Vibrio eleionomae sp. nov., isolated from shrimp (Penaeus vannamei) pond water

A novel Vibrio strain (CAIM 722^T=SW9^T=DSM 24596^T) was isolated in 2003 from water of a shrimp (Penaeus vannamei) culture pond located in Los Mochis, Sinaloa, Mexico, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence clustered within those of the genus Vibrio, showing high similarity to the type strains of the Porteresiae clade. Multilocus sequence analysis using eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the strain forms an independent branch. Whole genome sequencing and genomic analyses (average nucleotide identity, OrthoANI, average amino acid identity and in silico DNA-DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strain from related taxa. The results obtained demonstrate that the strain represent a novel species, for which the name Vibrio eleionomae sp. nov. is proposed.

Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes

The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.

Vibrio salinus sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll in the western Pacific Ocean

A marine, facultatively anaerobic, nitrogen-fixing bacterium, designated strain DNF-1^T, was isolated from the lagoon sediment of Dongsha Island, Taiwan. Cells grown in broth cultures were Gram-negative rods that were motile by means of monotrichous flagella. Cells grown on plate medium produced prosthecae and vesicle-like structures. NaCl was required and optimal growth occurred at about 2-3% NaCl, 25-30 °C and pH 7-8. The strain grew aerobically and was capable of anaerobic growth by fermenting D-glucose or other carbohydrates as substrate. Both the aerobic and anaerobic growth could be achieved with NH₄Cl as a sole nitrogen source. When N₂ served as the sole nitrogen source only anaerobic growth was observed. Major cellular fatty acids were C_14:0, C_16:0 and C_16:1 ω7c, while major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 42.2 mol% based on the genomic DNA data. Phylogenetic analyses based on 16S rRNA genes and the housekeeping genes, gapA, pyrH, recA and gyrB, revealed that the strain formed a distinct lineage at species level in the genus Vibrio of the family Vibrionaceae. These results and those from genomic, chemotaxonomic and physiological studies strongly support the assignment of a novel Vibrio species. The name Vibrio salinus sp. nov. is proposed for the novel species, with DNF-1^T (= BCRC 81209^T = JCM 33626^T) as the type strain. This newly proposed species represents the second example of the genus Vibrio that has been demonstrated to be capable of anaerobic growth by fixing N₂ as the sole nitrogen source.

Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll

A nitrogen-fixing isolate of facultatively anaerobic, marine bacterium, designated strain NFV-1^T, was recovered from the lagoon sediment of Dongsha Island, Taiwan. It was a Gram-negative rod which exhibited motility with monotrichous flagellation in broth cultures. The strain required NaCl for growth and grew optimally at about 25-35 °C, 3% NaCl and pH 7-8. It grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other carbohydrates as substrates. NH₄Cl could serve as a sole nitrogen source for growth aerobically and anaerobically, whereas growth with N₂ as the sole nitrogen source was observed only under anaerobic conditions. Cellular fatty acids were predominated by C_16:1 ω7c, C_16:0, and C_18:1 ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1^T had a DNA G + C content of 42.5 mol%, as evaluated according to the chromosomal DNA sequencing data. Analyses of sequence similarities and phylogeny based on the 16S rRNA genes, together with the housekeeping genes, gyrB, ftsZ, mreB, topA and gapA, indicated that the strain formed a distinct species-level lineage in the genus Vibrio of the family Vibrionaceae. These phylogenetic data and those from genomic and phenotypic characterisations support the establishment of a novel Vibrio species, for which the name Vibrio nitrifigilis sp. nov. (type strain NFV-1^T = BCRC 81211^T = JCM 33628^T) is proposed.

Genomics-Metabolomics Profiling Disclosed Marine Vibrio spartinae 3.6 as a Producer of a New Branched Side Chain Prodigiosin

A wide range of prescreening tests for antimicrobial activity of 59 bacterial isolates from sediments of Ria Formosa Lagoon (Algarve, Portugal) disclosed Vibrio spartinae 3.6 as the most active antibacterial producing strain. This bacterial strain, which has not previously been submitted for chemical profiling, was subjected to de novo whole genome sequencing, which aided in the discovery and elucidation of a prodigiosin biosynthetic gene cluster that was predicted by the bioinformatic tool KEGG BlastKoala. Comparative genomics led to the identification of a new membrane di-iron oxygenase-like enzyme, annotated as Vspart_02107, which is likely to be involved in the biosynthesis of cycloprodigiosin and analogues. The combined genomics-metabolomics profiling of the strain led to the isolation and identification of one new branched-chain prodigiosin (5) and to the detection of two new cyclic forms. Furthermore, the evaluation of the minimum inhibitory concentrations disclosed the major prodigiosin as very effective against multi-drug-resistant pathogens including Stenotrophomonas maltophilia, a clinical isolate of Listeria monocytogenes, as well as some human pathogens reported by the World Health Organization as prioritized targets.

The production and bioactivity of prodigiosin: quo vadis?

Prodigiosin (PG), a red tripyrrole pigment, belongs to a member of the prodiginine family and is normally secreted by various sources including Serratia marcescens and other Gram-negative bacteria. The studies of PG have received innovative devotion as a result of reported antimicrobial, larvicidal and anti-nematoid immunomodulation and antitumor properties, owing to its antibiotic and cytotoxic activities. This review provides a comprehensive summary of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, the current evidence-based understanding of the biological activities and medicinal potential of PG is employed to determine the efficacy, with some reports of information related to pharmacokinetics, pharmacodynamics and toxicology.

Vibrio zhugei sp. nov., a moderately halophilic bacterium isolated from pickling sauce

Strain HBUAS61001^T was isolated from the pickling sauce used to make a traditional fermented food product, datoucai, in China. The strain belonged to the genus Vibrio, but was placed in a clade separate from any known Vibrio species based on the 16S rRNA gene and MLSA results. The genome consisted of two chromosomes: chromosome I was 2 901 449 bp long with a G+C content of 45.4 mol%; and chromosome II was 1 107 930 bp long with a G+C content of 45.5 mol%. The most abundant fatty acids were C16 : 0 (28.1 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 29.4 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 10.1 %). The isoprenoid quinones detected were Q7 and Q8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Strain HBUAS61001^T could grow in the presence of up to 17 % NaCl. The calculated average nucleotide identity and in silico DNA-DNA hybridization (GGDC) values of the strain against the closest related type strains were all lower than 95 and 70 %, respectively. Putative genes in the genome associated with survival under high salinity stress were identified. Based on whole genome sequence analysis and phenotypic characteristics, strain HBUAS61001^T is a new species in the genus Vibrio, and the name Vibrio zhugei (=GDMCC 1.1416^T=KCTC 62784^T) is proposed.

Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy

Strain Corallo1^T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1^T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1^T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1^T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1^T. A draft genome sequence of strain Corallo1^T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1^T are C_16:1, n-C_16:0 and C_18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1^T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1^T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1^T (= DSM 27495^T = CIP 110630^T).