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.

Screening of Spore-Forming Bacteria with Probiotic Potential in Pristine Algerian Caves

The interest and exploration of biodiversity in subsurface ecosystems have increased significantly during the last 2 decades. The aim of this study was to investigate the in vitro probiotic properties of spore-forming bacteria isolated from deep caves. Two hundred fifty spore-forming microbes were enriched from sediment samples from 10 different pristine caves in Algeria at different depths. Isolates showing nonpathogenic profiles were screened for their potential to produce digestive enzymes (gliadinase and beta-galactosidase) in solid and liquid media, respectively. Different probiotic potentialities were studied, including (i) growth at 37°C, (ii) survival in simulated gastric juice, (iii) survival in simulated intestinal fluid, and (iv) antibiotic sensitivity and cell surface properties. The results showed that out of 250 isolates, 13 isolates demonstrated nonpathogenic character, probiotic potentialities, and ability to hydrolyze gliadin and lactose in solution. These findings suggest that a selection of cave microbes might serve as a source of interesting candidates for probiotics.

IMPORTANCE Previous microbial studies of subsurface ecosystems like caves focused mainly on the natural biodiversity in these systems. So far, only a few studies focused on the biotechnological potential of microbes in these systems, focusing in particular on their antibacterial potential, antibiotic production, and, to some extent, enzymatic potential. This study explores whether subsurface ecosystems can serve as an alternative source for microbes relevant to probiotics. The research focused on the ability of cave microbes to degrade two substrates (lactose and gliadin) that cause common digestive disorders. Since these enzymes may prove to be useful in food processing and in reducing the effect of lactose and gliadin digestion within intolerant patients, isolation of microbes such as in this study may expand the possibilities of developing alternative strategies to deal with these intolerances.

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.

Caulobacter endophyticus sp. nov., an endophytic bacterium harboring three lasso peptide biosynthetic gene clusters and producing indoleacetic acid isolated from maize root

A novel Gram-stain-negative, aerobic and rod-shaped bacterium with a single polar flagellum or a stalk at the end of the cell, was isolated from maize roots in the Fangshan District of Beijing, People's Republic of China. The new strain designated 774^T produced indole acetic acid (IAA). The 16S rRNA gene sequence analysis indicated that strain 774^T belongs to the genus Caulobacter and is closely related to Caulobacter flavus RHGG3^T, Caulobacter zeae 410^Tand Caulobacter radices 695^T, all with sequence similarities of 99.9%. The genome size of strain774^T was 5.4 Mb, comprising 5042 predicted genes with a DNA G+C content of 68.7%.Three striking lasso peptide biosynthetic gene clusters and two IAA synthesis genes belonging to the TPM pathway were also found in the genome of strain 774^T. The average nucleotide identity values and digital DNA-DNA hybridization values of the strain774^T with its closely phylogenetic neighbours were less than 91.5% and 45.0%, respectively, indicating a new Caulobacter species. The major fatty acids of strain774^T were identified as C16: 0 (27.7%), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) (12.6%) and summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) (42.9%).The major polar lipids consisted of phosphatidyl-glycerol and glycolipids. The predominant ubiquinone was identified as Quinone 10. Based on the polyphasic characterization, strain 774^T represents a novel species of the genus Caulobacter, for which the name Caulobacter endophyticus sp. nov. is proposed with 774^T (= CGMCC 1.16558^T = DSM 106777^T) as the type strain.

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).

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 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).

Bacillus aciditolerans sp. nov., isolated from paddy soil

A Gram-stain-positive, motile, rod-shaped bacterial strain, YN-1^T, was isolated from a rice field in the town of Jietou, Yunnan Province, PR China. Colonies were circular, 1-2 mm in diameter, creamy white, with slightly irregular margins. The isolate grew optimally at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence similarity comparisons, YN-1^T clustered together with other species of the genus Bacillus and showed highest similarities with Bacillus onubensis 0911MAR22V3^T (98.0 %), Bacillus humi LMG22167^T (97.5 %), 'Bacillus timonensis' 10403023 (97.4 %) and 'Bacillussinesaloumensis' P3516 (97.1 %). However, the DNA-DNA hybridization values between YN-1^T and closely related strains of species of the genus Bacillus were well below 47 %, indicating that they represent different taxa. The average nucleotide identity and the Genome-to-Genome Distance Calculator also revealed low relatedness (below 95 and 70 %, respectively) between YN-1^T and type strains of closely related species of the genus Bacillus. The DNA G+C content of the strain was 40 mol%. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids and two other unidentified lipids. Physiological and biochemical test results were also different from those of the most closely related species. On the basis of the phenotypic, genetic and chemotaxonomic data, strain YN-1^T is considered to represent a novel species of the genus Bacillus, for which the name Bacillusaciditolerans sp. nov. is proposed, with strain YN-1^T (=CCTCC AB 2017280^T=JCM 32973^T) as the type strain.