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°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 α-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). The EMBL accession number for the 16S rRNA sequence of Halomonas sinaiensis strain Sharm^T is AM238662.     

<Emphasis Type="Italic">Halomonas qijiaojingensis</Emphasis> sp. nov. and <Emphasis Type="Italic">Halomonas flava</Emphasis> sp. nov., two moderately halophilic bacteria isolated from a salt lake

Two moderately halophilic, Gram-negative, rod-shaped bacteria, designated YIM 93003^T and YIM 94343^T, were isolated from a salt lake in Xinjiang province, north-west China. The two strains YIM 93003^T and YIM 94343^T grew at 20–40°C, pH 6–9, 0.5–24% (w/v) NaCl and at 20–40°C, pH 6–9, 0.5–23% (w/v) NaCl, respectively. No growth occurred in absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 93003^T and YIM 94343^T were phylogenetically affiliated to the genus Halomonas and exhibited sequence similarity of 97.5% and 97.4% to the type strain Halomonas anticariensis DSM 16096^T, respectively. The strains possessed chemotaxonomic markers that were consistent with their classification in the genus Halomonas (Q-9 as predominant respiratory quinine; C18:1ω7c, C16:0 and C16:1 ω7c/iso-C15:02-OH as the major fatty acids). The DNA–DNA hybridization values for strains YIM 93003^T and YIM 94343^T, YIM 93003^T and DSM 16096^T, YIM 94343^T and DSM 16096^T were 38.1 ± 3.0, 18.3 ± 4.7, and 20.8 ± 4.6%, respectively. The G+C contents of the strains YIM 93003^T and YIM 94343^T were 63.4 and 64.0 mol%, respectively. Based on comparative analysis of physiological, biochemical and chemotaxonomic data, including low DNA–DNA hybridization results, two novel species, Halomonas qijiaojingensis sp. nov., and Halomonas flava sp. nov., are proposed. The type strains are YIM 93003^T (=CCTCC AB 208133^T =KCTC 22228^T) and YIM 94343^T (=CCTCC AB 2010382^T =KCTC 23356^T), respectively.     

<Emphasis Type="Italic">Halomonas sediminis</Emphasis> sp. nov., a new halophilic bacterium isolated from salt-lake sediment in China

A novel Gram-negative, slightly halophilic, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-C248^T, was isolated from a sediment sample collected from a salt-lake in the Qaidam Basin in Qinghai, north-west China. Cells were non-sporulating short rods, occurring singly or as doublets, motile with peritrichous flagella. Growth occurred with 1–15% (w/v) NaCl [optimum 2–4% (w/v) NaCl], at pH 6.0–10.0 (optimum pH 7.5) and at 4–35°C (optimum 25–30°C). The major cellular fatty acids were C_18:1 ω7c, C_12:0 3-OH, cyclo C_19:0 ω8c, C_16:0 and C_16:1. The predominant respiratory quinone was Q-9 and the genomic DNA G + C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C248^T should be assigned to the genus Halomonas. The sequence similarities between the isolate and the type strains of members of the genus Halomonas were in the range of 92.5–97.5%. The combination of phylogenetic analysis, DNA–DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain YIM-C248^T represents a new species of the genus Halomonas, for which the name Halomonas sediminis sp. nov. is proposed, with YIM-C248^T (=CCTCC AA 207031 = KCTC 22167) as the type strain. The GenBank/EMBL/DBBJ accession number for the 16S rRNA gene sequence of strain YIM-C248^T is EU135707.     

Halomonas nanhaiensis sp. nov., a halophilic bacterium isolated from a sediment sample from the South China Sea

A novel Gram-negative, aerobic, slightly halophilic, yellow-pigmented, oxidase-negative, Voges–Proskauer positive, non-spore-forming bacterium, designated YIM M 13059^T, was isolated from a sediment sample collected from the South China Sea at a depth of 310 m. Optimal growth was found to occur at 28–30 °C, pH 7.0 and in the presence of 3–4 % (w/v) NaCl. Cells were observed to be rod-shaped and motile by peritrichous flagella. The polar lipids of strain YIM M 13059^T were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a ninhydrin-positive phospholipid, one glycolipid and two unknown phospholipids. The predominant respiratory quinone was determined to be Q-9. The major fatty acids were identified as C_18:1 ω7c, C_16:1 ω6c/C_16:1 ω7c, C_16:0 and C_12:0 3-OH. The genomic DNA G+C content was determined to be 54.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belongs to the genus Halomonas in the family Halomonadaceae. The 16S rRNA gene sequence similarities between strain YIM M 13059 ^T and the type strains of members of the genus Halomonas were in the range 93.3–98.3 %. However, the levels of DNA–DNA relatedness values between YIM M 13059 and the type strains of the most closely related species, Halomonas zhangjiangensis, Halomonas variabilis, Halomonas neptunia, Halomonas boliviensis and Halomonas sulfadieris were 50.2 ± 0.68 %, 46.8 ± 1.9 %, 28.5 ± 0.74 %, 42.9 ± 0.55 % and 37.1 ± 0.68 %, respectively. Based on phylogenetic, chemotaxonomic and phenotypic data, the strain YIM M 13059^T is proposed to represent a novel member of the genus Halomonas, with the name Halomonas nanhaiensis sp. nov. The type strain is YIM M 13059^T (=JCM 18142^T =CCTCC AB 2012911^T).     

Phylogenetic Analysis of Bacterial Isolates from Man-Made High-pH, High-Salt Environments and Identification of Gene-Cassette–Associated Open Reading Frames

Environmental samples were collected from high-pH sites in Pakistan, including a uranium heap set up for carbonate leaching, the lime unit of a tannery, and the Khewra salt mine. Another sample was collected from a hot spring on the shore of the soda lake, Magadi, in Kenya. Microbial cultures were enriched from Pakistani samples. Phylogenetic analysis of isolates was carried out by sequencing 16S rRNA genes. Genomic DNA was amplified by polymerase chain reaction using integron gene-cassette–specific primers. Different gene-cassette–linked genes were recovered from the cultured strains related to Halomonas magadiensis, Virgibacillus halodenitrificans, and Yania flava and from the uncultured environmental DNA sample. The usefulness of this technique as a tool for gene mining is indicated.     

Halomonas borealis sp. nov. and Halomonas niordiana sp. nov., two new species isolated from seawater

Two Gram-negative strains obtained from tank water in a scallop hatchery in Norway, were phenotypically and genotypically characterized in order to clarify their taxonomic position. On the basis of 16S rRNA gene sequence analysis, these isolates, ATF 5.2^T and ATF 5.4^T, were included in the genus Halomonas, being their closest relatives H. smyrnensis and H. taeanensis, with similarities of 98.9% and 97.7%, respectively. Sequence analysis of the housekeeping genes atpA, ftsZ, gyrA, gyrB, mreB, rpoB, rpoD, rpoE, rpoH, rpoN and rpoS clearly differentiated the isolates from the currently described Halomonas species, and the phylogenetic analysis using concatenated sequences of these genes located them in two robust and independent branches. DNA–DNA hybridization (eDDH) percentage, together with average nucleotide identity (ANI), were calculated using the complete genome sequences of the strains, and demonstrate that the isolates constitute two new species of Halomonas, for which the names of Halomonas borealis sp. nov. and Halomonas niordiana sp. nov. are proposed, with type strains ATF 5.2^T (=CECT 9780^T = LMG 31367^T) and ATF 5.4^T (=CECT 9779^T = LMG 31227^T), respectively.     

Biotechnological Coproduction of Compatible Solutes and Polyhydroxyalkanoates using the Genus Halomonas

An increased usage of poly‐β‐hydroxyalkanoates (PHA), for instance as bulk biodegradable and biocompatible plastics, will require a cheaper production and downstream processing. If the synthesis of this intracellular biopolyester could be combined with the production of another valuable intracellular product, the economic balance of the process could be improved. It was found that the moderately halophilic bacterium Halomonas elongata simultaneously synthesizes PHA and a protector molecule, called ectoine. Whereas the synthesis of PHA is a response to the shortage of nutrients, the production of ectoine counteracts osmotic imbalances. This behavior is in so far surprising as the conditions of a bi‐factorial stress initiate the fast simultaneous synthesis of ectoine and PHA. In the presence of 100 g/L NaCl, Halomonas elongata accumulated up to 50 % w/w PHA and up to 14 % ectoine within 2–3 days under so far non‐optimized conditions. Furthermore, it was found that other Halomonas species (e.g. Halomonas halodenitrificans and own isolates of Halomonas halodeneurihalina and Halomonas salina) were able to produce both ectoine and PHA.     

<Emphasis Type="Italic">Halomonas jeotgali</Emphasis> sp. nov., a new moderate halophilic bacterium isolated from a traditional fermented seafood

A moderate halophilic, Gram-negative, non-motile, rod-shape, and aerobe designated as strain Hwa^T was isolated from traditional fermented Korean seafood, which presented as a single cell or paired cells. Optimal growth occurred at 25°C in 10% (w/v) salts at pH 7.0–8.0; however, growth occurred in a temperature range of 10–32°C, a salts concentration of 5–25% (w/v) and pH 5.0–10.0. Tests for oxidase and catalase were positive. The cells produced poly-β-hydroxybutyric acid, but not exopolysaccharide. Based on the 16S rRNA gene sequence, not only was there low similarity between strain Hwa^T and all other species (94.1% similarity with H. subglaciescola DSM 4683^T, 94.0% similarity with H. sulfidaeris Esulfide1^T, 93.6% similarity with H. cerina SP4^T and 93.0% similarity with H. halodurans DSM 5160^T), but the phylogenetic analysis revealed that the isolate may be classified as a novel species belonging to the genus Halomonas in the class Gammaproteobacteria. The predominant fatty acids of strain Hwa^T were C_18:1 ω7c, C_16:0, C_12:0 3-OH and C_16:1 ω7c/C_15:0 iso 2-OH. The DNA G+C content was calculated as 61.7 mol%. Based on phenotypic, genotypic, and phylogenetic characteristics, it is proposed that the strain designated as Hwa^T be assigned to the genus Halomonas as Halomonas jeotgali sp. nov. (=KCTC 22487^T =JCM 15645^T).     

Utilization of arylaliphatic nitriles by haloalkaliphilic Halomonas nitrilicus sp. nov. isolated from soda soils

An enrichment culture from saline soda soils, using acetate as carbon and energy source and 2-phenylpropionitrile as nitrogen source (PPN) at pH 10, resulted in the isolation of strain ANL-αCH3. The strain was identified as a representative of the genus Halomonas in the Gammaproteobacteria. The bacterium was capable of PPN utilization as a nitrogen source only, while phenylacetonitrile (PAN) served both as carbon, energy and nitrogen source. This capacity was not described previously for any other haloalkaliphilic bacteria. Apart from the nitriles mentioned above, resting cells of ANL-αCH3 also hydrolyzed mandelonitrile, benzonitrile, acrylonitrile, and phenylglycinonitrile, presumably using nitrilase pathway. Neither nitrile hydratase nor amidase activity was detected. The isolate showed a capacity to grow with benzoate and salicylate as carbon and energy source and demonstrated the ability to completely mineralize PAN. These clearly indicated a potential to catabolize aromatic compounds. On the basis of unique phenotype and distinct phylogeny, strain ANL-αCH3 is proposed as a novel species of the genus Halomonas—Halomonas nitrilicus sp. nov. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

<Emphasis Type="Italic">Halomonas chromatireducens</Emphasis> sp. nov., a new denitrifying facultatively haloalkaliphilic bacterium from solonchak soil capable of aerobic chromate reduction

A heterotrophic bacterial strain AGD 8-3 capable of denitrification under extreme haloalkaline conditions was isolated from soda solonchak soils of the Kulunda steppe (Russia). The strain was classified within the genus Halomonas. According to the results of 16S rRNA gene sequencing, Halomonas axialensis, H. meridiana, and H. aquamarina are most closely related to strain AGD 8-3 (96.6% similarity). Similar to other members of the genus, the strain can grow within a wide range of salinity and pH. The strain was found to be capable of aerobic reduction of chromate and selenite on mineral media at 160 g/l salinity and pH 9.5–10. The relatively low level of phylogenetic similarity and the phenotypic characteristics supported classification of strain AGD 8-3 as a new species Halomonas chromatireducens.     

Isolation and characterisation of bacteria from the haloalkaline Lake Elmenteita, Kenya

Culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. In this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from Lake Elmenteita. Different media were prepared using filter-sterilised water from the lake. The isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. Phylogenetic analysis of 181 partial 16S rRNA gene sequences with excellent quality showed that the majority of the isolates were affiliated to the class Gammaproteobacteria and to the genus Bacillus. Isolates from the genus Halomonas and Bacillus constituted 37 and 31% of the total sequenced isolates, respectively. Other groups recovered were related to Marinospirillum, Idiomarina, Vibrio, Enterococcus, Alkalimonas, Alkalibacterium, Amphibacillus, Marinilactibacillus and the actinobacteria Nocardiopsis and Streptomyces. Fifty-one different genera were represented with 31 and 15 cultures scoring with their nearest neighbour similarities below 98 and 97%, respectively. Some novel taxa were identified which had not been isolated previously from the soda environment. The results show that the use of different media with varying compositions can help retrieve novel bacterial diversity from the soda lake environment.     

Diversity of isolates of Acinetobacter from activated sludge systems based on their whole cell protein patterns

Whole cell protein extracts from strains of the currently recognized genomic species of Acinetobacter, together with those from a range of isolates of several genomic species identified using the Biolog system and obtained from a biological nutrient-removal activated sludge plant were analysed by SDS-PAGE. The dendrograms obtained after numerical analysis for the known genomic species generally supported the taxonomic relationships suggested from earlier DNA–DNA hybridisation data. In some cases the activated sludge isolates identified to genomic species level clustered closely with the corresponding genomic species reference strains, although isolates 5 and 8/9 were scattered throughout the dendrogram. Considerable variations were seen in the protein patterns of the 27 different environmental isolates of genomic species 7 that were analysed. Three unidentified Acinetobacter isolates examined formed their own subcluster. Received 06 September 1996/ Accepted in revised form 10 December 1996     

Natronobacillus azotifigens gen. nov., sp. nov., an anaerobic diazotrophic haloalkaliphile from soda-rich habitats

Gram-positive bacteria capable of nitrogen fixation were obtained in microoxic enrichments from soda soils in south-western Siberia, north-eastern Mongolia, and the Lybian desert (Egypt). The same organisms were obtained in anoxic enrichments with glucose from soda lake sediments in the Kulunda Steppe (Altai, Russia) using nitrogen-free alkaline medium of pH 10. The isolates were represented by thin motile rods forming terminal round endospores. They are strictly fermentative saccharolytic anaerobes but tolerate high oxygen concentrations, probably due to a high catalase activity. All of the strains are obligately alkaliphilic and highly salt-tolerant natronophiles (chloride-independent sodaphiles). Growth was possible within a pH range from 7.5 to 10.6, with an optimum at 9.5–10, and within a salt range from 0.2 to 4 M Na⁺, with an optimum at 0.5–1.5 M for the different strains. The nitrogenase activity in the whole cells also had an alkaline pH optimum but was much more sensitive to high salt concentrations compared to the growing cells. The isolates formed a compact genetic group with a high level of DNA similarity. Phylogenetic analysis based on 16S-rRNA gene sequences placed the isolates into Bacillus rRNA group 1 as a separate lineage with Amphibacillus tropicus as the nearest relative. In all isolates the key functional nitrogenase gene nifH was detected. A new genus and species, Natronobacillus azotifigens gen. nov., sp. nov., is proposed to accommodate the novel diazotrophic haloalkaliphiles. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The GenBank accession numbers for the 16S rRNA gene of the novel strains are EU143681-EU143690 and EU850814-EU850816; for the nifH gene the accession numbers are EU542601, EU563380-EU563386 and EU850817-EU850819.     

Screening and isolation of halophilic bacteria producing extracellular hydrolyses from Howz Soltan Lake,Iran

Screening of bacteria from different areas of Howz Soltan playa, a hypersaline lake in the central desert zone of Iran, led to the isolation of 231 moderately halophilic bacteria, which were able to grow optimally in media with 5–15% of salt, and 49 extremely halophilic microorganisms that required 20–25% of salt for optimal growth. These isolates produced a great variety of extracellular hydrolytic enzymes. A total of 195, 177, 100, 95, 92, 68, 65, 33, and 28 strains produced lipases, amylases, proteases, inulinases, xylanases, cellulases, pullulanases, DNases, and pectinases, respectively. In comparison with gram-negative bacteria, the gram-positive halophilic rods, showed more hydrolytic activities. Several combined activities were showed by some of these isolates. One strain presented 9 hydrolytic activities, 4 strains presented 8 hydrolytic activities, 10 strains presented 7 hydrolytic activities and 29 strains presented 6 hydrolytic activities. No halophilic isolate without hydrolytic activity has been found in this study. According to their phenotypic characteristics and comparative partial 16S rRNA sequence analysis, the halophilic strains were identified as members of the genera: Salicola, Halovibrio, Halomonas, Oceanobacillus, Thalassobacillus, Halobacillus, Virgibacillus, Gracilibacillus, Salinicoccus, and Piscibacillus. Most lipase and DNase producers were members of the genera Gracilibacillus and Halomonas, respectively, whereas most of the isolates able to produce hydrolytic enzymes such as amylase, protease, cellulose (CMCase) and inulinase, belonged to gram-positive genera, like Gracilibacillus, Thalassobacillus, Virgibacillus, and Halobacillus.     

Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil,and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996

Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17^T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7W^T and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8–91.3% and 84.1–92.6%, respectively. The major polar lipids of M5N1S17^T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C_18:1 ω6c and/or C_18:1 ω7c, C_16:0, and C_16:1 ω7c and/or C_16:1 ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17^T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17^T (= CGMCC 1.19023^T = KCTC 92130^T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443^T clustered tightly with Halomonas desiderata FB2^T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.     

Halomonas qiaohouensis sp. nov., isolated from salt mine soil in southwest China

Two Gram-stain negative, moderately halophilic, aerobic, motile bacteria, designated strains YIM QH88^T and YIM QH103, were isolated from the Qiaohou salt mine in Yunnan, southwest China. Cells of the strains were observed to be rod-shaped and produce creamy-coloured colonies. Growth of the two strains was observed at 10–45 °C (optimum 25–37 °C), at pH 6.0–10.0 (optimum 7.0–8.0), and in the presence of 0.5–20 % (w/v) NaCl (optimum 2–6 %). The two strains were found to contain summed feature 8 (C18:1 ω7c/ω6c), C19:0 cyclo ω8c and C16:0 as the major cellular fatty acids. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipid. The G+C content of the genomic DNA of strains YIM QH88^T and YIM QH103 were determined to be 64.6 and 64.2 mol%, respectively, and the predominant respiratory quinone detected was ubiquinone 9. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains YIM QH88^T and YIM QH103 formed a distinct lineage within the genus Halomonas and were most closely related to Halomonas pantelleriensis DSM 9661^T with 97.3 and 97.5 % of 16S rRNA sequence similarity respectively. The DNA–DNA hybridization relatedness value for strains YIM QH88^T and YIM QH103 was 95.2 ± 0.8 %. The levels of DNA–DNA relatedness between each of these two strains and the type strains of phylogenetically closely related Halomonas species were clearly below 70 %. On the basis of their phylogenetic analysis, DNA–DNA hybridization relatedness, phenotypic and chemotaxonomic characteristics, strains YIM QH88^T and YIM QH103 should be classified as a novel species of the genus Halomonas, for which the name Halomonas qiaohouensis sp. nov. is proposed. The type strain is YIM QH88^T (=DSM 26770^T =CCTCC AB 2012965^T).     

Reidentification of the keratinase-producing facultatively alkaliphilic Bacillus sp. AH-101 as Bacillus halodurans

Alkaliphilic Bacillus sp. AH-101 was characterized in terms of physiological and biochemical characteristics, and 16S rDNA sequence homology and DNA–DNA hybridization analyses were performed. Phylogenetic analysis of strain AH-101 based on comparison of 16S rDNA sequences revealed that this strain is closely related to Bacillus halodurans. DNA–DNA hybridization of AH-101 and related Bacillus reference strains showed that the highest level of DNA–DNA relatedness (88%) was found between strain AH-101 and the B. halodurans type strain (DSM497). Our findings demonstrate that strain AH-101 is a member of the species B. halodurans. Received: June 10, 1999 / Accepted: August 6, 1999     

New species in the genus <Emphasis Type="Italic">Francisella</Emphasis> (Gammaproteobacteria; Francisellaceae); <Emphasis Type="Italic">Francisella piscicida</Emphasis> sp. nov. isolated from cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>)

A Francisella strain, GM2212, previously isolated from moribund farmed Atlantic cod (Gadus morhua) in Norway, is closely related to Francisella philomiragia among Francisella spp. according to its complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S–5S intergenic spacer, 5S rDNA, FopA, lipoprotein TUL4 (LpnA), malate dehydrogenase and hypothetical lipoprotein (LpnB) sequences. A comparison between GM2212 and the type strain of Francisella philomiragia were performed by DNA–DNA hybridization and fatty acid analysis. The DNA–DNA hybridization showed a 70% similarity. The fatty acid analysis showed only minor differences between the Francisella isolates. Due to the inconclusive result from the DNA–DNA hybridisation, major emphasis concerning the status of this isolate is made on previously published molecular, phenotypic and biochemical characters. All characteristics taken together support the establishment of GM2212 as a novel species, for which the name Francisella piscicida sp. nov. is proposed (=CNCM I-3511^T = DSM 18777^T = LMG registration number not yet available).     

Cultivable Bacterial Diversity of Alkaline Lonar Lake, India

Aerobic, alkaliphilic bacteria were isolated and characterized from water and sediment samples collected in the winter season, January 2002 from alkaline Lonar lake, India, having pH 10.5. The total number of microorganisms in the sediment and water samples was found to be 10²–10⁶ cfu g⁻¹ and 10²–10⁴ cfu ml⁻¹, respectively. One hundred and ninety-six strains were isolated using different enrichment media. To study the bacterial diversity of Lonar lake and to select the bacterial strains for further characterization, screening was done on the basis of pH and salt tolerance of the isolates. Sixty-four isolates were subjected to phenotypic, biochemical characterization and 16S rRNA sequencing. Out of 64, 31 bacterial isolates were selected on the basis of their enzyme profile and further subjected to phylogenetic analysis. Phylogenetic analysis indicated that most of the Lonar lake isolates were related to the phylum Firmicutes, containing Low G+C, Gram-positive bacteria, with different genera: Bacillus, Paenibacillus, Alkalibacillus, Exiguobacterium, Planococcus, Enterococcus and Vagococcus. Seven strains constituted a Gram-negative bacterial group, with different genera: Halomonas, Stenotrophomonas and Providencia affiliated to γ-Proteobacteria, Alcaligenes to β-Proteobacteria and Paracoccus to α-Proteobacteria. Only five isolates were High G+C, Gram-positive bacteria associated with phylum Actinobacteria, with various genera: Cellulosimicrobium, Dietzia, Arthrobacter and Micrococcus. Despite the alkaline pH of the Lonar lake, most of the strains were alkalitolerant and only two strains were obligate alkaliphilic. Most of the isolates produced biotechnologically important enzymes at alkaline pH, while only two isolates (ARI 351 and ARI 341) showed the presence of polyhydroxyalkcanoate (PHA) and exopolysaccharide (EPS), respectively.     

Acidithiobacillus ferrivorans, sp. nov.; facultatively anaerobic, psychrotolerant iron-, and sulfur-oxidizing acidophiles isolated from metal mine-impacted environments

Phenotypic and genotypic analysis was carried out on four iron- and sulfur-oxidizing acidophilic bacteria (the “NO-37 group”) isolated from different parts of the world. 16S rRNA phylogeny showed that they are highly related to each other, but are less related to the type strain of Acidithiobacillus ferrooxidans. The NO-37 group isolates are obligate chemolithoautotrophs, facultative anaerobes, diazotrophic, and psychrotolerant. They are less tolerant of extremely low pH, and in contrast to At. ferrooxidans ^T, all of the NO-37 group isolates are motile. The GC contents of genomic DNA of the NO-37 group isolates were around 56 mol% and the DNA–DNA hybridization value between genomic DNA of isolate NO-37 and At. ferrooxidans ^T was 37%. It also appears that the bacteria of the NO-37 group have a different biochemical mechanism for oxidizing ferrous iron than At. ferrooxidans ^T; the gene coding for the archetypal rusticyanin (RusA) was not detected in any of the NO-37 group isolates, rather a gene coding for a homologous protein (RusB) was amplified from three of the four novel isolates. Isolates of the NO-37 group clearly belong to a species that is different to those already recognized in the genus Acidithiobacillus, for which the name Acidithiobacillus ferrivorans is proposed.