Family Vibrionaceae Research Articles

CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species

BackgroundBacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. Species within the bacterial family Vibrionaceae are marine organisms that encounter large numbers of phages. Our goal was to determine the significance of CRISPR-Cas systems as a mechanism of defense in this group by investigating their prevalence, phylogenetic distribution, and genome context.ResultsHerein, we describe all the CRISPR-Cas system types and their distribution within the family Vibrionaceae. In Vibrio cholerae genomes, we identified multiple variant type I-F systems, which were also present in 41 additional species. In a large number of Vibrio species, we identified a mini type I-F system comprised of tniQcas5cas7cas6f, which was always associated with Tn7-like transposons. The Tn7-like elements, in addition to the CRISPR-Cas system, also contained additional cargo genes such as restriction modification systems and type three secretion systems. A putative hybrid CRISPR-Cas system was identified containing type III-B genes followed by a type I-F cas6f and a type I-F CRISPR that was associated with a prophage in V. cholerae and V. metoecus strains. Our analysis identified CRISPR-Cas types I-C, I-E, I-F, II-B, III-A, III-B, III-D, and the rare type IV systems as well as cas loci architectural variants among 70 species. All systems described contained a CRISPR array that ranged in size from 3 to 179 spacers. The systems identified were present predominantly within mobile genetic elements (MGEs) such as genomic islands, plasmids, and transposon-like elements. Phylogenetic analysis of Cas proteins indicated that the CRISPR-Cas systems were acquired by horizontal gene transfer.ConclusionsOur data show that CRISPR-Cas systems are phylogenetically widespread but sporadic in occurrence, actively evolving, and present on MGEs within Vibrionaceae.

Strain-specific changes in the gut microbiota profiles of the white shrimp Litopenaeus vannamei in response to cold stress

The gut microbiota is closely related to shrimp growth and health. However, the response patterns of gut bacterial communities to environmental stresses (such as cold) in distinct shrimp strains and their association with host status are still unclear. In this study, stress tolerance and its potential association with the gut microbiota in two white shrimp Litopenaeus vannamei strains (ZT and PM) were investigated using 16S rRNA gene amplicon sequencing. The stable body weight of PM relative to the obvious weight loss of ZT after both were subjected to cold stress (at the adult life stage) suggests that PM possess stronger tolerance to cold stress. Meanwhile, the α-diversity indices of PM gut bacteria were significantly higher than those of ZT, and the bacterial community structure in the PM gut was more stable as well. Furthermore, cold stress led to domination of the bacterial composition in the ZT gut by the families Erysipelotrichaceae, Mycoplasmataceae, and Vibrionaceae, which have potential pathogenic members. On the other hand, the relative abundances of 18 discriminatory families, represented by Rhodobacteraceae (33.8%), in the PM gut were significantly higher than those in the ZT gut, suggesting that distinct gut bacterial assemblages may reflect the stress resistance potential of shrimp. The taxonomic signature of gut microbiota of the cold-resistant strain could be a guidance for isolation of novel probiotics from bacterial groups such as Rhodobacteraceae, which could be potentially applied to reduce the influence of cold stress in white shrimp.

Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding

With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.

Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi).

SummaryThe supply of quality juveniles via land‐based larviculture represents a major bottleneck to the growing finfish aquaculture industry. As the microbiome plays a key role in animal health, this study aimed to assess the microbial community associated with early larval development of commercially raised Yellowtail Kingfish (Seriola lalandi). We used qPCR and 16S rRNA gene amplicon sequencing to monitor changes in the microbiome associated with the development of S. lalandi from larvae to juveniles. We observed an increase in the bacterial load during larval development, which consisted of a small but abundant core microbiota including taxa belonging to the families Rhodobacteraceae, Lactobacillaceae and Vibrionaceae. The greatest change in the microbiome occurred as larvae moved from a diet of live feeds to formulated pellets, characterized by a transition from Proteobacteria to Firmicutes as the dominant phylum. A prediction of bacterial gene functions found lipid metabolism and secondary metabolite production were abundant in the early larval stages, with carbohydrate and thiamine metabolism functions increasing in abundance as the larvae age and are fed formulated diets. Together, these results suggest that diet is a major contributor to the early microbiome development of commercially raised S. lalandi.

Ascitic Bacterial Composition Is Associated With Clinical Outcomes in Cirrhotic Patients With Culture-Negative and Non-neutrocytic Ascites.

Ascites bacterial burden is associated with poor clinical outcomes in patients with end-stage liver disease. However, the impact of ascitic microbial composition on clinical course was still not clear. In this study, the ascitic microbiota composition of 100 cirrhotic patients with culture-negative and non-neutrocytic ascites were researched with 16S rRNA pyrosequencing and enterotype-like cluster analysis.Results: By characterizing the ascitic microbial composition, two distinct microbial clusters were observed, Cluster 1 (86 patients) and Cluster 2 (14 patients). Cluster 1 showed lower microbial richness than Cluster 2. At the phylum level, Cluster 1 had greater abundance of Bacteroidetes and Firmicutes, but less abundance of Proteobacteria and Actinobacteria than Cluster 2. At the family level, family Bacteroidales S24-7 group, Prevotellaceae, Lachnospiraceae, Lactobacillaceae, Rikenellaceae, and Vibrionaceae were found over-represented in Cluster 1. And family Acetobacteraceae, Erysipelotrichaceae, Rickettsiaceae, and Streptococcaceae were found enriched in Cluster 2. The levels of plasma cytokine IL-17A, IL-7, and PDGF-BB were found significantly higher in Cluster 1 than in Cluster 2. There were four OTUs closely correlated with plasma cytokines, which were OTU 140 and OTU 271 (both from Bacteroidales S24-7 group), OTU 68 (Veillonellaceae), and OTU 53 (Helicobacteraceae). Patients from Cluster 1 showed significant higher short-term mortality than patients from Cluster 2.Conclusion: Our study demonstrated that the microbial composition of culture-negative and non-neutrocytic ascites in cirrhotic patients is associated with short-term clinical outcomes. The results here offer a rational for the identification of patients with high risk, and provide references for selective use of prophylactic methods.

Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs

The Coorong estuary lies at the terminus of Australia’s largest river system, the Murray-Darling; both are strongly influenced by human activities; including farming and extensive flow modification. Metagenomic approaches were used to determine the planktonic bacterial community composition and potential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-like salinity, and the hypersaline upper-reaches of the estuary. Significant shifts in taxa and metabolic function were seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceae and Alteromonadaceae; families readily able to adapt to change in nutrient conditions; and the potentially pathogenic families Brucellaceae, Enterobacteriaceae and Vibrionaceae. Metabolisms over-represented include motility and chemotaxis, RNA metabolism and membrane transport, all of which are involved in actively searching for and obtaining nutrients. Also over-represented were metabolisms involved in population succession and stress response. An over-representation of taxa and metabolisms indicative of environmental change is reflective of anthropogenically affected riverine input. In the hypersaline upper reaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were the families Flavobacteriaceae, Cytophagaceae and Nocardioidaceae, members of which are able to survive over a wide salinity range. Metabolisms over-represented here were reflective of increased bacterial growth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide and nucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically with other planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity, respectively. This indicates that the Coorong exhibits a unique planktonic bacterial community that is influenced by riverine input at the river mouth and salinity in the upper-reaches.

Bacterial Communities in Tissues and Surficial Mucus of the Cold-Water Coral Paragorgia arborea

Coral bacterial associates can play important functional roles for the holobiont, such as nitrogen cycling, nutrient processing, and supporting immunity. While bacteria found within the microbiome of corals may benefit the host, they can also be linked to pathogenesis. In the deep-sea, cold-water corals, like their warm shallow-water counterparts, host bacterial communities, but have received little attention due to logistical constraints in sampling. In particular, bacteria associated with surficial mucus of cold-water corals have not yet been investigated. Here, tissue and mucus samples of Paragorgia arborea were collected from three submarine canyons along the continental slope of the Gulf of Maine. Bacterial DNA was extracted from tissue and mucus samples and sequencing of the V6-V8 hypervariable region of the 16S rRNA gene was performed using Illumina MiSeq. The bacterial communities associated with P. arborea compartments (tissue and mucus) and sampling locations (canyon) differed significantly in composition. Proteobacteria, Tenericutes, and Spirochaetes were the dominant phyla across the majority of coral tissue samples, with Gammaproteobacteria and Alphaproteobacteria identified as the largest Proteobacteria contributors across all samples. OTUs belonging to the taxa Spirochaeta, Mycoplasma, Flavobacteriaceae, Terasakiellaceae, Campylobacterales and Rickettsiales were identified as biomarkers (bacterial taxa significantly more abundant in a specific coral microhabitat) of P. arborea tissues, while Paracoccus was a biomarker of P. arborea mucus. Many of the recovered biomarker taxa may be involved in nitrogen cycling. Representatives from several bacterial families (Vibrionaceae, Campylobacteraceae, Rhodobacteraceae, Flavobacteraceae, and Burkholderiaceae) previously reported in diseased scleractinians, were present in P. arborea as rare bacterial taxa. Characterizing the bacterial associates present in visibly healthy coral colonies provides a benchmark of dominant and rare bacterial groups present in the cold-water coral holobiont. This is the first characterization of bacterial groups associated with P. arborea, examining both tissue- and mucus-specific communities.

Rotavirus analyses by SYBR Green real-time PCR and microbiological contamination in bivalves cultivated in coastal water of Amazonian Brazil.

The contamination of mussels and oysters by viruses and bacteria is often associated with water contamination and gastroenteritis in humans. The present study evaluated viral and bacterial contamination in 380 samples, from nine mollusk-producing regions in coastal water north of the Brazilian Amazon. Rotavirus contamination was studied for groups A to H, using a two-step SYBR Green RT-qPCR (quantitative reverse transcription polymerase chain reaction), and bacterial families Enterobacteriaceae, Vibrionaceae, and Aeromonadaceae by classical and molecular methods. From the 19 pools analyzed, 26.3% (5/19) were positive for group A Rotavirus, I2 genotype for VP6 region, without amplifications for groups B-H. Bacteriological analysis identified Escherichia coli isolates in 89.5% (17/19) with identification of atypical enteropathogenic E. coli aEPEC in 10.5% (2/19), Salmonella (Groups C1 and G) (10.5%, 2/19), Vibrio alginolyticus (57.9%, 11/19) V. parahaemolyticus (63.2%, 12/19), V. fluvialis (42.1%, 8/19), V. vulnificus (10.5%, 2/19), V. cholerae non-O1, non O139(10.5%, 2/19) and Aeromonas salmonicida (52.6%, 10/19). All the samples investigated presented some level of contamination by enterobacteria, rotavirus, or both, and these results may reflect the level of contamination in the Northern Amazon Region, due to the natural maintenance of some of these agents or by the proximity with human populations and their sewer.

Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata)

There is substantial evidence showing that the microbiome of teleosts plays a key role in host health and wellbeing. Aquaculture practices increase the risk of dysbiosis (i.e. microbial imbalance), which is known to facilitate pathogen infections. The skin and gills are the primary defense organs against pathogens, thus, characterizing their microbiome composition in farmed fish is pivotal for detecting potential alterations that may lead to disease susceptibility. Here, we assessed the skin and gill microbiomes of two of the most important adult fish species farmed in southern Europe, the seabass and the seabream, during winter months. We coupled next-generation sequencing (MiSeq) of the 16S rRNA V4 region with the DADA2 bioinformatic pipeline to assess microbial composition and structure. Variation in microbial alpha-diversity (intra-sample) and taxa proportions were assessed using analysis of variance. Differences in beta-diversity (between-sample) were tested using permutational multivariate analysis of variance. Microbiomes of both tissues (n = 30 per species) identified 19 bacteria phyla, dominated by the phyla Proteobacteria (44–68%) and Bacteroidetes (15–37%); the families Flavobacteriaceae (11–28%), Rhodobacteraeae (4–8%) and Vibrionaceae (2–17%); and the genera Rubritalea (4–13%), Pseudomonas (4–8%) and the NS3a marine group (4–12%). Mean relative proportion of these taxa, some alpha-diversity indices and all beta-diversity distances varied significantly between tissues within and between species. ASVs belonging to the genera Polaribacter and Vibrio, which include several species that are pathogenic, were detected in the core microbiomes of seabass or seabream.

The influence of surface microbial diversity and succession on microbiologically influenced corrosion of steel in a simulated marine environment.

To explore how a succession of bacteria grown on steel coupons in a marine environment can influence their corrosion process, we designed a microcosm in laboratory to evaluate corrosion kinetics and microbial diversity over 30 days. The results described a clear influence of corrosion by a succession of different bacterial groups. During the initial period, 2-7days, a sharp increase in the rate of corrosion was detected accompanied by the presence of Alteromonadaceae, Vibrionaceae, Oceanospirillaceae, Rhodobacteraceae, Rhodospirillaceae and Flavobacteriaceae bacteria families. After 15 days, representatives of families Piscirickettsiaceae and Pseudomonadaceae were also described, accompanied by a continuous corrosion process over the coupons. After 30 days, there was a sudden change in the profile of the bacteria present on the steel coupons, with a prevalence of Halomonadaceae family species, and establishment and continuity of the corrosion process by the biofilm grown on the coupons. The results describe differences in microbial diversity over the time, highlighting certain bacterial lithotrophic species that persisted for most of the experiment, through a complex association between bacteria and metal surfaces, which can be a new starting point for development and maintenance of a favorable microenvironment to accelerate corrosion processes.

Exploring the Impact of the Biofloc Rearing System and an Oral WSSV Challenge on the Intestinal Bacteriome of Litopenaeus vannamei

We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition and abundance of bacterial communities from the midgut of shrimp reared in the super-intensive biofloc technology (BFT) and clear seawater system (CWS). The predominant bacterial group belonged to the phylum Proteobacteria, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes. Within Proteobacteria, the family Vibrionaceae, which includes opportunistic shrimp pathogens, was more abundant in CWS than in BFT-reared shrimp. Whereas the families Rhodobacteraceae and Enterobacteriaceae accounted for almost 20% of the bacterial communities of shrimp cultured in BFT, they corresponded to less than 3% in CWS-reared animals. Interestingly, the WSSV challenge dramatically changed the bacterial communities in terms of composition and abundance in comparison to its related unchallenged group. Proteobacteria remained the dominant phylum. Vibrionaceae was the most affected in BFT-reared shrimp (from 11.35 to 20.80%). By contrast, in CWS-reared animals the abundance of this family decreased from 68.23 to 23.38%. Our results provide new evidence on the influence of both abiotic and biotic factors on the gut bacteriome of aquatic species of commercial interest.

Structure of the GH9 glucosidase/glucosaminidase from Vibrio cholerae.

Glycoside hydrolase family 9 (GH9) of carbohydrate-processing enzymes primarily consists of inverting endoglucanases. A subgroup of GH9 enzymes are believed to act as exo-glucosidases or exo-glucosaminidases, with many being found in organisms of the family Vibrionaceae, where they are proposed to function within the chitin-catabolism pathway. Here, it is shown that the GH9 enzyme from the pathogen Vibrio cholerae (hereafter referred to as VC0615) is active on both chitosan-derived and β-glucoside substrates. The structure of VC0615 at 3.17 Å resolution is reported from a crystal form with poor diffraction and lattice disorder. VC0615 was highly refractory to crystallization efforts, with crystals only appearing using a high protein concentration under conditions containing the precipitant poly-γ-glutamic acid (PGA). The structure is highly mobile within the crystal lattice, which is likely to reflect steric clashes between symmetry molecules which destabilize crystal packing. The overall tertiary structure of VC0615 is well resolved even at 3.17 Å resolution, which has allowed the structural basis for the exo-glucosidase/glucosaminidase activity of this enzyme to be investigated.

Patterns of triclosan resistance in Vibrionaceae.

The antimicrobial additive triclosan has been used in personal care products widely across the globe for decades. Triclosan resistance has been noted among Vibrio spp., but reports have been anecdotal and the extent of phenotypic triclosan resistance across the Vibrionaceae family has not been established. Here, triclosan resistance was determined for Vibrionaceae strains across nine distinct clades. Minimum inhibitory concentrations (MIC) were determined for 70 isolates from clinical (n = 6) and environmental sources (n = 64); only two were susceptible to triclosan. The mean MIC for all resistant Vibrionaceae was 53 µg mL−1 (range 3.1–550 µg mL−1), but was significantly different between clades (p < 0.001). The highest mean triclosan MIC was observed in the Splendidus clade (200 µg mL−1; n = 3). Triclosan mean MICs were 68.8 µg mL−1 in the Damselae clade and 45.3 µg mL−1 in the Harveyi clade. The lowest mean MIC was observed in the Cholerae clade with 14.4 µg mL−1, which was primarily represented by clinical strains. There were no significant differences in triclosan MIC among individual species or among environmental strains isolated from different locations. Overall, phenotypic triclosan resistance appears to be widespread across multiple clades of Vibrionaceae.

BACTERIAL COMMUNITIES OF THE OYSTERS Crassostrea corteziensis AND C. sikamea OF COSPITA BAY, SINALOA, MEXICO

This work aimed to quantify the bacterial loads and determine the taxonomic composition of the microbial communities of oysters Crassostrea corteziensis and C. sikamea , as well as the surrounding waters of Cospita Bay, using two sets of samples (M1 and M4) obtained in the dry season and two (M2 and M3) in the rainy season. Bacterial loads were quantified with the viable count technique and out of the 320 strains isolated for their different morphologies, 84 were identified with molecular techniques to the species level. These species pertained to the families Vibrionaceae, Bacillaceae, Brucellaceae, Micrococcaceae, Pseudoalteromonaceae, Rhodobactereceae, Shewanellaceae and Staphylococcaceae. The higher concentrations of total bacteria were in the rainy season (samples M2 and M3), when families Vibrionaceae and Brucellaceae dominated. The highest Vibrio spp. and Pseudomonas spp. concentrations were in winter (samples M4). Probably because of its poor health conditions, the Kumamoto oyster C. sikamea had the highest diversity of bacterial species and the highest number of known pathogens for aquatic organisms.

Corallibacterium pacifica gen. nov., sp. nov., a Novel Bacterium of the Family Vibrionaceae Isolated from Hard Coral.

A gram-negative, rod-shaped, motile, oxidase- and catalase-positive, non-pigmented marine bacterium, designated strain OS-11M-2T, was isolated from a coral sample collected from the Osakura coastal area in Micronesia. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences indicated that strain OS-11M-2T is a member of the family Vibrionaceae, its closest neighbors being Photobacterium damselae subsp. piscicida NCIMB 2058T (94.9%), Photobacterium damselae subsp. damselae CIP 102761T (94.75%), Grimontia marina IMCC5001T (94.5%), Enterovibrio coralii LMG 22228T (94.5%), and Grimontia celer 96-237T (94.5%). The major cellular fatty acids were summed feature 3 (21.4%), summed feature 8 (18.5%), iso-C16:0 (13.8%), and C16:0 (11.9%). The major respiratory quinone of the bacterium was ubiquinone-8 (Q-8) and its major polar lipid phosphatidylethanolamine. Six amino lipids, two phospholipids, and one polar lipid, all unidentified, were detected. The DNA G+C content was 49.7mol%. The 16S rRNA gene sequence of OS-11M-2T was registered in GenBank under accession number MF359550. On the basis of phenotypic, genotypic, and phylogenetic analyses, strain OS-11M-2T represents a novel genus of the family Vibrionaceae, for which we propose the name Corallibacterium pacifica gen. nov., sp. nov., with the type strain of the type species being OS-11M-2T (= KCCM 43265T). The digital protologue database (DPD) taxon number for strain OS-11M-2T is GA00041.

Carrageenanolytic enzymes from marine bacteria associated with the red alga Tichocarpus crinitus

One hundred six bacterial strains (106 strains) were isolated from the Pacific red alga Tichocarpus crinitus, collected from the Troitsa Bay of Gulf of Peter the Great (Sea of Japan, Russia), and studied on their ability to degrade different samples of carrageenan as substrates. Some of the studied strains exhibited hydrolytic activity selectively to a total polysaccharide (kappa and lambda) from Chondrus armatus, other strains, to κ/β-carrageenan from T. crinitus, which did not possess the same effect to a total polysaccharide from T. crinitus. The strains with the highest enzyme activity (28 strains) were identified using 16S rRNA gene sequence techniques and classified to the phyla Bacteroidetes and Proteobacteria. Most (75%) of the studied carrageenase producers belong to phylum Bacteroidetes (21 strains). These strains were related with 7 phylotypes of the genera Aquimarina, Cellulophaga, Maribacter, and Zobellia (family Flavobacteriaceae of the class Flavobacteriia). Cellulophaga strains were the dominant group (35.7% of total) and closely related to species C. baltica and C. lytica with 99.8 and 99.9% sequence similarity, respectively. The remaining strains (7 strains) were represented by members of the genera Altererythrobacter (the family Erythrobacteraceae), Phaeobacter, Sulfitobacter, Tateyamaria (the family Rhodobacteraceae), and Sphingomonas (the family Sphingobacteriaceae) of the class Alphaproteobacteria and Psychrobacter (the family Moraxellaceae) and Vibrio (the family Vibrionaceae) of the class Gammaproteobacteria.

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae.

Members of the family Vibrionaceae are metabolically versatile and ubiquitous in natural environments, with extraordinary genome feature of two chromosomes. Here we reported the complete genome of Paraphotobacterium marinum NSCS20N07DT, a recently described novel genus-level species in the family Vibrionaceae. It contained two circular chromosomes with a size of 2,593,992 bp with G+C content of 31.2 mol%, and a plasmid with a size of 5,539 bp. The larger chromosome (Chr. I) had a genome size of 1,426,504 bp with G+C content of 31.6 mol%, and the smaller one (Chr. II) had a genome size of 1,161,949 bp with G+C content of 30.8 mol%. The two chromosomes have strikingly similar G+C contents with difference of <1% and similar percentages of coding regions. Interestingly, by comparison to 134 species affiliated with seven genera within the family Vibrionaceae, P. marinum NSCS20N07DT possessed the smallest genome size and lowest G+C content. Clusters of orthologous groups of proteins functional categories revealed that the two chromosomes had different distributions of functional classes, indicating they take different cellular functions. Surprisingly, Chr. II had a large proportion of unknown genes than Chr. I. Metabolic characteristics predicted that Chr. I performed the essential metabolism, which can be complemented by the Chr. II, such as amino acids biosynthesis. Microbial community analysis of in situ surface seawater revealed that P. marinum accounted for one to four sequences among more than 20,000 of 16S ribosomal RNA gene V4 contigs, representing it apparently appeared as a rare species. What’s more, P. marinum was anticipated to be specific to the pelagic ocean. This study will provide new insight into more understanding the genomic and metabolic features of multiple chromosomes in prokaryote and emphasize the ecological distribution of the members in the family Vibrionaceae as a rare species.

Interactive regulations by viruses and dissolved organic matter on the bacterial community

AbstractViruses and dissolved organic matter (DOM) are major top–down and bottom–up factors, respectively, which control the abundance and diversity of bacterial communities. However, the relative strength and interaction between these two regulators in different marine ecosystems are not fully understood. We applied viral reduction and cross‐transplantation of eutrophic estuarine and pristine coastal waters to examine the separate and combined effects of viruses and DOM on the bacterial community composition. We showed that bacteria were more abundant in the virus‐depleted groups, particularly in those from the eutrophic estuarine water (i.e., &gt; 7 times higher, when compared with the virus‐rich groups). Cluster analyses showed that the bacterial communities in the virus‐rich groups were most similar to the in situ populations. Bacterial community richness, evenness and diversity were reduced at high DOM concentrations but were sustained by viruses. This allowed bacteria that were less vulnerable to viral infection to thrive (such as those in the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae, and SAR11), while suppressing those capable of fast growth at elevated DOM concentrations but which were more vulnerable to viral attack (such as those from the family Vibrionaceae). Our results showed that viral regulation occurring at the strain level can affect the bacterial community structure at higher phylogenetic levels. In addition, some less abundant groups, such as Vibrio and Alteromonas, might actually win the competition for resources, providing viral control is removed. Our results also showed that the population dynamics of certain bacterial groups was controlled by viruses, and the strength of such control was modulated by the concentration of DOM. We suggest that the composition of the bacterial community in aquatic environments results from the interactive regulation by DOM and viruses among other regulators.

Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan

Two phylogenetically distinct Vibrionaceae strains C4II189T and C4V358T isolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189T (=DSM 101554T=JCM 31629T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358T (=DSM 101555T=JCM 31630T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.

Photobacterium alginatilyticum sp. nov., a marine bacterium isolated from bottom seawater.

A Gram-straining-negative, facultatively aerobic, rod-shaped strain, motile by a polar flagellum and designated P03D4T, was isolated from the bottom seawater of the East China Sea. Growth occurred at 10-50 °C (optimum 32 °C), pH 5.0-10.0 (optimum pH 6.0) and in the presence of 1-7 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequence placed P03D4T within the genus Photobacterium of the family Vibrionaceae in the class Gammaproteobacteria, and revealed that strain P03D4T was most closely related to Photobacterium frigidiphilum SL13T with 96.9 % sequence similarity and had sequence similarities with other species of the genus Photobacterium in the range 94.6-96.9 %. The dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The polar lipids of strain P03D4T comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unknown lipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain P03D4T was 44.3 mol%. On the basis of the evidence from this polyphasic study, strain P03D4T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium alginatilyticum sp. nov. is proposed. The type strain is P03D4T (=KCTC 52365T=MCCC 1K03200T=CGMCC 1.15764T).