Genomic and transcriptomic analyses of jeotgalibacillus malaysiensis to provide insights inti its osmotic adaption

The genus Jeotgalibacillus under the family of Planococcaceae is one of the understudy genera. In this project, a bacterium strain D5 was isolated from Desaru beach, Johor. This study aimed to characterize strain D5 from morphological, physiological and biochemical aspects, in addition to examine the genomic feature and RNA expression response under saline stress. To achieve this objective, polyphasic analyses (phenotypic and genotypic), genome sequencing and RNA-Seq-based transcriptome analyses were performed. The result showed that strain D5 was mostly similar to Jeotgalibacillus alimentarius DSM 18867T with 99.87% 16S rRNA sequence similarity, and lower in similarity to other species. Strain D5 is distinguished from the other Jeotgalibacillus type strains due to the differences in phenotypic and genotypic characteristics which include morphology, endospore position, and shape, acid production from carbohydrates, tolerance to NaCl, fatty acid composition, DNA G+C content and DNA–DNA relatedness values. The D5 was proposed as a new type strain with the name of J. malaysiensis (DSM 28777T =KCTC 33350T). The complete genome of J. malaysiensis (3.52 Mbp) was sequenced using PacBio RS II sequencing system and was compared with draft genomes of J. alimentarius, J. campisalis, and J. soli. In total, 224 complete metabolic pathways were detected in J. malaysiensis genome, which include glycolysis, Krebs cycle, TCA cycle, pentose phosphate and others. J. malaysiensis shared 1,158 orthologous genes with the other Jeotgalibacillus spp. Which are involved in central metabolism, such as genes for flagellar activity, amino acid transport, translation, ribosomal structure, and biogenesis. To understand the mechanism of osmotic adaptation in J. malaysiensis, cells were cultivated in marine broth supplemented with 2% NaCl (control), saline stress of 10% and 20% (w/v) NaCl. The pairwise differentially expressed gene (DEGs) detected during the osmotic upshift were analyzed and categorized according to eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) groups. At 10% (w/v) NaCl, 195 genes were differentially expressed while at 20 % (w/v) NaCl, 166 DEGs were differentially expressed. Osmotic stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. J. malaysiensis apply a combination of approaches which include utilization of the TRK system for the regulation of K+ uptake, uptake and synthesis of various osmoprotectants especially proline and glutamate. As a conclusion, this study has provided new insights into the biology of this genus and showed that J. malaysiensis established halotolerance via a global cooperative mechanism, rather than by one single approach

Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan

The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis

Draft Genome Sequence of the Sulfate-Reducing Bacterium <i>Desulfotomaculum copahuensis</i> Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment.Centro de Investigación y Desarrollo en Fermentaciones Industriale

Modification of media formulation for enhancing production of extracellular polysaccharides by porphyridium cruentum

The red microalgae Porphyridium cruentum produce many valuable compounds such as extracellular polysaccharides (EPS) that are extensively used in the industry. In this study modification of media formulation for optimal production of EPS from Porphyridium cruentum was carried out by varying nitrate, sulfate and glucose concentrations in the Jones 1962 media. Different concentration of each nutrient was used in the media formulation. For nitrate, the highest concentration provided in the medium at 50 mM showed the highest growth rate and EPS production, but by inhibiting the nitrate concentration, the growth is reduced while the production of EPS is increased as when a high concentration of nitrate was provided to the medium. For sulfate, increasing concentration in the media showed great decrease in growth rate, but increasing EPS production, the highest production of EPS was at 50 mM which was the highest concentration of sulfate provided in the media modification. Addition of glucose in the medium on the other hand substantially increased the growth rate and the biomass production but as the glucose concentration kept on increasing, it also inhibited the production of EPS by the algae. The growth rate of the algae did not correlate with the EPS production. The result showed that high concentration of glucose and low concentration of nitrate and sulfate inhibited the production of EPS by the microalgae and in order to increase the EPS production, medium without nitrate or a very high concentration of nitrate or and sulfate must be provided. Therefore, the optimum medium formulation for optimal growth and EPS production by Porphyridium cruentum is at either 20 mM of nitrate or without nitrate at all, 50 mM of sulfate and 0.5% (w/v) of glucose. The compositions of the EPS were also confirmed by using HPLC that showed the composition of glucose, galactose and xylose of the EPS

Complete genome of Jeotgalibacillus malaysiensis D5T consisting of a chromosome and a circular megaplasmid

Jeotgalibacillus spp. are halophilic bacteria within the family Planococcaceae. No genomes of Jeotgalibacillus spp. have been reported to date, and their metabolic pathways are unknown. How the bacteria survive in hypertonic conditions such as seawater is yet to be discovered. As only few studies have been conducted on Jeotgalibacillus spp., potential applications of these bacteria are unknown. Here, we present the complete genome of J. malaysiensis D5T (=DSM 28777T =KCTC 33350T), which is invaluable in identifying interesting applications for this genus

Draft genome of Jeotgalibacillus campisalis SF-57T, a moderate halophilic bacterium isolated from marine saltern

Jeotgalibacillus campisalis SF-57T (= KCCM 41644T, JCM 11810T) is a moderate halophilic bacterium isolated from a Korean marine saltern. In this study, we describe the high-quality draft genome of strain SF-57T, which was assembled into 24 contigs containing 3,650,490 bp with a G + C content of 41.06%. Availability of the genome sequence of J. campisalis SF-57T will contribute to a better understanding of the genus Jeotgalibacillus

Draft genome sequence of yellow pigmented jeotgalibacillus alimentarius jy-13t, the first halophile strain of the genus jeotgalibacillus

Jeotgalibacillus alimentarius JY-13T (=KCCM 80002T=JCM 10872T) is a moderate halophile. In 2001, this was the first strain of the newly proposed Jeotgalibacillus genus. The draft genome of J. alimentarius was found to consist of 32 contigs (N50, 315,125 bp) with a total size of 3,364,745 bp. This genome information will be helpful for studies on pigmentation as well as applications for this bacterium

Isolation of Jeotgalibacillus malaysiensis sp. nov. from a sandy beach, and emended description of the genus Jeotgalibacillus

A Gram-stain-positive, endospore-forming, rod-shaped bacterial strain, designated D5T, was isolated from seawater collected from a sandy beach in a southern state of Malaysia and subjected to a polyphasic taxonomic study. Sequence analysis of the 16S rRNA gene demonstrated that this isolate belongs to the genus Jeotgalibacillus, with 99.87% similarity toJeotgalibacillus alimentarius JCM 10872T. DNA–DNA hybridization of strain D5T with J. alimentarius JCM 10872T demonstrated 26.3% relatedness. The peptidoglycan type was A1a linked directly to L-lysine as the diamino acid. The predominant quinones identified in strain D5Twere menaquinones MK-7 and MK-8.The major fatty acids were iso-C15:0 and anteiso-C15:0. The G+C content of its DNA was 43.0mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and sulfoquinovosyl diacylglycerol, as well as two unknown phospholipids and three unknown lipids. The phenotypic, chemotaxonomic and genotypic data indicated that strain D5T represents a novel species of the genus Jeotgalibacillus, for which the nameJeotgalibacillus malaysiensis sp. nov. is proposed (type strain D5T=DSM 28777T=KCTC33550T). An emended description of the genus Jeotgalibacillus is also provided

Draft genome sequence of erythrobacter vulgaris strain o1, a glycosyl hydrolase-producing bacterium

Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium

Draft genome sequence of jeotgalibacillus soli dsm 23228, a bacterium isolated from alkaline sandy soil

Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a nonmarine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N-acyl homoserine lactonases are presented