Large-Scale Bioinformatics Analysis of
            <i>Bacillus</i>
            Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

Grubbs, Kirk J.; Bleich, Rachel M.; Maria, Kevin C. Santa; Allen, Scott E.; Farag, Sherif; Team, AgBiome; Shank, Elizabeth A.; Bowers, A.

doi:10.1128/msystems.00040-17

Cited by 84 publications

(72 citation statements)

References 65 publications

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“…NRPs and PKs-NRPs BGCs in Bacillus species are encoding highly conserved known compounds as well as various novel variants. These findings are consistent with KirK J. Grubbs [64] reported. They found that many of the highly conserved BGCs in Bacillus genomes set encode NRPSs; a few additional PKS-NRPSs, such as zwittermicin and bacillaene, are also well conserved.…”

Section: Disscussionsupporting

confidence: 93%

Antimicrobial Activity Screening of Rhizosphere Soil Bacteria from Tomato and Genome-Based Analysis of their Antimicrobial Biosynthetic Potential

Zhou

Cui

et al. 2020

Preprint

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Background: Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowadays. Plant Growth Promoting Rhizobacteria (PGPR) can promote plant growth through biological activity. Their use is considered to be a promising sustainable approach for crop growth. Moreover, a vast number of biosynthetic gene clusters (BGCs) for secondary metabolite production are being revealed in PGPR, which helps to find potential anti-microbial activities for tomato disease control.Results: We isolated 351 bacterial strains (181 of which are Bacillus sp.) from healthy tomato, rhizosphere soil, and tomato tissues. In vitro antagonistic assays revealed that 34 Bacillus strains have antimicrobial activity against Erwinia carotovora, Pseudomonas syringae; Rhizoctonia solani; Botrytis cinerea; Verticillium dahliae and Phytophthora infestans. The genomes of 10 Bacillus and Paenibacillus strains with good antagonistic activity were sequenced. Via genome mining approaches, we identified 120 BGCs encoding NRPs, PKs-NRPs, PKs, terpenes and bacteriocins, including known compounds such as fengycin, surfactin, bacillibactin, subtilin, etc. In addition, several novel BGCs were identified. We discovered that the NRPs and PKs-NRPs BGCs in Bacillus species are encoding highly conserved known compounds as well as various novel variants.Conclusions: This study highlights the great number of varieties of BGCs in Bacillus strains. These findings pave the road for future usage of Bacillus strains as biocontrol agents for tomato disease control and are a resource arsenal for novel antimicrobial discovery.

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Section: Disscussionsupporting

confidence: 93%

Antimicrobial Activity Screening of Rhizosphere Soil Bacteria from Tomato and Genome-Based Analysis of their Antimicrobial Biosynthetic Potential

Zhou

Cui

et al. 2020

Preprint

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“…Fengycin, bacillaene, iturin, and difficidin were essentially observed only within the B. subtilis group. This suggests that the different environmental niches inhabited by members of the B. subtilis clade may select for conservation of metabolites with distinct (or potentially redundant) beneficial functions (78). We here describe one such function, that of outcompeting S. plymuthica in nonfavorable growth temperature.…”

Section: Discussionmentioning

confidence: 94%

The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers

Ogran

Yardeni

Keren-Paz

et al. 2019

Appl Environ Microbiol

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Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have coevolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically toward S. plymuthica, while expressing a nonribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms outcompeted S. plymuthica for successful colonization of the host. Strikingly, the plant host was able to enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria. IMPORTANCE Our study sheds mechanistic light on how multicellular biofilm units compete to successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey, followed by nonribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms, as they activate the synthesis of polyketides; therefore, our study provides evidence of a mechanism by which the host can indirectly select for beneficial microbiota members.on July 10, 2020 by guest http://aem.asm.org/ Downloaded from RESULTSB. subtilis biofilm actively expands toward a competing S. plymuthica colony. When grown on a solid biofilm-inducing medium, B. sutbilis biofilms form symmetrical, circular colonies. To determine the effect of a competing S. plymuthica colony on the development of a B. subtilis biofilm, the two species were inoculated next to each other on a solid biofilm medium. After 2 days, the B. subtilis colony reached S. plymuthica, forming a thick wrinkle around its edge and penetrating toward its center. By the third day, B. subtilis biofilm completely engulfed the S. plymuthica colony, covering it with a thin, unstructured film and enclosing it within the circular wrinkle (Fig. 1A). The location and shape of the B. subtilis center of the biofilm did not change during the interaction with S. plymuthica. However, the biofilm colony advanced asymmetrically toward the S. plymuthica colony, breaking from its usual circular shape ( Fig. 1A).We next examined the mechanisms that could mediate this asymmetric expansion toward a competitor. Many bacterial cells are capable of directional swimming using their flagella (2...

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“…produce different lipopeptide isoforms belonging to the families of surfactins, fengycins or iturins (11). A comparison of predicted BGCs from distinct Bacillus genomes assigned 11 BGCs to B. subtilis strains (12). Notably, a predicted BGC is not proof of the synthesis of the natural product.…”

Section: Introductionmentioning

confidence: 99%

Genomic and chemical diversity ofBacillus subtilissecondary metabolites against plant pathogenic fungi

Kiesewalter

Lozano-Andrade

Wibowo

et al. 2020

Preprint

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Bacillus subtilis produces a wide range of secondary metabolites providing diverse plant-growth-promoting and biocontrol abilities. These secondary metabolites include non-ribosomal peptides (NRPs) with strong antimicrobial properties, causing either cell lysis, pore formation in fungal membranes, inhibition of certain enzymes, or bacterial protein synthesis. However, the natural products of B. subtilis are mostly studied either in laboratory strains or in individual isolates and therefore, a comparative overview of B. subtilis secondary metabolites is missing.In this study, we have isolated 23 B. subtilis strains from eleven sampling sites, compared the fungal inhibition profiles of wild types and their NRPs mutants, followed the production of targeted lipopeptides, and determined the complete genomes of 13 soil isolates. We discovered that non-ribosomal peptide production varied among B. subtilis strains co-isolated from the same soil samples. In vitro antagonism assays revealed that biocontrol properties depend on the targeted plant pathogenic fungus and the tested B. subtilis isolate. While plipastatin alone is sufficient to inhibit Fusarium sp., a combination of plipastatin and surfactin is required to hinder the growth of Botrytis cinerea. Detailed genomic analysis revealed that altered NRP production profiles in certain isolates is due to missing core genes, nonsense mutation, or potentially altered gene regulation.Our study combines microbiological antagonism assays with chemical NRPs detection and biosynthetic gene cluster predictions in diverse B. subtilis soil isolates to provide a broader overview of the secondary metabolite chemodiversity of B. subtilis.IMPORTANCESecondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which non-ribosomally produced lipopeptides in particular display strong antifungal activity. To facilitate prediction of the biocontrol potential of new Bacillus subtilis isolates, we have explored the in vitro antifungal inhibitory profiles of recent B. subtilis isolates, combined with analytical natural product chemistry, mutational analysis, and detailed genome analysis of biosynthetic gene clusters. Such a comparative analysis helped to explain why selected B. subtilis isolates lack production of certain secondary metabolites.

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Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

Cited by 84 publications

References 65 publications

Antimicrobial Activity Screening of Rhizosphere Soil Bacteria from Tomato and Genome-Based Analysis of their Antimicrobial Biosynthetic Potential

Antimicrobial Activity Screening of Rhizosphere Soil Bacteria from Tomato and Genome-Based Analysis of their Antimicrobial Biosynthetic Potential

The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers

Genomic and chemical diversity ofBacillus subtilissecondary metabolites against plant pathogenic fungi

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