Bacteria

Commensal bacteria associated with marine invertebrates are underappreciated sources of chemically novel natural products. Using mass spectrometry, we had previously detected the presence of peptidic natural products in obligate marine bacteria of the genus Microbulbifer cultured from marine sponges. In this report, the isolation and structural characterization of a panel of ureidohexapeptide natural products, termed the bulbiferamides, from Microbulbifer strains is reported wherein the tryptophan side chain indole participates in a macrocyclizing peptide bond formation. Genome sequencing identifies biosynthetic gene clusters encoding production of the bulbiferamides and implicates the involvement of a thioesterase in the indolic macrocycle formation. The structural diversity and widespread presence of bulbiferamides in commensal microbiomes of marine invertebrates point toward a possible ecological role for these natural products.

nov., three marine bacteria isolated from a tidal flat

Three strains, TT30^T, TT37^T and L3^T, were isolated from tidal flat samples. Cells were Gram-stain-negative, non-motile and rod shaped. Cells of strains TT30^T and TT37^T were able to grow in a medium containing 1.0-15.0 % (w/v) NaCl (optimum, 3.0 and 4.0 %, respectively), and cells of strain L3^T was able to grow in a medium containing 1.0-10.0 % (w/v) NaCl (optimum, 1.0 %). Growth of the three strains was observed at pH 6.0-10.0 and at 10-40 °C. Strains TT30^T, TT37^T and L3^T showed the highest similarity to Microbulbifer hydrolyticus DSM 11525^T (97.7 %), M. yueqingensis CGMCC 1.10658^T (98.0 %) and M. elongatus DSM 6810^T (97.9 %), respectively. Results of phylogenetic analyses indicated that the three isolates represented two distinct lineages within the genus Microbulbifer. The DNA G+C contents of strains TT30^T, TT37^T and L3^T were 61.3, 60.9 and 60.2%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among strains TT30^T, TT37^T and L3^T and the reference strains were 84.4-87.4 and 19.6-28.9 %, respectively. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data, demonstrated that strains TT30^T, TT37 ^T and L3^T represent novel species of the genus Microbulbifer, which are named Microbulbifer zhoushanensis sp. nov. (TT30^T=KCTC 92167^T=MCCC 1K07276^T), Microbulbifer sediminum sp. nov. (TT37^T=KCTC 92168^T=MCCC 1K07277^T) and Microbulbifer guangxiensis sp. nov. (L3^T=KCTC 92165^T=MCCC 1K07278^T).

Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway

Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO₄ was slower than that in the presence of MgSO₄. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.

Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp

(2Z,4E)-3-Methyl-2,4-decadienoic acid (1) was identified as a major metabolite from a culture extract of a marine bacterium Microbulbifer which was collected from a stony coral Porites sp. NMR-based spectroscopic analysis revealed that 1 is an unsaturated fatty acid in which a methyl group is located in an uncommon position as a natural product. Feeding experiments of ¹³C-labeled precursors clarified that ʟ-methionine-derived methylation takes place at the carbon which is derived from the carbonyl carbon of acetate. Compound 1 showed weak growth inhibition against Saccharomyces cerevisiae.

Strain A4B-17 and the Characterization of Its Metabolic Pathways for 4-Hydroxybenzoic Acid Synthesis

The marine bacterium Microbulbifer sp. A4B-17 produces secondary metabolites such as 4-hydroxybenzoic acid (4HBA) and esters of 4HBA (parabens). 4HBA is a useful material in the synthesis of the liquid crystal. Parabens are man-made compounds that have been extensively used since the 1920s in the cosmetic, pharmaceutical, and food industries for their effective antimicrobial activity. In this study, we completed the sequencing and annotation of the A4B-17 strain genome and found all genes for glucose utilization and 4HBA biosynthesis. Strain A4B-17 uses the Embden-Meyerhof-Parnas (EMP), hexose monophosphate (HMP), and Entner-Doudoroff (ED) pathways to utilize glucose. Other sugars such as fructose, sucrose, xylose, arabinose, galactose, mannitol, and glycerol supported cell growth and 4HBA synthesis. Reverse transcriptional analysis confirmed that the key genes involved in the glucose metabolism were functional. Paraben concentrations were proportionally increased by adding alcohols to the culture medium, indicating that strain A4B-17 synthesizes the 4HBA and the alcohols separately and an esterification reaction between them is responsible for the paraben synthesis. A gene that codes for a carboxylesterase was proposed to catalyze this reaction. The temperature and NaCl concentration for optimal growth were determined to be 35°C and 22.8 g/L.

Q7

Alginate lyases play an important role in preparation of alginate oligosaccharides. Although a large number of alginate lyases have been characterized, reports on directional preparation of alginate oligosaccharides by alginate lyases are still rather less. Here, a gene alyM encoding a new alginate lyase AlyM was cloned from Microbulbifer sp. Q7 and expressed in Escherichia coli. AlyM exhibited the maximumactivity at pH 7.0 and 55°C and showed special preference to poly-guluronic acid (polyG). Glycine promoted the extracellular secretion of AlyM by 3.6 times. PBS and glycerol significantly improved the thermal stability of AlyM, the enzyme activity remained 75 and 78% after heat-treatment at 45°C for 2 h, respectively. ESI-MS analysis suggested that AlyM mainly produced oligosaccharides with degrees of polymerization (DP) of 2-5. The results of ¹H-NMR showed that guluronic acid (G) occupied the reducing end of the end products, indicating that AlyM preferred to degrade the glycosidic bond at the G-X linkage. HPLC analysis showed that the hydrolysis products with a lower degree of polymerization contained more G. Therefore, AlyM shows good potential to produce alginate oligosaccharides with specific M/G ratio and molecular weights.

CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia

Microbulbifer sp. CCB-MM1 is a halophile isolated from estuarine sediment of Matang Mangrove Forest, Malaysia. Based on 16S rRNA gene sequence analysis, strain CCB-MM1 is a potentially new species of genus Microbulbifer. Here we describe its features and present its complete genome sequence with annotation. The genome sequence is 3.86 Mb in size with GC content of 58.85%, harbouring 3313 protein coding genes and 92 RNA genes. A total of 71 genes associated with carbohydrate active enzymes were found using dbCAN. Ectoine biosynthetic genes, ectABC operon and ask_ect were detected using antiSMASH 3.0. Cell shape determination genes, mreBCD operon, rodA and rodZ were annotated, congruent with the rod-coccus cell cycle of the strain CCB-MM1. In addition, putative mreBCD operon regulatory gene, bolA was detected, which might be associated with the regulation of rod-coccus cell cycle observed from the strain.