Phenotypic and genotypic characterization of Marinobacterium weihaiense sp. nov. and Marinobacterium marinum sp. nov., isolated from marine sediment, and genomic properties of the genus Marinobacterium

Abstract

In this study, two novel bacterial strains were isolated from coastal sediment of Weihai, China. The two strains were Gram-stain-negative and facultatively aerobic, designated 3-1745^T and A346^T. Based on phenotypic, genetic and phylogenetic properties, strains 3-1745^T and A346^T represent two novel species of the genus Marinobacterium. The results of genome analysis revealed many central carbohydrate metabolism pathways such as gluconeogenesis, pyruvate oxidation, tricyclic acid cycle, pentose phosphate pathway and PRPP biosynthesis in the genus Marinobacterium. The ability of strains 3-1745^T and A346^T to utilize volatile fatty acids was experimentally confirmed. Polyhydroxyalkanoate synthases (PhaA, PhaB and PhaC) for the synthesis of polyhydroxyalkanoates were prevalent in the genus Marinobacterium. Multiple BGCs (biosynthetic gene clusters) including betalactone, ectoine, ranthipeptide, redox-cofactor, RiPPs (ribosomally synthesized post-translationally modified peptides) and T3PKS (polyketide synthases) in the genome of the genus Marinobacterium were found. Additional genome analyses suggested that the genus Marinobacterium contained diverse potential mechanisms of salt tolerance and mainly utilized oligosaccharides. This is the first report on broad genomic analyses of the genus Marinobacterium with the description of two novel species and potential ecological and biotechnological implications.

Keywords: Marinobacterium; comparative genomic analysis; polyhydroxyalkanoates; polyphasic taxonomy.

Fig. 1.

Map showing the sample collection site. The blue dot represents the sampling site, and the upper right corner shows an enlarged image of the sample collection site.

Fig. 2.

Maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showing the position of strains A346^T and 3-1745^T. Bootstrap values >70 % are shown at branch nodes. Celerinatantimonas diazotrophica S-G2-2^T (DQ913890.1) was used as an outgroup. The 16S rRNA gene sequences of strains A346^T and 3-1745^T were extracted from the genome. Bar, 0.050 substitutions per nucleotide position.

Fig. 3.

IQ-TREE based on a group of 120 conserved genes showing the relationships between strains A346^T, 3-1745^T and related taxa. Bootstrap values >70 % are shown at branch nodes. Celerinatantimonas diazotrophica S-G2-2^T (NZ_SMGD01000011.1) was used as an outgroup. Bar, 0.20 substitutions per nucleotide position.

Fig. 4.

Comparisons of the average nucleotide identity (ANI), DNA–DNA hybridization (DDH) and average amino acid identity (AAI) values between strains A346^T, 3-1745^T and related Marinobacterium type strains. (a) ANI and DDH values; (b) AAI values. Strains: 1, M. weihaiense A346^T; 2, M. marinum 3-1745^T; 3, M. stanieri DSM 7027^T; 4, M. georgiense JCM 21667^T; 5, M. halophilum DSM 17586^T; 6, M. aestuarii ST58-10^T; 7, M. alkalitolerans AK62^T; 8, M. arenosum CAU 1594^T; 9, M. jannaschii DSM 6295^T; 10, M. litorale DSM 23545^T; 11, M. lutimaris DSM 22012^T; 12, M. mangrovicola DSM 27697^T; 13, M. nitratireducens CGMCC 1.7286^T; 14, M. profundum PAMC 27536^T; 15, M. ramblicola D7^T; 16, M. rhizophilum DSM 18822^T; 17, M. zhoushanense CGMCC 1.15341^T; 18, M. sedimentorum KMM 9957^T.

Fig. 5.

Complete and incomplete metabolism pathways of the KEGG database in the genus Marinobacterium: 0, incomplete metabolism pathways; 1, complete metabolism pathways. Different colour codes in the y-axis represent different module types.

Fig. 6.

PHA synthase genes in Marinobacterium genomes. Numbers represent the gene count. K00626: ACAT, atoB; acetyl-CoA C-acetyltransferase; K00023: phbB; acetoacetyl-CoA reductase; K03821: phaC, phbC; poly[(R)−3-hydroxyalkanoate] polymerase subunit PhaC; K22881: phaE; poly[(R)-3-hydroxyalkanoate] polymerase subunit PhaE; K03737: por, nifJ; pyruvate-ferredoxin/flavodoxin oxidoreductase.

Fig. 7.

PHA synthetic pathways in the genus Marinobacterium. The enzymes shown in yellow are present in strains A346^T and 3-1745^T.

Fig. 8.

Prediction of biosynthetic gene clusters for Marinobacterium strains annotated by the antiSMASH database. Bubble sizes represent the number of gene clusters.

Fig. 9.

Comparison of carbohydrate-active enzymes (CAZymes) between various Marinobacterium strains. AA: auxiliary activities; CBM: carbohydrate-binding module; CE: carbohydrate esterases; GH: glycoside hydrolases; GT: glycosyltransferases; PL: polysaccharide lyases.

Fig. 10.

Predicted number of carbohydrate-active enzymes detected in the genus Marinobacterium. The shade of the colour represents the number of genes.

Fig. 11.

Flagella synthase genes in Marinobacterium sp. genomes. Numbers represent the gene count.