The recA gene is crucial to mediate colonization of Bacillus cereus 905 on wheat roots

Nutrient Requirements Shape the Preferential Habitat of Allorhizobium vitis VAR03-1, a Commensal Bacterium, in the Rhizosphere of Arabidopsis thaliana

A diverse range of commensal bacteria inhabit the rhizosphere, influencing host plant growth and responses to biotic and abiotic stresses. While root-released nutrients can define soil microbial habitats, the bacterial factors involved in plant-microbe interactions are not well characterized. In this study, we investigated the colonization patterns of two plant disease biocontrol agents, Allorhizobium vitis VAR03-1 and Pseudomonas protegens Cab57, in the rhizosphere of Arabidopsis thaliana using Murashige and Skoog (MS) agar medium. VAR03-1 formed colonies even at a distance from the roots, preferentially in the upper part, while Cab57 colonized only the root surface. The addition of sucrose to the agar medium resulted in excessive proliferation of VAR03-1, similar to its pattern without sucrose, whereas Cab57 formed colonies only near the root surface. Overgrowth of both bacterial strains upon nutrient supplementation inhibited host growth, independent of plant immune responses. This inhibition was reduced in the VAR03-1 ΔrecA mutant, which exhibited increased biofilm formation, suggesting that some activities associated with the free-living lifestyle rather than the sessile lifestyle may be detrimental to host growth. VAR03-1 grew in liquid MS medium with sucrose alone, while Cab57 required both sucrose and organic acids. Supplementation of sugars and organic acids allowed both bacterial strains to grow near and away from Arabidopsis roots in MS agar. These results suggest that nutrient requirements for bacterial growth may determine their growth habitats in the rhizosphere, with nutrients released in root exudates potentially acting as a limiting factor in harnessing microbiota.

Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress

Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.

Plant Growth Promotion Using Bacillus cereus

Plant growth-promoting bacteria (PGPB) appear to be a sensible competitor to conventional fertilization, including mineral fertilizers and chemical plant protection products. Undoubtedly, one of the most interesting bacteria exhibiting plant-stimulating traits is, more widely known as a pathogen, Bacillus cereus. To date, several environmentally safe strains of B. cereus have been isolated and described, including B. cereus WSE01, MEN8, YL6, SA1, ALT1, ERBP, GGBSTD1, AK1, AR156, C1L, and T4S. These strains have been studied under growth chamber, greenhouse, and field conditions and have shown many significant traits, including indole-3-acetic acid (IAA) and aminocyclopropane-1-carboxylic acid (ACC) deaminase production or phosphate solubilization, which allows direct plant growth promotion. It includes an increase in biometrics traits, chemical element content (e.g., N, P, and K), and biologically active substances content or activity, e.g., antioxidant enzymes and total soluble sugar. Hence, B. cereus has supported the growth of plant species such as soybean, maize, rice, and wheat. Importantly, some B. cereus strains can also promote plant growth under abiotic stresses, including drought, salinity, and heavy metal pollution. In addition, B. cereus strains produced extracellular enzymes and antibiotic lipopeptides or triggered induced systemic resistance, which allows indirect stimulation of plant growth. As far as biocontrol is concerned, these PGPB can suppress the development of agriculturally important phytopathogens, including bacterial phytopathogens (e.g., Pseudomonas syringae, Pectobacterium carotovorum, and Ralstonia solanacearum), fungal phytopathogens (e.g., Fusarium oxysporum, Botrytis cinerea, and Rhizoctonia solani), and other phytopathogenic organisms (e.g., Meloidogyne incognita (Nematoda) and Plasmodiophora brassicae (Protozoa)). In conclusion, it should be noted that there are still few studies on the effectiveness of B. cereus under field conditions, particularly, there is a lack of comprehensive analyses comparing the PGP effects of B. cereus and mineral fertilizers, which should be reduced in favor of decreasing the use of mineral fertilizers. It is also worth mentioning that there are still very few studies on the impact of B. cereus on the indigenous microbiota and its persistence after application to soil. Further studies would help to understand the interactions between B. cereus and indigenous microbiota, subsequently contributing to increasing its effectiveness in promoting plant growth.

Harnessing Native Bacillus spp. for Sustainable Wheat Production

The genus Bacillus has been widely applied in contemporary agriculture as an environmentally-friendly biological agent. However, the real effect of commercial Bacillus-based fertilizers and pesticides varies immensely in the field. To harness Bacillus for efficient wheat production, we reviewed the diversity, functionality, and applicability of wheat-associated native Bacillus for the first time. Our main findings are: (i) Bacillus spp. inhabit the rhizosphere, root, stem, leaf, and kernel of wheat; (ii) B. subtilis and B. velezensis are the most widely endophytic species that can be isolated from both below and aboveground tissues; (iii) major functions of these representative strains are promotion of plant growth and alleviation of both abiotic and biotic stresses in wheat; (iv) stability and effectiveness are 2 major challenges during field application; (v) a STVAE pipeline that includes 5 processes, namely, Screen, Test, Validation, Application, and Evaluation, has been proposed for the capture and refinement of wheat-associated Bacillus spp. In particular, this review comprehensively addresses possible solutions, concerns, and criteria during the development of native Bacillus-based inoculants for sustainable wheat production.

Watermelon Root Exudates Enhance Root Colonization of Bacillus amyloliquefaciens TR2

Bacillus amyloliquefaciens TR2, one of plant growth-promoting rhizobacteria (PGPR), is capable of colonizing plant roots in a large population size. However, the interaction of watermelon root exudates and colonization of the strain TR2 has not yet been clearly elucidated. In this investigation, we demonstrated that B. amyloliquefaciens TR2 promoted watermelon plants growth and exhibited biocontrol efficacy against watermelon Fusarium wilt under greenhouse conditions. Collected watermelon root exudates significantly induced chemotaxis, swarming motility, and biofilm formation of the strain TR2. We also tested the components of root exudates (organic acids: malic acid, citric acid, succinic acid, and fumaric acid; amino acids: methionine, glutamic acid, alanine, and aspartic acid; phenolic acid: benzoic acid) and the results showed that a majority of these compounds could promote chemotactic response, swarming motility, and biofilm formation in a different degree. Benzoic acid induced the strongest chemotactic response; however, the swarming motility and biofilm formation of the strain TR2 were maximumly enhanced by supplement of fumaric acid and glutamic acid, respectively. In addition, the root colonization examination indicated that the population of B. amyloliquefaciens TR2 colonized on watermelon root surfaces was dramatically increased by adding concentrated watermelon root exudates. In summary, our studies provide evidence suggesting that root exudates are important for colonization of B. amyloliquefaciens TR2 on plant roots and help us to understand the interaction between plants and beneficial bacteria.

A Potential Biofertilizer—Siderophilic Bacteria Isolated From the Rhizosphere of Paris polyphylla var. yunnanensis

The increasing demands for crop production have become a great challenge while people also realizing the significance of reductions in synthetic chemical fertilizer use. Plant growth-promoting rhizobacteria (PGPR) are proven biofertilizers for increasing crop yields by promoting plant growth via various direct or indirect mechanisms. Siderophilic bacteria, as an important type of PGPR, can secrete siderophores to chelate unusable Fe³⁺ in the soil for plant growth. Siderophilic bacteria have been shown to play vital roles in preventing diseases and enhancing the growth of plants. Paris polyphylla var. yunnanensis (PPVY) is an important traditional Chinese herb. However, reports about its siderophilic bacteria are still rare. This study firstly isolated siderophilic bacteria from the rhizosphere soil of PPVY, identified by morphological and physio-biochemical characteristics as well as 16S rRNA sequence analysis. The dominant genus in the rhizobacteria of PPVY was Bacillus. Among 22 isolates, 21 isolates produced siderophores. The relative amount of siderophores ranged from 4 to 41%. Most of the isolates produced hydroxamate siderophores and some produced catechol. Four isolates belonging to Enterobacter produced the catechol type, and none of them produced carboxylate siderophores. Intriguingly, 16 strains could produce substances that have inhibitory activity against Candida albicans only in an iron-limited medium (SA medium). The effects of different concentrations of Fe³⁺ and three types of synthetic chemical fertilizers on AS19 growth, siderophore production, and swimming motility were first evaluated from multiple aspects. The study also found that the cell-free supernatant (CFS) with high siderophore units (SUs) of AS19 strain could significantly promote the germination of pepper and maize seeds and the development of the shoots and leaves of Gynura divaricata (Linn.). The bacterial solution of AS19 strain could significantly promote the elongation of the roots of G. divaricata (Linn.). Due to its combined traits promoting plant growth and seed germination, the AS19 has the potential to become a bioinoculant. This study will broaden the application prospects of the siderophilic bacteria-AS19 as biofertilizers for future sustainable agriculture.

Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food

Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEA_DAFG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization.