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 SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546T (98.6 %), Halobacillus locisalis KCTC 3788T (98.6 %) and Halobacillus yeomjeoni KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T 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-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 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 SKP4-6T represents a novel species of the genus Halobacillus , for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).

Halomonas Salinarum sp. nov., a Moderately Halophilic Bacterium, Isolated from Saline Soil in Yingkou, China

Strains of Halomonas, thought to play vital roles in the environment for their versatility, are ubiquitous in hypersaline environments. A Gram-staining-negative, moderately halotolerant, facultatively aerobic, motile bacterium, designated G5-11T, was isolated from saline soil in Yingkou of Liaoning, China. The cells of strain G5-11T grew at 4-35 ℃ (optimum 30 ℃), at pH 6.0-9.0 (optimum 8.0) and in the presense of 3-15 % (w/v) NaCl (optimum 5 %). The strain could be clearly distinguished from the related species of the genus Halomonas by its phylogenetic position and biochemical characteristics. It presented Q-9 as the major respiratory quinone and the dominant cellular fatty acids were summed feature 8 (C18:1 ω7c/ C18:1 ω6c), C16:0 and summed feature 3 (C16:1 ω7c/ C16:1 ω6c). The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol as the major components. The G+C content of strain G5-11T genome was 61.0 mol%. 16S rRNA analysis showed that strain G5-11T had the highest similarity to Halomonas niordiana LMG 31227T and Halomonas taeanensis DSM 16463T, both reaching 98.3 %, followed by Halomonas pacifica NBRC 102220T with a value of 95.8 %. Based on phenotypic, chemotaxonomic and phylogenetic inferences, strain G5-11T represents a novel species of the genus Halomonas, for which the name Halomonas salinarum sp. nov. is proposed. The type strain of Halomonas salinarum is G5-11T (=CGMCC 1.12051T=LMG 31677T).

Salt Tolerance Mechanism of the Rhizosphere Bacterium JZ-GX1 and Its Effects on Tomato Seed Germination and Seedling Growth

Salinity is one of the strongest abiotic factors in nature and has harmful effects on plants and microorganisms. In recent years, the degree of soil salinization has become an increasingly serious problem, and the use of plant growth-promoting rhizobacteria has become an option to improve the stress resistance of plants. In the present study, the salt tolerance mechanism of the rhizosphere bacterium Rahnella aquatilis JZ-GX1 was investigated through scanning electron microscopy observations and analysis of growth characteristics, compatible solutes, ion distribution and gene expression. In addition, the effect of JZ-GX1 on plant germination and seedling growth was preliminarily assessed through germination experiments. R. aquatilis JZ-GX1 was tolerant to 0–9% NaCl and grew well at 3%. Strain JZ-GX1 promotes salt tolerance by stimulating the production of exopolysaccharides, and can secrete 60.6983 mg/L of exopolysaccharides under the high salt concentration of 9%. Furthermore, the accumulation of the compatible solute trehalose in cells as the NaCl concentration increased was shown to be the primary mechanism of resistance to high salt concentrations in JZ-GX1. Strain JZ-GX1 could still produce indole-3-acetic acid (IAA) and siderophores and dissolve inorganic phosphorus under salt stress, characteristics that promote the ability of plants to resist salt stress. When the salt concentration was 100 mmol/L, strain JZ-GX1 significantly improved the germination rate, germination potential, fresh weight, primary root length and stem length of tomato seeds by 10.52, 125.56, 50.00, 218.18, and 144.64%, respectively. Therefore, R. aquatilis JZ-GX1 is a moderately halophilic bacterium with good growth-promoting function that has potential for future development as a microbial agent and use in saline-alkali land resources.

A Novel pH and Thermo-Tolerant Halophilic Alpha-amylase From Moderate Halophile Nesterenkonia Sp.Strain F: Gene Analysis, Molecular Cloning, Heterologous Expression and Biochemical Characterization

A novel pH and thermo-tolerate halophilic alpha-amylase from moderately halophilic bacterium, Nesterenkonia sp.strain F was cloned and expressed in Escherichia coli. 16S rRNA sequence of the strain shared 99.46 % similarities with closely related type species. Also, the genome sequence shared ANI values below 92 % and dDDH values below 52 % with the closely related type species. Consequently, it is proposed that strain F represents a novel species. The AmyF gene was 1390 bp long and encodes an alpha-amylase of 463 amino acid residues with pI of 4.62. The deduced AmyF shared very low sequence similarity (<24%) with functionally characterized recombinant halophilic alpha- amylases. The recombinant alpha-amylase was successfully purified from Ni-NTA columns with a molecular mass of about 52 KDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active over a wide range of temperature (25–75 °C) and pH (4–9) with optimum activity at 45 °C and 7.5, respectively. Also, although it was active over a various concentrations of NaCl and KCl (0–4 M), increasing activity of the enzyme was observed with increasing concentration of these salts. Low concentrations of Ca2+ ion had no activating effect, but high concentrations of the ion (40 - 200 mM) enhanced activity of AmyF. The enzyme activity was increased by increasing concentrations of Mg2+, Zn2+, Hg2+ and Fe3+. However, it was inhibited only at very high concentrations of these metal ions. Cu2+ did not decrease the amylase activity and the highest activity was observed at 100 mM of the ion. These properties indicate wide potential applications of this recombinant enzyme in starch processing industries. This is the first isolation, cloning and characterization of a gene encoding alpha-amylase from Nesternkonia genus.

Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow

A Gram-stain-positive, facultatively anaerobic, endospore-forming, rod-shaped strain, AGMB 02131T, which grew at 20–40 °C (optimum 30 °C), pH 3.0–11.0 (optimum pH 4.0) and in the presence of 0–18 % (w/v) NaCl (optimum 10 %), was isolated from a cow faecal sample and identified as a novel strain using a polyphasic taxonomic approach. The phylogenetic analysis based on 16S rRNA gene sequences along with the whole genome (92 core gene sets) revealed that AGMB 02131T formed a group within the genus Peribacillus , and showed the highest sequence similarity with Peribacillus endoradicis DSM 28131T (96.9 %), following by Peribacillus butanolivorans DSM 18926T (96.6 %). The genome of AGMB 02131T comprised 70 contigs, the chromosome length was 4 038 965 bp and it had a 38.5 % DNA G+C content. Digital DNA–DNA hybridization revealed that AGMB 02131T displayed 21.4 % genomic DNA relatedness with the most closely related strain, P. butanolivorans DSM 18926T. AGMB 02131T contains all of the conserved signature indels that are specific for members of the genus Peribacillus . The major cellular fatty acids (>10 %) of AGMB 02131T were C18 : 1ω9c, C18:0 and C16 : 0. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, AGMB 02131T represents a novel species of the genus Peribacillus , for which the name Peribacillus faecalis sp. nov. is proposed. The type strain is AGMB 02131T (=KCTC 43221T=CCTCC AB 2020077T).

Halomonas Maris Sp. Nov., a Moderately Halophilic Bacterium Isolated From Marine Sediment in the Southwest Indian Ocean

A halophilic, Gram-staining-negative, rod-shaped, flagellated and motile bacterium, strain QX-1T, was isolated from deep-sea sediment at a depth of 3332 m in the southwestern Indian Ocean. Strain QX-1T growth was observed at 4–50 °C (optimum 37 °C), pH 5.0–11.0 (optimum pH 7.0), 3%–25% NaCl (w/v; optimum 7%), and it did not grow without NaCl. A phylogenetic analysis based on the 16S rRNA gene placed strain QX-1T in the genus Halomonas and most closely related to Halomonas sulfidaeris (97.90%), Halomonas zhaodongensis (97.80%), Halomonas songnenensis (97.59%), Halomonas hydrothermalis (97.37%), Halomonas subterranea (97.25%), Halomonas salicampi (97.09%), and Halomonas arcis (97.01%). DNA–DNA hybridization (< 26.50%) and average nucleotide identity values (< 83.54%) between strain QX-1T and the related type strains meet the accepted criteria for a new species. The principal fatty acids (> 10%) of strain QX-1T are C16:0 (25.50%), C17:0 cyclo (14.02%), C19:0 cyclo ω8c (18.72%), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c, 18.08%). The polar lipids of strain QX-1T are mainly diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid, unidentified aminophospholipid, and five unidentified lipids. The main respiratory quinone is Q-9. The G+C content of its chromosomal DNA is 54.4 mol%. Its fatty acid profile, respiratory quinones, and G+C content also support the placement of QX-1T in the genus Halomonas. These phylogenetic, phenotypic, and chemotaxonomic analyses indicate that QX-1T is a novel species, for which the name Halomonas maris is proposed. The type strain is QX-1T (=MCCC 1A17875T = KCTC 82198T = NBRC 114670T).

Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India

A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1T, belonging to the genus Halomonas , was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of gyrB and rpoD genes revealed that strain D1-1T belonged to the genus Halomonas and was most closely related to Halomonas alimentaria YKJ-16T (98.1 %) followed by Halomonas ventosae Al12T (97.5 %), Halomonas sediminicola CPS11T (97.5 %), Halomonas fontilapidosi 5CRT (97.4 %) and Halomonas halodenitrificans DSM 735T (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4–30 % and 79.5–85.4 % with close relatives of H. halodenitrificans DSM 735T, H . alimentaria YKJ-16T, H. ventosae Al12T and H. fontilapidosi 5CRT were lower than the threshold recommended for species delineation (70 % and 95–96 % for dDDH and ANI, respectively). Further, strain D1-1T formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4–45 °C) and 2–8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0 and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1T represents a novel species in the genus Halomonas , for which we propose the name Halomonas icarae sp. nov., within the family Halomonadaceae . The type strain is D1-1T (=JCM 33602T=KACC 21317T=NAIMCC-B-2254T).