Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov

A Gram-stain-positive, facultative anaerobic endospore-forming bacterium, which originated from roots/rhizosphere of maize (Zea mays), was investigated for its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain JJ-3T was grouped together with Neobacillus species showing the highest similarities to Neobacillus bataviensis (98.8 %) and the three species Neobacillus dendrensis, Neobacillus soli and Neobacillus cucumis (all 98.6 %). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were lower than 98.5 %. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-3T genome assembly and those of the other Neobacillus type strains were <83, <85 and <27 %, respectively. Chemotaxonomic features supported the grouping of the strain to the genus Neobacillus, e.g. the major fatty acids were C15 : 0 anteiso and C15 : 0 iso, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major quinone was menaquinone MK-7. Physiological and biochemical test results were slightly different from those of the most closely related species. For this reason, JJ-3T represents a novel species of the genus Neobacillus , for which we propose the name Neobacillus rhizosphaerae sp. nov., with JJ-3T (= CIP 111895T=LMG 32087T=DSM 111784T=CCM 9084T) as the type strain. We also propose to reclassify Bacillus dielmonensis as Neobacillus dielmonensis comb. nov. based mainly on the results of phylogenomic and conserved signature indel analyses.

Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere

A facultative anaerobic, Gram-stain-positive, endospore-forming bacterium, isolated from the rhizosphere of maize roots (Zea mays), was taxonomically studied. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-79T clustered only loosely with Neobacillus species and showed the highest similarity to Neobacillus soli (97.9%). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were 97.5 % and below. Chemotaxonomic features supported the grouping of the strain to the Neobacillus group, e.g. the major fatty acids were C15 : 0 anteiso, C15 : 0 iso and C16 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, the major quinone was menaquinone MK-7, and major compound in the polyamine pattern was spermidine. However, the JJ-79T genome assembly did not share most of the 11 conserved signature indels that are indicative of the genus Neobacillus . The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-79T genome assembly and those of the closest relative Bacillaceae type strains were <71, <71 and <25 %, respectively. Physiological and biochemical test results were also different from those of the most closely related Bacillaceae species. As a consequence, JJ-79T represents a novel genus for which we propose the name Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., with JJ-79T (=CIP 111885T=CCM 9045T) as the type strain.

Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov., isolated from the citrus rhizosphere soil

Two Gram-staining positive strains, FJAT-49825^T and FJAT-50051^T were isolated from a citrus rhizosphere soil sample. Strains FJAT-49825^T and FJAT-50051^T showed the highest 16S rRNA gene sequence similarity with the type strain of Neobacillus cucumis (98.4-98.5%). The 16S rRNA gene sequence similarity between strains FJAT-49825^T and FJAT-50051^T was 99.8%. Strain FJAT-49825^T optimally grew at 35 °C, pH 6.0 in the absence of NaCl while strain FJAT-50051^T grew at 40 °C, pH 7.0 and in presence of 2% NaCl (w/v). Both strains contained meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The respiratory quinone of strains FJAT-49825^T and FJAT-50051^T was MK-7. The polar lipids of strain FJAT-49825^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipid and unidentified lipid whereas strain FJAT-50051^T polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid and unidentified lipid. The major fatty acids (> 10%) in both strains were iso-C_15:0 and anteiso-C_15:0. The genomic DNA G + C content of strains FJAT-49825^T and FJAT-50051^T were 40.8 and 41.1%, respectively. The average nucleotide identity and digital DNA-DNA hybridization value between strains FJAT-49825^T and FJAT-50051^T and with other members of the genus Neobacillus were lower than the cut-off value (95-96/70%) for interspecies identity. Based on the results, strains FJAT-49825^T and FJAT-50051^T represent two novel species of the genus Neobacillus, for which the names Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov. are proposed. The type strains are FJAT-49825^T (= GDMCC 1.2592^T = JCM 34834^T) and FJAT-50051^T (= GDMCC 1.2593^T = JCM 34835^T).

Neobacillus kokaensis sp. nov., isolated from soil

A Gram-stain-variable, motile, aerobic, spore-forming, rod-shaped bacterium, designated as strain LOB 377T, was isolated from soil sampled in Koka County (now Konan City), in Shiga Prefecture, Japan. To determine its taxonomic position, the bacterium was evaluated by a polyphasic approach based on genomic, phenotypic and chemotaxonomic tests. From phylogenetic analysis based on 16S rRNA gene sequences, strain LOB 377T (LC570960) was revealed to have the highest similarity to the type strain of Neobacillus mesonae FJAT-13985T (9.1 %). The average nucleotide identity and digital DNA–DNA hybridization values between both strains based on whole genome sequences were 84.1 and 42.8 %, respectively, which were below the recommended thresholds. The strain grew at 15–45 °C (optimum, 25–37 °C), at pH 5.5–9.5 (optimum, pH 6.5–8.5) and with 1.0–2.0 % (w/v) NaCl. Cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid. The major menaquinone was menaquinone-7. Predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and C16 : 1 ω11c. The polar lipids were phosphatidylglycerol, unidentified phospholipid and unidentified aminophospholipid. The DNA G+C content was 40.5 mol%. According to the genomic, phenotypic and chemotaxonomic results, strain LOB 377T represents a novel species in the genus Neobacillus , for which the name Neobacillus kokaensis sp. nov. is proposed. The type strain is LOB 377T (=ATCC 31382T=NBRC 114637T=DSM 113418T).

Neobacillus paridis sp. nov., an endophyte of Paris polyphylla Smith var. yunnanensis

A novel endophytic strain, designated YIM B02564^T, was isolated from the root of Paris polyphylla Smith var. yunnanensis obtained from Yunnan Province, southwest China. By using a polyphasic approach, cells of the strain were characterized as facultative anaerobic, Gram-positive and rod-shaped. The growth conditions of the strain were found to occur at 20-55 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0). Strain YIM B02564^T can tolerate 2% NaCl concentration. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02564^T belonged to the genus Neobacillus and the 16S rRNA gene sequence similarity values of strain YIM B02564^T to the type strains of members of this genus ranged from 95.6 to 97.8%. The DNA G+C content of strain YIM B02564^T calculated from the whole genome sequence was 41.6 mol%. Values of the ANI and the dDDH between strain YIM B02564^T and its closely related Neobacillus species were below 77.9% and 21.5%. Strain YIM B02564^T contained MK-7 as the major menaquinone, iso-C_15:0 and anteiso-C_15:0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and four unidentified lipids. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. On the basis of polyphasic analysis, strain YIM B02564^T could be differentiated genotypically and phenotypically from recognized species of the genus Neobacillus. The isolate therefore represents a novel species, for which the name Neobacillus paridis is proposed. The type strain is YIM B02564^T (= JCM 34668^T = CGMCC 1.18655^T).

Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1^T was isolated from the surface-sterilized Selaginella involvens roots. Growth of strain BRMEA1^T was found to occur at pH 6.0-8.0 (optimum, pH 7.0), 15-50 °C (optimum, 25-30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1^T formed a lineage within the genus Neobacillus (family Bacillaceae) and showed the highest sequence similarity to Neobacillus drentensis DSM 15600^T (98.3 %) and Neobacillus fumarioli KCTC 13885^T (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus Neobacillus. Whole-genome analysis of strain BRMEA1^T comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA-DNA hybridization analyses revealed that strain BRMEA1^T showed 20.5 and 22.0% genomic DNA relatedness with the closest species, N. drentensis DSM 15600^T and N. fumarioli KCTC 13885^T, respectively. The whole-genome sequence of strain BRMEA1^T showed the presence of 11 specific conserved signature indels for the genus Neobacillus. The major cellular fatty acids (>10 %) of strain BRMEA1^T were found to be iso-C_15 : 0 and anteiso-C_15 : 0, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1^T represents a novel species of the genus Neobacillus, with the proposed name Neobacillus endophyticus sp. nov. The type strain is BRMEA1^T (=KCTC 43208^T=CCTCC AB 2020071^T).

Neobacillus sedimentimangrovi sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment

Two Gram-stain positive, rod-shaped, endospore-forming, aerobic, thermophilic strains, designated FJAT-2464^T and FJAT-52740, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. The 16S rRNA gene sequence similarity between strains FJAT-2464^T and FJAT-52740 was 100%. The result suggests that strains FJAT-2464^T and FJAT-52740 belong to the same genome species, hence only FJAT-2464^T was considered for further analysis. Strain FJAT-2464^T showed the highest 16S rRNA gene sequence similarities to the type strains of Neobacillus thermocopriae SgZ-7^T (99.9%), Neobacillus cucumis AP-6^T (97.6%) and Neobacillus drentensis LMG 21831^T (97.5%). Growth was observed at 25-65 °C (optimum 60 °C), pH 7.0-8.0 (optimum 8.0) with NaCl tolerance up to 1.0% (w/v) (optimum without NaCl %). The cell-wall peptidoglycan contained meso-diaminopimelic acid and MK-7 was the only respiratory quinone. The major fatty acids were iso-C_15:0 and anteiso-C_15:0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid and unidentified lipids. The average nucleotide identity and digital DNA-DNA hybridization values between strain FJAT-2464^T and the most closely related strain N. thermocopriae SgZ-7^T was below the threshold value for species delineation. Based on the above results, strain FJAT-2464^T represents a novel species of the genus Neobacillus, for which the name Neobacillus sedimentimangrovi sp. nov. is proposed. The type strain is FJAT-2464^T (= MCCC 1K04406^T = KCTC 43264^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.

Bacillus xiapuensis sp. nov., isolated from marine sediment

A rod-shaped, endospore-forming, aerobic bacterium, designated FJAT-46582^T, was isolated from a sediment sample of the coastal region in Xiapu County, Fujian Province in China. Growth was observed at 10-30 °C (optimum, 25 °C), in 0-7.0 % NaCl (0 %) and at pH 6.0-11.0 (pH 8.0), respectively. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the isoprenoid quinone was MK-7. The main fatty acids were anteiso-C17 : 0 (26.5 %), anteiso-C15 : 0 (19.6 %), iso-C15 : 0 (14.4 %) and C16 : 0 (10.5 %). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidyl ethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain FJAT-46582^T with the genus Bacillus, and showed the highest sequence similarity to Bacillus thermotolerans SGZ-8^T (97.6 %) and Bacillus ectoinformans (97.1 %). The average nucleotide identity and in silico DNA-DNA hybridization values between strain FJAT-46582^T and the most closely related species were 72.3 and 22.9 %, respectively, which were much lower than the thresholds commonly used to define species (96 and 70 %, respectively) indicating that it belonged to a different taxon. The DNA G+C content was 44.2 mol%. The phenotypic characters and taxono-genomics study revealed that strain FJAT-46582^T represents a novel Bacillus species, for which the name Bacillus xiapuensis sp. nov. is proposed. The type strain is FJAT-46582^T (=JCM 33155=CCTCC AB 2017047^T).

Bacillus gobiensis sp. nov., isolated from a soil sample

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated FJAT-4402T, was isolated from the weed rhizosphere soil of the Gobi desert in the Xinjiang Autonomous Region in the north-west of China. Isolate FJAT-4402T grew at 15-40 °C (optimum 30 °C), pH 5-10 (optimum pH 7) and in 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses, based on 16S rRNA gene sequences, showed that isolate FJAT-4402T was a member of the genus Bacillus and was most closely related to Bacillus licheniformis DSM 13T (96.2 %). The isolate showed 33.3 % DNA-DNA relatedness to the closest reference isolate, B. licheniformis DSM 13T. The diagnostic diamino acid of the peptidoglycan of isolate FJAT-4402T was meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (28.5 %), iso-C15 : 0 (20.1 %), anteiso-C17 : 0 (14.3 %), iso-C16 : 0 (9.6 %), C16 : 0 (8.4 %), iso-C17 : 0 (6.2 %) and iso-C14 : 0 (4.7 %) and the DNA G+C content was 42.0 mol%. The phenotypic, chemotaxonomic and genotypic properties indicated that strain FJAT-4402T represents a novel species within the genus Bacillus, for which the name Bacillus gobiensis sp. nov. is proposed. The type strain is FJAT-4402T ( = DSM 29500T = CGMCC 1.12902T).

Bacillus taiwanensis sp. nov., isolated from a soil sample from Taiwan

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium (FJAT-14571T) was isolated from a soil sample in Taiwan. Strain FJAT-14571T grew at 20–40 °C (optimum 35 °C), pH 6–10 (optimum pH 8) and 0–2 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FJAT-14571T was a member of the genus Bacillus and was most closely related to Bacillus oceanisediminis DSM 24771T (96.2 %). DNA–DNA relatedness between strain FJAT-14571T and B. oceanisediminis DSM 24771T was low (32.0 % ± 0.88 %). The diagnostic diamino acid of the peptidoglycan of strain FJAT-14571T was meso-diaminopimelic acid and the predominant menaquinone was MK-7 (96.6 %). The major cellular fatty acids were iso-C15 : 0 (46.4 %), anteiso-C15 : 0 (7.6 %), iso-C17 : 0 (8.2 %) and iso-C16 : 0 (10.0 %) and the DNA G+C content was 40.8 mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that strain FJAT-14571T represents a novel species within the genus Bacillus, for which the name Bacillus taiwanensis sp. nov. is proposed. The type strain is FJAT-14571T ( = DSM 27845T = CGMCC1.1 2698T).

Bacillus wuyishanensis sp. nov., isolated from rhizosphere soil of a medical plant, Prunella vulgaris

A Gram-staining-positive, rod-shaped, endospore-forming, aerobic bacterium (FJAT-17212T) was isolated from the rhizosphere soil of a medical plant, Prunella vulgaris (common selfheal), on the Wuyishan mountain of China. Isolate FJAT-17212T grew at 10–50 °C (optimum 30 °C), pH 5–11 (optimum pH 7) and with 0–6  % (w/v) NaCl (optimum 2  %). Phylogenetic analyses based on 16S rRNA gene sequences showed that isolate FJAT-17212T was a member of the genus Bacillus and was most closely related to Bacillus galactosidilyticus DSM 15595T (97.3  %). DNA–DNA relatedness between isolate FJAT-17212T and B. galactosidilyticus DSM 15595T was low (35.2  % ± 2.3). The diagnostic diamino acid of the peptidoglycan of isolate FJAT-17212T was meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7 (80.8  %). The major cellular fatty acids were iso-C15 : 0 (35.7  %), anteiso-C15 : 0 (29.8  %), iso-C14 : 0 (9.9  %) and iso-C16 : 0 (9.9  %) and the DNA G+C content was 39.8  mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate FJAT-17212T represents a novel species within the genus Bacillus, for which the name Bacillus wuyishanensis sp. nov. is proposed. The type strain is FJAT-17212T ( = DSM 27848T = CGMCC 1.12709T).