Halobacillus salicampi sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment

Halobacillus rhizosphaerae sp. nov., a moderately halophilic bacterium with protease activities isolated from the rhizosphere soil of the mangrove Acanthus ebracteatus

A Gram-positive, moderately halophilic, rod-shaped and facultatively anaerobic strain T66T, was isolated from the rhizosphere soil of mangrove Acanthus ebracteatus in Guangxi, China. Strain T66T was observed to grow at 15-40 ℃ (optimum 30 ℃), pH 5-8 (optimum 6-7) and with 2-20% (w/v) NaCl (optimum 6%). The phylogenetic tree of the 16S rRNA gene sequences depicted a cluster of strain T66T to be closely related to Halobacillus litoralis SL-4 T (98.72%), Halobacillus dabanensis D-8 T (98.70%) and Halobacillus campisalis ASL-17 T (98.66%). The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain T66T belonged to the genus Halobacillus and formed a separate branch. The digital DNA-DNA hybridisation and average nucleotide identify values between strain T66T and its related species were 17.80-19.80% and 70.78-73.22%, respectively, which were lower than the threshold recommended for species delineation. The genomic DNA G + C content was 40.9%. The predominant isoprenoid quinone was MK-7, the cell-wall peptidoglycan contained meso-diaminopimelic acid, and the major fatty acids that accounted for more than 10.0% were anteiso-C15:0 (68.4%) and anteiso-C17:0 (13.4%). Phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids and an unidentified glycolipid were found in the polar lipid extraction. Strain T66T could hydrolyse casein and contains several genes (e. g. vanY, vpr, pbpG and elpC) involved in protease. Therefore, strain T66T is salt-tolerant and produces protease, and it may have development and utilisation value in flavouring agents and food curing. Based on phenotypic, chemotaxonomic data and genotypic characteristics, strain T66T represents a novel species of the genus Halobacillus, for which the name Halobacillus rhizosphaerae sp. nov. is proposed. The type strain is T66T (= JCM 36534 T = MCCC 1K08701T).

Draft genome sequence of Halobacillus campisalis strain ASL-17

We report here the genome sequence of moderately halophilic Halobacillus campisalis ASL-17, isolated from hypersaline sediment from the Yellow Sea, Korea. The bacterium was Gram variable, oval or coccoid, and mesophilic. The genome of H. campisalis ASL-17 has 3.8 Mbp, with 3,910 coding sequences, 76 RNAs, and 41.3% G + C content.

Halobacillus salinarum sp. nov., Halobacillus shinanisalinarum sp. nov. and Halobacillus amylolyticus sp. nov., isolated from saltern soil

Three bacterial strains, designated SSBR10-3T, SSTM10-2T and SSHM10-5T, were isolated from saltern soil sampled in Jeollanam-do, Republic of Korea. Cells were aerobic, Gram-stain-positive, flagellated and rod-shaped. The strains grew optimally at 28°C and at pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains SSBR10-3T, SSTM10-2T and SSHM10-5T were placed within the genus Halobacillus, showing the highest similarity to Halobacillus alkaliphilus FP5T (98.6 %), 'Halobacillus ihumii' Marseille-Q1234T (98.5 %) and Halobacillus locisalis MSS-155T (98.6 %), respectively. The genomic similarity values between strains SSBR10-3T, SSTM10-2T and SSHM10-5T and their related species were 17.6-22.6 % for digital DNA-DNA hybridization (dDDH) and 69.6-78.5 % for orthologous average nucleotide identity (OrthoANI), which were lower than the thresholds recommended for species delineation. The dDDH and OrthoANI values among the three strains were below 38.3 and 89.4 %, respectively. Besides the differences in genomic features, strains SSBR10-3T, SSTM10-2T and SSHM10-5T were distinct from each other and from members of the genus in terms of phenotypic traits related to substrate assimilation. The cell-wall peptidoglycan contained meso-diaminopimelic acid, the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, and the predominant menaquinone was MK-7 for all three strains. Diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid were present in their polar lipid profiles. Based on a polyphasic approach incorporating genomic data, strains SSBR10-3T, SSTM10-2T and SSHM10-5T represent novel species, for which the names Halobacillus salinarum sp. nov. (SSBR10-3T=DSM 114353T=KACC 21935T=NBRC 115504T), Halobacillus shinanisalinarum sp. nov. (SSTM10-2T=DSM 114354T=KACC 21936T=NBRC 115505T) and Halobacillus amylolyticus sp. nov. (SSHM10-5T=DSM 114355T= KACC 21937T=NBRC 115506T) are proposed.

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6^T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6^T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546^T (98.6 %), Halobacillus locisalis KCTC 3788^T (98.6 %) and Halobacillus yeomjeoni KCTC 3957^T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6^T and its related species were 18.2-19.3 % and 69.84-84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30-40 °C, at pH 7.0 and with 10-15 % (w/v) NaCl. It contained l-Orn-d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C_15 : 0, anteiso-C_15 : 0 and anteiso-C_17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA-DNA relatedness and ANI values, strain SKP4-6^T represents a novel species of the genus Halobacillus, for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6^T (=JCM 32624^T=TISTR 2595^T).

HaloDom: a new database of halophiles across all life domains

Background

Halophilic organisms may thrive in or tolerate high salt concentrations. They have been studied for decades and a considerable number of papers reporting new halophilic species are being published every year. However, an extensive collection of these salt-loving organisms does not exist nowadays. Halophilic life forms have representatives from all three life domains, Archaea, Bacteria and Eukarya. The purpose of this study was to search for all documented halophilic species in the scientific literature and accommodate this information in the form of an online database.

Results

We recorded more than 1000 halophilic species from the scientific literature. From these, 21.9% belong to Archaea, 50.1% to Bacteria and 27.9% to Eukaryotes. Our records contain basic information such as the salinity that a particular organism was found, its taxonomy and genomic information via NCBI and other links. The online database named “HaloDom” can be accessed at http://www.halodom.bio.auth.gr.

Conclusions

Over the last few years, data on halophiles are growing fast. Compared to previous efforts, this new halophiles database expands its coverage to all life domains and offers a valuable reference system for studies in biotechnology, early life evolution and comparative genomics.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.