Accumulation of osmoprotectants and lipid pattern modulation in response to growth conditions by Halomonas pantelleriense

Ligilactobacillus cholophilus sp. nov., isolated from pickled potherb mustard (Brassica juncea Coss.)

Strain BD7642T was isolated from Chinese pickled potherb mustard (Brassica juncea Coss.) purchased from a local market in Shanghai, PR China. A polyphasic approach, including 16S rRNA gene sequence, housekeeping gene, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), G+C content and phenotypic analyses, was employed to characterize strain BD7642T. Cells of the bacterium were short round rods, Gram-stain-positive, non-spore-forming and catalase-negative. The strain grew at 30-45 °C and pH 4.0-8.0. Optimum growth occurred at 35-40 °C and pH 6.0-7.0. The strain exhibited growth with salt (NaCl) concentrations of up to 5 % (w/v). The G+C content of the strain's genomic DNA was 31.37 mol%. The major fatty acids were C16 : 0, C18 : 1 c9 and summed feature 10 (C18 : 1 c11/t9/t6). 16S rRNA gene sequencing revealed that strain BD7642T represents a member of the genus Ligilactobacillus and it had high sequence similarity to Ligilactobacillus aviarius NBRC 102162T (96.73 %), Ligilactobacillus araffinosus LGM 23560 (96.66 %) and Ligilactobacillus salivarius JCM 1231T (95.82 %). The dDDH values between strain BD7642T and its phylogenetically related species within the genus Ligilactobacillus ranged from 12.6 to 25.4 %. The ANI values between strain BD7642T and its closely related taxa were far lower than the threshold (95 %-96 %) used for species differentiation. Results of phylogenetic, physiological and phenotypic characterization confirmed that strain BD7642T represents a novel species within the genus Ligilactobacillus, for which the name Ligilactobacillus cholophilus sp. nov. is proposed. The type strain is BD7642T (=CCTCC AB 2022398T=JCM 36074T).

Kingella pumchi sp. nov., an organism isolated from human vertebral puncture tissue

A Gram-negative, non-motile rod and strictly aerobic bacterium, designated as 18B16333^T, was isolated from vertebral puncture tissue of a patient at Peking union medical college hospital in China. Growth occurred in NaCl concentrations of 0-1% (w/v) (optimum growth at 0% NaCl), at temperatures of 25-40 °C (optimum growth at 37 °C) and at pH 6.0-9.0 (optimum growth at pH 8.0). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids, and the major fatty acids were C_16:0, C_18:1 ω7c/C_18:1 ω6c and C_16:1 ω7c/C_16:1 ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain 18B16333^T was most closely related to Kingella potus CCUG 49773 ^T (97.3%, 16S rRNA gene sequence identity) and Neisseria bacilliformis CCUG 50858 ^T (96.8%). The ANI values between strain 18B16333^T and the type strains K. potus CCUG 49773 ^T, N. bacilliformis CCUG 50858 ^T, Kingella kingae CCUG 352 ^T and Neisseria gonorrhoeae CCUG 26876 ^T were 77.3%, 79.1%, 72.1% and 75.4%, respectively. The dDDH values between strain 18B16333^T and the four reference strains mentioned above were 24.8%, 26.9%, 24.2% and 20.7%. Further core gene analysis distinctively clustered strain 18B16333^T with four Kingella species but not with Neisseria species. Based on the phenotypic, chemotaxonomic, and phylogenetic properties, strain 18B16333^T represents a novel species of the genus Kingella, for which the name Kingella pumchi sp. nov. is proposed. The type strain is Kingella pumchi 18B16333^T (= CICC 24913 ^T = CCUG 75125 ^T).

Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China

A facultatively anaerobic, Gram-negative, rod-shaped bacterial strain designated as LLDRA6T, was isolated from heavy metal contaminated soils collected near a ceased smelting factory at Zhuzhou, Hunan Province, China. Strain LLDRA6T has the ability to oxidize Mn(II) and generate biogenic manganese oxides. The strain can grow in a wide range of temperature from 10–42°C and pH from 5 to 10. Comparative analysis of its complete 16S rRNA gene sequence suggests that strain LLDRA6T is highly similar to species within the genus Providencia . The complete genome of LLDRA6T is 4 342 370 bp with 40.18 mol% of G+C content and contains no plasmids. In comparison to the genomes of type strains in Providencia , LLDRA6T shows average nucleotide identity values between 76.60 and 80.89 %, and digital DNA–DNA hybridization values in a range of 21.2–24.6 %. Both multilocus sequence analysis and genomic phylogenetics indicate a new taxonomic status for LLDRA6T in Providencia . Chemotaxonomic analyses for LLDRA6T show that the predominant cellular fatty acids are C16 : 0, C14 : 0 and cyclo-C17 : 0, accounting for 32.7, 16.1 and 10.3 % of total fatty acids, respectively. The polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids, one unidentified phospholipid and three unidentified lipids. Within the cell wall, ribose and meso-diaminopimelic acid are the characteristic constituents for saccharides and amino acids, respectively. Respiratory quinones on cell membranes are composed of menaquinone (MK) and ubiquinone (coenzyme Q), including MK-8 (100.0 %), Q-7 (13.7 %) and Q-8 (86.3 %). Moreover, the positive results from d-lyxose and d-mannitol fermentation tests indicate that LLDRA6T is totally different from all the type strains within the genus Providencia . In summary, strain LLDRA6T represents a novel species in the genus Providencia , for which the name Providencia manganoxydans sp. nov. (type strain LLDRA6T=CCTCC AB 2021154T=KCTC 92091T) is proposed.

Paenibacillus tianjinensis sp. nov., isolated from corridor air

A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019^T, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15-40 °C (optimum growth at 37 °C), pH 6.0-8.0 (pH 7.0) and in the presence of 0-2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019^T was most closely related to Paenibacillus typhae CGMCC 1.11012^T (98.63%), Paenibacillus albidus Q4-3^T (98.19%), Paenibacillus borealis DSM 13188^T (97.55%), Paenibacillus helianthi P26E^T (97.33%) and Paenibacillus odorifer DSM 15391^T (97.19%). The digital DNA-DNA hybridization and the average nucleotide identity values between TB2019^T and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was meso-diaminopimelic acid. The polar lipids of TB2019^T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C_15:0 (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus tianjinensis sp. nov. is proposed. The type strain is TB2019^T (=CICC 25065^T=JCM 34610^T).

Physiological response of the moderately halophilic psychrotolerant strain Chromohalobacter sp. N1 to salinity change and low temperature

The available information on de novo synthesized compatible solutes in response to high medium salinity by bacteria of the Chromohalobacter genus is limited to studies of the mesophilic moderately halophilic strain Chromohalobacter salexigens DSM 3043^T. Therefore, there is a need for studies of representatives of other species of the Chromohalobacter genus of the Halomonadaceae family. A moderately halophilic psychrotolerant bacterium, strain N1, closely related to the species Chromohalobacter japonicus was isolated from the salt crust of a rock salt waste pile in Berezniki, Perm Krai, Russia. An intracellular pool of compatible solutes of strain N1 was investigated by NMR spectroscopy. Cells grown in the presence of 5% NaCl at optimal growth temperature (28 °C) accumulated ectoine, glutamate, N(4)-acetyl-l-2,4-diaminobutyrate (NADA), alanine, trehalose, hydroxyectoine, and valine. Such a combination of compatible solutes is unique and distinguishes the strain from C. salexigens DSM 3043^T. Hyperosmotic stress induced by 15% NaCl caused the accumulation of ectoine, NADA, and hydroxyectoine but led to a decrease in the amount of alanine, valine, and trehalose. The intracellular pool of glutamate was not significantly changed. A reduction of the growth temperature from 28 to 5 °C led to an increase in the amount of ectoine, NADA, trehalose, and hydroxyectoine. Ectoine was the major compatible solute.

Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu

A Gram-stain-positive, strictly aerobic and rod-shaped bacterium, designated as 3 H-10^T, was isolated from a yellow water sample collected from the manufacturing process of strong flavor Chinese baijiu in Yibin region of Sichuan province (PR China). Oval endospores were formed at the subtermini of cells with swollen sporangia. The isolate was able to grow at temperatures of 20-45 °C (optimum growth at 37 °C), at pH 6.0-10.0 (optimum growth at pH 8.0) and in the presence of 0-2 % (w/v) NaCl (optimum growth with 0 % NaCl). Ribose was the major cell-wall sugar, and meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of 3 H-10^T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). MK-7 was predominant menaquinone and iso-C_15 : 0 (60.7 %) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that 3 H-10^T was most closely related to Bacillus mesophilus SA4^T (96.30 %), Bacillus ginsengihumi Gsoil 114^T (96.27 %) and Bacillus shackletonii LMG 18435^T (96.27 %). The average nucleotide identity (ANI) values between strain 3 H-10^T and the three type strains mentioned above were 69.56, 70.19 and 70.67 %, respectively. The genomic DNA G+C content was 35.4 mol%. On the basis of its phenotypic, chemotaxonomic and phylogenetic properties, strain 3 H-10^T represents a novel species of the genus Bacillus, for which the name Bacillus aquiflavi sp. nov. is proposed. The type strain is Bacillus aquiflavi 3 H-10^T (=CICC 24755^T=JCM 33703^T).

Tabrizicola alkalilacus sp. nov., isolated from alkaline Lake Dajiaco on the Tibetan Plateau

A novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Lake Dajiaco on the Tibetan Plateau. Strain DJC^T grew without NaCl and tolerated up to 3 % (w/v) NaCl. Growth occurred at pH 6.0-10.0 (optimum, pH 7.0-8.0) and 15-37 °C (optimum, 25-30 °C). Vitamins were not required for growth. The main polar lipids of strain DJC^T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-10. The major fatty acid was C_18 : 1ω7c. Genome sequencing revealed a genome size of 4.61 Mbp and a G+C content of 62.9 mol%. Analysis of 16S rRNA sequences showed that strain DJC^T belonged to the genus Tabrizicola, with the closest neighbour Tabrizicola aquatica RCRI19^T (97.5 %). DNA-DNA relatedness between strain DJC^T and the closest phylogenetically related strain T. aquatica RCRI19^T was 40.8 %. Stain DJC^T was clearly distinguished from the type strain mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristic comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain DJC^T could be classified as a representative of a novel species of the genus for which the name Tabrizicola alkalilacus sp. nov. is proposed. The type strain is DJC^T (=CICC 24242^T=KCTC 62173^T).

Flavobacterium tibetense sp. nov., isolated from a wetland

A novel, Gram-stain-negative, non-motile and rod-shaped bacterium, designated YH5^T, was isolated from the YonghuCo wetland on the Tibetan Plateau. The strain was able to grow optimally with 1 % (w/v) NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6-9 (optimum pH 7) and 10-37 °C (optimum 30 °C). Vitamins were not required for growth. The major polar lipid of strain YH5^T was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone 6 (MK-6). The major fatty acids were iso-C15 : 0, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Genome sequencing revealed a genome size of 2.74 Mbp and a G+C content of 33.3 mol%. Analysis of 16S rRNA gene sequences showed that strain YH5^T belonged to the genus Flavobacterium, with the closest neighbours Flavobacterium luticocti xz20^T (96.7 % similarity), Flavobacterium jejuense EC11^T (96.4 %), Flavobacterium jumunjinense HME7102^T (95.9 %) and Flavobacterium dongtanense LW30^T (95.6 %). DNA-DNA relatedness between strain YH5^T and the closest phylogenetically related strain F. luticocti xz20^T was 27.0 %. Strain YH5^T was clearly distinguished from the reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. Based on its phenotypic and chemotaxonomic characteristics, strain YH5^T is classified as a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium tibetense sp. nov. is proposed. The type strain is YH5^T (=CICC 24247^T=KCTC 62174^T).

Halomonas alkalicola sp. nov., isolated from a household product plant

A Gram-stain-negative, alkaliphilic and moderately halophilic bacterium, designated 56-L4-10aEnT, was isolated from a household product plant in China. Cells of the novel isolate were rod-shaped, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 56-L4-10aEnT belongs to the genus Halomonas, with the six closest neighbours being Halomonas mongoliensis Z-7009T (97.59 % 16S rRNA gene sequence similarity), Halomonas ventosae Al12T (97.35 %), Halomonas campaniensis 5AGT (97.22 %), Halomonas alimentaria YKJ-16T (97.22 %), Halomonas shengliensis SL014B-85T (97.12 %) and Halomonas fontilapidosi 5CRT (97.09 %). The main polar lipids of strain 56-L4-10aEnT contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-9, with Q-8 as a minor component. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0. Strain 56-L4-10aEnT was clearly distinguished from the type strains mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. It is evident from the genotypic and phenotypic data that strain 56-L4-10aEnTcould be classified as a representative of a novel species of the genus Halomonas, for which the name Halomonas alkalicola sp. nov. is proposed. The type strain is 56-L4-10aEnT (=CICC 11012sT=DSM 103354T).

Scopulibacillus daqui sp. nov., a thermophilic bacterium isolated from high temperature daqu

A Gram-stain-positive, facultatively anaerobic, thermophilic bacterium, designated ZQ18-1T, was isolated from a high temperature daqu sample collected from the sesame-flavour liquor-making process. Oval endospores were formed at the centre of cells with swollen sporangia. The isolate was able to grow at temperatures of 20-60 °C (optimum growth at 50 °C), at pH 4-9 (optimum growth at pH 8) and in the presence of 0-10 % (w/v) NaCl (optimum growth with 2 % NaCl). Glucose and galactose were major cell-wall sugars, and meso-diaminopimelic acid was the diagnostic amino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and three glycolipids. The major cellular fatty acids were anteiso-C17 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ18-1T was most closely related to Scopulibacillus darangshiensis DLS-06T, Pullulanibacillus pueri YN3T, Tuberibacillus calidus 607T, Pullulanibacillus naganoensis ATCC 53909T, Pullulanibacillus uraniitolerans UG-2T, Sporolactobacillus terrae DSM 11697T and Sporolactobacillus inulinus NRIC 1133T. Strain ZQ18-1T showed low DNA-DNA relatedness (40.7, 23.1, 46.5, 27.2, 45.6, 33.7 and 55.1 %) with the strains mentioned above. Based on morphological characteristics, chemotaxonomic characteristics, DNA-DNA hybridization data and physiological properties, strain ZQ18-1T represents a novel species of the genus Scopulibacillus, for which the name Scopulibacillus daqui sp. nov. is proposed. The type strain is Scopulibacillus daqui ZQ18-1T (=DSM 28236T=CICC 10824T). An emended description of the genus Scopulibacillus is provided.

Structural characterization of the lipid A from the LPS of the haloalkaliphilic bacterium Halomonas pantelleriensis

Halomonas pantelleriensis DSM9661(Τ) is a Gram-negative haloalkaliphilic bacterium isolated from the sand of the volcanic Venus mirror lake, closed to seashore in the Pantelleria Island in the south of Italy. It is able to optimally grow in media containing 3-15 % (w/v) total salt and at pH between 9 and 10. To survive in these harsh conditions, the bacterium has developed several strategies that probably concern the bacteria outer membrane, a barrier regulating the exchange with the environment. In such a context, the lipopolysaccharides (LPSs), which are among the major constituent of the Gram-negative outer membrane, are thought to contribute to the restrictive membrane permeability properties. The structure of the lipid A family derived from the LPS of Halomonas pantelleriensis DSM 9661(T) is reported herein. The lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different numbers of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of ESI FT-ICR mass spectrometry and chemical analysis. Preliminary immunological assays were performed, and a comparison with the lipid A structure of the phylogenetic proximal Halomonas magadiensis is also reported.

Physiological features of Halomonas lionensis sp. nov., a novel bacterium isolated from a Mediterranean Sea sediment

A novel halophilic bacterium, strain RHS90(T), was isolated from marine sediments from the Gulf of Lions, in the Mediterranean Sea. Its metabolic and physiological characteristics were examined under various cultural conditions, including exposure to stressful ones (oligotrophy, high pressure and high concentrations of metals). Based on phylogenetic analysis of the 16S rRNA gene, the strain was found to belong to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are Halomonas axialensis and Halomonas meridiana (98% similarity). DNA-DNA hybridizations indicated that the novel isolate is genotypically distinct from these species. The DNA G + C content of the strain is 54.4 mol%. The main fatty acids (C18:1ω7c, 2-OH iso-C15:0, C16:0 and/or C19:0 cyclo ω8c), main polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified phosphoglycolipid) and major respiratory quinone (ubiquinone Q9) were determined. The novel isolate is heterotrophic, mesophilic, euryhaline (growth optimum ranging from 2 to 8% w/v NaCl) and is able to grow under stressful conditions. The strain accumulates poly-β-hydroxyalkanoates granules and compatible solutes. Based on genotypic, chemotaxonomic and phenotypic distinctiveness, this isolate is likely to represent a novel species, for which the name Halomonas lionensis is proposed. The type strain of H. lionensis is RHS90(T) (DSM 25632(T) = CIP 110370(T) = UBOCC 3186(T)).

Microbiology and epidemiology of Halomonas species

Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.

Pseudomonas chengduensis sp. nov., isolated from landfill leachate

Strain MBRT was isolated from landfill leachate in a solid-waste disposal site in Chengdu, Sichuan, China. An analysis of 16S rRNA gene sequences revealed that the isolate was closely related to members of the genus Pseudomonas , sharing the highest sequence similarities with Pseudomonas toyotomiensis HT-3T (99.8 %), Pseudomonas alcaliphila AL15-21T (99.7 %) and Pseudomonas oleovorans ATCC 8062T (99.4 %). Multi-locus sequence analysis based on three housekeeping genes (gyrB, rpoB and rpoD) provided higher resolution at the species level than that based on 16S rRNA gene sequences, which was further confirmed by less than 70 % DNA–DNA relatedness between the new isolate and P. toyotomiensis HT-3T (61.3 %), P. alcaliphila AL15-21T (51.5 %) and P. oleovorans ATCC 8062T (57.8 %). The DNA G+C content of strain MBRT was 61.9 mol% and the major ubiquinone was Q-9. The major cellular fatty acids (>10 %) were C18 : 1ω7c and/or C18 : 1ω6c, C16 : 0, and C16 : 1ω7c and/or C16 : 1ω6c. Polyphasic analysis indicates that strain MBRT represents a novel species of the genus Pseudomonas , for which the name Pseudomonas chengduensis sp. nov. is proposed. The type strain is MBRT ( = CGMCC 2318T = DSM 26382T).

Fulvitalea axinellae gen. nov., sp. nov., a member of the family Flammeovirgaceae isolated from the Mediterranean sponge Axinella verrucosa

The yellow-pigmented, non-motile, Gram-negative, strictly aerobic, rod-shaped bacterial strain VI.18T was isolated from the Mediterranean sponge Axinella verrucosa collected off the coast near Sdot Yam, Israel. Results from 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flammeovirgaceae . The highest nucleotide similarity (91.4 %) occurred with Aureibacter tunicatorum A5Q-118T. The predominant cellular fatty acids of strain VI.18T were iso-C15 : 0 (56.0 %), iso-C17 : 1ω9c (22.8 %) and C16 : 0 (7.4 %) and its major respiratory quinone was MK-7. The DNA G+C content was 47.5 mol%. The strain could readily be distinguished from its phylogenetically closest relatives by phenotypic, physiological and chemotaxonomic properties. On the basis of the data from the present polyphasic study, we propose a novel genus and species within the family Flammeovirgaceae , with the name Fulvitalea axinellae gen. nov., sp. nov. Strain VI.18T ( = ATCC BAA-2395T  = LMG 26722T) is the type strain of Fulvitalea axinellae.

Luteivirga sdotyamensis gen. nov., sp. nov., a novel bacterium of the phylum Bacteroidetes isolated from the Mediterranean sponge Axinella polypoides

A novel aerobic bacterium, designated strain PIII.02T, was isolated from a Mediterranean sponge (Axinella polypoides) collected off the Israeli coast near Sdot Yam. The non-motile cells were Gram-staining-negative, oxidase-positive and catalase-positive. The orange pigment of colonies growing on marine agar was neither diffusible nor flexirubin-like. Strain PIII.02T grew at 15–35 °C, at pH 6.0–9.0, with 2.0–7.0 % (w/v) NaCl, and with 1.0-8.0 % (w/v) sea salts. The predominant fatty acids were iso-C15 : 0, iso-C16 : 1 H, iso-C16 : 0, C16 : 0, anteiso-C15 : 0 and C16 : 1ω7c. The major respiratory quinone was MK-7. The genomic DNA G+C content of the novel strain was 38.1 mol%. Results from 16S rRNA gene sequence analysis indicated that strain PIII.02T was distantly related to established members of the phylum Bacteroidetes . The established species found to be most closely related to the novel strain was Persicobacter diffluens NCIMB 1402T (87.6 % 16S rRNA gene sequence similarity). Based on the phenotypic and chemotaxonomic data and the results of the phylogenetic analyses, strain PIII.02T represents a novel species of a new genus, for which the name Luteivirga sdotyamensis gen. nov., sp. nov. is proposed. The type strain is PIII.02T ( = ATCC BAA-2393T  = LMG 26723T).

Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

Biodegradation of benzene homologues in contaminated sediment of the East China Sea

This study focused on acclimating a microbial enrichment to biodegrade benzene, toluene, ethylbenzene and xylenes (BTEX) in a wide range of salinity. The enrichment degraded 120 mg/L toluene within 5d in the presence of 2M NaCl or 150 mg/L toluene within 7d in the presence of 1-1.5M NaCl. PCR-DGGE (polymerase chain reaction-denatured gradient gel electrophoresis) profiles demonstrated the dominant species in the enrichments distributed between five main phyla: Gammaproteobacteria, Sphingobacteriia, Prolixibacter, Flavobacteriia and Firmicutes. The Marinobacter, Prolixibacter, Balneola, Zunongwangia, Halobacillus were the dominant genus. PCR detection of genotypes involved in bacterial BETX degradation revealed that the degradation pathways contained all the known initial oxidative attack of BTEX by monooxygenase and dioxygenase. And the subsequent ring fission was catalysed by catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. Nuclear magnetic resonance (NMR) spectroscopy profiles showed that the bacterial consortium adjusted the osmotic pressure by ectoine and hydroxyectoine as compatible solutes to acclimate the different salinity conditions.

Pseudomonas litoralis sp. nov., isolated from Mediterranean seawater

Strains 2SM5T and 2SM6, two strictly aerobic chemo-organotrophic gammaproteobacteria, were isolated from Mediterranean seawater off the coast of Vinaroz, Castellón, Spain, in February, 1990. They were extensively characterized by a polyphasic study that placed them in the genus Pseudomonas. Phylogenetic analysis of 16S rRNA gene sequences showed that both strains shared 100 % sequence similarity and were closely related to members of the Pseudomonas pertucinogena clade, with less than 97.3 % similarity to strains of established species; Pseudomonas xiamenensis was the closest relative. Analysis of sequences of three housekeeping genes, rpoB, rpoD and gyrB, further confirmed the phylogenetic assignment of the Mediterranean isolates. Chemotaxonomic traits such as quinone and polar lipid composition also corroborated the placement of strains 2SM5T and 2SM6 in the gammaproteobacteria. Other phenotypic traits, including fatty acid composition, enabled clear differentiation of both isolates from other species of Pseudomonas. We therefore conclude that strains 2SM5T and 2SM6 represent a novel species of Pseudomonas, for which the name Pseudomonas litoralis is proposed; the type strain is 2SM5T ( = CECT 7670T = KCTC 23093T).

Bacillus daliensis sp. nov., an alkaliphilic, Gram-positive bacterium isolated from a soda lake

A Gram-positive, alkaliphilic bacterium, designated strain DLS13T, was isolated from Dali Lake in Inner Mongolia Autonomous Region, China. The isolate was able to grow at pH 7.5-11.0 (optimum at pH 9), in 0-8 % (w/v) NaCl (optimum at 2 %, w/v) and at 10-45 °C (optimum at 30 °C). Cells of the isolate were facultatively anaerobic, spore-forming rods with peritrichous flagella. The predominant isoprenoid quinone was MK-7 and its cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C15:0. The genomic DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DLS13T was a member of the genus Bacillus and most closely related to Bacillus saliphilus DSM 15402T (96.9 % similarity). The DNA-DNA relatedness value between strain DLS13T and B. saliphilus DSM 15402T was 38.7±1.9 %. Comparative analysis of genotypic and phenotypic features indicated that strain DLS13T represents a novel species of the genus Bacillus, for which the name Bacillus daliensis sp. nov. is proposed; the type strain is DLS13T (=CGMCC 1.10369T=JCM 17097T=NBRC 107572T).

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 contained MK6 as the sole respiratory quinone. Phosphatidylethanolamine (PE) was the only identifiable polar lipid, although other lipids were also detected. The predominant cellular fatty acids were saturated C15 and monounsaturated C15. The DNA G+C content was around 40 mol%. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the new strain represents a novel genus and species, for which the name Euzebyella saccharophila gen. nov., sp. nov., is proposed. The type strain of the type species is 7SM30T (=CECT 7477T=KCTC 22655T).

Halomonas sinaiensis sp. nov., a novel halophilic bacterium isolated from a salt lake inside Ras Muhammad Park, Egypt

An alkalitolerant and halotolerant bacterium, designated strain Sharm was isolated from a salt lake inside Ras Muhammad. The morphological, physiological and genetic characteristics were compared with those of related species of the genus Halomonas. The isolate grew optimally at pH 7.0, 5-15% NaCl at 35 degrees C. The cells were Gram-negative rods, facultative anaerobes. They accumulated glycine-betaine, as a major osmolyte, and ectoine and glutamate as minor components. The strain Sharm(T) biosynthetised alpha-glucosidase. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and a novel phosphoglycolipid as major components. Ubiquinone with nine repetitive unities (Q9) was the only quinone found and, nC16:0 and C19:0 with cyclopropane were the main cellular fatty acids, accounting for 87.3% of total fatty acids. The G + C content of the genomic DNA was 64.7 mol %. The 16S rRNA sequence analysis indicated that strain Sharm was a member of the genus Halomonas. The closest relatives of the strain Sharm were Halomonas elongata and Halomonas eurihalina. However, DNA-DNA hybridisation results clearly indicated that strain Sham was a distinct species of Halomonas. On the basis of the evidence, we propose to assign strain Sharm as a new species of the genus Halomonas, H. sinaiensis sp. nov, with strain Sharm(T) as the type strain (DSM 18067(T); ATCC BAA-1308(T)).

Oceanobacillus oncorhynchi subsp. incaldanensis subsp. nov., an alkalitolerant halophile isolated from an algal mat collected from a sulfurous spring in Campania (Italy), and emended description of Oceanobacillus oncorhynchi

A halophilic, alkalitolerant bacterium, strain 20AGT, was isolated from an algal mat collected from a sulfurous spring located in Santa Maria Incaldana (Mondragone, Campania Region, southern Italy). The isolate is Gram-positive, ferments several carbohydrates and has motile, rod-shaped cells that do not sporulate. The isolate grows at pH 6.5-9.5 and in 5-20 % NaCl. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Oceanobacillus; strain 20AGT showed 96.6 % 16S rRNA gene sequence similarity to the type strain of Oceanobacillus iheyensis, DSM 14371T, and 99.5 % similarity to Oceanobacillus oncorhynchi NCIMB 14022T. Levels of DNA-DNA relatedness between strain 20AGT and O. iheyensis DSM 14371T and O. oncorhynchi NCIMB 14022T were respectively 29.4 and 59.0 %. The G+C content of the DNA of strain 20AGT was 40.1 mol%. The predominant respiratory quinone was MK-7, phosphatidylglycerol and phosphatidylcholine were the predominant polar lipids and minor phospholipids were also detected. ai-C14 : 0, ai-C15 : 0 and i-C15 : 0 were the major fatty acids. Strain 20AGT accumulated osmolytes and produced exopolysaccharide. On the basis of phenotypic characteristics, phylogenetic data and DNA-DNA relatedness data, isolate 20AGT should be designated as the type strain of a subspecies of Oceanobacillus oncorhynchi, for which the name Oceanobacillus oncorhynchi subsp incaldanensis subsp. nov. is proposed. The type strain is 20AGT (=DSM 16557T = ATCC BAA-954T).

Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy)

A halotolerant and alkaliphilic Gram-negative bacterium, strain 18bAG(T), that grows aerobically at the optimum temperature of 37 degrees C, and at pH 7.5-10 (optimum 9.0), was isolated from a salt pool located in Montefredane in Campania Region (South of Italy). The isolate tolerated high concentration of NaCl up to 20%. Strain 18bAG(T) accumulated osmolytes and polyhydroxybutyrate, produced exopolysaccharide and possessed alpha-glucosidase activity. The predominant respiratory quinones were ubiquinones, Q8 and Q6(6H); phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. Major fatty acids were C16 : 1, C16 : 0, and C18 : 0. On the basis of 16S rRNA gene sequence similarity, 18bAG(T) was shown to belong to Halomonas genus. Analysis of 16S rRNA gene revealed a high similarity of strain 18bAG(T) to Halomonas venusta (DSM 4743(T)) and Halomonas hydrothermalis (DSM 15725(T)). Level of DNA-DNA relatedness between strain 18bAG(T) and the most related species Halomonas venusta and Halomonas hydrothermalis was 56.0% and 41.2%, respectively. The G+C content (mol%) of DNA was 53.0. The RiboPrinting patterns of Halomonas venusta and 18AG(T) showed a pattern similarity of 0.50. On the basis of genomic information and phenotypic characteristics strain 18bAG(T) represents a new species, for which the name Halomonas alkaliphila sp. nov. is proposed. The type strain is 18bAG(T) (=DSM 16354T =ATCC BAA-953T).

Alkalibacillus filiformis sp. nov., isolated from a mineral pool in Campania, Italy

A halo-alkaliphilic, Gram-positive, non-motile bacterium, designated strain 4AGT, was isolated from a mineral pool located in Malvizza, Campania, southern Italy. On the basis of 16S rRNA gene sequence analysis, strain 4AGT was shown to belong to the genus Alkalibacillus within the phylum Firmicutes; its phylogenetic distance from recognized Alkalibacillus species was <95·0 %. Chemotaxonomic data (MK-7 as the major menaquinone; directly cross-linked meso-diaminopimelic acid in the cell wall; phosphatidylglycerol and diphosphatidylglycerol as major polar lipids; iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 as major fatty acids; and glycine betaine and glutamate as major compatible solutes) supported the affiliation of the strain to the genus Alkalibacillus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 4AGT from the two recognized Alkalibacillus species. Strain 4AGT therefore represents a novel species, for which the name Alkalibacillus filiformis sp. nov. is proposed. The type strain is 4AGT (=DSM 15448T=ATCC BAA-956T).

Halomonas campaniensis sp. nov., a haloalkaliphilic bacterium isolated from a mineral pool of Campania Region, Italy

A Gram-negative, aerobic, motile and rod-shaped haloalkaliphilic bacterial strain 5AGT (DSM 15293 and ATCC BAA-966) was isolated from water with algal mat of a mineral pool in Malvizza site (Campania-Italy) and was subjected to a polyphasic study. The isolate grew at temperature of 10.0-43.0 degrees C with an optimum at 37.0 degrees C. Strain 5AGT grew optimally in the presence of 10% NaCl and grew also in the absence of salt. The isolate grew in the pH range 7.0-10.0 with an optimum at pH 9.0. It accumulated glycine-betaine, ectoine, and glutamate, as osmoprotectants. Strain 5AGT was also characterized chemotaxonomically by having ubiquinone-8 (Q8) as the predominant isoprenoid quinone, phosphoethanolamine (PEA), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG), as major polar lipids and aiC16:0 and C18:1cis as the major fatty acids. The DNA G+C content was 63.7mol%. Phylogenetic analyses based on 16S rRNA gene sequence showed that the isolate belonged to the genus Halomonas. The DNA-DNA hybridization of the type strain 5AGT with the most related Halomonas campisalis showed a re-association value of 35.0%. On the basis of phenotypic properties and phylogeny, strain 5AGT should be placed in the genus Halomonas as a member of a novel species for which we propose the name Halomonas campaniensis sp. nov.

Fatty acid, compatible solute and pigment composition of obligately chemolithoautotrophic alkaliphilic sulfur-oxidizing bacteria from soda lakes

Salt adaptation in chemolithotrophic alkaliphilic sulfur-oxidizing strains belonging to genera Thioalkalimicrobium and Thioalkalivibrio has been studied by determination of salt-dependent changes in fatty acid and compatible solute composition. In both alkaliphilic groups, represented by the low salt-tolerant Thioalkalimicrobium aerophilum strain AL 3T and the extremely salt-tolerant Thioalkalivibrio versutus strain ALJ 15, unsaturated fatty acids predominate over saturated fatty acids. In strain AL 3T, C18:1, C16:0 and C16:1 were the dominant fatty acids. In strain ALJ 15, the concentrations of C18:1 and C19cyclo were salt-regulated in an inverse proportional relationship, suggesting the stimulation of cyclopropyl-synthetase activity. Squalene has been found in substantial amounts only in strain ALJ 15. Ectoine and glycine betaine were found to be the main osmolytes in Thioalkalimicrobium aerophilum and Thioalkalivibrio versutus, respectively. The production of ectoine and glycine betaine was positively correlated with the salt concentration in the growth medium. A novel type of membrane-bound yellow pigments was uniformly detected in the extremely salt-tolerant strains of Thioalkalivibrio with a backbone consisting of C15-polyene, whose specific concentration correlated with increasing salinity of the growth medium. The results suggest that the mechanisms of haloalkaliphilic adaptation in Thioalkalimicrobium sp. and Thioalkalivibrio sp. involve the production of cyclopropane fatty acids, organic compatible solutes and, possibly specific pigments.

Salinivibrio costicola subsp. alcaliphilus subsp. nov., a haloalkaliphilic aerobe from Campania Region (Italy)

Phenotypic and phylogenetic studies were performed on unidentified Gram-negative staining, haloalkaliphilic aerobe and protease producer Salinivibrio-like organism recovered from a saltish spring with algal mat in the "Pozzo del Sale" site (Salt's Well) in the Campania Region (South Italy). Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was related to species of Salinivibrio genus. The DNA-DNA hybridization of the type strain 18AG(T) with the most related Salinivibrio costicola subsp. costicola showed a reassociation value of 72%. Based on the phenotypic distinctiveness of 18AG(T) strain and molecular, chemical and genetic evidence, it is proposed that strain 18AG(T) can be classified as S. costicola subsp. alcaliphilus, subsp. nov. The type strain of S. costicola subsp. alcaliphilus, is ATCC BAA-952(T); DSM 16359(T).

Bacillus saliphilus sp. nov., isolated from a mineral pool in Campania, Italy

A haloalkaliphilic Gram-positive bacterium, strain 6AGT, that grew aerobically at an optimum temperature of 37 °C and at pH 7–10 (optimum 9·0), was isolated from algal mat from a mineral pool located in Malvizza in the Campania region (southern Italy). The isolate tolerated high concentrations of NaCl, up to 25 %. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Bacillus. Analysis of the 16S rRNA gene sequence revealed high similarity between strain 6AGT and an unidentified isolate from Hailaer soda lake (China) (99·9 % identity) and two Kenyan isolates, 3E1 and WE4 (98·3 and 97·8 % identity, respectively). The G+C content of the DNA was 48·4 mol%. The predominant respiratory quinones were MK-7(H2), MK-7(H4) and DMK-7(H2); phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. iC15 : 0 and aiC15 : 0 were the major fatty acids. Strain 6AGT accumulated osmolytes. The phylogenetic distance of strain 6AGT (=DSM 15402T=ATCC BAA-957T) from any recognized species within the genus Bacillus allowed it to be classified as the type strain of Bacillus saliphilus sp. nov.

Haloalkaliphilic sulfur-oxidizing bacteria in soda lakes

The existence of chemolithoautotrophic sulfur-oxidizing bacteria (SOB) capable of growth in an extremely alkaline and saline environment has not been recognized until recently. Extensive studies of saline, alkaline (soda) lakes located in Central Asia, Africa and North America have now revealed the presence, at relatively high numbers, of a new branch of obligately autotrophic SOB in these doubly extreme environments. Overall more than 100 strains were isolated in pure culture. All of them have the potential to grow optimally at around pH 10 in media strongly buffered with sodium carbonate/bicarbonate and cannot grow at pH<7.5 and Na(+) concentration <0.2 M. The majority of the isolates fell into two distinct groups with differing phylogeny and physiology, that have been described as two new genera in the Gammaproteobacteria; Thioalkalimicrobium and Thioalkalivibrio. The third genus, Thioalkalispira, contains a single obligate microaerophilic species T. microaerophila. The Thioalkalimicrobium group represents a typical opportunistic strategy, including highly specialized, relatively fast-growing and low salt-tolerant bacteria, dominating in hyposaline steppe soda lakes of Central Asia. The genus Thioalkalivibrio includes mostly slowly growing species better adapted to life in hypersaline conditions and with a more versatile metabolism. It includes denitrifying, thiocyanate-utilizing and facultatively alkaliphilic species.

Rapid and sensitive NMR method for osmolyte determination

We propose a rapid and sensitive method for osmolyte determination, based on one-dimensional and two-dimensional 1H NMR spectroscopy applied directly on culture of haloalkalophilic Halomonas pantelleriensis and acidothermophilic archaeon Sulfolobus solfataricus, without any extraction procedure. The osmoprotectants hydroxyectoine, ectoine, glutamate, glycine-betaine and treahalose can easily be quantified by integrating the peak areas with respect to an internal standard, and the concentrations evaluated with this method are in excellent agreement with the values previously reported. Furthermore, trace amount of osmoprotectants, often undetectable after extraction procedures, can also be evaluated.

Planococcus rifietensis sp. nov, Isolated from Algal Mat Collected from a Sulfurous Spring in Campania (Italy)

The taxomony of strain M8, isolated from algal mat formed at the origin of a sulfurous spring in Rifieto (Savignano Irpino, Campania, Italy), was investigated in a polyphasic approach. The morphological, physiological and genetic characteristics were compared with of Planococcus and Planomicrobium species. The isolate grew optimally at pH 9.0, 1.8 M NaCl at 37 degrees C. The cells were Gram-positive cocci that form pairs, tetrads and aggregates of several cells. The isolate was aerobic/microaerophilic and accumulated glycine-betaine, as a major osmolyte, with minor components glutamate and an unknown compound. M8 was able to hydrolyse X-Glc (5-bromo-4-chloro-3-indoyl beta-d-glucopyranoside). The polar lipid profile consisted of phosphatidylglycerol and diphosphatidylglycerol as major components, and phosphocholine as a minor compound. MK8 was the only quinone found and the fatty acid composition was dominated by branched acids, mainly aiC15:0. The G+C content of DNA was 47.9% and its phylogenetic position was established by 16S rRNA gene sequencing as a member of the genus Planococcus. The DNA/DNA similarity of M8 to the type species Planococcus citreus was less than 55%. For this reason and for physiological and chemotaxonomic features, it is proposed to create a new species Planococcus rifietensis sp. nov.