimum, 33°) and pH 6.0–8.5 (optimum, 7.0). The similarity of 16S rRNA gene sequence between the two strains was 95.2%. The phylogenetic analysis based on 16S rRNA gene sequence showed that strains A6E486T and 5E331T belong to the genus Kordiimonas, sharing the highest similarity to the genus Kordiimonas (94.6%–96.8%, 94.9%–96.1%, respectively). Strains A6E486T and 5E331T had percentage of conserved protein (POCP) values of 56.0%–67.3% and average nucleotide identity (ANI) values of 68.8%–73.1% to members of the genus Kordiimonas. The major polar lipids detected in the two strains were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and unidentified glycolipids, aminolipids, and lipids. The predominant respiratory quinone of the two strains was Q-10. Based upon the results presented in this study, strains A6E486T and 5E331T represent two novel species of the genus Kordiimonas, for which the names Kordiimonas marina and Kordiimonas laminariae are proposed with the type strains A6E486T (= KCTC 82758T = MCCC 1H00470T) and 5E331T (= KCTC 92199T = MCCC 1H00515T), respectively. Comparative genomic analysis showed that seven species of the genus Kordiimonas shared 1,258 core genes and had differences in carbohydrate metabolism, energy metabolism, and cofactor and vitamin metabolism. The pan-genome of the genus Kordiimonas was open. The prediction of secondary metabolites showed that most strains of the genus Kordiimonas had the ability to produce homoserine lactones, one of the most important signal molecules in the quorum-sensing system of Gram-negative bacteria. Additionally, numerous genes involved in bacterial defense, motility and chemotaxis, cold adaptation, and environment stress response were found in the genus Kordiimonas, indicating the marine-adapted lifestyle of members of the genus Kordiimonas.

Description of Aequorivita aurantiaca sp. nov. Isolated from Coastal Sediment, and Comparative Genomic Analysis and Biogeographic Distribution of the Genus Aequorivita

“…Amplification of the 16S rRNA gene was performed using PCR technology with the primer pairs 27F and 1492R [18]. To obtain the nearly complete cloned 16S rRNA gene sequence of SDUM287046 T , the clone operation was performed as described previously [19]. The purified PCR product was ligated into the pMD18-T vector (Takara Bio Inc., Dalian, China), and then the ligation product was transferred into Escherichia coli DH5a receptor cells.…”

“…The percentage of accessory genes in each Aequorivita genome ranged from 28.8% to 44.9% and unique genes from 5.9% to 24.9%. Moreover, the analysis of KEGG distribution showed that the core genes were more involved in the metabolisms supporting basic life activities, such as nucleotide metabolism and translation, while unique genes were more distributed in carbohydrate metabolism, cell motility, cellular community, and membrane transport pathways (Figure S3), which might give the genus Aequorivita species metabolic diversity and flexibility [19]. According to the KEGG annotation analysis (Figure 4), the TCA cycle pathway (M00009) and F-type ATPase (M00157) were complete in all Aequorivita genomes, while the glycolysis pathway (M00001) was not.…”

Gimibacter soli gen. nov. sp. nov., isolated from mangrove soil and insight into its ecological distribution and metabolic potential

“…The first two genera currently include only one species, Eilatimonas milleporae and Temperatibacter marinus . The genus Kordiimonas currently consists of nine species with correct names validly published under the International Code of Nomenclature of Prokaryotes [4], including Kordiimonas aestuarii [5], Kordiimonas aquimaris [6], Kordiimonas gwangyangensis (type species) [3], Kordiimonas lacus [7], Kordiimonas laminariae [8], Kordiimonas lipolytica [9], Kordiimonas marina [8], Kordiimonas pumila [10] and Kordiimonas sediminis [11]. The family Temperatibacteraceae bacteria are often isolated from marine environments, such as the hydrocoral Millepora dichotoma [2], seawater [1, 6, 7] and sediments [3, 5, 8, 10].…”

“…The genus Kordiimonas currently consists of nine species with correct names validly published under the International Code of Nomenclature of Prokaryotes [4], including Kordiimonas aestuarii [5], Kordiimonas aquimaris [6], Kordiimonas gwangyangensis (type species) [3], Kordiimonas lacus [7], Kordiimonas laminariae [8], Kordiimonas lipolytica [9], Kordiimonas marina [8], Kordiimonas pumila [10] and Kordiimonas sediminis [11]. The family Temperatibacteraceae bacteria are often isolated from marine environments, such as the hydrocoral Millepora dichotoma [2], seawater [1, 6, 7] and sediments [3, 5, 8, 10]. Several studies demonstrated that some members of this family could degrade carbazole [12] and diesel oil [13]; some may play important roles in the biogeochemical cycles of carbon, nitrogen, sulphur, phosphorus and others [14].…”