Bacillus litorisediminis sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment

Two aerobic, Gram-staining-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-47801^T and FJAT-47835, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. Growth was observed at 25-55 °C (optimum, 50 °C) and pH 7.0-9.0 (optimum, pH 7.0), with up to 4.0% (w/v) NaCl (optimum, without NaCl). Strains FJAT-47801^T and FJAT-47835 showed the highest 16S rRNA gene sequence similarity to Bacillus oleivorans (98.5%). The 16S rRNA gene sequence similarity between FJAT-47801^T and FJAT-47835 was 99.9% indicating they were the same species. Phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 120 conserved bacterial single-copy genes) trees showed that strains FJAT-47801^T and FJAT-47835 should be affiliated to the genus Bacillus. The of menaquinone of strain FJAT-47801^T was MK-7. The major fatty acids of strain FJAT-47801^T were iso-C_15:0, anteiso-C_15:0, iso-C_17:0, and C_16:0. The major polar lipids strain FJAT-47801^T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The genomic DNA G+C content of strain FJAT-47801^T was 39.3%. The average nucleotide identity (84.3%) and the digital DNA-DNA hybridization value (28.1%) between strain FJAT-47801^T and B. oleivorans CCTCC AB 2013353^T were below the cut-off level for species delineation. Based on the above results, strain FJAT-47801^T represents a novel species of the genus Bacillus, for which the name Bacillus litorisediminis sp. nov., is proposed. The type strain is FJAT-47801^T (=GDMCC 1.2712^T = JCM 34875^T).

Neobacillus massiliamazoniensis sp. nov., a new bacterial species isolated from stool sample of an inhabitant of the Amazon region

Using a culturomics approach, a strain was isolated, identified and characterised following the taxonogenomics concept. Neobacillus massiliamazoniensis sp. nov., strain LF1^T (=CSURP1359) was isolated from human stool. The 16S rRNA gene sequence analysis of strain LF1^T (accession number: LK021124) exhibits 98.32% similarity levels with Neobacillus bataviensis strain IDA1115 (accession number: NR_036766.1), the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain LF1^T (accession number: CVRB00000000) is 4.6 Mbp with a G+C content of 34.1 mol%. Analysis of phylogenic tree, genomic analysis and phenotypic criteria described here sufficiently prove that this bacterium is different from previously known bacterial species with standing in nomenclature and represents a new Neobacillus species belonging to Firmicutes phylum.

Mesobacillus aurantius sp. nov., isolated from an orange-colored pond near a solar saltern

An endospore producing, strict aerobic, Gram-stain-positive, orange-colored colony forming bacterium designated as strain JC1013^T was isolated from an orange pond near a solar saltern of Tamil Nadu, India. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain was affiliated to the family Bacillaceae of the phylum Firmicutes. Strain showed highest 16S rRNA gene sequence identity of 98.7% with Mesobacillus selenatarsenatis SF-1 ^T and below 98.3% with other members of the genus Mesobacillus. Strain JC1013^T produced carotenoid pigments and indole compounds. Major cellular fatty acids of strain JC1013^T were iso-C_15:0, anteiso-C_15:0, C_16:0 3-OH, iso-C_17:0ω10c and summed feature 4 (iso-C_17:1 I/ anteisoB). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and four unidentified phospholipids. Strain JC1013^T constituted m-diaminopimelic acid as diagnostic cell wall amino acids. MK-7 is the predominant menaquinone of strain JC1013^T. The genome size of strain JC1013^T was 4.6 Mbp and its G + C content was 42.7 mol%. For the affirmation of strain's taxonomic status, a detailed phylogenomic study was done. Based on the phylogenetic analyses, low ANI (84.6%), AAI (88.5%) values, in-silico DDH (< 29%) value, morphological, physiological and chemo-taxonomical characteristics, strain JC1013^T was clearly distinguished from the nearest phylogenetic neighbor, Mesobacillus selenatarsenatis SF-1^T to conclude that it is a new species of the genus Mesobacillus. We propose the name as Mesobacillus aurantius with type strain JC1013^T (= NBRC 114146^T = KACC 21451 ^T).

Mesobacillus harenae sp. nov., isolated from the sandy soil of a cold desert

A bacterial strain, designated Y40^T, was isolated from sandy soil sampled on the Qinghai-Tibet Plateau. A polyphasic study confirmed the affiliation of the strain with the genus Mesobacillus. Strain Y40^T was found to be an aerobic, Gram-stain-positive, motile and rod-shaped bacterium. The strain grew at 10-42 °C, pH 6-9 and with 0-2 % (w/v) NaCl. The diagnostic amino acid was meso-diaminopimeilic acid. MK7 was predominant menaquinone, and iso-C_15:0, iso-C_17:1 ω10c and anteiso-C_15:0 were the major fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content was 40.6 mol%. Based on he results of 16S rRNA gene sequence analysis, strain Y40^T was phylogenetically closely related to Mesobacillus zeae JJ-247^T and Mesobacillus foraminis CV53^T, with similarities of 98.0 and 97.7 %, respectively. The average nucleotide identity (ANIb) values between strain Y40^T and Mesobacillus zeae JJ-247^T and Mesobacillus foraminis CV53^T were 69.9 and 70.0 %, respectively. Based on the morphological, physiological, and chemotaxonomic data, it is proposed that strain Y40^T (=CICC 24459^T=JCM 32794^T) should be classified into the genus Mesobacillus as Mesobacillus harenae sp. nov.

Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L

A novel Gram-positive and endospore-forming bacterium assigned as strain SPB7^T which is also a new source of a cyclic diketopiperazine (3S,6S)-3,6-diisobutylpiperazine-2,5-dione is described. A polyphasic (biochemical, phenotypic and genotypic) approach was used to clarify the taxonomic affiliation of this strain. The partial and complete 16S rRNA gene sequences revealed that strain SPB7^T is a member of the Bacillus genus [showing high similarity (> 98.70%) with Bacillus spizizenii NRRL B-23049^T, Bacillus tequilensis KCTC 13622^T, Bacillus inaquosorum KCTC 13429^T and Bacillus cabrialesii TE3^T]. The maximum values for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (GGDC, Formula 2) of strain SPB7^T was obtained for twenty-five strains of Bacillus spizizenii (ANI 95.01-95.48% and GGDC 62.70-60.00%). The whole-genome phylogenetic relationship showed that SPB7^T formed an individual and separated clade with the Bacillus spizizenii group. Principal cellular fatty acids identified in strain SPB7^T were anteiso C_15:0, anteiso C_17:0, iso C_15:0, iso C_17:0, C_16:0, C_10:0 3OH and iso C_{17:1 ϖ10c}. Polar lipid profile showed presence of diphosphotidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and five unknown lipids. Cells were rod shaped, catalase, oxidase-positive and motile. Growth occurred at 20-45 °C (optimal 35 °C), at pH 6.0-10.0 (optimal pH 8) and 0-10% (w/v) NaCl (optimal 2%). The phenotypic, biochemical, and genotypic traits of strain SPB7^T strongly supported its taxonomic affiliation as a novel species of the Bacillus genus, for which the name Bacillus rugosus sp. nov. is proposed. The type strain is SPB7^T (= NRRL B-65559^T, = CICC 24827^T, = MCC 4185^T).

Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu

A Gram-stain-positive, strictly aerobic and rod-shaped bacterium, designated as 3 H-10^T, was isolated from a yellow water sample collected from the manufacturing process of strong flavor Chinese baijiu in Yibin region of Sichuan province (PR China). Oval endospores were formed at the subtermini of cells with swollen sporangia. The isolate was able to grow at temperatures of 20-45 °C (optimum growth at 37 °C), at pH 6.0-10.0 (optimum growth at pH 8.0) and in the presence of 0-2 % (w/v) NaCl (optimum growth with 0 % NaCl). Ribose was the major cell-wall sugar, and meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of 3 H-10^T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). MK-7 was predominant menaquinone and iso-C_15 : 0 (60.7 %) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that 3 H-10^T was most closely related to Bacillus mesophilus SA4^T (96.30 %), Bacillus ginsengihumi Gsoil 114^T (96.27 %) and Bacillus shackletonii LMG 18435^T (96.27 %). The average nucleotide identity (ANI) values between strain 3 H-10^T and the three type strains mentioned above were 69.56, 70.19 and 70.67 %, respectively. The genomic DNA G+C content was 35.4 mol%. On the basis of its phenotypic, chemotaxonomic and phylogenetic properties, strain 3 H-10^T represents a novel species of the genus Bacillus, for which the name Bacillus aquiflavi sp. nov. is proposed. The type strain is Bacillus aquiflavi 3 H-10^T (=CICC 24755^T=JCM 33703^T).

A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov

The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.

Statistical Optimization for Coproduction of Chitinase and Beta 1, 4-Endoglucanase by Chitinolytic Paenibacillus elgii PB1 Having Antifungal Activity

A bacterial strain PB1 with antagonistic activity against pathogenic fungi was isolated from marine soil and was identified as Paenibacillus elgii based on phenotypic and genotypic characterization. The isolate showed good antifungal activity against "Aspergillus niger (MTCC 282), Trichophyton rubrum (MTCC 791), Microsporum gypseum (MTCC 2819), Candida albicans (MTCC 227), and Saccharomyces cerevisiae (MTCC 170)". Chitinase and beta 1, 4-endoglucanase are known for their capability to degrade fungal cell wall, thus we analyzed its productivity in PB1 strain using Plackett-Burman and Central Composite Design. The factors that affect the productivity of chitinase and beta 1, 4-endoglucanase were identified and optimized. A 7.77-fold increase (3.157 to 24.53 ± 1.33 U/mL) in chitinase and 7.422-fold increase (6.476 to 48.066 ± 0.676 U/mL) in beta 1, 4-endoglucanase versus basal medium was achieved. Chitinase and beta 1, 4-endoglucanase produced by Paenibacillus elgii strain PB1 represents the new source for biotechnological, medical, and agricultural applications.

Description of Bacillus kexueae sp. nov. and Bacillus manusensis sp. nov., isolated from hydrothermal sediments

Two Gram-staining-positive, strictly aerobic bacilli, designated as strains Ma50-5^T and Ma50-6^T, were isolated from the hydrothermal sediments of Manus Basin in the western Pacific Ocean. Based on 16S rRNA gene sequence, strains Ma50-5^T and Ma50-6^T were most closely related to Bacillus alveayuensis (97.0 and 97.2 % identity, respectively). The 16S rRNA gene sequence identity between strains Ma50-5^T and Ma50-6^T was 97.4 %. The identities between strains Ma50-5^T and Ma50-6^T and other closely related organisms were below 97.0 %. The G+C contents of the genomic DNA of strains Ma50-5^T and Ma50-6^T were 43.4 and 47.6 mol%, respectively. The major fatty acids (>10 %) of both strains were iso-C15 : 0 and iso-C17 : 0. The predominant isoprenoid quinone detected in both strains was menaquinone-7. Phylogenetic, physiological, biochemical and morphological analyses suggested that strains Ma50-5^T and Ma50-6^T represent two novel species of the genus Bacillus, for which the names Bacillus kexueae sp. nov. (type strain Ma50-5^T=KCTC 33881^T=CCTCC AB 2017020^T) and Bacillus manusensis sp. nov. (type strain Ma50-6^T=KCTC 33882^T=CCTCC AB 2017019^T), respectively, are proposed.