Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment

Two aerobic, Gram-stain-positive, spore-forming motile bacterial strains, designated SSPM10-3T and SSWR10-1T, were isolated from salterns in Jeollanam province of South Korea. Both strains were halotolerant and grew well in 5 % NaCl but not in 20 and 25% NaCl, respectively. Optimal growth was observed with 5 % NaCl, at 30 °C and at pH 7.0-8.0. On the basis of the results of phylogenetic analysis using 16S rRNA gene sequence, both the strains were placed within the genus Gracilibacillus with Gracilibacillus massiliensis (98.65 % similarity) as their nearest neighbour. Menaquinone-7 (MK-7) (97 %) was the major isoprenoid quinone in both strains and major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Orthologous average nucleotide identity with usearch (OrthoANIu) and digital DNA-DNA hybridisation (dDDH) percentage comparison indicated that SSPM10-3T and SSWR10-1T exhibited highest similarity with G. massiliensis Awa-1T at 74.27 % and 21.0 and 74.23 % and 20.0 %, respectively. The DNA G+C contents of the strains were 39.1 % (SSPM10-3T) and 38.5 % (SSWR10-1T). Members of the genus Gracilibacillus, both strains were distinct from each other with respect to their ability to produce urease, β-glucosidase, assimilation of inulin and methyl-α-d-glucopyranoside and degradation of casein. Compared with each other, ANI and d4 dDDH calculations were only 88.2 % and 36.3 %, well below the cut-off values for species delineation for each index. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics,SSPM10-3T and SSWR10-1T represent distinct novel species for which names Gracilibacillus salinarum SSPM10-3T and Gracilibacillus caseinilyticus SSWR10-1T are proposed. The type strains are SSPM10-3T (=KACC 21933T =NBRC 115502T) and SSWR10-1T (=KACC 21934T =NBRC 115503T).

Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa

A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30^T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30^T grew at pH 6.0-11.0 (optimum, pH 7.0), 10-40 °C (35 °C) and in the presence of 1-15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30^T were iso-C_15:0, C_15:1 ω5c and anteiso-C_15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30^T clustered with Gracilibacillus thailandensis TP2-8^T, Gracilibacillus saliphilus YIM 91119^T and Gracilibacillus lacisalsi BH312^T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8^T, G. saliphilus YIM 91119^T, G. lacisalsi BH312^T and all other current type strains, respectively. The digital DNA-DNA hybridization and average nucleotide identity based on blast values between strain LD4P30^T and G. saliphilus YIM 91119^T, G. thailandensis TP2-8^T and G. lacisalsi BH312^T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30^T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30^T (=CGMCC 1.17697^T=KCTC 82375^T).

Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri

Purpose

Gracilibacillus dipsosauri strain DD1 is a salt-tolerant Gram-positive bacterium that can hydrolyze the synthetic substrates o-nitrophenyl-β-d-galactopyranoside (β-ONP-galactose) and p-nitrophenyl-α-d-galactopyranoside (α-PNP-galactose). The goals of this project were to characterize the enzymes responsible for these activities and to identify the genes encoding them.

Methods

G. dipsosauri strain DD1 was grown in tryptic soy broth containing various carbohydrates at 37 °C with aeration. Enzyme activities in cell extracts and whole cells were measured colorimetrically by hydrolysis of synthetic substrates containing nitrophenyl moieties. Two enzymes with β-galactosidase activity and one with α-galactosidase activity were partially purified by ammonium sulfate fractionation, ion-exchange chromatography, and gel-filtration chromatography from G. dipsosauri. Coomassie Blue-stained bands corresponding to each activity were excised from nondenaturing polyacrylamide gels and subjected to peptide sequencing after trypsin digestion and HPLC/MS analysis.

Result

Formation of β-galactosidase and α-galactosidase activities was repressed by d-glucose and not induced by lactose or d-melibiose. β-Galactosidase I had hydrolytic and transgalactosylation activity with lactose as the substrate but β-galactosidase II showed no activity towards lactose. The α-galactosidase had hydrolytic and transgalactosylation activity with d-melibiose but not with d-raffinose. β-Galactosidase I had a lower Km with β-ONP-galactose as the substrate (0.693 mmol l−1) than β-galactosidase II (1.662 mmol l−1), was active at more alkaline pH, and was inhibited by the product d-galactose. β-Galactosidase II was active at more acidic pH, was partially inhibited by ammonium salts, and showed higher activity with α-PNP-arabinose as a substrate. The α-galactosidase had a low Km with α-PNP-galactose as the substrate (0.338 mmol l−1), a pH optimum of about 7, and was inhibited by chloride-containing salts. β-Galactosidase I activity was found to be due to the protein A0A317L6F0 (encoded by gene DLJ74_04930), β-galactosidase II activity to the protein A0A317KZG3 (encoded by gene DLJ74_12640), and the α-galactosidase activity to the protein A0A317KU47 (encoded by gene DLJ74_17745).

Conclusions

G. dipsosauri forms three intracellular enzymes with different physiological properties which are responsible for the hydrolysis of β-ONP-galactose and α-PNP-galactose. BLAST analysis indicated that similar β-galactosidases may be formed by G. ureilyticus, G. orientalis, and G. kekensis and similar α-galactosidases by these bacteria and G. halophilus.

Gracilibacillus oryzae sp. nov., isolated from rice seeds

A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8^T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8^T should be placed within the genus Gracilibacillus (95.2-99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727^T (99.0 %), 'Gracilibacillus xinjiangensis' CGMCC 1.12449^T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642^T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0, iso-C_15 : 0, C_16 : 0 and iso-C_16 : 0, which supported the allocation of the strain to the genus Gracilibacillus. The digital DNA-DNA hybridization value between strain TD8^T and Gracilibacillus ureilyticus CGMCC 1.7727^T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8^T represented a novel species in the genus Gracilibacillus. The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8^T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8^T (=ACCC 61556^T=CICC 24889^T=JCM 33537^T).

Gracilibacillus salitolerans sp. nov., a moderate halophile isolated from saline soil in Northwest China

A moderately halophilic strain, designated SCU50T, was recovered from a saline soil sample and characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain SCU50T belonged to the genus Gracilibacillus and was most closely related to Gracilibacillus thailandensis TP2-8T (98.1 % similarity) and Gracilibacillus orientalis XH-63T (97.7 %). Genomic average nucleotide identity and digital DNA–DNA hybridization analyses confirmed the separate species status of the new isolate relative to other recognized Gracilibacillus species. The genome size was about 5.09 Mbp and the DNA G+C content was 36.7 mol%. The strain grew optimally at 10–15 % (w/v) NaCl, pH 6.5–7.5 and 25–30 °C. It contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the dominant fatty acids and menaquinone-7 as the major respiratory quinone. The polar lipid profile was examined and found to comprise diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The cell-wall peptidoglycan type was A1γ based on meso-diaminopimelic acid. Combining the data from phenotypic, chemotaxonomic, genomic and phylogenetic characterization, it was concluded that strain SCU50T should be assigned as representing a novel species within the genus Gracilibacillus . Thus, a novel taxon named Gracilibacillus salitolerans sp. nov. was first established, with SCU50T (=CGMCC 1.17336T=KCTC 43107T) as the type strain.

Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase

Gracilibacillus dipsosauri is a moderately-halophilic Gram-positive bacterium which forms an extracellular α-amylase that is induced by starch, repressed by D-glucose, and active in 2.0 M KCl. Previous studies showed that while enzyme activity could be measured with the synthetic substrate 2-chloro-4-nitrophenyl-α-D-maltotrioside (CNPG3), other assays were inconsistent and the protein showed aberrant mobility during nondenaturing gel electrophoresis. To clarify the properties of this enzyme, the genome of G. dipsosauri was sequenced and was found to be 4.19 Mb in size with an overall G+C content of 36.9%. A gene encoding an α-amylase composed of 691 amino acids was identified. The protein was a member of the glycosyl hydrolase 13 family, which had a molecular mass of 77,396 daltons and a pI of 4.39 due to an unusually large number of aspartate and glutamate residues (95/691 or 13.7%). BLAST analysis of the amino acid sequence revealed significant matches to other proteins with cyclodextrin glycosyltransferase activity. Partial purification of the protein from G. dipsosauri showed that fractions catalyzing the hydrolysis of CNPG3 and p-nitrophenyl-D-maltoheptoside also catalyzed the formation of β-cyclodextrin but not α-cyclodextrin or γ-cyclodextrin. Formation of β-cyclodextrin was not stimulated by high salt concentrations but did occur with rice, potato, wheat, and corn starches and amylopectin. These studies explain the unusual features of the α-amylase from G. dipsosauri and indicate it should be classified as EC 2.4.1.19. The availability of the complete genomic sequence of G. dipsosauri will provide the basis for studies on other enzymes from this halophile which may be useful for biotechnology.

Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species

The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.

Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora

Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille‐P2481 (= CSUR P2481 =  DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram‐positive, strictly aerobic, spore‐forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille‐P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0–8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12‐methyl‐tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille‐P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103^T, the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille‐P2481^T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.

Gracilibacillus eburneus sp.nov., a moderately halophilic bacterium isolated from Xinjiang province, China

A novel Gram-staining positive, moderately halophilic, endospore-forming, motile, rod-shaped and strictly aerobic strain, designated YIM 93565^T, was isolated from a salt lake in Xinjiang province of China and subjected to a polyphasic taxonomic study. Strain YIM 93565^T grew in the range of pH 6.0-9.0 (optimum pH 7.0), 10-45 °C (optimum 35-40 °C) and at salinities of 2-24% (w/v) NaCl (optimum 7-10%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 93565^T clustered with members of the genera Gracilibacillus and form a clade with Gracilibacillus bigeumensis KCTC 13130^T (95.6% similarity) and Gracilibacillus halophilus DSM 17856^T (94.9%), which was well separated from others. The DNA G + C content of this novel strain was 36.8 mol%. The major fatty acids were anteiso-C_15:0, iso-C_15:0, C_16:0 and anteiso-C_17:0 and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and two unidentified phospholipids. The predominant menaquinone was MK-7. The cell-wall peptidoglycan was based on meso-diaminopimelic acid. Based on the results of phylogenetic, physiological and chemotaxonomic comparative analyses, the isolate is assigned to a novel species of the genus Gracilibacillus, for which the name Gracilibacillus eburneus sp. nov. is proposed, with the type strain YIM 93565^T (= DSM 23710^T = CCTCC AB 2013249^T).

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001^T. Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C_15:0, anteiso C_17:0, iso C_15:0. The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8^T (96.84%), followed by Gracilibacillus saliphilus YIM 91119^T (96.78%) and Gracilibacillus ureilyticus MF38^T (96.57%), thus confirming the affiliation of strain YIM 98001^T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001^T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001^T (=KCTC 42683^T = DSMZ 104330^T).

Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi

A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).

Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing

A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SG103T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample for dyeing prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that SG103T is a member of the genus Gracilibacillus with the closest relatives being ‘Gracilibacillus xinjiangensis’ J2 (similarity: 97.06 %), Gracilibacillus thailandensis TP2-8T (97.06 %) and Gracilibacillus halotolerans NNT (96.87 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew at temperatures between 13 and 48 °C with the optimum at 39 °C. It grew in the range pH 7–10 with the optimum at pH 9. The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 41.3 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Unlike other reported species of the genus Gracilibacillus , the strain lacked diphosphatidylglycerol as a major polar lipid. DNA–DNA hybridization experiments with strains exhibiting greater than 96.87 % 16S rRNA gene sequence similarity, ‘G. xinjiangensis’ J2, G. thailandensis TP2-8T and G. halotolerans NNT, revealed 2±4 %, 4±9 % and 3±2 % relatedness, respectively. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported species of the genus Gracilibacillus , strain SG103T merits classification as a members of a novel species, for which the name Gracilibacillus alcaliphilus sp. nov. is proposed. The type strain is SG103T ( = JCM 17253T = NCIMB 14683T).

Gracilibacillus marinus sp. nov., isolated from the northern South China Sea

Two gram-positive, aerobic, spore-forming, rod-shaped bacteria, designated HB09003(T) and HB12160, were isolated from seawater and sediment in the northern South China Sea, respectively. Cells were found to be motile by means of peritrichous flagella. The strains were found to grow with 0-15 % (w/v) NaCl, at 10-45 °C and pH 5.0-10.7, with an optimum of 3 % NaCl, 28 °C and pH 8.5, respectively. The predominant isoprenoid quinone of strain HB09003(T), selected as the representative strain, was identified as MK-7. This strain was found to possess anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major fatty acids. The G+C contents of strain HB09003(T) and HB12160 were determined to be 34.1 and 34.3 mol%, respectively. Analysis of the 16S rRNA gene sequences of the two strains showed an affiliation with the genus Gracilibacillus, with Gracilibacillus kekensis CGMCC 1.10681(T) (similarity of 97.4, 98.0 %, respectively) and Gracilibacillus ureilyticus CGMCC 1.7727(T) (similarity of 97.1, 97.8 %, respectively) as their closest relatives. The DNA-DNA hybridization values between strain HB09003(T) and the two type strains were 42.2 and 54.1 %, respectively. On the basis of phenotypic and genotypic data, strain HB09003(T) and HB12160 are proposed to represent a novel species of the genus Gracilibacillus, for which the name Gracilibacillus marinus sp. nov. is proposed. The type strain is HB09003(T) (=CGMCC 1.10343(T) = DSM 23372(T)).

Gracilibacillus xinjiangensis sp. nov., a new member of the genus Gracilibacillus isolated from Xinjiang region, China

A Gram-positive, endospore-forming, rod-shaped bacterium, designated isolate J2(T) was isolated from a soil sample from Xinjiang Uyghur Autonomous Region, China. The isolate was observed to grow at 16-46 °C and pH 6.5-8.0. Chemotaxonomic analysis showed menaquinone-7 (MK-7) to be the major isoprenoid quinone; diphosphatidylglycerol, phosphatidylglycerol, one aminophospholipid, two phosphoglycolipids and one glycolipid as the major cellular polar lipids; and anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major fatty acids. Comparative analyses of the 16S rRNA gene sequence showed that strain J2(T) is most closely related to Gracilibacillus ureilyticus (with 98.8 % similarity), Gracilibacillus dipsosauri (97.2 %), Gracilibacillus quinghaiensis (97.1 %) and Gracilibacillus thailandensis (97.0 %). The DNA-DNA reassociation values between strain J2(T) and G. ureilyticus MF38(T), G. dipsosauri DD1(T), G. quinghaiensis YIM-C229(T) and G. thailandensis TP2-8(T) were 29.8 ± 3.7, 23.0 ± 3.5, 15.8 ± 4.9 and 15.9 ± 5.0 %, respectively. The genomic DNA G+C content of strain J2(T) was determined to be 36.5 mol%. Based on these data, strain J2(T) is considered as a novel species of the genus Gracilibacillus, for which the name Gracilibacillus xinjiangensis sp. nov. is proposed. The type species is J2(T) (= CGMCC 1.12449(T) = JCM 18859(T)).