Genomic analysis of a novel species Halomonas shambharensis isolated from hypersaline lake in Northwest India.

Genome analysis of Halomonas shambharensis, a novel species, was performed to understand the osmoprotectant strategies used by the strain to overcome the salinity stress and to explore the prospective industrial uses. It will also help to better understand the ecological roles of Halomonas species in hypersaline habitats. Ultrastructure of the cell was determined by using transmission electron microscopy. Standard microbiological methods were used to find out growth parameters and heterotrophic mode of nutrition. For Genome analysis, complete bacterial genome sequencing was performed using the Oxford Nanopore MinION DNA Sequencer. Assembly, annotation and finishing of the obtained sequence were done by using a Prokaryotic Genome Annotation Pipeline (PGAP) (SPAdes v. 3.10.1). Predicted Coading sequences (CDSs) obtained through the PGAP were used for functional annotation using Clusters of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms. The H. shambharensis was found to be a Gram-stain-negative, rod-shaped bacterium, motile with a peritrichous flagella. The H. shambharensis bacterium can grow in a wide range of temperature (from 25 to 65 °C), pH (pH 4 to pH 12.0) and salt concentration (5.0% NaCl to 30.0% NaCl). After annotation and assembly, the total genome size obtained was 1,533,947 bp, which revealed 146 subsystems, 3847 coding sequences, and 19RNAs with G+C content of 63.6%. Gene annotation identified the genes related to various metabolic pathways, including carbohydrate metabolism, fatty acid metabolism and stress tolerance. The genomic dataset of H. shambharensis will be useful for analysis of protein-coding gene families and how these coding genes are significant for the survival and metabolism among the different species of Halomonas. The complete genome sequence presented here will help to unravel the biotechnological potential of H. shambharensis for production of the high-value products such as betaine, or as a source of gene-mining for individual enzymes.

Halomonas sambharensis sp. nov., a Moderately Halophilic Bacterium Isolated from the Saltern Crystallizer Ponds of the Sambhar Salt Lake in India.

Two moderately halophilic strains SBS 10T and SSO 06 were isolated from the saltern crystallizer ponds of the hypersaline Sambhar Salt Lake in India. Strains were aerobic, Gram-stain-negative, and rod shaped. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that two strains belong to the genus Halomonas in the Gammaproteobacteria, with highest 16S rRNA gene sequence similarities with Halomonas gudaonensis LMG 23610T (98.2% similarity) and Halomonas campaniensis 5AGT (99.0% similarity). Strains grew optimally at 37 °C, pH 7.5-8.0 in the presence of 5-8% (w/v) NaCl. The major fatty acids of the strain SBS 10T were C18:1ω7c (54.37%), C16:0 (25.69%), C16:1 × 7c/C16:1 × 6c (13.28%), and C12:0 (1.21%). The G+C content was 63.6 mol % (Tm). Phenotypic features, fatty acids profile, and DNA G+C content supported placement of the strain SBS 10T in the genus Halomonas having distinct characteristics with related strains. Analysis of the housekeeping genes: gryB and rpoD and in silico DNA-DNA hybridization between the strain SBS 10T and its type strain Halomonas gudaonensis (LMG 23610T) further revealed the strain SBS 10T to be a distinct species. On the basis of the phenotypic, chemotaxonomic and phylogenetic analysis, the strain SBS 10T is considered to represent a novel species for which the name Halomonas sambharensis is proposed. The type strain is SBS 10T (= MTCC 12313T = LMG 30344T).

Betaine accumulation suppresses the de-novo synthesis of ectoine at a low osmotic concentration in Halomonas sp SBS 10, a bacterium with broad salinity tolerance.

The study aims to find out osmoadaptive mechanism used to overcome the salinity stress by Halomonas sp SBS 10 isolated from the saltern crystallizer ponds of the Sambhar Salt Lake and its taxonomic position using neighbor-joining algorithm. The strain SBS 10 was tested for accumulation of two major compatable solutes betaine and ectoine and was observed that osmoprotection in the strain SBS 10 is achieved by the accumulation of betaine or by the de-novo synthesis of betaine or ectoine. Amount of endogenous content of the betaine and ectoine per milligram of cell biomass was estimated to be 581 µg, 587 µg, 588 µg, 617 µg, and 761 µg for betaine and 1.52 µg, 2.74 µg, 3.14 µg, 3.50 µg, and 52.67 µg for ectoine, when exposed to 5, 10, 15, 20 and 25% of NaCl concentration. Results obtained from HPLC analysis showed that the betaine accumulation suppresses the de-novo synthesis of ectoine partially at low NaCl concentration in the growth medium. However, at a high NaCl concentration, the ectoine concentration increases abruptly as compared to the betaine. This indicates that the ectoine accumulation is transcriptionally up-regulated by the salinity stress. Phylogenetic analysis based on the neighbor-joining algorithm included the strain SBS 10 in the genus Halomonas of the family Halomonadaceae belonging to the class Gammaproteobacteria. Most closely related type strain was found to be Halomonas gudaonensis SL014B-69T (98.2% similarity). Ultrastructure characteristics showed the strain to be non-spore forming rod, 0.3-0.4 × 0.75-1.65 µm in size and motile with the help of peritrichous flagella.

Sulfur oxidation by Achromobacter xylosoxidans strain wsp05 reveals ecological widening over which thiotrophs are distributed.

Achromobacter xylosoxidans is a versatile bacterium known for its ability to degrade aromatic compounds. However, its ability to oxidize sulfur compounds for electron and energy source is not reported much. In the present work, the Gram-negative bacterium Achromobacter xylosoxidans strain wsp05 isolated from a waste stabilization ponds (WSPs) system was studied for its ability to oxidize reduced sulfur compounds. The strain was able to oxidize thiosulfate and sodium sulfite. To observe the effect of physicochemical parameters on the rate of sulfur oxidation, strain wsp05 was grown in thiosulfate (20 mM) containing minimal salt medium at varied pH, temperature and ammonium and phosphate ions concentration. Maximum thiosulfate oxidation was observed at 30 °C with initial pH of 7-7.2. The strain was characterized using universal 16S rRNA gene primers revealing high similarity (> 99%) with Achromobacter xylosoxidans NBRC 15126T belonging to ß-proteobacteria. In the present study, we investigated the sulfur oxidation properties of the Achromobacter xylosoxidans strain wsp05, which revealed an ecological and phylogenetic widening over which the thiotrophs are distributed.

Whole-Genome Shotgun Sequence of Halomonas sp. Strain SBS 10, Isolated from a Hypersaline Lake in India.

The whole-genome shotgun sequence of a moderately halophilic bacterium, Halomonas sp. strain SBS 10, was assembled and studied. The assembled genome size was 1.5 Mb, with a G+C content of 63.6%. The genome sequence of this Halomonas sp. SBS 10 isolate will be valuable in understanding gene clusters and functions involved in the adaptability of this bacterium to hypersaline conditions.