Simply Versatile: The Use of Peribacillus simplex in Sustainable Agriculture

Peribacillus simplex is a Gram-positive, spore-forming bacterium derived from a vast range of different origins. Notably, it is part of the plant-growth-promoting rhizobacterial community of many crops. Although members of the Bacillaceae family have been widely used in agriculture, P. simplex has, so far, remained in the shadow of its more famous relatives, e.g., Bacillus subtilis or Bacillus thuringiensis. Recent studies have, however, started to uncover the bacterium's highly promising and versatile properties, in particular in agricultural and environmental applications. Hence, here, we review the plant-growth-promoting features of P. simplex, as well as its biocontrol activity against a variety of detrimental plant pests in different crops. We further highlight the bacterium's potential as a bioremediation agent for environmental contaminants, such as metals, pesticide residues, or (crude) oil. Finally, we examine the recent developments in the European regulatory landscape to facilitate the use of microorganisms in plant protection products. Undoubtedly, further studies on P. simplex will reveal additional benefits for agricultural and environmentally friendly applications.

Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain

A strictly aerobic, chemoheterotrophic, endospore-forming, Gram-positive, rod-shaped bacterial strain N3^T was isolated from the feces of a river otter in Castril (Granada, southern Spain). It is halotolerant, motile, and catalase-, oxidase-, ACC deaminase-, and C4- and C8-lipase-positive. It promotes tomato plant growth and can reduce virulence in Erwinia amylovora CECT 222^T and Dickeya solani LMG 25993^T through interference in their quorum-sensing systems, although other antagonistic mechanisms could also occur. A phylogenetic analysis of the 16S rRNA gene sequence as well as the phenotypic and phylogenomic analyses indicated that the strain N3^T is a novel species of the genus Peribacillus, with the highest 16S rRNA sequence similar to that of Bacillus frigoritolerans DSM 8801^T (99.93%) and Peribacillus simplex DSM 1321^T (99.80%). Genomic digital DNA-DNA hybridization (dDDH) between the strain N3^T and Bacillus frigoritolerans DSM 8801^T and Peribacillus simplex was 12.8 and 69.1%, respectively, and the average nucleotide identity (ANIb) of strain N3^T and Bacillus frigoritolerans DSM 8801^T and Peribacillus simplex was 67.84 and 93.21%, respectively. The genomic G + C content was 40.3 mol%. Its main cellular fatty acids were anteiso-C_15:0 and iso-C_15:0. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with the chemotaxonomic and phenotypic data, we demonstrated that the type strain N3^T (=CECT 30509^T = LMG 32505^T) is a novel species of the genus Peribacillus and the name Peribacillus castrilensis sp. nov. is proposed.

Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow

A Gram-stain-positive, facultatively anaerobic, endospore-forming, rod-shaped strain, AGMB 02131^T, which grew at 20-40 °C (optimum 30 °C), pH 3.0-11.0 (optimum pH 4.0) and in the presence of 0-18 % (w/v) NaCl (optimum 10 %), was isolated from a cow faecal sample and identified as a novel strain using a polyphasic taxonomic approach. The phylogenetic analysis based on 16S rRNA gene sequences along with the whole genome (92 core gene sets) revealed that AGMB 02131^T formed a group within the genus Peribacillus, and showed the highest sequence similarity with Peribacillus endoradicis DSM 28131^T (96.9 %), following by Peribacillus butanolivorans DSM 18926^T (96.6 %). The genome of AGMB 02131^T comprised 70 contigs, the chromosome length was 4 038 965 bp and it had a 38.5 % DNA G+C content. Digital DNA-DNA hybridization revealed that AGMB 02131^T displayed 21.4 % genomic DNA relatedness with the most closely related strain, P. butanolivorans DSM 18926^T. AGMB 02131^T contains all of the conserved signature indels that are specific for members of the genus Peribacillus. The major cellular fatty acids (>10 %) of AGMB 02131^T were C_18 : 1ω9c, C_18:0 and C_16 : 0. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, AGMB 02131^T represents a novel species of the genus Peribacillus, for which the name Peribacillus faecalis sp. nov. is proposed. The type strain is AGMB 02131^T (=KCTC 43221^T=CCTCC AB 2020077^T).

Reclassification of Brevibacterium frigoritolerans DSM 8801T as Bacillus frigoritolerans comb. nov. Based on Genome Analysis

16S rRNA gene sequence analysis showed that the type strain Brevibacterium frigoritolerans DSM 8801^T had the highest similarity (99.7%) with the reference strain Bacillus simplex NBRC 15720^T, followed by Bacillus muralis DSM 16288^T (99.6%), Bacillus butanolivorans DSM 18926^T (99.5%), and Bacillus loiseleuriae FJAT-27997^T (97.9%). This relationship is confirmed by the phylogenetic analysis indicating that Bre. frigoritolerans DSM 8801^T fell in the genus Bacillus group and formed a clade with the closely related Bacillus species. Average nucleotide identity and in silico DNA-DNA hybridization (isDDH) values between strain DSM 8801^T and the most closed reference strain Bac. simplex NBRC 15720^T were both much lower than species definition threshold values of 95% and 70%, respectively, which indicated strain DSM 8801^T should not be affiliated to one of the validly named Bacillus species. The percentage of conserved protein (POCP) values between the strain DSM 8801^T and the type strains of the above species were 80.7%, 69.2%, 72.2%, 53.6%, and 50.0%, respectively, higher than the genus definition threshold value of 50%. The main isoprenoid quinone of strain DSM 8801^T was MK-7, the main polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidyl ethanolamine (PE), and the major fatty acids were anteiso-C_15:0 and iso-C_15:0. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, Bre. frigoritolerans DSM 8801^T should belong to the genus Bacillus, and be proposed to reclassify as Bacillus frigoritolerans comb. nov., with the type strain DSM 8801^T (=ATCC 25097^T = CCUG 43489^T= CIP 67.20^T= JCM 11681^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 terrae sp. nov. isolated from Cistus ladanifer rhizosphere soil

A bacterial strain designated RA9T was isolated from a root of Cistus ladanifer in Spain. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate into the genus Bacillus with its closest relatives being Bacillus fortis R-6514T and Bacillus fordii R-7190T with 98.2 % similarity in both cases. DNA-DNA hybridization studies showed mean relatedness values of 29 and 30 %, respectively, between strain RA9T and the type strains of B. fortis and B. fordii. Cells of the isolate were Gram-stain-positive, motile, sporulating rods. Catalase and oxidase were positive. Gelatin, starch and casein were not hydrolysed. Menaquinone MK-7 was the only menaquinone detected and iso-C15 : 0 and anteiso-C15 : 0 were the major fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, one unidentifed glycolipid and one unidentified lipid. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 43.1 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RA9T should be considered as representing a novel species of the genus Bacillus, for which the name Bacillus terrae sp. nov. is proposed. The type strain is RA9T (=LMG 29736T=CECT 9170T).