Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea

Halomonas gemina sp. nov. and Halomonas llamarensis sp. nov., two siderophore-producing organisms isolated from high-altitude salars of the Atacama Desert

Introduction

This study aimed to identify and characterize novel siderophore-producing organisms capable of secreting high quantities of the iron-binding compounds. In the course of this, two not yet reported halophilic strains designated ATCHA^T and ATCH28^T were isolated from hypersaline, alkaline surface waters of Salar de Llamará and Laguna Lejía, respectively. The alkaline environment limits iron bioavailability, suggesting that native organisms produce abundant siderophores to sequester iron.

Methods

Both strains were characterized by polyphasic approach. Comparative analysis of the 16S rRNA gene sequences revealed their affiliation with the genus Halomonas. ATCHA^T showed close similarity to Halomonas salicampi and Halomonas vilamensis, while ATCH28^T was related closest to Halomonas ventosae and Halomonas salina. The ability of both strains to secrete siderophores was initially assessed using the chromeazurol S (CAS) liquid assay and subsequently further investigated through genomic analysis and NMR. Furthermore, the effect of various media components on the siderophore secretion by strain ATCH28^T was explored.

Results

The CAS assay confirmed the ability of both strains to produce iron-binding compounds. Genomic analysis of strain ATCHA^T revealed the presence of a not yet reported NRPS-dependant gene cluster responsible for the secretion of siderophore. However, as only small amounts of siderophore were secreted, further investigations did not lie within the scope of this study. Via NMR and genomic analysis, strain ATCH28^T has been determined to produce desferrioxamine E (DFOE). Although this siderophore is common in various terrestrial microorganisms, it has not yet been reported to occur within Halomonas, making strain ATCH28^T the first member of the genus to produce a non-amphiphilic siderophore. By means of media optimization, the produced quantity of DFOE could be increased to more than 1000 µM.

Discussion

Phenotypic and genotypic characteristics clearly differentiated both strains from other members of the genus Halomonas. Average nucleotide identity (ANI) values and DNA-DNA relatedness indicated that the strains represented two novel species. Therefore, both species should be added as new representatives of the genus Halomonas, for which the designations Halomonas llamarensis sp. nov. (type strain ATCHA^T = DSM 114476 = LMG 32709) and Halomonas gemina sp. nov. (type strain ATCH28^T = DSM 114418 = LMG 32708) are proposed.

Halomonas getboli sp. nov., a halotolerant bacteria isolated from a salt flat

A novel Gram-stain-negative, rod-shaped, cream-coloured, motile, halotolerant bacterium, designated as YJPS3-2^T, was isolated from saltern sediment of the Yellow sea in Yongyu-do, Republic of Korea. Strain YJPS3-2^T grew at pH 5.0-10.0 (optimum, pH 7.0), 4-40 °C (optimum, 30 °C) and with 1-15% (w/v) NaCl (optimum 3 %). The 16S rRNA gene sequence analysis indicated that strain YJPS3-2^T was closely related to those of Halomonas halophila F5-7^T (98.75 %), Halomonas salina F8-11^T (98.74 %), Halomonas smyrnensis AAD6^T (98.66 %), Halomonas organivorans G-16.1^T (98.34 %), Halomonas koreensis SS20^T (97.98 %) and Halomonas beimenensis NTU-107^T (96.93 %). The average nucleotide identity and digital DNA-DNA hybridization values between YJPS3-2^T and related type strains were 86.9-91.6 % and 32.0-44.8 %. Strain YJPS3-2^T was characterized as having Q-9 as the predominant respiratory quinone and the principal fatty acids (>10 %) were C_16 : 0 (31.4 %), C_19 : 0 ω8c cyclo (16.3 %), C_17 : 0 cyclo (11.9 %) and C_12 : 0 3-OH (10.4 %). The polar lipids consisted of phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain YJPS3-2^T is 68.1mol %. Based on the polyphasic taxonomic evidence presented in this study, YJPS3-2^T should be classified as representing a novel species within the genus Halmonas, for which name Halomonas getboli is proposed, with the type strain YJPS3-2^T (= KCTC 92124^T=KACC 22561^T=JCM 35085^T).

Halomonas litopenaei sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium isolated from a shrimp hatchery

Two Gram-stain negative, moderately halophilic, exopolysaccharide-producing bacteria, designated strains SYSU ZJ2214^T and SYSU XM8, were isolated from rearing water and larvae from shrimp hatcheries, respectively. Cells of the strains were aerobic, motile and short-rod-shaped. They grew at NaCl concentrations of 0.5-22 % (w/v), at 4-45 °C and at pH 6-9. Pairwise comparison of 16S rRNA gene sequences revealed that strains SYSU ZJ2214^T and SYSU XM8 were most closely related to Halomonas denitrificans M29^T (98.3 and 98.2 % similarity, respectively). Strains SYSU ZJ2214^T and SYSU XM8 shared an average nucleotide identity of 99.9 % between them. The DNA G+C contents were calculated at 64.1 % for both strains from the draft genome information. The major cellular fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 3-OH, and the predominant respiratory quinone was ubiquinone Q-9. Their main polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, four unidentified phospholipids and three unidentified lipids. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU ZJ2214^T and SYSU XM8 merit recognition as representatives of a novel species of the genus Halomonas, for which the name Halomonas litopenaei sp. nov. is proposed. The type strain is SYSU ZJ2214^T (=NBRC 111829^T=KCTC 42974^T).

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing

This study explored the bacterial diversity of brines used for cheesemaking in Italy, as well as their physicochemical characteristics. In this context, 19 brines used to salt soft, semi-hard, and hard Italian cheeses were collected in 14 commercial cheese plants and analyzed using a culture-independent amplicon sequencing approach in order to describe their bacterial microbiota. Large NaCl concentration variations were observed among the selected brines, with hard cheese brines exhibiting the highest values. Acidity values showed a great variability too, probably in relation to the brine use prior to sampling. Despite their high salt content, brine microbial loads ranged from 2.11 to 6.51 log CFU/mL for the total mesophilic count. Microbial community profiling assessed by 16S rRNA gene sequencing showed that these ecosystems were dominated by Firmicutes and Proteobacteria, followed by Actinobacteria and Bacteroidetes. Cheese type and brine salinity seem to be the main parameters accountable for brine microbial diversity. On the contrary, brine pH, acidity and protein concentration, correlated to cheese brine age, did not have any selective effect on the microbiota composition. Nine major genera were present in all analyzed brines, indicating that they might compose the core microbiome of cheese brines. Staphylococcus aureus was occasionally detected in brines using selective culture media. Interestingly, bacterial genera associated with a functional and technological use were frequently detected. Indeed Bifidobacteriaceae, which might be valuable probiotic candidates, and specific microbial genera such as Tetragenococcus, Corynebacterium and non-pathogenic Staphylococcus, which can contribute to sensorial properties of ripened cheeses, were widespread within brines.

Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat

Strain Hb3^T was isolated from a tidal flat in Jeollabuk-do Gunsan, Republic of Korea. Cells were Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and motile. The strain grew optimally at 25-35 °C, at pH 6.0-6.5 and with 3.0-10.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Hb3^T belonged to the genus Halomonas. Strain Hb3^T was related most closely to Halomonas ventosae Al12^T (98.6 % 16S rRNA gene sequence similarity), Halomonas denitrificans M29^T (98.6 %) and Halomonas saccharevitans AJ275^T (98.4 %). Moreover, multilocus sequence analysis using the gyrB, rpoD and secA genes supported the phylogenetic position of strain Hb3^T. The genomic G+C content of strain Hb3^T was 67.9 mol%. DNA-DNA hybridization values for strain Hb3^T versus H. ventosae Al12^T, H. denitrificans M29^T and H. saccharevitans AJ275^T were 38.0, 54.5 and 47.4 %, respectively. The major quinone was ubiquinone Q-9 and the major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, amino lipid, six unidentified phospholipids and an unidentified lipid comprised the polar lipid profile. On the basis of the data presented in this report, strain Hb3^T represents a novel species of the genus Halomonas. The name Halomonas aestuarii sp. nov. is proposed for this novel species. The type strain is Hb3^T (=KCTC 52253^T=JCM 31415^T).

Complete genome sequence of Halomonas ventosae virulent halovirus QHHSV-1

A virulent halovirus QHHSV-1 which lyses Halomonas ventosae QH52-2 originating from the Qiaohou salt mine in Yunnan, Southwest China was characterized. The complete genome of QHHSV-1 is composed of a circular double-stranded DNA of 37,270 base pairs in length, with 66.8% G+C content and 69 putative open reading frames (ORFs), which were classified into five functional groups, including morphogenesis, replication/regulation, packaging, lysis and lysogeny. A putative Cro repressor gene and an integrase gene were found in the genome, showing that QHHSV-1 may utilize a lambda-like repression system under unfavorable conditions. QHHSV-1 is the first report of the whole genome sequence of the virulent Halomonas phage belonging to the family Siphoviridae.

Identification and Characterization of Early Mission Phase Microorganisms Residing on the Mars Science Laboratory and Assessment of Their Potential to Survive Mars-like Conditions

Planetary protection is governed by the Outer Space Treaty and includes the practice of protecting planetary bodies from contamination by Earth life. Although studies are constantly expanding our knowledge about life in extreme environments, it is still unclear what the probability is for terrestrial organisms to survive and grow on Mars. Having this knowledge is paramount to addressing whether microorganisms transported from Earth could negatively impact future space exploration. The objectives of this study were to identify cultivable microorganisms collected from the surface of the Mars Science Laboratory, to distinguish which of the cultivable microorganisms can utilize energy sources potentially available on Mars, and to determine the survival of the cultivable microorganisms upon exposure to physiological stresses present on the martian surface. Approximately 66% (237) of the 358 microorganisms identified are related to members of the Bacillus genus, although surprisingly, 22% of all isolates belong to non-spore-forming genera. A small number could grow by reduction of potential growth substrates found on Mars, such as perchlorate and sulfate, and many were resistant to desiccation and ultraviolet radiation (UVC). While most isolates either grew in media containing ≥10% NaCl or at 4°C, many grew when multiple physiological stresses were applied. The study yields details about the microorganisms that inhabit the surfaces of spacecraft after microbial reduction measures, information that will help gauge whether microorganisms from Earth pose a forward contamination risk that could impact future planetary protection policy. Key Words: Planetary protection-Spore-Bioburden-MSL-Curiosity-Contamination-Mars. Astrobiology 17, 253-265.

Halomonas xiaochaidanensis sp. nov., isolated from a salt lake sediment

A short-rod-shaped moderately halophilic bacterium, designated CUG 00002(T), was isolated from the sediment of Xiaochaidan salt lake in Qinghai Province, China by using R2A medium. The cells were Gram-staining negative, aerobic, forming creamy and circular colonies with diameters of 2-3 mm on R2A agar when incubated at 30 °C for 3 days. 16S rRNA gene-based phylogenetic analysis indicated that strain CUG 00002(T) belonged to the genus Halomonas in the class Gammaproteobacteria, showing highest sequence similarity of 97.1 and 96.7 % to Halomonas mongoliensis Z-7009(T) (=DSM 17332=VKM B2353) and Halomonas shengliensis SL014B-85(T) (=CGMCC 1.6444(T)=LMG 23897(T)), respectively. The predominant isoprenoid quinone was ubiquinone-9 (Q9), and the major fatty acids were C16:0, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (comprising C18:1 ω7c or C18:1 ω6c). The genomic DNA G+C content of strain CUG 00002(T) was 61.8 mol%. The above characteristics were consistent with the placement of the organism in the genus Halomonas. The level of DNA-DNA relatedness between CUG 00002(T) and its most closely related strain H. mongoliensis Z-7009(T) was 41.0 ± 1.6 %. Based on the results of phenotypic, phylogenetic and biochemical analyses, strain CUG 00002(T) represents a novel species of the genus Halomonas, for which the name Halomonas xiaochaidanensis sp. nov. is proposed. The type strain is CUG 00002(T) (=CCTCC AB 2014152(T)=KCTC 42685(T)).

Halomonas urumqiensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake

A moderately halophilic, aerobic bacterium, strain BZ-SZ-XJ27T, belonging to the genus Halomonas, was isolated from a saline-alkaline lake in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences and a multilocus sequence analysis using the 16S rRNA, gyrB and rpoD genes demonstrated that strain BZ-SZ-XJ27T represents a member of the genus Halomonas. On the basis of 16S rRNA gene sequence similarity, the closest relatives were Halomonas campaniensis 5AGT, H. fontilapidosi 5CRT, H. korlensis XK1T and H. sinaiensis ALO SharmT, with similarities of 96.2-97.2 %. DNA-DNA hybridization with H. korlensis CGMCC 1.6981T (the nearest phylogenetic neighbour) and H. campaniensis DSM 15293T (the highest 16S rRNA gene sequence similarity) showed relatedness values of 53 and 38 %, respectively, demonstrating the separateness of the three taxa. The bacterium stained Gram-negative and the cells were motile and rod-shaped. The strain formed creamy-white colonies and grew under optimal conditions of 1.42 M Na+ (range 0.22-4.32 M Na+), pH 8.0-8.5 (range pH 6.0-10.0) and 39 °C (range 4-43 °C). The dominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 36.6 %), C16 : 0 (25.9 %) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.2 %). The dominant polar lipids were two unknown phospholipids, phosphatidylethanolamine and phosphatidylglycerol, and the main respiratory quinones were ubiquinone 9 (Q-9; 89 %) and ubiquinone 8 (Q-8; 10 %). The genomic DNA G+C content was 61.7 ± 0.8 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ27T is proposed to represent a novel species, Halomonas urumqiensis sp. nov., within the genus Halomonas of the family Halomonadaceae. The type strain is BZ-SZ-XJ27T ( = JCM 30202T = CGMCC 1.12917T).

Halomonas garicola sp. nov., isolated from saeu-jeot, a Korean salted and fermented shrimp sauce

A Gram-stain-negative, moderately halophilic and facultatively aerobic bacterium capable of respiration with nitrate, designated strain JJ-M1^T, was isolated from saeu-jeot, a traditional Korean fermented shrimp sauce. Cells of the strain were non-motile short rods showing oxidase-negative and catalase-positive reactions and the production of pale-yellow pigments. Growth of strain JJ-M1^T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.5 (optimum, pH 7.0) and in the presence of 3-22.5 % (w/v) sea salts (optimum, 10 %). Strain JJ-M1^T contained ubiquinone 9 (Q-9) as the predominant isoprenoid quinone and summed feature 8 (comprising C_18 : 1ω7c and/or C_18 : 1ω6c), C_16 : 0, summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c) and C_12 : 0 3-OH as the major cellular fatty acids. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content of strain JJ-M1^T was 62.4 mol%. Phylogenetic and comparative analyses, based on 16S rRNA gene sequences, indicated that strain JJ-M1^T formed a tight phyletic lineage with Halomonas jeotgali Hwa^T within the genus Halomonas and was most closely related to Halomonas jeotgali Hwa^T with 96.2 % 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic features, strain JJ-M1^T represents a novel species of the genus Halomonas, for which the name Halomonas garicola sp. nov. is proposed. The type strain is JJ-M1^T ( = KACC 18117^T = JCM 30151^T).

The heterotrophic eubacterial and archaeal co-inhabitants of the halophilic Dunaliella salina in solar salterns fed by Bay of Bengal along south eastern coast of India

Halophilic microbes are studied to understand the metabolic pathways adopted by organisms in such extreme environment and for their biotechnological exploitation. In thallosohaline environments worldwide, the autotrophic alga Dunaliella salina Teodoresco is omnipresent, but it is being recently realised that the heterotrophic components vary in different regions. The unexplored eastern coastline of India abutted by Bay of Bengal was investigated for the heterotrophic halophilic microbes in this region. The waters in the salterns – replicas of natural hyper-saline water bodies of that region, were collected at four sites along 650 km of the coastal belt. In cultures set up from these waters, green and pink colonies were observed. The green colonies were found to be those of D. salina while the pink colonies were of heterotrophs. To identify the heterotrophic microbes, light microscopy, 16S rRNA typing and pigment profiling through spectrophotometry and HPLC were done. The cells in pink colonies were rod shaped. 16S rRNA typing of cells in these colonies detected the presence of Halomonas sp. – a eubacterium. The pigment profile of cells in pink cultures matched that of the archaea – Halobacterium; bacterioruberin derivatives were found. Thus, it was concluded that Halomonas and Halobacterium spp. are among the co-inhabitant heterotrophs of D. salina. Cultures of D. salina established from these salterns showed the typical three colours seen in the ponds of different sub-plots of salterns. They were green until 30 days, turning dark orange by 60 days and pink when 90 day old. In the 90 day old cultures, innumerable rod shaped cells were found. These cells were similar to the cells of the waters from the ponds of pink sub-plots of salterns and the pink colonies established from saltern waters in the laboratory. In the old (90 days) laboratory cultures of D. salina, the glycerol and proteins released from degenerating cells and the increase in salt concentration to super saturation levels due to evaporation of water in the medium led to the gregarious appearance of the heterotrophs – the co-inhabitants in natural environment.

Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil

A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T).

Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils

A moderately halophilic bacterium (strain NEAU-ST10-39T) was isolated from saline and alkaline soils in the oilfield of Daqing City, Heilongjiang Province, China. The strain was strictly aerobic, Gram-stain-negative, rod-shaped and motile by peritrichous flagella. Its colonies were yellow. It grew at NaCl concentrations of 0.2–15 % (w/v) (optimum 4 %, w/v), at temperatures of 4–40 °C (optimum 35 °C) and at pH 5–10 (optimum pH 7). It did not produce acids from sugars or alcohols. Its DNA G+C content was 57.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that it belonged to the genus Halomonas in the class Gammaproteobacteria . The most phylogenetically related species were Halomonas axialensis , Halomonas meridiana and Halomonas aquamarina , whose types shared 98.3 % (16S rRNA), 82.7 % (gyrB) and 83.9–84.5 % (rpoD) sequence similarity with strain NEAU-ST10-39T. The results of DNA–DNA hybridization assays showed 20±2 %–50±1 % relatedness between strain NEAU-ST10-39T and the most closely related species including Halomonas axialensis DSM 15723T, Halomonas meridiana DSM 5425T, Halomonas aquamarina DSM 30161T, Halomonas johnsoniae DSM 21197T, Halomonas stevensii DSM 21198T, Halomonas nanhaiensis CCTCC AB 2012911T, Halomonas hamiltonii DSM 21196T and Halomonas arcis CGMCC 1.6494T. The major fatty acids were C18 : 1ω7c (47.2 %), C16 : 1ω7c and/or C16 : 1ω6c (18.9 %) and C16 : 0 (16.3 %), the only respiratory quinone detected was ubiquinone 9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and three unknown lipids. The new isolate is proposed to represent a novel species with the name Halomonas songnenensis sp. nov., NEAU-ST10-39T ( = CGMCC 1.12152T = DSM 25870T) being the type strain.

Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium

Four Gram-negative, moderately halophilic, exopolysaccharide-producing strains, designated AAD6T, AAD4, AAD17 and AAD21, were isolated from Çamaltı Saltern Area, a wildlife reserve in Sasalı, İzmir province located in the Aegean Region of Turkey. The isolates grew at an optimum NaCl concentration of 10 % (w/v). The major cellular fatty acids were C16 : 0, C18 : 1ω7c, C16 : 1ω7c and C12 : 0 3OH, respectively and the predominant lipoquinone was ubiquinone Q-9. The G+C content of the genomic DNA of strains AAD6T, AAD4, AAD17 and AAD21 was 63.0, 63.3, 62.8 and 62.6 mol%, respectively. Comparative 16S rRNA gene sequence studies showed that the isolates belonged to the genus Halomonas . The DNA–DNA hybridization mean values between the representative strain AAD6T and the closely related species Halomonas salina DSM 5928T, Halomonas halophila DSM 4770T, Halomonas maura DSM 13445T, Halomonas organivorans DSM 16226T, Halomonas elongata DSM 2581T, Halomonas koreensis JCM 12237T and Halomonas nitroreducens LMG 24185, were 40.8, 39.6, 24.2, 23.3, 12.6, 14.5 and 12.2 %, respectively. Based on these data the strains represent a novel species of the genus Halomonas for which the name Halomonas smyrnensis sp. nov. is proposed. The type strain is AAD6T ( = DSM 21644T = JCM 15723T).

Halomonas beimenensis sp. nov., isolated from an abandoned saltern

A Gram-staining negative, motile, non-spore-forming, short rod-shaped (0.8–1.5×1.5–2.0 µm), halophilic bacterium, designated strain NTU-107T, was isolated from brine samples collected from the abandoned Beimen saltern in southern Taiwan. The novel strain grew with 0–15 % (w/v) NaCl (optimum between 5 % and 10 %), at 15–55 °C (optimum 40 °C) and at pH 5.5–9.5 (optimum pH 7.5). The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C19 : 0 cyclo ω8c, the genomic DNA G+C content was 66.5 mol%, and the predominant ubiquinone was Q-9. The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. In a phylogenetic analysis based on 16S rRNA gene sequences, strain NTU-107T clustered with members of the genus Halomonas . In hybridization experiments, however, the levels of DNA–DNA relatedness between strain NTU-107T and the type strains of its closest phylogenetic neighbours ( Halomonas koreensis , H. organivorans and H. ventosae ) were all found to be less than 40 %. Based on the phenotypic, chemotaxonomic and genetic data, strain NTU-107T represents a novel species within the genus Halomonas , for which the name Halomonas beimenensis sp. nov. is proposed. The type strain is NTU-107T ( = BCRC 17999T = KCTC 22876T = JCM 16084T).

Halomonas cibimaris sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

Two moderately halophilic, facultatively aerobic, motile bacteria with flagella, designated strains 10-C-3(T) and 30-C-3, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of the strains were observed to be ovoid-rods showing catalase- and oxidase-positive reactions and production of creamy-pink pigments. Growth of strain 10-C-3(T) was observed at 15-35 °C (optimum, 25-30 °C), at pH 5.5-9.0 (optimum, pH 7.0-7.5), and in the presence of 3-15 % (w/v) salts (optimum: 5-10 %). The two strains were found to contain C(18:1) ω7c, C(16:0), summed feature 3 (as defined by the MIDI system, comprising C(16:1) ω7c and/or C(16:1) ω6c), and C(12:0) 3-OH as the major cellular fatty acids. The G+C contents of the genomic DNA of strains 10-C-3(T) and 30-C-3 were determined to be 63.2 and 63.1 mol%, respectively and the respiratory quinone detected was ubiquinone 9 (Q-9) only. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains 10-C-3(T)and 30-C-3 formed a distinct phyletic lineage within the genus Halomonas and are most closely related to Halomonas fontilapidosi 5CR(T) with 95.2 % of 16S rRNA sequence similarity. Strains 10-C-3(T)and 30-C-3 shared 99.2 % of 16S rRNA gene sequence similarity and their DNA-DNA relatedness value was 96.6 ± 0.9 %. On the basis of phenotypic, chemotaxonomic and molecular features, strains 10-C-3(T)and 30-C-3 represent a novel species of the genus Halomonas, for which the name Halomonas cibimaris sp. nov. is proposed. The type strain is 10-C-3(T) (= KACC 14932(T) = JCM 16914(T)).

Halomonas stenophila sp. nov., a halophilic bacterium that produces sulphate exopolysaccharides with biological activity

We have undertaken a polyphasic taxonomic study of two halophilic, Gram-negative bacterial strains, N12T and B-100, that produce sulphated exopolysaccharides with biological activity. They were isolated from two different saline soil samples. Both strains grow at NaCl concentrations within the range 3–15 % (w/v) [optimum 5–10 % (w/v)], at 15–37 °C (optimum 20–32 °C) and at pH 6–8 (optimum pH 7–8). Their 16S rRNA gene sequences indicate that they belong to the genus Halomonas in the class Gammaproteobacteria. Their closest relative is Halomonas nitroreducens, to which our strains show maximum 16S rRNA gene sequence similarity values of 98.7 % (N12T) and 98.3 % (B-100). Their DNA G+C contents are 61.9 and 63.8 mol%, respectively. The results of DNA–DNA hybridizations showed 43.9 % relatedness between strain N12T and H. nitroreducens CECT 7281T, 30.5 % between N12T and Halomonas ventosae CECT 5797T, 39.2 % between N12T and Halomonas fontilapidosi CECT 7341T, 46.3 % between N12T and Halomonas maura CECT 5298T, 52.9 % between N12T and Halomonas saccharevitans LMG 23976T, 51.3 % between N12T and Halomonas koreensis JCM 12237T and 100 % between strains N12T and B-100. The major fatty acids of strain N12T are C12 : 0 3-OH (5.42 %), C15 : 0 iso 2-OH/C16 : 1ω7c (17.37 %), C16 : 0 (21.62 %) and C18 : 1ω7c (49.19 %). The proposed name for the novel species is Halomonas stenophila sp. nov. Strain N12T ( = CECT 7744T  = LMG 25812T) is the type strain.

Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis

A phylogenetic study of the family Halomonadaceae was carried out based on complete 16S rRNA and 23S rRNA gene sequences. Several 16S rRNA genes of type strains were resequenced, and 28 new sequences of the 23S rRNA gene were obtained. Currently, the family includes nine genera (Carnimonas, Chromohalobacter, Cobetia, Halomonas, Halotalea, Kushneria, Modicisalibacter, Salinicola and Zymobacter). These genera are phylogenetically coherent except Halomonas, which is polyphyletic. This genus comprises two clearly distinguished clusters: group 1 includes Halomonas elongata (the type species) and the species Halomonas eurihalina, H. caseinilytica, H. halmophila, H. sabkhae, H. almeriensis, H. halophila, H. salina, H. organivorans, H. koreensis, H. maura and H. nitroreducens. Group 2 comprises the species Halomonas aquamarina, H. meridiana, H. axialensis, H. magadiensis, H. hydrothermalis, H. alkaliphila, H. venusta, H. boliviensis, H. neptunia, H. variabilis, H. sulfidaeris, H. subterranea, H. janggokensis, H. gomseomensis, H. arcis and H. subglaciescola. Halomonas salaria forms a cluster with Chromohalobacter salarius and the recently described genus Salinicola, and their taxonomic affiliation requires further study. More than 20 Halomonas species are phylogenetically not within the core constituted by the Halomonas sensu stricto cluster (group 1) or group 2 and, since their positions on the different phylogenetic trees are not stable, they cannot be recognized as additional groups either. In general, there is excellent agreement between the phylogenies based on the two rRNA gene sequences, but the 23S rRNA gene showed higher resolution in the differentiation of species of the family Halomonadaceae.

A constructed alkaline consortium and its dynamics in treating alkaline black liquor with very high pollution load

Background

Paper pulp wastewater resulting from alkaline extraction of wheat straw, known as black liquor, is very difficult to be treated and causes serious environmental problems due to its high pH value and chemical oxygen demand (COD) pollution load. Lignin, semicellulose and cellulose are the main contributors to the high COD values in black liquor. Very few microorganisms can survive in such harsh environments of the alkaline wheat straw black liquor. A naturally developed microbial community was found accidentally in a black liquor storing pool in a paper pulp mill of China. The community was effective in pH decreasing, color and COD removing from the high alkaline and high COD black liquor.

Findings

Thirty-eight strains of bacteria were isolated from the black liquor storing pool, and were grouped as eleven operational taxonomy units (OTUs) using random amplified polymorphic DNA-PCR profiles (RAPD). Eleven representative strains of each OTU, which were identified as genera of Halomonas and Bacillus, were used to construct a consortium to treat black liquor with a high pH value of 11.0 and very high COD pollution load of 142,600 mg l⁻¹. After treatment by the constructed consortium, about 35.4% of color and 39,000 mg l⁻¹ (27.3%) COD_cr were removed and the pH decreased to 7.8. 16S rRNA gene polymerase chain reaction denaturant gradient gel electrophoresis (PCR-DGGE) and gas chromatography/mass spectrometry (GC/MS) analysis suggested a two-stage treatment mechanism to elucidate the interspecies collaboration: Halomonas isolates were important in the first stage to produce organic acids that contributed to the pH decline, while Bacillus isolates were involved in the degradation of lignin derivatives in the second stage under lower pH conditions.

Conclusions/Significance

Tolerance to the high alkaline environment and good controllability of the simple consortium suggested that the constructed consortium has good potential for black liquor treatment. Facilitating the treatment process by the constructed consortium would provide a promising opportunity to reduce the pollution, as well as to save forest resources and add value to a waste product.

Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea

A moderately halophilic, Gram-negative bacterium, designated strain BH843T, was isolated from a solar saltern in Korea and subjected to a taxonomic analysis. Strain BH843T grew at salinities of 1–14 % (w/v) NaCl and at temperatures of 10–40 °C. The cells were motile cocci or short rods with single flagella and contained C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo as the major fatty acids. The G+C content of the genomic DNA was 66 mol% and the predominant ubiquinone was Q-9. Comparative 16S rRNA gene sequence analyses showed that strain BH843T formed a distinct phyletic line within the genus Halomonas, and the levels of 16S rRNA gene sequence similarity with respect to recognized Halomonas species were below 95.1 %. The levels of DNA–DNA relatedness between strain BH843T and the type strains of phylogenetically closely related Halomonas species were below 25 %. On the basis of phenotypic, chemotaxonomic and molecular data, strain BH843T represents a novel species within the genus Halomonas, for which the name Halomonas kribbensis is proposed. The type strain is BH843T (=KCTC 12584T=DSM 17892T).

Recommended minimal standards for describing new taxa of the family Halomonadaceae

Following Recommendation 30b of the Bacteriological Code (1990 Revision), a proposal of minimal standards for describing new taxa within the family Halomonadaceae is presented. An effort has been made to evaluate as many different approaches as possible, not only the most conventional ones, to ensure that a rich polyphasic characterization is given. Comments are given on the advantages of each particular technique. The minimal standards are considered as guidelines for authors to prepare descriptions of novel taxa. The proposals presented here have been endorsed by the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halomonadaceae.

Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico

A Gram-negative, short rod to oval-shaped bacterium (strain MW2a(T)) was isolated from the surface of leaves of the black mangrove Avicennia germinans and subjected to a polyphasic taxonomic study. Strain MW2a(T) was moderately halophilic, growing at NaCl concentrations in the range 0-25 % (w/v) with optimum growth at 5 % (w/v) NaCl. Growth occurred at 12-40 degrees C (optimum, 30-35 degrees C) and at pH 5.0-9.0 (optimum, pH 7.0-8.0). Strain MW2a(T) was strictly aerobic. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Halomonas. The closest relative was Halomonas marisflavi, with 98.6 % 16S rRNA gene sequence similarity. The DNA G+C content of strain MW2a(T) was 61.5 mol%, which is in the range of values for Halomonas species. DNA-DNA hybridization with H. marisflavi showed a relatedness of 42 % and lower values were obtained with respect to other related Halomonas species. The major fatty acids were C(16 : 0), C(19 : 0) cyclo omega8c, C(18 : 1)omega7c and C(12 : 0) 3-OH. Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MW2a(T) represents a novel species within the genus Halomonas. The name Halomonas avicenniae sp. nov. is proposed, with strain MW2a(T) (=CECT 7193(T)=CCM 7396(T)) as the type strain.

Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China

Three strains of Gram-negative, aerobic, neutrophilic and halophilic bacteria were isolated from samples of a salt lake on the Qinghai–Tibet Plateau and a subterranean saline well in the Si-Chuan Basin of China. These isolates, designated AJ275T, AJ282Tand ZG16T, were investigated using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the isolates could be affiliated to the genusHalomonas. Genomic DNA G+C contents were 65.9 mol% for AJ275T, 56.7 mol% for AJ282Tand 57.6 mol% for ZG16T. The results of DNA–DNA hybridizations, fatty acid analysis and physiological and biochemical tests allowed the isolates to be differentiated genotypically and phenotypically from closely related species. It is proposed that strains AJ275T(=CGMCC 1.6493T=JCM 14606T=LMG 23976T), AJ282T(=CGMCC 1.6494T=JCM 14607T=LMG 23978T) and ZG16T(=CGMCC 1.6495T=JCM 14608T=LMG 23977T) represent the type strains of three novel species in the genusHalomonas:Halomonas saccharevitanssp. nov.,Halomonas arcissp. nov. andHalomonas subterraneasp. nov., respectively.

Halomonas gudaonensis sp. nov., isolated from a saline soil contaminated by crude oil

Two moderately halophilic strains, SL014B-69T and SL014B-62A2, were isolated from a saline soil contaminated with crude oil in Gudao in the coastal Shengli oilfield in China; the isolates were Gram-negative, rod-shaped and carried lateral flagella. Growth occurred at NaCl concentrations of 1–20 % (w/v), at temperatures of 10–42 °C and at pH 8.0–9.0. Strain SL014B-69T had C18 : 1 ω7c (28.61 %), C19 : 1 cyclo ω7c (27.97 %), C16 : 0 (19.66 %) and C12 : 0 3-OH (8.87 %) as the predominant fatty acids and Q9 as the major ubiquinone, with the G+C content of genomic DNA being 64.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains belonged to genus of Halomonas in the Gammaproteobacteria, with the highest 16S rRNA gene sequence similarities of 96.4 % with Halomonas campisalis ATCC 700597T and 96.0 % with Halomonas desiderata FB2T. DNA–DNA relatedness of strain SL014B-69T with strain SL014B-62A2, H. campisalis ATCC 700597T and H. desiderata DSM 9502T was 97.4, 42.9 and 36.8 %, respectively. On the basis of these data, a novel species of the genus Halomonas, Halomonas gudaonensis sp. nov., is proposed for strain SL014B-69T and SL014B-62A2. The type strain is SL014B-69T (=LMG 23610T=CGMCC 1.6133T).

Halomonas taeanensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea

A moderately halophilic, Gram-negative bacterium, strain BH539(T), which was isolated from a solar saltern at Taean in Korea, was considered to be a member of the genus Halomonas. Strain BH539(T) grew at salinities of 1-25% (w/v) and at temperatures of 10-45 degrees C. Cells were short rods that were motile by means of several flagella. Their major fatty acids were C(18:1)omega7c, C(16:0) and C(19:0) cyclo omega8c. The genomic DNA G+C content was about 65 mol% and the predominant ubiquinone was Q-9. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate formed a branch of the species Cobetia marina. However, 23S and 16S rRNA gene sequence similarities revealed that strain BH539(T) was related more closely to the type strains of the genus Halomonas. Phylogenetic analyses based on 23S rRNA gene sequences also indicated that the strain formed a phyletic line within the genus Halomonas. Therefore, it was concluded that strain BH539(T) should be classified within the genus Halomonas, rather than Cobetia. On the basis of physiological and molecular properties, strain BH539(T) represents a novel species of the genus Halomonas, for which the name Halomonas taeanensis sp. nov. is proposed. The type strain is BH539(T) (=KCTC 12284(T)=DSM 16463(T)).

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.