Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method

Ectobacillus ponti sp. nov., a novel bacterium isolated from Pearl River Estuary

A Gram-staining-positive, aerobic, motile, and rod-shaped strain, designated SYSU M60031^T, was isolated from a Pearl River Estuary sediment sample, Guangzhou, Guangdong, China. The isolate could grow at pH 5.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-1 % (w/v) NaCl (optimum, 0 %). The predominant respiratory menaquinone of SYSU M60031^T was MK-7. The cellular polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, and one unidentified aminolipid. The major fatty acids (>10 % of total) were iso-C_14 : 0, iso-C_15 : 0, anteiso-C_15 : 0, iso-C_16 : 0, and C_16 : 0. The genomic DNA G+C content was 51.2 %. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60031^T belonged to the genus Ectobacillus and showed the highest sequence similarity to Ectobacillus funiculus NAF001^T (96.16%), followed by Ectobacillus antri SYSU K30001^T (95.08 %). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M60031^T should be considered to represent a novel species of the genus Ectobacillus, for which the name Ectobacillus ponti sp. nov. is proposed. The type strain of the proposed novel isolate is SYSU M60031^T (=CGMCC 1.19243^T =NBRC 115614^T).

Ectobacillus aegiceratis sp. nov., a novel bacterium isolated from branch of Aegiceras corniculatum

A Gram-stain-positive, non-motile, endospore-forming, rod-shaped and aerobic bacterium was isolated from surface-sterilized branch of Aegiceras corniculatum in Guangxi Zhuang Autonomous Region, China. The isolate, designated strain 165^T, grew at 20-45 °C (optimum, 30 °C), pH 6.0-7.0 (optimum, 6.0) and with 0-3 % (w/v) NaCl (optimum, 1 %). The major respiratory quinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified glycolipid. The major fatty acids were iso-C_15:0, anteiso-C_15:0 and iso-C_16:0. On the basis of 16 S rRNA gene sequence and multiple genes of conserved core proteins analysis, strain 165^T was a member of the genus Ectobacillus. Its closest phylogenetic neighbor was Ectobacillus panaciterrae Gsoil 1517^T, with sequence similarity of 97.1 %. The average nucleotide identity value between strain 165^T and type strain of Ectobacillus panaciterrae was 73.0 %. The estimated DDH value between strain 165^T and type strain of Ectobacillus panaciterrae was 19.7 %. The genome of strain 165^T was 3, 545, 051 bp long with a DNA G + C content of 38.2 % and encodes 3459 predicted proteins, 25 rRNAs, 87 tRNAs and 5 ncRNA. The genome of strain 165^T comprised gene clusters of type 3 PKS, terpene, betalactone and lanthipeptide-class-ii for secondary metabolites. Phenotypic, chemotaxonomic and phylogenetic analyses supported the strain 165^T as a representative of a novel species of the genus Ectobacillus, for which the name Ectobacillus aegiceratis sp. nov. is proposed, with strain 165^T (= JCM 33,414^T = CGMCC 1.13742^T) as the type strain.

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

Bacillus acidinfaciens sp. nov., isolated from farmland soil

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).

Current knowledge and perspectives of Paenibacillus: a review

Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.