Gracilibacillus pellucidus sp. nov., a moderately halophilic bacterium isolated from saline soil in Xinjiang province, China

A motile, Gram-positive, moderately halophilic, catalase-positive and oxidase-negative, obligate aerobic, slender rod-shaped bacterium, strain S3-1-1T was isolated from the plant rhizosphere soil in saline soil of Xinjiang Uygur Autonomous Region. Strain S3-1-1T grew in the presence of 1-21% NaCl and at pH 7.0-9.0, with optimum growth at 3% NaCl and pH 7.5. It grew at 16-45 °C, with optimum growth at 40 °C.Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S3-1-1T should be placed within the genus Gracilibacillus and formed a separate branch. It exhibited highest similarities to Gracilibacillus ureilyticus MF38T (sequence similarity 97.7%), Gracilibacillus massiliensis Awa-1T (sequence similarity 97.5%), Gracilibacillus xinjiangensis J2T (sequence similarity 97.4%) and Gracilibacillus salitolerans SCU50T (sequence similarity 97.4%). Genomic comparisons revealed that strain S3-1-1T shares closest phylogenetic relationships with Gracilibacillus saliphilus YIM 91119T (ANI 77.4%, AAI 78.4%), Gracilibacillus thailandensis TP2-8T (ANI 77.2%, AAI 78.3%), and Gracilibacillus salitolerans SCU50T (ANI 77.3%, AAI 78.1%). However, the digital DNA-DNA hybridization (19.3-22.1%), average nucleotide identity (71.1-77.4%), and average amino acid identity (66.9-78.6%) values all fell below the recommended thresholds for species delineation, supporting its novel taxonomic status. The major cellular fatty acids were anteiso-C15:0, C16:0, iso-C15:0, and anteiso-C17:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and aminophospholipids. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics, S3-1-1T represented a novel species of the genus Gracilibacillus, for which the name Gracilibacillus pellucidus sp. nov. is proposed, with S3-1-1T (= JCM 36422T = GDMCC 1.4017T) as the type strain.

Remediation of hexavalent chromium contaminated soils by stimulating indigenous microorganisms: Optimization, community succession and applicability

Microbial remediation has become an environmental-friendly and promising remediation method for Hexavalent chromium [Cr(VI)] contaminated soils. However, it is hard for exogenous microorganisms to adapt to different contaminated soils. In this study, Cr(VI) contaminated soils were remediated by the indigenous iron reducing bacteria and Cr(VI) reducing bacteria under the stimulation of sodium lactate, ferrihydrite and humic acid. The Cr(VI) removal rates of contaminated soils with the Cr(VI) concentration of 2234.92 mg/kg reached 71.61% on the 24th day with a sodium lactate dosage of 5.80%, a ferrihydrite dosage of 2.00% and a humic acid dosage of 0.93% that obtained after the optimization of Box-Benhnken design. The total abundance of iron reducing bacteria and Cr(VI) reducing bacteria increased from 9.78% to 64.64% after the remediation. Bacillus, Salipaludibacillus, Gracilibacillus, Virgibacillus and Delftia played a critical role in the remediation. Adding the above three exogenous substances to Cr(VI) contaminated soils in other three regions still had an excellent remediation effect. When the initial Cr(VI) concentrations were no more than 1000 mg/kg, they could decrease to below 60.53 mg/kg after the remediation of 24 days. The Cr(VI) removal rate could still reach 89.49% even if the initial concentration exceeded 2000 mg/kg. Our results provide an attractive strategy to utilize indigenous microorganisms to remediate Cr(VI) contaminated soils.

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).

The halophilic bacteria Gracilibacillus dipsosauri GDHT17 alleviates salt stress on perennial ryegrass seedlings

Introduction

Adverse abiotic environmental conditions including excess salt in the soil, constantly challenge plants and disrupt the function of plants, even inflict damage on plants. Salt stress is one of the major limiting factors for agricultural productivity and severe restrictions on plant growth. One of the critical ways to improve plant salt tolerance is halotolerant bacteria application. However, few such halotolerant bacteria were known and should be explored furtherly.

Methods

Halophilic bacterium strain was isolated from saline soil with serial dilution and identified with classical bacteriological tests and 16S rRNA analysis. Perennial ryegrass (Lolium perenne L) was used in this study to evaluate the potential effect of the bacteria.

Results and discussion

A halophilic bacterium strain GDHT17, was isolated from saline soil, which grows in the salinities media with 1.0%, 5.0%, and 10.0% (w/v) NaCl, and identified as Gracilibacillus dipsosauri. Inoculating GDHT17 can significantly promote ryegrass's seedling height and stem diameter and increase the root length, diameter, and surface area at different salt concentrations, indicating the significant salt stress alleviating effect of GDHT17 on the growth of ryegrass. The alleviating effect on roots growth showed more effective, especially on the root length, which increased significantly by 26.39%, 42.59%, and 98.73% at salt stress of 100 mM, 200 mM, and 300 mM NaCl when the seedlings were inoculated with GDHT17. Inoculating GDHT17 also increases perennial ryegrass biomass, water content, chlorophyll and carotenoid content under salt stress. The contents of proline and malonaldehyde in the seedlings inoculated with GDHT17 increased by 83.50% and 6.87%, when treated with 300 mM NaCl; however, the contents of MDA and Pro did not show an apparent effect under salt stress of 100 mM or 200 mM NaCl. GDHT17-inoculating maintained the Na+/K+ ratio in the salt-stressed ryegrass. The Na+/K+ ratio decreased by 26.52%, 6.89%, and 29.92% in the GDHT17-inoculated seedling roots treated with 100 mM, 200 mM, and 300 mM NaCl, respectively. The GDHT17-inoculating increased the POD and SOD activity of ryegrass seedlings by 25.83% and 250.79%, respectively, at a salt stress of 300 mM NaCl, indicating the properties of GDHT17, improving the activity of antioxidant enzymes of ryegrass at the salt-stress condition. Our results suggest that G. dipsosauri GDHT17 may alleviate salt stress on ryegrass in multiple ways; hence it can be processed into microbial inoculants to increase salt tolerance of ryegrass, as well as other plants in saline soil.

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.

Isolation of a novel halothermophilic strain of the genus Gracilibacillus from Howz-e Sultan hypersaline lake in Iran

Background and Objectives:

Halothermophilic bacteria are adapted to high osmolarity and can grow in high saline environments and high temperatures. This study was aimed at the isolation of halothermophilic bacteria from Howz-e Sultan hypersaline lake in the central desert zone in Iran.

Materials and Methods:

Samples were collected and after preparing dilutions, the samples were cultured on Molten haloid agar with different salt concentrations (5–35%), then the plates were incubated at 35–70ºC in both aerobic and anaerobic conditions. Biochemical characterizations, utilization of carbon sources, production of exoenzymes and antibiotic susceptibility were investigated. Taxonomic and phylogenetic analyses were performed using 16S rRNA gene sequences.

Results:

One of the isolated bacteria was found to be Gram-positive, hyperhalophilic, thermophilic, endospore-forming, and was named as 1–9 h isolate. The bacterial cells were bacilli-shaped, which produced endospores at a subterminal position. This isolate was an aerobe and facultative anaerobe and grew between pH 5.0 and 10.0 (optimal growth at pH 7.0–7.5), at temperature between 15°C and 65°C (optimal growth at 40–45°C) and at salinity of 9–32% (w/v) NaCl, growing optimally at 18% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, isolate 1–9 h belongs to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity to Gracilibacillus sp. IBP-V003 (99.0%).

Conclusion:

Based on the results of its phenotypic and genotypic properties, strain 1–9 h represents a novel strain of the genus Gracilibacillus. It can be used in various fields of industry and biotechnology.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool

Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.

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).

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.

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 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).

Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov

Background

Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome.

Methods

By using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined.

Results

Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp. nov., type strain Awa-1^T (=CSUR P1441=DSM 29726), is a moderately halophilic gram-positive, non-spore-forming rod, and is motile by using a flagellum. Strain Awa-1^T shows catalase activity but no oxidase activity. It is not only an aerobic bacterium but also able to grow in anaerobic and microaerophilic atmospheres. The draft genome of G. massiliensis is 4,207,226 bp long, composed of 13 scaffolds with 36.05% of G+C content. It contains 3,908 genes (3,839 protein-coding and 69 RNA genes). At least 1,983 (52%) orthologous proteins were not shared with the closest phylogenetic species. Hundred twenty-six genes (3.3%) were identified as ORFans.

Conclusions

Microbial culturomics can dramatically improve the characterization of the food and environmental microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in environment, health, and disease.

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)).

Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan

A Gram-staining positive, non-spore forming, non-pigmented and non-motile bacterium, designated as NCCP-1340(T), was isolated from a hot water spring, Tatta Pani, Pakistan. Cells of strain NCCP-1340(T) were observed to be aerobic, rod shaped, catalase and urease positive but H2S production and oxidase negative. Growth was observed at pH 6.0-8.0 (optimum pH 7.0) and at 20-40 °C (optimum 37 °C). The strain could tolerate 0-8 % NaCl (optimum 2 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain NCCP-1340(T) belongs to the genus Nocardioides and is closely related to Nocardioides iriomotensis JCM 17985(T) (96.8 %), Nocardioides daedukensis KCTC 19601(T) (96.6 %), Nocardioides jensenii KCTC 9134(T) (96.1 %) and Nocardioides daejeonensis KCTC 19772(T) (96.1 %). The DNA-DNA relatedness values of strain NCCP-1340(T) with N. iriomotensis JCM 17985(T), N. daedukensis KCTC 19601(T) and N. jensenii KCTC 9134(T) were found to be less than 53 %. The DNA G+C content of strain NCCP-1340(T) was determined to be 71.8 mol  %. The affiliation of strain NCCP-1340(T) to the genus Nocardioides was further supported by chemotaxonomic data which showed the presence of MK-8(H4) as major menaquinone system; iso-C16:0, C17:0, C16:0 10-methyl, iso-C15:0 and C 15:0 as major cellular fatty acids; and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and unidentified glycolipids and polar lipids in the polar lipids profile. The cell wall peptidoglycan contained LL-diaminopimelic acid as the diagnostic amino acid. On the basis of physiological and biochemical characteristics and the phylogenetic analyses, strain NCCP-1340(T) can be distinguished from the closely related taxa and thus represents a novel species of the genus Nocardioides, for which the name Nocardioides pakistanensis sp. nov. is proposed with the type strain NCCP-1340(T) (= DSM 29942(T) = JCM 30630(T)).

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.

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).

Diversity of cultivable halophilic archaea and bacteria from superficial hypersaline sediments of Tunisian solar salterns

Prokaryotes in the superficial sediments are ecologically important microorganisms that are responsible for the decomposition, mineralization and subsequent recycling of organic matter. The aim of this study was to explore the phylogenetic and functional diversity of halophilic archaea and bacteria isolated from the superficial sediments of solar salterns at Sfax, Tunisia. Sixty four strains were isolated from crystallizer (TS18) and non-crystallizer (M1) ponds and submitted to genotypic characterization and evaluation by amplified ribosomal RNA restriction analysis (ARDRA) techniques. Our findings revealed that the archaeal diversity observed for 29 isolates generated five distinct patterns from the non-crystallizer M1 pond, with Halorubrum chaoviator as the most prevalent cultivable species. However, in the TS18 crystallizer pond, ten restriction patterns were observed, with the prevalence of haloarchaea EB27K, a not yet identified genotype. The construction of a neighbour-joining tree of 16S rRNA gene sequences resulted in the division of the potential new species into two major groups, with four strains closely related to the sequence of the unculturable haloarchaeon EB27K and one strain to the recently described Halovenus aranensis strain. The 35 bacterial strains observed in this work were present only in the non-crystallizer pond (M1) and presented two distinct ARDRA patterns. These strains belonged to the γ-proteobacteria subdivision, with members of Salicola marasensis (83%) being the most predominant species among the isolates. 16S rRNA gene sequencing revealed that Salicola strains displayed different degrees of homogeneity. The results from pulsed field gel electrophoresis assays showed that the Salicola isolates could be clustered in two distinct groups with different genome sizes.

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)).

Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil

A Gram-staining-positive, moderately halophilic bacterium, designated strain BH097T, was isolated from solar saltern soil of Bigeum Island in south-west Korea. Cells were motile rods, producing spherical endospores at a terminal position in swollen sporangia. Strain BH097T was strictly aerobic, grew at pH 5.5–9.5 (optimum, pH 8.0), at 10–52 °C (optimum, 37 °C) and at salinities of 1–22 % (w/v) NaCl (optimum, 7 % NaCl). On the basis of 16S rRNA gene sequence analysis, strain BH097T was shown to belong to the genus Gracilibacillus within the phylum Firmicutes , and showed closest sequence similarity to Gracilibacillus saliphilus DSM 19802T (95.8 %), Gracilibacillus thailandensis TP2-8T (95.6 %), Gracilibacillus boraciitolerans DSM 17256T (95.5 %), ‘Gracilibacillus quinghaiensis’ DSM 17858 (95.4 %) and Gracilibacillus halophilus DSM 17856T (95.2 %). The DNA G+C content of this novel isolate was 37.9 mol%. The major cellular fatty acids of strain BH097T were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol two unknown phospholipids and a glycolipid. The isoprenoid quinone was MK-7, and the peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of polyphasic evidence from this study, strain BH097T represents a novel species of the genus Gracilibacillus for which the name Gracilibacillus bigeumensis sp. nov. is proposed. The type strain is BH097T ( = KCTC 13130T = DSM 19028T).

Gracilibacillus kekensis sp. nov., a moderate halophile isolated from Keke Salt Lake

A novel moderately halophilic bacterium, designated strain K170(T), was isolated from Keke Salt Lake in Qinghai, China. The strain grew with 0-22 % (w/v) NaCl, at 4-50 °C and at pH 6-11, with optimum growth in 3 % (w/v) NaCl, at 40 °C and at pH 8. The predominant respiratory quinone was menaquinone 7 (MK-7). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, aminolipids and glycolipids. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the full-length 16S rRNA gene sequence revealed that strain K170(T) was a member of the genus Gracilibacillus. High levels of 16S rRNA gene sequence similarity were found between strain K170(T) and Gracilibacillus boraciitolerans DSM 17256(T) (97.3 %) and Gracilibacillus thailandensis JCM 15569(T) (97.1 %). 16S rRNA gene sequence similarities between strain K170(T) and the type strains of other recognized members of the genus Gracilibacillus were below 97 %. The DNA-DNA hybridization values of strain K170(T) with G. boraciitolerans DSM 17256(T) and G. thailandensis JCM 15569(T) were 21.9 % and 34.3 %, respectively. On the basis of these results, strain K170(T) is considered to represent a novel species of the genus Gracilibacillus, for which the name Gracilibacillus kekensis sp. nov. is proposed; the type strain is K170(T) ( = CGMCC 1.10681(T) = DSM 23178(T)).

Bioprospecting microbial natural product libraries from the marine environment for drug discovery

Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.

Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline–alkaline soil

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.

Terribacillus aidingensis sp. nov., a moderately halophilic bacterium

Three Gram-positive, moderately halophilic bacteria, designated YI7-61(T), IA7 and DB2, were isolated from sediments of Aiding salt lake in the Xinjiang region of China. Cells of the strains were rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Colonies were pale yellow in colour. The strains grew optimally at 30-37 °C, pH 6-7 and 3-7 % (w/v) NaCl. The diamino acid in the murein was meso-diaminopimelic acid and the major quinone system was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 44.6-45.0 mol%. 16S rRNA gene sequence analysis revealed that strains YI7-61(T), IA7 and DB2 were closely related to members of the genus Terribacillus and showed 96.8-97.6, 96.4-97.2 and 95.4-95.5 % 16S rRNA gene sequence similarity with Terribacillus halophilus 002-051(T), Terribacillus saccharophilus RB589 and Terribacillus goriensis CL-GR16(T), respectively. DNA-DNA relatedness among the isolates was 88-92 % and strain YI7-61(T) shared 24, 18 and 18 % DNA-DNA relatedness with T. halophilus JCM 21760(T), T. saccharophilus JCM 21759(T) and T. goriensis DSM 18252(T), respectively. On the basis of phenotypic and phylogenetic distinctiveness, the three isolates should be placed in the genus Terribacillus as representatives of a novel species, for which the name Terribacillus aidingensis sp. nov. is proposed. The type strain is YI7-61(T) (=CGMCC 1.8913(T) =NBRC 105790(T)).

Gracilibacillus thailandensis sp. nov., from fermented fish (pla-ra)

A novel strain, designated TP2-8(T), was isolated from fermented fish (pla-ra) in Thailand. It stained Gram-positive and the cells were aerobic, endospore-forming rods. The strain grew at pH 6-8 (optimum pH 7), 15-55 degrees C (optimum 37 degrees C) and 1-22 % (w/v) NaCl (optimum 5-10 %). It contained meso-diaminopimelic in the cell-wall peptidoglycan. MK-7 and cellular fatty acids anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0) were major components. Polar lipids diphosphatidylglycerol and phosphatidylglycerol and unidentified lipids were detected. The DNA G+C content was 37.6 mol%. Comparison of the 16S rRNA gene sequence of strain TP2-8(T) with those of other members of the family Bacillaceae indicated that it was a member of the genus Gracilibacillus (94.9-99.2 % sequence similarity) and was closely related to Gracilibacillus saliphilus YIM 91119(T) (99.2 % similarity), G. lacisalsi BH312(T) (98.6 %), G. orientalis XH-63(T) (97.7 %), 'G. quinghaiensis' YIM C229 (97.7 %) and G. boraciitolerans T-16X(T) (97.2 %). Strain TP2-8(T) showed low DNA-DNA relatedness (< or = 49%) to G. saliphilus YIM 91119(T), G. lacisalsi DSM 19029(T), G. orientalis CCM 7326(T), 'G. quinghaiensis' DSM 17858 and G. boraciitolerans JCM 21714(T). On the basis of the physiological and biochemical characteristics and molecular data presented, strain TP2-8(T) is proposed to represent a novel species, Gracilibacillus thailandensis sp. nov. (type strain TP2-8(T) =JCM 15569(T) =PCU 304(T) =TISTR 1881(T)).