Thalassobacillus cyri sp. nov., a moderately halophilic Gram-positive bacterium from a hypersaline lake

The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov

The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.

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.

A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils

Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.

New Insights into the Effect of Fipronil on the Soil Bacterial Community

Fipronil is a broad-spectrum insecticide with remarkable efficacy that is widely used to control insect pests around the world. However, its extensive use has led to increasing soil and water contamination. This fact is of concern and makes it necessary to evaluate the risk of undesirable effects on non-target microorganisms, such as the microbial community in water and/or soil. Studies using the metagenomic approach to assess the effects of fipronil on soil microbial communities are scarce. In this context, the present study was conducted to identify microorganisms that can biodegrade fipronil and that could be of great environmental interest. For this purpose, the targeted metabarcoding approach was performed in soil microcosms under two environmental conditions: fipronil exposure and control (without fipronil). After a 35-day soil microcosm period, the 16S ribosomal RNA (rRNA) gene of all samples was sequenced using the ion torrent personal genome machine (PGM) platform. Our study showed the presence of Proteobacteria, Actinobacteria, and Firmicutes in all of the samples; however, the presence of fipronil in the soil samples resulted in a significant increase in the concentration of bacteria from these phyla. The statistical results indicate that some bacterial genera benefited from soil exposure to fipronil, as in the case of bacteria from the genus Thalassobacillus, while others were affected, as in the case of bacteria from the genus Streptomyces. Overall, the results of this study provide a potential contribution of fipronil-degrading bacteria.

Thalassobacillus, a genus of extreme to moderate environmental halophiles with biotechnological potential

Thalassobacillus is a moderately halophilic genus that has been isolated from several sites worldwide, such as hypersaline lakes, saline soils, salt flats, and volcanic mud. Halophilic bacteria have provided functional stable biomolecules in harsh conditions for industrial purposes. Despite its potential biotechnological applications, Thalassobacillus has not been fully characterized yet. This review describes the Thalassobacillus genus, with the few species reported, pointing out its possible applications in enzymes (amylases, cellulases, xylanases, and others), biosurfactants, bioactive compounds, biofuels production, bioremediation, and plant growth promotion. The Thalassobacillus genus represents a little-explored biological resource but with a high potential.

Emended description of Salinivibrio proteolyticus, including Salinivibrio costicola subsp. vallismortis and five new isolates

We carried out a comparative taxonomic study of Salinivibrio proteolyticus and Salinivibrio costicola subsp. vallismortis, as well as of five halophilic strains (IB574, IB872, PR5, PR919 and PR932), isolated from salterns in Spain and Puerto Rico that were closely related to these bacteria. Multilocus sequence analysis of concatenated gyrB, recA, rpoA and rpoD housekeeping genes showed that they constituted a single cluster separate from the other species and subspecies of Salinivibrio. Experimental and in silico DNA-DNA hybridization studies indicated that they are members of the same species, with relatedness of 100-74 % and 97.8-70.0 %, respectively. The average nucleotide identity (ANI) determined for these strains was 99.7-95.6 % for ANIb and 99.7-95.7 % for OrthoANI. However, the ANI values for S. costicolasubsp.vallismortis DSM 8285^T with respect to S. costicolasubsp.costicola DSM 11403^T and S. costicolasubsp.alcaliphilus DSM 16359^T were 78.7 and 78.9 % (ANIb) and 79.4 and 79.4 % (OrthoANI), respectively. The phylogenomic tree based on 1072 concatenated orthologous single-copy core genes confirmed that S. proteolyticus, S. costicolasubsp.vallismortis and the five new isolates constitute a coherent single phylogroup, separated from the other species and subspecies of Salinivibrio. All these data indicate that S. costicolasubsp.vallismortis is a heterotypic synonym of S. proteolyticus and we propose an emended description of this species.

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns

Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184^T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAG^T (99.6-98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508^T (99.0-98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472^T (96.8-95.4% and 94.9-94.7%, respectively) and S. sharmensis DSM 18182^T (94.0-92.6% and 92.9-92.7%, respectively). In silico DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3-44.8% and 80.2-91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio. Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184^T were C_16:0 and C_18:1. The DNA G+C content range was 51.9-52.5mol% (T_m) and 50.2-50.9mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184^T (=CECT 9177^T=LMG 29817^T).

Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium

A novel filamentous, endospore-forming, thermophilic and moderately halophilic bacterium designated strain Nari2AT was isolated from soil collected from an Algerian salt lake, Chott Melghir. The novel isolate was Gram-staining-positive, aerobic, catalase-negative and oxidase-positive. Optimum growth occurred at 50–55 °C, 7–10 % (w/v) NaCl and pH 7–8. The strain exhibited 95.4, 95.4 and 95.2 % 16S rRNA gene sequence similarity to Thalassobacillus devorans G19.1T, Sediminibacillus halophilus EN8dT and Virgibacillus kekensis YIM-kkny16T, respectively. The major menaquinone was MK-7. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were iso-C15 : 0 and iso-C17 : 0. The DNA G+C content was 41.9 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain Nari2AT is considered to represent a novel species of a new genus in the family Bacillaceae , order Bacillales , for which the name Melghiribacillus thermohalophilus gen. nov., sp. nov. is proposed. The type strain of Melghiribacillus thermohalophilus is Nari2AT ( = DSM 25894T = CCUG 62543T).

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.

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).

Thalassobacillus pellis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from salted hides

A Gram-positive, moderately halophilic and endospore-forming bacterium, designated strain 18OM(T), was isolated from salted animal hides. The cells were rods and produced ellipsoidal endospores at a terminal position. Strain 18OM(T) was motile, strictly aerobic and grew at 0.5-25 % (w/v) NaCl [optimal growth at 10 % (w/v) NaCl], at between pH 5.0 and 9.0 (optimal growth at pH 7.5) and at temperatures between 15 and 45 °C (optimal growth at 37 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 18OM(T) was closely related to species of the genus Thalassobacillus within the phylum Firmicutes. The closest phylogenetic similarity was with Thalassobacillus devorans G-19.1(T) (98.4 %), Thalassobacillus cyri HS286(T) (97.9 %) and Thalassobacillus hwangdonensis AD-1(T) (97.4 %). The major cellular fatty acids were anteiso-C(15 : 0) (57.9 %), anteiso-C(17 : 0) (14.0 %), iso-C(15 : 0) (10.8 %) and iso-C(16 : 0) (8.1 %). The respiratory isoprenoid quinones were MK-7 (98.5 %) and MK-6 (1.5 %). The DNA G+C content was 42.9 mol%. These features confirmed the placement of strain 18OM(T) within the genus Thalassobacillus. The DNA-DNA hybridization values between strain 18OM(T) and T. devorans G-19.1(T), T. cyri HS286(T) and T. hwangdonensis AD-1(T) were 49 %, 9 % and 15 %, respectively, showing unequivocally that strain 18OM(T) constituted a novel genospecies. On the basis of phylogenetic analysis and phenotypic, genotypic and chemotaxonomic characteristics, strain 18OM(T) is considered to represent a novel species of the genus Thalassobacillus, for which the name Thalassobacillus pellis sp. nov. is proposed. The type strain is 18OM(T) ( = CECT 7566(T) = DSM 22784(T) = JCM 16412(T)).

Thalassobacillus hwangdonensis sp. nov., isolated from a tidal flat sediment

A Gram-staining-positive, endospore-forming, motile, rod-shaped bacterium, strain AD-1(T), was isolated from a tidal flat sediment of the coast of Hwangdo on the Yellow Sea, Korea. Strain AD-1(T) grew optimally at pH 7.0-7.5 and 40 degrees C and in the presence of 5-10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AD-1(T) was most closely related to Thalassobacillus devorans G-19.1(T) (98.0 % sequence similarity) and Thalassobacillus cyri HS286(T) (97.8 %). The cell-wall peptidoglycan was based on meso-diaminopimelic acid and MK-7 was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified lipids. The major fatty acids (>10 % of total fatty acids) were iso-C(15 : 0), iso-C(17 : 0) and anteiso-C(15 : 0). The DNA G+C content of strain AD-1(T) was 45.2 mol%. It appears reasonable to classify strain AD-1(T) as a member of the genus Thalassobacillus. There were differences in fatty acid profiles and phenotypic and genetic characteristics between strain AD-1(T) and the type strains of the two Thalassobacillus species. On the basis of the data presented, strain AD-1(T) represents a novel species within the genus Thalassobacillus, for which the name Thalassobacillus hwangdonensis sp. nov. is proposed. The type strain is AD-1(T) (=KCTC 13254(T) =CCUG 56607(T)).