Numerical Taxonomy of Aerobic, Gram-negative Bacteria associated with Oysters and Surrounding Seawater of the Mediterranean Coast
Abstract A numerical taxonomic study was performed on 245 strains of heterotrophic, aerobic, marine bacteria, plus 26 reference strains. The isolates were obtained from oysters and seawater sampled monthly over one year, by direct plating on Marine Agar. The strains were characterised by 93 morphological, biochemical, physiological and nutritional tests. Clustering yielded 46 phena at 0.60 S level (S J coefficient). Some could be identified as species of Alteromonas, Shewanella, Deleya, Flavobacterium, Oceanospirillum, Pseudomonas and marine Agrobacterium -like organisms, others were unidentified groups. Several phena seem to correspond to as yet undescribed taxa.
A comparison of strategies for the detection and recovery of Vibrio vulnificus from marine samples of the Western Mediterranean coast
Summary We have compared the effectiveness of culture-based methods and a DNA-based method for the detection, of Vibrio vulnificus from seawater and three types of shellfish collected from the coastal waters of Valencia, Spain. For culture-based method, we used two selective media, thiosulphate-citrate-bile salts-sucrose (TCBS), and cellobiose-polymyxin B-colistin (CPC) agars with and without previous enrichment in alkaline-saline-peptone-water (APWS). Presumptive colonies were confirmed as V. vulnificus by the polymerase chain reaction (PCR) using previously described 23S rRNA V. vulficus -specific sequences as primers (Dvu 9V and Dvu 45R). Direct detection was accomplished by a nested-PCR…
Marinomonas spartinae sp. nov., a novel species with plant-beneficial properties.
Two strains of Gram-stain-negative, chemo-organotrophic, aerobic and halophilic gammaproteobacteria, isolated from within the stem and roots of Spartina maritima in salt marshes from the south Atlantic Spanish coast, were found to represent a novel species in the genus Marinomonas through phylogenetic analysis of their 16S rRNA genes and phenotypic characterization. 16S rRNA gene sequences of the two strains shared < 96.2 % similarity with other Marinomonas species, with Marimonas alcarazii being the most similar in sequence. They required sodium ions for growth, were able to thrive at low (4 °C) temperatures and at salinities of 12–15 %, were unable to hydrolyse any tested macromolecule ex…
Diversity and distribution of marine heterotrophic bacteria from a large culture collection
16 pages, 5 figures, 3 tables, supplementary information https://doi.org/10.1186/s12866-020-01884-7
Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.
A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113T, CECT 5114, CECT 5118T, and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non- motile coccobacilli, aerobic chemoorganotrophs, with an optimum temperature of 26°C and salinity of 3.5–5%. Major cellular fatty acids of strains CECT 5113T and CECT 5114 were C18 : 1 ω7c/ω6c and C10 : 0 3OH, G+C content was 54.4–54.5 mol% and were able to utilize propionate, L-threonine, L- arginine, and L-aspartate as carbon sources. They exhibited 98.3% 16S rRNA gene s…
Draft genomic sequence of Nereida ignava CECT 5292T, a marine bacterium of the family Rhodobacteraceae
Nereida ignava strain 2SM4T (= CECT 5292T = DSM 16309T = CIP 108404T = CCUG 49433T) is a marine bacterium belonging to the Roseobacter group of the family Rhodobacteraceae within the class Alphaproteobacteria. The strain was isolated from sea water surrounding cultivated oysters 2–3 miles off the Mediterranean coast near Valencia (Spain) and was phylogenetically related to uncultured clones of gall symbiont bacteria of some species of Prionitis alga. Here we describe the genome sequence and annotation of this organism, the type strain of the single species of this genus. The genome comprised 2,888,349 bp, 2,872 protein-coding genes and 52 RNA genes. The annotation revealed the capacity to p…
Draft Genome Sequences of Vibrio renopiscarius Strains CECT 8603T and CECT 8604, Two Marine Gammaproteobacteria Isolated from Cultured Gilthead Sea Bream (Sparus aurata).
ABSTRACT Vibrio renopiscarius DCR 1-4-2 T (CECT 8603 T ) and DCR 1-4-12 (CECT 8604) were isolated from healthy gilthead sea bream ( Sparus aurata ) from Mediterranean fish farms (Castellón, Spain). Their draft genome sequences (30 and 44 contigs, respectively) have 4.3 Mbp and a G+C content of 45.2 mol% and contain almost 3,700 protein-encoding genes.
Multilocus sequence analysis of putative Vibrio mediterranei strains and description of Vibrio thalassae sp. nov.
A multilocus sequence analysis based on partial gyrB, mreB, rpoD and pyrH genes was undertaken with 61 putative Vibrio mediterranei/V. shilonii strains from different hosts (mussels, oysters, clams, coral, fish and plankton) or habitat (seawater and sediment) and geographical origins (Mediterranean, Atlantic and Pacific). A consistent grouping was obtained with individual and concatenated gene sequences, and the clade, comprising 54 strains, was split into three subclades by all methods: subclade A (40 strains, including AK1, the former type strain of Vibrio shilonii), subclade B (8 strains) corresponding to the species V. mediterranei, and subclade C (six strains) representing a new specie…
Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater.
Strain MD5T, an aerobic marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized in a polyphasic study and was placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae . Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD5T is related to Tropicibacter naphthalenivorans C02T, Phaeobacter inhibens T5T, P. gallaeciensis BS107T and P. daeponensis TF-218T, with 96.9, 96.2, 96.1 and 96.1 % sequence similarity, respectively. Phylogenetic analyses also showed that strain MD5T forms a stable clade only with T. naphthalenivorans C02T. Strain MD5T requires Na+ plus a diva…
Euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae.
Strain 7SM30T , an aerobic marine, Gram-negative, heterotrophic and yellow- to orange-pigmented bacterium isolated from seawater from Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that the isolate represented a novel lineage within the family Flavobacteriaceae. The most closely related genera were Pseudozobellia, Zobellia and Kriegella. Cells of strain 7SM30T were non-motile rods that required sea salts for growth, used a wide variety of carbohydrates as sole carbon and energy sources and, unlike species of the genera Pseudozobellia and Zobellia, did not possess flexirubin-type pigment or hydrolyse agar. Strain 7SM30T containe…
Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes.
The central clade of the genus Vibrio, also called the Vibrio core group, comprises six species that are tightly related (DNA–DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA–DNA hybridization assays. The genes selected, 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR, were amplified by direct PCR from 44 Vibr…
Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009.
Abstract A facultatively anaerobe, moderately halophilic, Gram-negative, filamentous, non motile and unpigmented bacterium, designated M30 T , was isolated from coastal Mediterranean Sea water in Valencia, Spain. Phylogenetic analysis based on 16S rRNA sequences placed this strain in the phylum “ Bacteroidetes ” with Marinifilum fragile JC2469 T as its closest relative with 97% sequence similarity. Average nucleotide identity (ANI) values between both strains were far below the 95% threshold value for species delineation (about 89% using BLAST and about 90% using MUMmer). A comprehensive polyphasic study, including morphological, biochemical, physiological, chemotaxonomic and phylogenetic d…
Roseivivax atlanticus (Li, Lai, Liu, Sun and Shao, 2015) is a later heterotypic synonym of Roseivivax marinus (Dai, Shi, Gao, Liu and Zhang, 2014)
The genomes of the type strains of Roseivivax atlanticus and Roseivivax marinus ( Rhodobacteraceae , Alphaproteobacteria ), were analysed to determine their respective Average Nucleotide Identity (ANI) and in silico DNA–DNA hybridization (DDH) values. These species were proposed and effectively published relatively closely in time (February and August 2014, respectively) and so not taking account of the other. The intergenomic relatedness between both type strains, 97.0–97.4 % ANI and 82.8 % in silico DDH, confirm that they represent members of the same genomic species. This conclusion is also supported at the phenotypic level. Since the name Roseovarius marinus was validly published earlie…
Mesonia oceanica sp. Nov., isolated from oceans during the tara oceans expedition, with a preference for mesopelagic waters
10 pages, 4 figures, 3 tables
Photobacterium aphoticum sp. nov., isolated from coastal water
A facultatively anaerobic marine gammaproteobacterium, designated strain M46T, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized by using a polyphasic approach and was found to be situated within the genus Photobacterium in the family Vibrionaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M46T was closely related to P. rosenbergii CECT 7644T, P. halotolerans CECT 5860T and P. ganghwense CECT 7641T, showing sequence similarities of 96.8, 96.4 and 96.2 %, respectively. According to the results of phylogenetic analyses based on recA and gyrB gene sequences, the most closely related taxon was P. ganghwens…
Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis.
Strain CECT 5091T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria , in the family Rhodobacteraceae , with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae , Ruegeria atlantica and Ruegeria arenilitoris , respectively. Average nucleotide identities (ANI) and in silico DNA–DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091T with those of the type strains of 12 species of the genus Ruegeria : the values obtained were always below the thresholds…
Draft genomes of Nautella italica strains CECT 7645(T) and CECT 7321: Two roseobacters with potential pathogenic and biotechnological traits.
Nautella italica is a member of the family Rhodobacteraceae described in 2009. Strain LMG 24365(T) (=CECT 7645(T), =DSM 26436(T), =CCUG 55857(T)) was isolated from a marine electroactive biofilm growing in a stainless steel cathode exposed to natural water in Genoa, Italy. Strain AD 41 (=CECT 7321) was isolated from water surrounding cultivated gilthead seabream larvae in Cadiz, Spain. The genomes of strains CECT 7645(T) and CECT 7321 were sequenced, assembled, annotated and compared. Here we describe the most relevant findings: biofilm formation, quorum sensing, resistance to multiple drugs, heavy metals and oxidative stress, cytotoxins, and poly-β-hydroxybutyrate (PHB) production genes. T…
Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium.
7 pages, 1 figure, 1 table
Reinekea blandensis sp. nov., a marine, genome-sequenced gammaproteobacterium
6 pages, 2 figures, 2 tables
An MLSA approach for the taxonomic update of the Splendidus clade, a lineage containing several fish and shellfish pathogenic Vibrio spp.
A multilocus sequence analysis was undertaken in order to redefine the Splendidus clade of the genus Vibrio, a large group of species containing several pathogenic members that affect fish and shellfish, and are difficult to identify through both phenotypic and genotypic approaches. The study included analysis of partial sequences of recA, gyrB, mreB, rpoD and pyrH genes, as well as the 16S rRNA gene. Seventeen type strain species were included that were complemented with other reference strains and a collection of isolates tentatively identified as members of this clade, as well as a set of other Vibrio species. The clade was well defined and stable in all analyses, and was confirmed to co…
Surface and virulence properties of environmental Vibrio cholerae non-O1 from Albufera Lake (Valencia, Spain).
A total of 140 environmental Vibrio cholerae non-O1 isolates, together with several culture collection strains from both environmental and clinical sources, were studied in relation to hemagglutination, surface hydrophobicity, and the enzymatic, hemolytic, cytotoxic, and enterotoxic activities of their extracellular products. A total of 78 and 62% of the strains produced hemagglutinins and exohemagglutinins, respectively. Four different hemagglutinating and two exohemagglutinating activities were found by using eight sugars in the inhibition assays. Cell-bound mannose-sensitive hemagglutination was detected mainly in chicken blood, whereas fucose-sensitive hemagglutination was recorded only…
Actibacterium mucosum gen. nov., sp. nov., a marine alphaproteobacterium from Mediterranean seawater
Strain R46T, a marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. It is an aerobic chemo-organotrophic, mesophilic and slightly halophilic organism, with complex ionic requirements. Phylogenetic analyses based on the 16S rRNA and gyrB gene sequences showed that strain R46T formed a separate branch within the family Rhodobacteraceae , bearing similarities below 94.7 and 80.3 %, respectively, to any other recognized species. It contained Q10 as the predominant isoprenoid quinone and C18 : 1ω7c/C18 : 1ω6c as the major cellular fatty acid. Phosphatidylglycerol was the only identified polar lipid, although other lipids were also detected. …
Vibrio palustris sp. nov. and Vibrio spartinae sp. nov., two novel members of the Gazogenes clade, isolated from salt-marsh plants (Arthrocnemum macrostachyum and Spartina maritima)
Two bacterial strains, EAod9T and SMJ21T, isolated from salt-marsh plants, were determined to be related to species of the genus Vibrio from from 16S rRNA sequence comparisons. Their closest phylogenetic relatives are members of the Gazogenes clade, Vibrio mangrovi and Vibrio rhizosphaerae , which show the greatest similarity to the SMJ21TrRNA sequence (97.3 and 97.1 %, respectively), while EAod9T had less than 97.0 % similarity to any other species of the genus Vibrio . Both strains share the basic characteristics of the genus Vibrio , as they are Gram-stain negative, motile, slightly halophilic, facultatively anaerobic bacteria. In addition, they are oxidase-negative and unable to grow on…
Whole genome sequences reveal Vibrio hemicentroti Kim et al. 2013 as a later heterotypic synonym of Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981.
The synonymy between Vibrio hemicentroti Kim et al. 2013 and Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981 was suggested after a recent multilocus sequence analysis of the Splendidus clade, which included the type strains of both species. To clarify their status, we have determined genomic indexes from whole genome sequences of strains V. hemicentroti CECT 8714T and V. splendidus NCCB 53037T. Average Nucleotide Identities of 96.0–96.7 % and an in silico DNA–DNA hybridization value of 70.2 %, as well as similarity levels of selected housekeeping gene sequences support the consideration of V. hemicentroti as a later heterotypic synonym of V. splendidus .
Grimontia celer sp. nov., from sea water
Strain 96-237T, a Gram-reaction-negative, curved- to spiral-shaped motile bacterium, isolated from coastal marine water, was found to be related to species of the genus Grimontia by 16S rRNA gene sequence comparison, sharing 98.3 % similarity to Grimontia marina CECT 8713Tand 98.8 % to 'Grimontiaindica' AK16. Phenotypic analysis revealed that strain 96-237T is slightly halophilic, mesophilic and facultatively anaerobic, fermenting d-glucose, d-ribose, d-mannose, d-mannitol, maltose and sucrose. It was positive for oxidase and indole production and negative for arginine dihydrolase and lysine and ornithine decarboxylases. Its major fatty acids were C16 : 1ω7c/C16 : 1ω6c (SF3), C18 : 1ω7c and…
Shimia thalassica sp. nov., and reclassification of Pseudopelagicola gijangensis as Shimia gijangensis comb. nov., and Thalassobius activus as Cognatishimia activa comb. nov.
Strain CECT 7735T, a marine Gram-reaction negative, aerobic, non-motile bacterium, was isolated from coastal seawater in Valencia, Spain. Strain CECT 7735T is chemoorganotrophic, mesophilic, slightly halophilic, grows at 15–28 °C but not at 4 or 37 °C, requires seawater for growth and grows up to 6 % salinity. The major cellular fatty acid is summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The G+C content of the genome is 55.7 mol%. Comparative analysis of the 16S rRNA gene sequence shows the strain is affiliated to the family Rhodobacteraceae , in the class Alphaproteobacteria , with highest similarities to Phaeobacter species (97.0–97.5 %), Shimia species (96.5–97.3 %) and Pseudopelagico…
Draft genome sequence of Shimia marina CECT 7688T
Shimia marina is a member of the family Rhodobacteraceae described in 2006. Strain CL-TA03(T) (=CECT 7688(T)) was isolated from a biofilm formed on an acrylic slide submerged in surface water in a coastal fish farm in Tongyeong, Korea. Here we report the draft genome sequence and annotation of S. marina CECT 7688(T) which is composed by 4,001,860bp arranged in 45 scaffolds with a G+C content of 57.4%, 3878 protein coding genes, 40 tRNA genes, 4 rRNA genes and 1 repeat region. An overview of annotated genes revealed diverse genes encoding for exopolysaccharide and capsular biosynthesis enzymes, secondary metabolite biosynthesis enzymes, multiple antibiotic and metal resistance and the abilit…
Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae
9 pages, 1 figure, 3 tables
Ribotyping of Vibrio Populations Associated with Cultured Oysters (Ostrea edulis)
The intraspecific variability of Vibrio splendidus, V. harveyi and V. tubiashii recovered from oysters (Ostrea edulis) collected at the Mediterranean coast near Valencia, Spain, was analyzed by ribotyping. The two former species represented the most abundant ones, and the third one was the only species described as pathogenic for oysters. A total of 115 environmental strains were studied, 84 of V. splendidus, 23 of V. harveyi and 8 of V. tubiashii. Chromosomal DNA was digested with KpnI and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Ribotyping among natural populations of the three species rendered 5 to 9 bands, and showed a h…
Numerical Taxonomy of Vibrionaceae Isolated from Oysters and Seawater Along an Annual Cycle
Summary A numerical taxonomic study on Gram negative heterotrophic facultative anaerobic bacteria isolated from marine samples (oysters and seawater of Western Mediterranean Sea) was performed. Three hundred sixty eight strains, including reference strains of most species of the Vibrionaceae , were characterized (96 tests per strain). Cluster analysis of similarity matrices obtained with S SM and S J coefficients was performed and S J -based tree and 0.75 S level selected for definition of phena. Larger phena corresponded to non-luminescent Vibrio splendidus biotype 1 and V. harveyi . The species V. tubiashii (an oyster larvae pathogen), V. pelagius, V. mediterranei, V. orientalis and Photo…
Occurrence and virulence of Pseudoalteromonas spp. in cultured gilthead sea bream (Sparus aurata L.) and European sea bass (Dicentrarchus labrax L.). Molecular and phenotypic characterisation of P. undina strain U58
During two long-term bacteriological surveys in European sea bass (Dicentrarchus labrax L.) and gilthead sea bream (Sparus aurata L.) culture facilities on the Spanish Mediterranean coast, four different species of Pseudoalteromonas were found in the internal organs of animals. Pseudoalteromonas undina, Pseudoalteromonas haloplanktis, P. espejiana and Pseudoalteromonas sp. were isolated from 9% out of 177 European sea bass and 11.7% out of 547 gilthead sea bream and they were recovered as pure cultures in 50% of isolations. Among fish with positive bacterial growth, Pseudoalteromonas was more prevalent in sea bass showing clinical signs (27.7%) and in gilthead sea bream without clinical sig…
Haliea mediterranea sp. nov., a marine gammaproteobacterium.
Strain 7SM29T, an aerobic marine gammaproteobacterium isolated from seawater from Castellón, Spain, was characterized by classical phenotyping, chemotaxonomy and 16S rRNA gene sequence analysis. Strain 7SM29T was found to be closely related to strains in the genus Haliea and to Congregibacter litoralis KT71T, with which a genus-level cluster was formed within the NOR5/OM60 clade of the Gammaproteobacteria. Strain 7SM29T was a short, motile rod with a tuft of three polar flagella. The strain grew on marine agar and formed pale-yellow colonies. Strain 7SM29T required NaCl for growth, reduced nitrate to nitrite, degraded several polymers and showed a preference for organic acids and amino acid…
Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium.
A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3–95.7 % sequence similarities, respectively), within the family Oceanospirillaceae . Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be o…
Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.
Four strains (M15∅_3, M17(T), M49 and R37(T)) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8-96.4%), Phaeobacter inhibens (95.9-96.3%) and Phaeobacter gallaeciensis (95.9-96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF…
Vibrio renipiscarius sp. nov., isolated from cultured gilthead sea bream (Sparus aurata)
Two strains of Gram-negative, facultatively anaerobic, slightly halophilic bacteria, isolated from healthy gilthead sea bream (Sparus aurata) cultured in Spanish Mediterranean fish farms, were different from their closest relatives,Vibrio scophthalmiandV. ichthyoenteri, by phenotypic, phylogenetic and genomic standards. The strains were negative for decarboxylase tests and lacked extracellular hydrolytic activities, but were able to fermentd-mannitol, sucrose, cellobiose andd-gluconate, among other carbohydrates. The major cellular fatty acids were C16:1and C16:0, in agreement with other species of the genusVibrio. Their 16S rRNA gene sequences were 98.4 and 97.2 % similar to those of the t…
Multilocus Sequence Analysis of the redefined clade Scophthalmi in the genus Vibrio.
A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the aim of better defining boundaries between these two closely related, fish-associated species. The type strain of V. ponticus, recently added to the clade Scophthalmi, was also included. The study was based on partial sequences of the protein-coding housekeeping genes rpoD, mreB, recA, ftsZ, and gyrB, and the 16S rRNA. While the 16S rRNA gene-based trees were unable to pull apart members of V. scophthalmi or V. ichthyoent…
Draft genome of Leisingera aquaemixtae CECT 8399T, a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea
We report the draft genome sequence and annotation of Leisingera aquaemixtae CECT 8399T (DDBJ/EMBL/GenBank accession number CYSR00000000) which comprises 4,614,060 bp, 4313 protein coding genes, 54 tRNA coding genes and 7 rRNA coding genes. General findings of the annotated genome, such as pigment indigoidine operon, phenylacetate oxidation genes or predictable number of replicons, are commented in comparison to other Leisingera species. Average Nucleotide Identity between available genomes of type strains of species of Leisingera and Phaeobacter genera has been calculated to evaluate its current classification. Keywords: Rhodobacteraceae, Phaeobacter, Ectoine, Indigoidine, Phenylacetate de…
Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax
Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-beta-hydroxybutyrate granules. The G + C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene seq…
Vibrio Species in Seawater and Mussels: Abundance and Numerical Taxonomy
Summary Qualitative and quantitative studies were performed on Vibrio species from seawater and mussel samples at a hatchery in Valencia harbour, and from market mussels. Vibrio alginolyticus and V. harveyi were the most abundant species in all samples. Other species identified were V. pelagius, V. mediterranei, V. tubiashii, V. damsella, V. splendidus, V. fluvialis, V. parahaemolyticus, V. anguillarum, V. cholerae and Aeromonas spp . The abundance of V. harveyi and V. mediterranei was positively correlated with temperature whereas V. pelagius counts showed negative correlation with this parameter. The pathogenic species were recovered in very low numbers. A numerical taxonomic study was pe…
Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively
Abstract Two new Vibrio species, Vibrio aestivus and Vibrio quintilis , are described after a polyphasic characterization of strains M22 T , M61 and M62 T , isolated from seawater collected off a beach on the East coast of Spain (Valencia). All three strains are Gram negative, mesophilic, slightly halophilic, fermentative rods. V. aestivus (M22 T = CECT 7558 T = CAIM 1861 T = KCTC 23860 T and M61 = CECT 7559 = CAIM 1862 = KCTC 23861) is oxidase positive, reduces nitrates to nitrites, is negative for Voges Proskauer, arginine dihydrolase and indole and non hydrolytic on most substrates tested. The 16S rRNA gene sequences of M22 T and M61 are most similar to Vibrio marisflavi (97.1–97.2%) …
Draft genome sequence of Thalassobius gelatinovorus CECT 4357 T , a roseobacter with the potential ability to degrade polycyclic aromatic hydrocarbons
Abstract Thalassobius gelatinovorus is a member of the family Rhodobacteraceae previously classified in the genera Agrobacterium and Ruegeria . Strain Ahrens B6 T (= ATCC 25655 T , = B6 T , = CECT 4357 T , = CIP 105976 T , = DSM 5887 T , = IAM 12617 T , = JCM 20688 T , = KCTC 22092 T , = LMG 129 T , = NBRC 15761 T , = NCIMB 2206 T ) was isolated in 1967 from a sea water sampled in Kiel Fjord in Baltic Sea. Genomic DNA sequence of T. gelatinovorus CECT 4357 T was assembled into a draft genome and annotated. Here we report the main features of this draft genome composed by 3,902,797 bp arranged in 30 contigs with a G + C content of 58.4%, 3770 protein coding genes, 44 tRNA genes, 7 rRNA genes…
Draft Genome Sequence of Actibacterium mucosum KCTC 23349, a Marine Alphaproteobacterium with Complex Ionic Requirements Isolated from Mediterranean Seawater at Malvarrosa Beach, Valencia, Spain
ABSTRACT Strain R46 (CECT 7668; KCTC 23349), a nomenclatural type of Actibacterium mucosum , was isolated from surface seawater collected at Malvarrosa Beach (Valencia, Spain) in July 2008. The draft genome sequence of strain R46 (approximately 3.72 Mbp) contains 22 scaffolds and 3,619 protein-encoding genes, with a G+C content of 60.8 mol%.
Vibrio agarivorans sp. nov., a novel agarolytic marine bacterium.
It is proposed that the new Vibrio species Vibrio agarivorans accommodates two agarolytic, halophilic, fermentative bacterial strains isolated from Mediterranean sea water. The cells were gram-negative, oxidase-positive, polarly flagellated bacilli that fermented glucose without gas production and that produced no decarboxylases. They used a wide range of compounds as sole carbon and energy sources. The DNA G+C content was 44.8 mol%. Phylogenetic analysis based on complete 16S and 23S rDNA sequences revealed that the strains belong to the gamma-Proteobacteria, and are specifically related to Vibrio species. Their nearest relatives were species of the Vibrio fischeri group, sharing 16S rDNA …
Draft genome sequence of Thalassobius mediterraneus CECT 5383T, a poly-beta-hydroxybutyrate producer
Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an abundant representative of marine bacteria. T. mediterraneus XSM19T (=CECT 5383T) was isolated from the Western Mediterranean coast near Valencia (Spain) in 1989. We present here the draft genome sequence and annotation of this strain (ENA/DDBJ/NCBI accession number CYSF00000000), which is comprised of 3,431,658 bp distributed in 19 contigs and encodes 10 rRNA genes, 51 tRNA genes and 3276 protein coding genes. Relevant findings are commented, including the complete set of genes required for poly-beta-hydroxybutyrate (PHB) synthesis and genes related to degradation of aromatic …
The Family Rhodobacteraceae
The family Rhodobacteraceae can be considered a paradigm of modern taxonomy of prokaryotes. Taking into account the number of species and genera that conforms the family, together with the knowledge about their abundance and vast global distribution, it surprises that most of them have been described relatively recent to our days. Two notable exceptions are Rhodonostoc capsulatum (Molisch, Die purpurbakterien nach neuen untersuchungen, vols i–vii. G. Fischer, Jena, pp 1–95, 1907) and Micrococcus denitrificans Beijerinck and Minkman (Zentbl Bakteriol, Parasitenkd, Infektionskr Hyg. Abt II 25:30–63, 1910), early basonyms of Rhodobacter capsulatus and Paracoccus denitrificans, respectively. Th…
Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems
A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them…