Lentibacillus persicus sp. nov., a moderately halophilic species isolated from a saline lake

Microbial diversity in polyextreme salt flats and their potential applications

Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.

Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea

A novel moderately halophilic bacterial strain, designated YIM 93176^T, was isolated from a saltern in Korea and subjected to a polyphasic taxonomic study. This isolate YIM 93176^T was observed to grow in the presence of 0-22% (w/v) NaCl and at pH 6.0-10.0 and 10-45 °C; optimum growth was observed with 5-10% (w/v) NaCl and at pH 7.0-9.0 and 28-37 °C. Based on 16S rRNA gene sequences analysis, the nearest relatives were Lentibacillus alimentarius M2024^T (96.5% similarity), followed by Virgibacillus carmonensis LMG 20964^T (96.0%) and the other type strains of the family Bacillaceae, but phylogenetic analysis indicated that strain YIM 93176^T belonged to the cluster comprising type species of the genus Lentibacillus. Genome sequencing of strain YIM 93176^T revealed a genome size of 3.2 Mb and a DNA G + C content of 40.5 mol%. The major fatty acids were anteiso-C_15:0 (40.7%) and iso-C_15:0 (26.4%), while the predominant respiratory quinone was menaquinone 7. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. These genotypic and chemotaxonomic characteristics supported affiliation of strain YIM 93176^T to the genus Lentibacillus. In addition, phenotypic characteristics could distinguish strain YIM 93176^T from its closely related species in genus Lentibacillus. Based on the cumulative evidences from the polyphasic taxonomic study, strain YIM 93176^T represents a novel species of the genus Lentibacillus, for which name Lentibacillus saliphilus sp. nov. (type strain YIM 93176^T = CCTCC AB 208139^T = DSM 21375^T) is proposed.

Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food

Two bacterial strains designated NKC220-2^T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5-9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3-99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3^T (97.4-97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1-9^T (79.5-79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC-220-2^T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C_15:0 and anteiso-C_17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2^T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2^T (= KACC 21232^T = JCM 33390^T).

Lentibacillus lipolyticus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi)

A Gram-stain-positive, aerobic, spore-forming, moderately halophilic bacterium, SSKP1-9^T, was isolated from traditional salted shrimp paste (Ka-pi) produced in Samut Sakhon Province, Thailand. This strain grew optimally at 37-40 °C, pH 7.0 and in the presence of 8-16 % (w/v) NaCl. The 16S rRNA gene sequence similarity values between strain SSKP1-9^T and Lentibacillus juripiscarius TISTR 1535^T and Lentibacillus halophilus TISTR 1549^T were 98.7 and 97.2 %, respectively. Based on 16S rRNA gene sequence similarity, strain SSKP1-9^T represents a distinct novel species, as shown by phenotypic traits, DNA-DNA hybridization and average nucleotide identity values. In addition, the whole-cell protein profile confirmed the novelty of the taxon. The genomic DNA G+C content was 44.6 mol%. The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis support that strain SSKP1-9^T represents a novel species of Lentibacillus, for which the name Lentibacilluslipolyticus sp. nov. is proposed. The type strain is SSKP1-9^T (=JCM 32625^T=TISTR 2597^T).

Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus salicampi ATCC BAA-719 T

Lentibacillus salicampi SF-20^T (=ATCC BAA-719^T) was first isolated from a Yellow Sea salt field in Korea in 2002. Here, we report that the L. salicampi ATCC BAA-719^T genome sequence has a predicted length of 3,897,716 bp, containing 3,945 total genes and a CRISPR array, with a G+C content of 43.0%.

Lentibacillus salicampi SF-20^T (=ATCC BAA-719^T) was first isolated from a Yellow Sea salt field in Korea in 2002. Here, we report that the L. salicampi ATCC BAA-719^T genome sequence has a predicted length of 3,897,716 bp, containing 3,945 total genes and a CRISPR array, with a G+C content of 43.0%.

Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6BT, was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6BT were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6BT was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5–20.0 % (w/v), with optimum growth occurring at 10.0 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6BT was shown to belong to the phylum Firmicutes and its closest phylogenetic similarities were with the species Virgibacillus koreensis BH30097T (97.5 %), Virgibacillus albus YIM 93624T (97.4 %), Sediminibacillus halophilus EN8dT (96.8 %), Sediminibacillus albus NHBX5T (96.6 %), Virgibacillus carmonensis LMG 20964T (96.3 %) and Paraliobacillus quinghaiensis YIM-C158T (96.0 %), respectively. Phylogenetic analysis revealed that strain B6BT, along with V. koreensis BH30097T and V. albus YIM 93624T, clustered in a separate clade in the family Bacillaceae . The DNA G+C content of the novel isolate was 35.8 mol%. DNA–DNA hybridization experiments revealed low levels of relatedness between strain B6BTand V. koreensis BH30097T (13 %) and V. albus YIM 93624T (33 %). The major cellular fatty acid of strain B6BT was anteiso-C15 : 0 (75.1 %) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90 %) and MK-6 (3 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6BT within the phylum Firmicutes . It is closely related to V. koreensis and V. albus , but with features that clearly distinguish it from species of the genus Virgibacillus or of other related genera. On the basis of the polyphasic evidence derived in this study, we propose that strain B6BT be placed within a new genus, as Aquibacillus halophilus gen. nov., sp. nov., with B6BT as the type strain ( = IBRC-M 10775T = KCTC 13828T). We also propose that V. koreensis and V. albus should be transferred to this new genus and be named Aquibacillus koreensis comb. nov. and Aquibacillus albus comb. nov., respectively. The type strain of Aquibacillus koreensis comb. nov. is BH30097T ( = KCTC 3823T = IBRC-M 10657T = JCM 12387T) and the type strain of Aquibacillus albus comb. nov. is YIM 93624T ( = DSM 23711T = IBRC-M 10798T = JCM 17364T).

Evolution in the Bacillaceae

The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae , the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.

Comparison of bacterial biodiversity and enzyme production in three hypersaline lakes; urmia, howz-soltan and aran-bidgol

This research is a comparative study on the diversity of halophilic bacteria with hydrolytic activities in three significant hypersaline lakes; Urmia in the northwest and Howz-Soltan and Aran-Bidgol in the central desert in Iran. Isolated strains from these saline lakes were found to be halotolerant, moderately and extremely halophilic bacteria. The bacteria in each saline lake were able to produce different hydrolytic enzymes including amylase, protease, lipase, DNase, inulinase, xylanase, carboxy methyl cellulase, pectinase and pullulanase. 188, 302, 91 halophilic strains were isolated from Urmia Lake, Howz-Soltan and Aran-Bidgol playa, respectively. The numbers of Gram-positive strains were more than Gram-negatives, and among Gram-positive bacteria; spore-forming bacilli were most abundant. Due to the unique physico-chemical conditions of the lake environments, the hydrolytic activities of isolated strains were significantly different. For instance, isolated strains from Howz-Soltan playa did not produce pectinase, DNase, amylase, lipase and inulinase, while the isolates from Aran-Bidgol playa had a great ability to produce pectinase and DNase. The strains from Urmia Lake were also good producers of DNase but failed to show any chitinase activity. The diversity of halophilic bacteria from the mentioned three saline lakes was also determined using PCR-amplified 16S rRNA followed by phylogenetic analysis of the partial 16S rRNA sequences.

Saliterribacillus persicus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a hypersaline lake

A novel Gram-positive, moderately halophilic bacterium, designated strain X4BT, was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain X4BT were motile rods and formed ellipsoidal endospores at a terminal or subterminal position in swollen sporangia. Strain X4BT was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5–22.5 % (w/v), with optimum growth occurring at 7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. Analysis of 16S rRNA gene sequence revealed that strain X4BT is a member of the family Bacillaceae , constituting a novel phyletic lineage within this family. Highest sequence similarities were obtained with the 16S rRNA gene sequences of the type strains of Sediminibacillus albus (96.0 %), Paraliobacillus ryukyuensis (95.9 %), Paraliobacillus quinghaiensis (95.8 %) and Sediminibacillus halophilus (95.7 %), respectively. The DNA G+C content of this novel isolate was 35.2 mol%. The major cellular fatty acids of strain X4BT were anteiso-C15 : 0 and anteiso-C17 : 0 and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids, an aminophospholipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (89 %) and MK-6 (11 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain X4BT represents a novel species in a new genus in the family Bacillaceae , order Bacillales for which the name Saliterribacillus persicus gen. nov., sp. nov. is proposed. The type strain of the type species (Saliterribacillus persicus) is X4BT ( = IBRC-M 10629T = KCTC 13827T).