Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.     

Arcobacter ellisii sp. nov., isolated from mussels

As part of a study carried out for detecting Arcobacter spp. in shellfish, three mussel isolates that were Gram-negative slightly curved rods, non-spore forming, showed a new 16S rDNA-RFLP pattern with a specific identification method for the species of this genus. Sequences of the 16S rRNA gene and those of the housekeeping genes rpoB, gyrB and hsp60 provided evidence that these mussel strains belonged to an unknown genetic lineage within the genus Arcobacter. The similarity between the 16S rRNA gene sequence of the representative strain (F79-6^T) and type strains of the other Arcobacter species ranged between 94.1% with A. halophilus and 99.1% with the recently proposed species A. defluvii (CECT 7697^T). DDH results between strain F79-6^T and the type strain of the latter species were below 70% (53 ± 3.0%). Phenotypic characteristics together with MALDITOF mass spectra differentiated the new mussel strains from all other Arcobacter species. All the results indicate that these strains represent a new species, for which the name Arcobacter ellisii sp. nov. with the type strain F79-6^T (=CECT 7837^T = LMG 26155^T) is proposed.     

Lacinutrix jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment and emended description of the genus Lacinutrix

A Gram-negative, strictly aerobic, non-motile, rod-shaped and psychrophilic bacterial strain, PAMC 27137^T, was isolated from the marine sediment of the Ross Sea, Antarctica. Strain PAMC 27137^T was observed to grow at 4–10 °C, at pH 6.5–7.5 and in the presence of 2.5–4.0 % (w/v) sea salts. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain PAMC 27137^T belongs to the genus Lacinutrix showing the high similarities with Lacinutrix mariniflava JCM 13824^T (97.6 %) and Lacinutrix algicola JCM 13825^T (97.1 %). Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 27137^T is clearly distinguished from the most closely related Lacinutrix species. The major fatty acids (>5 %) were identified as iso-C_15:1 G (19.9 %), iso-C_15:0 (19.3 %), iso-C_17:0 3-OH (11.3 %), summed feature 9 (C_16:0 10-methyl and/or iso-C_17:1 ω9c as defined by MIDI, 9.1 %), iso-C_15:0 3-OH (7.5 %), and anteiso-C_15:1 A (5.8 %). The polar lipids were found to consist of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and five unidentified phospholipids. The major respiratory quinone was identified as MK-6. The genomic DNA G+C content was determined to be 32.1 mol%. Based on the data from this polyphasic taxonomic study, strain PAMC 27137^T is considered to represent a novel species of the genus Lacinutrix, for which the name Lacinutrix jangbogonensis sp. nov. is proposed. The type strain is PAMC 27137^T (=KCTC 32573^T=JCM 19883^T).     

Desulfonauticus autotrophicus sp. nov., a novel thermophilic sulfate-reducing bacterium isolated from oil-production water and emended description of the genus Desulfonauticus

A novel moderately thermophilic and halophilic sulfate-reducing bacterium, strain TeSt^T, was isolated from production water of an oil field in Northern Germany near Hamburg. The cells were Gram-negative, straight to slightly curved rods and motile by a single polar flagellum. Only hydrogen and formate served as electron donors, whereas a wide variety of organic substrates and CO₂ could be used as carbon sources. Sulfate, sulfite, thiosulfate and sulfur were used as electron acceptors, but not nitrate or ferric iron. The novel isolate was negative for oxidase, catalase and desulfoviridin enzyme activity. Cytochromes were present and predominantly of the c-type. Whole-cells fatty acid patterns were dominated by the branched-chain fatty acids anteiso-C_15:0, iso-C_15:0, iso-C_17:0 and anteiso-C_17:0. As major respiratory lipoquinones partially saturated derivates of menaquinone 6 [MK-6(H₂) and probably MK-6(H₄)] were identified. The G + C content of the genomic DNA was 41.3 mol% (HPLC method). An analysis of the 16S rRNA gene sequence indicated that strain TeSt^T belongs to the family Desulfohalobiaceae within the class Deltaproteobacteria. The most closely related species with a sequence similarity of 95.0% was Desulfonauticus submarinus suggesting an affiliation of TeSt^T to the genus Desulfonauticus. The novel isolate could be clearly distinguished from Desulfonauticus submarinus by its ability to grow chemolithoautotrophically and hence should be assigned to a novel species for which the name Desulfonauticus autotrophicus sp. nov. is proposed. The type strain is TeSt^T (=DSM 4206^T = JCM 13028^T). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea

Journal of Microbiology - A Gram-stain-negative strictly aerobic, short-rod-shaped, and non-motile bacterial strain designated HSLHS9T was isolated from surface seawater collected from the South...     

Rouxiella aceris sp. nov., isolated from tree sap and the emended description of the genus Rouxiella

Antonie van Leeuwenhoek - Polyphasic taxonomic studies were performed for the seven strains, which were isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea. Cells...     

Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora

A novel actinomycete, designated strain NEAU-GRX11^T, was isolated from muddy soil collected from a stream of Jinlong Mountain in Harbin, north China. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora. The 16S rRNA gene sequence of strain NEAU-GRX11^T showed highest similarity to Micromonospora zamorensis CR38^T (99.2 %), Micromonospora saelicesensis Lupac 09^T (99.0 %), Micromonospora chokoriensis 2-19/6^T (98.7 %), Micromonospora coxensis 2-30-b/28^T (98.5 %), Micromonospora aurantiaca ATCC 27029^T (98.4 %) and Micromonospora lupini lupac 14N^T (98.3 %). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that strain NEAU-GRX11^T was a member of the genus Micromonospora and supported the closest phylogenetic relationship to M. zamorensis CR38^T, M. saelicesensis Lupac 09^T, M. chokoriensis 2-19/6^T and M. lupini lupac 14N^T. A combination of DNA–DNA hybridization and some phenotypic characteristics indicated that the novel strain could be readily distinguished from these closest phylogenetic relatives. Therefore, it is proposed that NEAU-GRX11^T represents a novel species of the genus Micromonospora, for which the name Micromonospora jinlongensis sp. nov. is proposed. The type strain is NEAU-GRX11^T (=CGMCC 4.7103^T=DSM 45876^T).     

Arcobacter molluscorum sp. nov., a new species isolated from shellfish

Nineteen bacteria isolates recovered from shellfish samples (mussels and oysters) showed a new and specific 16S rDNA-RFLP pattern with an Arcobacter identification method designed to recognize all species described up to 2008. These results suggested that they could belong to a new species. ERIC-PCR revealed that the 19 isolates belonged to 3 different strains. The sequence of the 16S rRNA gene of a representative strain (F98-3^T) showed 97.6% similarity with the closest species Arcobacter marinus followed by Arcobacter halophilus (95.6%) and Arcobacter mytili (94.7%). The phylogenetic analysis with the16S rRNA, rpoB, gyrB and hsp60 genes placed the shellfish strains within the same cluster as the three species mentioned (also isolated from saline habitats) but they formed an independent phylogenetic line. The DDH results between strain F98-3^T and A. marinus (54.8% ± 1.05), confirmed that it represents a new species. Several biochemical tests differentiated the shellfish isolates from all other Arcobacter species. Although the new species was different from A. mytili, they shared not only the same habitat (mussels) but also the characteristic of being so far the only Arcobacter species that are simultaneously negative for urea and indoxyl acetate hydrolysis. All results supported the classification of the shellfish strains as a new species, for which the name Arcobacter molluscorum sp. nov. with the type strain F98-3^T is proposed (=CECT 7696^T = LMG 25693^T).     

Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment

Antonie van Leeuwenhoek - A Gram-stain-negative, aerobic, rod-shaped, non-gliding and non-motile bacterium designated as N1E253T, was isolated from marine sediments collected from the coast of...     

Nevskia aquatilis sp. nov. and Nevskia persephonica sp. nov., isolated from a mineral water aquifer and the emended description of the genus Nevskia

Four isolates, with an optimum temperature of about 30°C and an optimum pH for growth of 6.0-6.5, were recovered from a borehole head of a mineral water aquifer in Portugal and from the stored bottles produced on site. Strains F2-63(T) and F2-178 were yellow-pigmented and formed non-motile rod-shaped cells. Strains G6M-30(T) and G6-54 were whitish-pigmented, translucent and form rod-shaped cells with a polar flagellum. The four strains were strictly aerobic, oxidase and catalase positive. The major fatty acids of strains F2-63(T) and F2-178 were C(18:1)ω7c and C(16:0), and the major fatty acids of strains G6M-30(T) and G6-54 were C(18:1)ω7c and C(16:1)ω7c. Ubiquinone 8 was the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics two new species of the genus Nevskia are described; Nevskia aquatilis represented by strains F2-63(T) (=LMG 26345 =CECT 7897) and F2-178 (=LMG 26344 =CECT 7898) and Nevskia persephonica represented by strains G6M-30(T) (=DSM 24987 =CECT 7975) and G6-54 (=DSM 25048 =CECT 7976).     

Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium

A Gram-negative bacterium designated AC-49T was isolated from an alkaline groundwater with a pH 11.4. This organism formed rod-shaped cells, was strictly aerobic, catalase and oxidase positive, with an optimum growth temperature of 35 degrees C and an optimum pH value of 8.0. Strain AC-49T assimilated primarily amino acids and some Krebs cycle metabolites, did not use sugars for growth. The organism did not grow on L-phenylalanine or antipyrin. The G+ C content of DNA was 66.9 mol%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relatives of strain AC-49T were Phenylobacterium lituiforme and Phenylobacterium immobile, indicating that the organism is a member of the order Caulobacterales of the Alphaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-49T, represents a novel species of the genus Phenylobacterium for which we propose the name Phenylobacterium falsum sp. nov.     

Fibrivirga algicola gen. nov., sp. nov., an algicidal bacterium isolated from a freshwater river

An aerobic, gram-stain-negative, pink-colored, non-motile and rod-shaped algicidal bacterium, designated as JA-25^T was isolated from freshwater in Geumgang River, Republic of Korea. Strain JA-25^T grew at 15–30 °C and pH 6–9, and did not require NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25^T belongs to the family ‘Spirosomaceae’ and is most closely related to Fibrella aestuarina BUZ 2^T (93.6%). Strain JA-25^T showed?<?90% sequence similarity to other members of the family ‘Spirosomaceae’. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and average amino acid identity(AAI) values based on the genomic sequences of JA-25^T and F. aestuarina BUZ 2^T were 74.4, 20.5, and 73.6%, respectively. Strain JA-25^T showed an algicidal effect on the marine flagellate alga Heterocapsa triquetra, but no effect on fresh water cyanobacterium (Nostoc). In genome analysis, RIPP-like peptides were detected and predicted to resemble the indolmycin biosynthetic gene cluster, which possibly influence its algicidal effect. Furthermore, a bacteriorhodopsin gene with photoheterotrophic characteristics was detected. The genomic DNA G?+?C content was 52.5 mol%. The major cellular fatty acids were summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (>?10%). The major respiratory quinone was menaquinone 7 and major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids, and five unidentified lipids. Considering the phylogenetic inference, phenotypic, and chemotaxonomic data, strain JA-25^T should be classified as a novel species in the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25^T (=?KCCM 43334^T?=?NBRC 114259^T).

     

Sinanaerobacter chloroacetimidivorans gen. nov., sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge

An obligate anaerobic bacterial strain (BAD-6^T) capable of degrading acetochlor and butachlor was isolated from an anaerobic acetochlor-degrading reactor. Cells were Gram-stain positive, straight to gently curved rods with flagella. The major fermentation products in peptone-yeast broth were acetate and butyrate. The optimum temperature and pH for growth was 30 °C and 7.2–7.5, respectively. The major cellular fatty acids (>?10%) were C_14:0 FAME, C_16:0 FAME and cyc-9,10-C_19:0 DMA. Genome sequencing revealed a genome size of 4.80 Mb, a G?+?C content of 43.6 mol% and 4741 protein-coding genes. The most closely related described species on the basis of 16S rRNA gene sequences was Anaerovorax odorimutans NorPut^T in the order Clostridiales of the class Clostridia with sequence similarity of 94.9%. The nucleotide identity (ANI) value and digital DNA–DNA hybridization (dDDH) between the genomes of strain BAD-6^T and Ana. odorimutans NorPut^T were 70.9% and 15.9%, respectively. Based on the distinct differences in phylogenetic and phenotypic characteristics between strain BAD-6^T and related species, Sinanaerobacter chloroacetimidivorans gen. nov., sp. nov. is proposed to accommodate the strain. Strain BAD-6^T is the type strain (=?CCTCC AB 2021092^T?=?KCTC 25290^T).

     

Luteimonas dalianensis sp. nov., an obligate marine bacterium isolated from seawater

A marine bacterial strain, designated OB44-3^T, was isolated from a crude oil-contaminated seawater sample collected near Dalian Bay, China. Cells of strain OB44-3^T were Gramnegative, aerobic, rod-shaped, and oxidase- and catalasepositive. The major fatty acids were branched-chain saturated iso-C_15:0 (27.9%) and unsaturated iso-C_17:1 ω9c (14.8%). The DNA G+C content was 64.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain OB44-3^T was a member of the genus Luteimonas (95–96% 16S rRNA gene sequence similarity); its closest neighbors were the type strains of Luteimonas terricola (96% sequence similarity), Luteimonas mephitis (96%), and Luteimonas lutimaris (96%). On the basis of phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain OB44-3^T was considered to represent a novel species of the genus Luteimonas. The name Luteimonas dalianensis sp. nov. is proposed, with strain OB44-3^T (=CGMCC 1.12191^T =JCM 18136^T) as the type strain.