M28 family peptidase derived from Peribacillus frigoritolerans initiates trained immunity to prevent MRSA via the complosome-phosphatidylcholine axis

Methicillin-resistant Staphylococcus aureus (MRSA) represents a major global health threat due to its resistance to conventional antibiotics. The commensal microbiota maintains a symbiotic relationship with the host, playing essential roles in metabolism, energy regulation, immune modulation, and pathogen control. Mammals harbor a wide range of commensal bacteria capable of producing unique metabolites with potential therapeutic properties. This study demonstrated that M28 family peptidase (M28), derived from commensal bacteria Peribacillus frigoritolerans (P. f), provided protective effects against MRSA-induced pneumonia. M28 enhanced the phagocytosis and bactericidal activity of macrophages by inducing trained immunity. RNA sequencing and metabolomic analyses identified the CFB-C3a-C3aR-HIF-1α axis-mediated phosphatidylcholine accumulation as the key mechanism for M28-induced trained immunity. Phosphatidylcholine, like M28, also induced trained immunity. To enhance M28-mediated therapeutic potential, it was encapsulated in liposomes (M28-LNPs), which exhibited superior immune-stimulating properties compared to M28 alone. In vivo experiments revealed that M28-LNPs significantly reduced bacterial loads and lung damage following MRSA infection, which also provided enhanced protection against Klebsiella pneumoniae and Candida albicans. We first confirmed a link between complement activation and trained immunity, offering valuable insights into the treatment and prevention of complement-related autoimmune diseases.

Diverse spore-forming bacterial populations in US organic raw milk are driven by climate region

Spore-forming bacteria pose significant challenges to the dairy industry, as they are present at high levels in the natural environment and can cause finished product spoilage. To improve organic raw milk quality and minimize spoilage caused by spore-forming bacteria, we used a farm-to-table approach, by assessing the levels and diversity of various spore types through longitudinal studies of United States (US) organic dairy supplies, including (1) raw milk from 100 organic dairy farms, (2) raw milk intended for organic cheese production from 5 processing plants, (3) pasteurized milk from 5 processing plants, and (iv) dairy powders from 2 processing plants. Based on a total of 4,194 isolates characterized by either rpoB or 16S rRNA gene sequencing, Bacillus spp. dominated the aerobic spore-formers isolated from farm raw milk, pasteurized milk, and powders. Nonmetric multidimensional scaling revealed that aerobic spore-former populations in organic farm raw milk differ significantly between climate zones at genus, species, and allelic type levels. The anaerobic/facultative anaerobic spore-formers isolated from farm and cheese raw milk samples represented the orders Clostridiales and Bacillales. Evaluation of the gas produced by anaerobic/facultative anaerobic spore-forming bacteria isolates showed that gas production varied significantly between Clostridiales clades, and 1 Bacillales clade produced gas amounts that were not significantly different from most Clostridiales clades. Overall, our data indicate (1) a substantial diversity of aerobic and anaerobic spore-formers in US organic dairy supplies with predominant genera and species similar between organic and conventional dairy supplies as previously described; (2) both anaerobic and facultative anaerobic spore-formers found in organic raw milk produce gas; and (3) climate may affect aerobic spore-former diversity in farm raw milk.

Bacterial Diversity of Marine Biofilm Communities in Terra Nova Bay (Antarctica) by Culture-Dependent and -Independent Approaches

Applying both culture-independent and -dependent approaches, bacterial diversity of marine biofilm communities colonising polyvinyl chloride panels submerged in Terra Nova Bay (Ross Sea, Antarctica) was investigated. Panels were deployed in two sites subjected to a different degree of anthropogenic impact (Road Bay [RB] impacted site and Punta Stocchino [PTS] control site). Biofilm samples were collected after 3 or 12 months to evaluate both short- and long-term microbial colonisation. Taxonomic composition of the microbial community was studied by 16S rRNA gene amplicon sequencing. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Actinobacteria, Verrucomicrobia and Firmicutes. Impacted RB biofilms were found to contain a relevant fraction of potentially pathogenic bacterial genera, accounting for 27.49% of the whole community. A total of 86 psychrotolerant bacterial strains were isolated from the biofilm samples using culture-dependent techniques designed to enrich in Actinobacteria. These strains were assigned to three different phyla: Actinobacteria (54.65%), Firmicutes (32.56%) and Proteobacteria (12.79%). 2.73% of genera identified by metabarcoding were recovered also through cultivation, while 11 additional genera were uniquely yielded by cultivation. Functional screening of the isolates revealed their hydrolytic and oxidative enzyme activity patterns, giving new insights into the metabolic and biotechnological potential of microbial biofilm communities in Terra Nova Bay seawater.

Whole-Genome Sequencing of Peribacillus frigoritolerans Strain d21.2 Isolated in the Republic of Dagestan, Russia

Pesticide-free agriculture is a fundamental pillar of environmentally friendly agriculture. To this end, there is an active search for new bacterial strains capable of synthesizing secondary metabolites and toxins that protect crops from pathogens and pests. In this study, we isolated a novel strain d21.2 of Peribacillus frigoritolerans from a soil sample collected in the Republic of Dagestan, Russia. Leveraging several bioinformatic approaches on Illumina-based whole-genome assembly, we revealed that the strain harbors certain insecticidal loci (coding for putative homologs of Bmp and Vpa) and also contains multiple BGCs (biosynthetic gene clusters), including paeninodin, koranimine, schizokinen, and fengycin. In total, 21 BGCs were predicted as synthesizing metabolites with bactericidal and/or fungicidal effects. Importantly, by applying a re-scaffolding pipeline, we managed to robustly predict MGEs (mobile genetic elements) associated with BGCs, implying high genetic plasticity. In addition, the d21.2's genome was free from genes encoding for enteric toxins, implying its safety in use. A comparison with available genomes of the Peribacillus frigoritolerans strain revealed that the strain described here contains more functionally important loci than other members of the species. Therefore, strain d21.2 holds potential for use in agriculture due to the probable manifestation of bactericidal, fungicidal, growth-stimulating, and other useful properties. The assembled genome is available in the NCBI GeneBank under ASM4106054v1.

Isolation and characterization of salt-stress-tolerant rhizosphere soil bacteria and their effects on plant growth-promoting properties

PGPR has a higher potential impact on agricultural crops. It enhances plant growth and development in a variety of adverse environmental conditions, including biotic and abiotic stresses. The PGPR is commercially vital since it is more efficient, safe for the environment, and beneficial to the economy. Nowadays, salt stress has an impact on the agricultural ecosystem. Salt-tolerant PGPR can directly stimulate plant growth and development by producing a variety of metabolites and phytohormones. The current study looked at the isolation of salt-tolerant bacterial species and their ability to stimulate plant development. Four bacterial species were chosen for their better salt stress tolerance (0-5%). They were identified by 16S rRNA sequencing: Solibacillus silvestris BR1, Peribacillus frigoritolerans BR2, Paenibacillus taichungensis CR1, and Solibacillus isronensis CR2. These strains were positive production of indole acetic acid with varying incubation periods (19.66 ± 1.528 to 646.111 ± 8.058 µg/mL), salt stress (ranging from 29.556 ± 1.171 to 147.8111 ± 2.086 µg/mL), phosphate solubilization (0.145 ± 0.011 to 0.921 ± 0.007 µg/mL), ammonium production (0.299 ± 0.047 to 1.202 ± 0.142 µg/mL), HCN production (0.308 ± 0.051 to 4.269 ± 0.069 µg/mL), and siderophore production (0.190 ± 0.064 to 1.543 ± 0.108 µg/mL) for control strains were used without salt stress. The production level was expressed using a standard curve containing various standards.

Induction of phytoextraction, phytoprotection and growth promotion activities in Lupinus albus under mercury abiotic stress conditions by Peribacillus frigoritolerans subsp., mercuritolerans subsp. nov

Strain SAICEUPBMT was isolated from soils of Almadén (Ciudad Real, Spain), subjected to a high mercury concentration. SAICEUPBMT significantly increased aerial plant weight, aerial plant length and the development of secondary roots under mercury stress; increased twice the absorption of mercury by the plant, while favoring its development in terms of biomass. Similarly, plants inoculated with SAICEUPBMT and grown in soils contaminated with mercury, express a lower activity of antioxidant enzymes; catalase enzymes (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR) for defense against ROS (reactive oxygen species). Whole genome analysis showed that ANI (95. 96 %), dDDH (72.9 %), AAI (93.3 %) and TETRA (0.99) values were on the thresholds established for differentiation a subspecies. The fatty acids analysis related the strain with the Peribacillus frigoritolerans species. And the synapomorphic analysis reveals a common ancestor with analysis related the strain with the Peribacillus frigoritolerans species. Results from genomic analysis together with differences in phenotypic features and chemotaxonomic analysis support the proposal of strain SAICEUPBMT as the type strain of a novel subspecies for which the name Peribacillus frigoritolerans subps. mercuritolerans sp. nov is proposed. The absence of virulence genes and transmissible resistance mechanisms reveals its safety for agronomic uses, under mercury stress conditions. The ability of Peribacillus frigoritolerans subsp. mercuritolerans subsp. nov to improve plant development was tested in a Lupinus albus model, demonstrating a great potential for plant phytoprotection against mercury stress.

Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana

AIMS

This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion.

METHODS AND RESULTS

Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4-5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40-73 µg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 µg/ml nitrite), along with production of exopolysaccharides (125 ± 20 µg/ml) and auxin-like compounds (42.6 ± 0.05 µg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < -1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5-2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2-4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani.

CONCLUSIONS

P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.

Plant growth-promoting rhizobacteria: Peribacillus frigoritolerans 2RO30 and Pseudomonas sivasensis 2RO45 for their effect on canola growth under controlled as well as natural conditions

Even though canola is one of the most important industrial crops worldwide, it has high nutrient requirements and is susceptible to pests and diseases. Therefore, natural methods are sought to support the development of these plants. One of those methods could be a plant growth-promoting rhizobacteria (PGPR) that have a beneficial effect on plant development. The aim of this study was a genomic comparison of two PGPR strains chosen based on their effect on canola growth: Peribacillus frigoritolerans 2RO30, which stimulated canola growth only in sterile conditions, and Pseudomonas sivasensis 2RO45, which promoted canola growth in both sterile and non-sterile conditions. First of all, six bacterial strains: RO33 (Pseudomonas sp.), RO37 (Pseudomonas poae), RO45 (Pseudomonas kairouanensis), 2RO30 (Peribacillus frigoritolerans), 2RO45 (Pseudomonas sivasensis), and 3RO30 (Pseudomonas migulae), demonstrating best PGP traits in vitro, were studied for their stimulating effect on canola growth under sterile conditions. P. frigoritolerans 2RO30 and P. sivasensis 2RO45 showed the best promoting effect, significantly improving chlorophyll content index (CCI) and roots length compared to the non-inoculated control and to other inoculated seedlings. Under non-sterile conditions, only P. sivasensis 2RO45 promoted the canola growth, significantly increasing CCI compared to the untreated control and to other inoculants. Genome comparison revealed that the genome of P. sivasensis 2RO45 was enriched with additional genes responsible for ACC deaminase (acdA), IAA (trpF, trpG), and siderophores production (fbpA, mbtH, and acrB) compared to 2RO30. Moreover, P. sivasensis 2RO45 showed antifungal effect against all the tested phytopathogens and harbored six more biosynthetic gene clusters (BGC), namely, syringomycin, pyoverdin, viscosin, arylpolyene, lankacidin C, and enterobactin, than P. frigoritolerans 2RO30. These BGCs are well known as antifungal agents; therefore, it can be assumed that these BGCs were responsible for the antifungal activity of P. sivasensis 2RO45 against all plant pathogens. This study is the first report describing P. sivasensis 2RO45 as a canola growth promoter, both under controlled and natural conditions, thus suggesting its application in improving canola yield, by improving nutrient availability, enhancing stress tolerance, and reducing environmental impact of farming practices.

Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera

Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.

Characterization of endophytic bacteria isolated from root nodules of lentil in intercropping with durum wheat

Legumes improve soil fertility by interacting symbiotically with nitrogen-fixing rhizobia allocated in root nodules. Some bacterial endophytes can coexist with rhizobia in nodules and might help legumes by enhancing stress tolerance, producing hormones stimulating plant growth, and increasing plant nutrient intake. Twenty-six bacterial endophytes from Lens culinaris root nodules cultivated in intercropping with Triticum durum were identified and characterized molecularly and biochemically. Potential plant growth-promoting strains have been selected according to the indole acetic acid and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, and for their inorganic phosphate solubilization ability. The presence of genes associated to ACC deaminase and nitrogenase was evaluated. Six selected strains were grown with varying NaCl and polyethylene glycol concentrations to test their salt and osmotic stress tolerance. Priestia megaterium 11NL3 and Priestia aryabhattai 19NL1, resulted to be tolerant to salinity and osmotic stress, were tested on four genotypes of T. durum seeds in different stress conditions. The effect of strain inoculation on seed germination, vigor, and root-to-shoot ratio varied depending on the type of stress and on the durum wheat genotypes. For future research, it will be necessary to test the selected bacterial strains at different plant phenological stages and to clarify the mechanisms involved in the different outcomes of plant-microbe interactions.

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.

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.

Isolation and Degradation Characteristics of PBAT Film Degrading Bacteria

In recent years, PBAT (polybutylene adipate-co-terephthalate) mulch has become one of the most commonly used biodegradable mulching films. In this paper, five potential strains of PBAT film degrading bacteria were screened from the soil sample using PBAT film as the sole carbon source. A highly efficient PBAT degrading strain JZ1 was isolated by comparing the degradation performance of PBAT mulching film identified as Peribacillus frigoritolerans S2313 by 16S rDNA sequence analysis. The capacity of the strain to degrade PBAT film was optimized by adjusting the cultivation conditions such as nitrogen source, pH, and inoculum volume. After 8 weeks of cultivation, the actual degradation rate of the strain to PBAT mulch film reached 12.45%. SEM (scanning electron microscopy) coupled with EDX (energy dispersive spectroscopy) analysis showed that microbial degradation is an oxidation process and is mainly due to the amorphous regions of the PBAT film. The biodegradation of PBAT film by Peribacillus frigoritolerans may provide a promising method for regulating the degradation progress of PBAT film in the farmlands.

In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity

Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.