Biology subjects

Kovacs, A. T.

Publications and source records attributed to Kovacs, A. T..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Expanding the genome information on Bacillales for biosynthetic gene cluster discovery

This study showcases 121 new genomes of spore-forming Bacillales from strains collected globally from a variety of habitats, assembled using Oxford Nanopore long-read and MGI short-read sequences. Bacilli are renowned for their capacity to produce diverse secondary metabolites with use in agriculture, biotechnology, and medicine. These secondary metabolites are encoded within biosynthetic gene clusters (smBGCs). smBGCs have significant research interest due to their potential for the discovery of new bioactivate compounds. Our dataset includes 62 complete genomes, 2 at chromosome level, and 57 at contig level, covering a genomic size range from 3.50 Mb to 7.15 Mb. Phylotaxonomic analysis revealed that these genomes span 16 genera, with 69 of them belonging to Bacillus. A total of 1,176 predicted BGCs were identified by in silico genome mining. We anticipate that the open-access data presented here will expand the reported genomic information of spore-forming Bacillales and facilitate a deeper understanding of the genetic basis of Bacillales potential for secondary metabolite production.

microbiology↗

bioRxiv2024

Disentangling the potential factors defining Bacillus subtilis abundance in natural soils

Bacillus subtilis is ubiquitously and broadly distributed in various environments but mostly isolated from soil. Given that species of B. subtilis are known as key plant growth-promoting rhizobacteria in agriculture, we here aimed to describe the natural distribution of this species and uncover how biotic and abiotic factors affect its distribution. When comparing different soils, we discovered that B. subtilis is most abundant in grasslands, but can rarely be isolated from forest soil, even if the sample sites for the two types of soil are situated in proximity. Differential analysis revealed that spore-forming bacteria exhibited enrichments in the grassland, suggesting niche overlap or synergistic interactions leading to the proliferation of certain Bacillus species in grassland environments. Network analysis further revealed that Bacillus and other Bacillota established a densely interconnected hub module in the grassland soil samples, characterized by positive associations indicating co-occurrence, a pattern not observed in the forest soil. Speculating that this difference was driven by abiotic factors, we next combined amplicon sequencing with physio-chemical analysis of soil samples, and found multiple chemical variables, mainly pH, to affect microbial composition. Our study pinpoints the factors that influence B. subtilis abundance in natural soils and, therefore, offers insights for designing B. subtilis-based biocontrol products in agricultural settings.

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bioRxiv2023

Taxonomy of Pseudomonas spp determines interactions with Bacillus subtilis

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil, and frequently co-isolated. Despite this, no systematic approach has been employed to assess the pairwise compatibility of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini, but in this case, cocultures with increased B. subtilis pellicle formation were spatially segregated. Our study is the first to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads, hence cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

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bioRxiv2023

Resistance towards and biotransformation of Pseudomonas-produced secondary metabolites during community invasion

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains ambiguous. Here, we use a four-species synthetic community to determine how antibiotic production contributes to P. protegens community invasion and identify community traits that alter the abundance of key P. protegens antimicrobial metabolites (DAPG, pyoluteorin and orfamide A). Surprisingly, mutants deficient in antimicrobial production caused similar perturbations in community composition compared to invasion by wildtype P. protegens. Intriguingly, while pyoluteorin and orfamide A are secreted at levels toxic to individual bacterial strains, community-level resistance circumvents toxicity. Here, we identify the underlying mechanism by which the cyclic lipopeptide, orfamide A, is inactivated and degraded by Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.

microbiology↗

bioRxiv2023

Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas

Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin in an antagonistic interaction with Pseudomonas marginalis. The presence of bacillibactin strongly influenced the outcome of the interaction in an iron-dependent manner. The bacillibactin producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of bacillibactin restricted B. subtilis colony growth in a mechanism reminiscent of a siderophore tug-of-war for iron. Our analysis revealed that the Bacillus-Pseudomonas interaction is conserved across fluorescent Pseudomonas spp., expanding our understanding of the interplay between two genera of the most well-studied soil microbes.

microbiology↗

bioRxiv2023

Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach

Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species, including agriculturally important species.

microbiology↗

bioRxiv2023

Enhanced niche colonisation and competition during bacterial adaptation to a fungus

Bacterial-fungal interactions (BFIs) influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Using a simple BFI system encompassing the Gram-positive bacterium Bacillus subtilis and the black mould fungus Aspergillus niger, we established a co-culture experimental evolution method to investigate bacterial adaptation to the presence of a fungus. In the evolving populations, B. subtilis was rapidly selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles and RlmA-dependent cell wall stress induction. Increased surfactin production typically enhances the competitive success of bacteria against fungi, which likely explains the primary adaption path in the presence of A. niger. Significance statementExperimental evolution and co-cultivation of different microbes are important and useful techniques for discovering new traits and unravelling cryptic regulatory connections. We combined these methods by evolving the Gram-positive bacterium Bacillus subtilis in the presence of the black mould fungus Aspergillus niger that were previously shown to engage in an intricate and physical interaction. Both are ubiquitous, environmentally and industrially relevant model microbes in the colonisation of rhizo- and endosphere and in the production of enzymes. Our results demonstrate how laboratory adaptation can be exploited to improve biocontrol properties of bacteria.

microbiology↗

bioRxiv2023

Parallel genetic adaptation of Bacillus subtilis to different plant species

Plant growth-promoting rhizobacteria benefit plants by stimulating their growth or protecting them against phytopathogens. Rhizobacteria must colonise and persist on plant roots to exert their benefits. However, little is known regarding the processes by which rhizobacteria adapt to different plant species, or behave under alternating host plant regimes. Here, we used experimental evolution and whole-population whole-genome sequencing to analyse how Bacillus subtilis evolves on Arabidopsis thaliana and tomato seedlings, and under an alternating host plant regime, in a static hydroponic setup. We observed parallel evolution across multiple levels of biological organisation in all conditions, which was greatest for the two heterogeneous, multi-resource spatially-structured environments at the genetic level. Species-specific adaptation at the genetic level was also observed, possibly caused by the selection stress imposed by different host plants. Furthermore, a trade-off between motility and biofilm development was supported by mutational changes in motility- and biofilm-related genes. Finally, we identified several condition-specific and common targeted genes in different environments by comparing three different B. subtilis biofilm adaptation settings. The results demonstrate a common evolutionary pattern when B. subtilis is adapting to the plant rhizosphere in similar conditions, and reveal differences in genetic mechanisms between different host plants. These findings will likely support strain improvements for sustainable agriculture. Data summarySequencing data associated with this article are available in the CNGB Sequence Archive (CNSA) [1] of the China National GeneBank DataBase (CNGBdb) [2] under accession numbers CNP0002416 and CNP0003952. Strain data for the DK1042 ancestor are available under accession number CNP0002416. Impact statementFor rhizobacteria to benefit plant growth and protect against phytopathogens, bacteria must colonise and persist on plant roots. Understanding how rhizobacteria adapt to different plant species will assist strain development in sustainable agriculture. To explore the rhizobacterial adaptation process for different plant species and alternating host regimes, B. subtilis was experimentally evolved on A. thaliana or tomato roots, or an alternating host regime. Both parallel and species-specific adaptation was revealed at the genetic level. Analysis of the trade-off between motility and biofilm formation revealed several condition-specific and commonly targeted genes based on experimentally evolving B. subtilis biofilms.

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bioRxiv2022

Species and condition dependent mutational spectrum in experimentally evolved biofilms of Bacilli

Laboratory experimental evolution provides a powerful tool for studying microbial adaptation to different environments. To understand the differences and similarities of the dynamic evolutionary landscapes of two model species from the Bacillus genus as they adapt to abiotic and biotic surfaces, we revived the archived population samples from our four previous experimental evolution studies and performed longitudinal whole-population genome sequencing. Surprisingly, higher number of mutations, higher genotypic diversity, and higher evolvability were detected in the biotic conditions with smaller population size. Different adaptation strategies were observed in different environments within each species, with more diversified mutational spectrum detected in biotic conditions. The insertion sequences of Bacillus thuringiensis are critical for its adaptation to the plastic bead-attached biofilm environment, but insertion sequence mobility was a general phenomenon in this species independent of the selection condition. Additionally, certain parallel evolution has been observed across species and environments, particularly when two species adapt to the same environment at the same time. Further, our results suggest that the population size might be an important driver of evolution. Together, these results provide the first comprehensive mutational landscape of two bacterial species biofilms that is adapted to an abiotic and biotic surface. ImportanceBiofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolved Bacillus thuringiensis and Bacillus subtilis that were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Further, the differences and similarities of adaptive mechanisms in B. thuringiensis and B. subtilis were not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species biofilms that is adapted to an abiotic and biotic surface.

microbiology↗

bioRxiv2022

Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans

Given the risk of Candida albicans overgrowth in the gut, novel complementary therapies should be developed to reduce fungal dominancy. This study highlights the antifungal characteristics of a Bacillus subtilis-derived secondary metabolite, surfactin with high potential against C. albicans. Surfactin inhibited the growth of C. albicans following a 1-hour exposure, in addition to reduced adhesion and morphogenesis. Specifically, surfactin did not affect the level of reactive oxygen species but increased the level of reduced glutathione. Surprisingly, ethanol production enhanced following 2 hours of surfactin exposure. Surfactin treatment caused a significant reduction in intracellular iron, manganese and zinc content compared to control cells, whereas the level of copper was not affected. Alongside these physiological properties, surfactin also enhanced fluconazole efficacy. To gain detailed insights into the surfactin-related effects on C. albicans, genome-wide gene transcription analysis was performed. Surfactin treatment resulted in 1390 differentially expressed genes according to total transcriptome sequencing (RNA-Seq). Of these, 773 and 617 genes with at least a 1.5-fold increase or decrease in transcription, respectively, were selected for detailed investigation. Several genes involved in morphogenesis or related to metabolism (e.g., glycolysis, fermentation, fatty acid biosynthesis) were down-regulated. Moreover, surfactin decreased the expression of ERG1, ERG3, ERG9, ERG10 and ERG11 involved in ergosterol synthesis, whereas genes associated with ribosome biogenesis and iron metabolism and drug transport-related genes were up-regulated. Our data demonstrate that surfactin significantly influences the physiology and gene transcription of C. albicans, and could contribute to the development of a novel innovative complementary therapy. ImportanceAlthough gut colonization by Candida albicans can be considered normal, it may be associated with intestinal diseases. Furthermore, Candida dominance in the gut may pose a potent risk for systemic candidiasis, especially for immunocompromised individuals. In recent years, interest has been growing for the use of Bacillus subtilis as a safe and effective probiotic for human healthcare. Surfactin is a B. subtilis-derived lipopeptide with potential antifungal activity; however, the mechanism underlying this remains unknown. In this study, surfactin negatively affected the adherence, morphogenesis and metabolism of C. albicans and increased ethanol production. These were associated with a reduction in intracellular iron, manganese and zinc while the copper content was not affected. Alongside these physiological modulations, surfactin also had a potent synergistic effect on fluconazole. Our results provide a definitive explanation for the surfactin-related antifungal effect of B. subtilis; furthermore, these data provide a good basis for future probiotic development.

microbiology↗

bioRxiv2022

Complex extracellular biology drives surface competition in Bacillus subtilis

In nature, many bacteria grow on surfaces, where they form cell collectives that compete for space. Within these collectives, cells often secrete molecules that benefit surface spreading by, for example, reducing surface tension or promoting filamentous growth. Although we have a detailed understanding of how these molecules are produced, much remains unknown about their role in surface competition. Here, we examine sliding motility in Bacillus subtilis and compare how secreted molecules, essential for sliding, affect cooperation and competition on the surface. We specifically examine (i) the lipopeptide surfactin, (ii) the hydrophobin protein BslA and (iii) exopolysaccharides (EPS). We find that these molecules have a remarkably different effect on competition: whereas surfactin acts like a common good, which is costly to produce and benefits cells throughout the surface, BslA and EPS are cost-free and act locally. Accordingly, surfactin deficient mutants can exploit the wild-type strain in competition for space, while BslA and EPS mutants cannot. Using a mathematical model, we show that three factors are important in predicting the outcome of surface competition: the costs of molecule synthesis, the private benefits of molecule production, and the diffusion rate. Our results underscore the intricate extracellular biology that can drive bacterial surface competition.

microbiology↗

bioRxiv2022

Keystone species determine the productivity of synthetic microbial biofilm communities

Microbes typically reside in multi-species communities, whose interactions have considerable impacts on the robustness and functionality of such communities. To manage microbial communities, it is essential to understand the factors driving their assemblage and maintenance. Even though the community composition could be easily assessed, interspecies interactions during community establishment remain poorly understood. Here, we combined co-occurrence network analysis with quantitative PCR to examine the importance of each species within synthetic communities (SynComs) of pellicle biofilms. Genome-scale metabolic models and in vitro experiments indicated that the biomass of SynComs was primarily affected by keystone species that are acting either as metabolic facilitators or as competitors. Our study sets an example of how to construct a model SynCom and investigate interspecies interactions.

microbiology↗

bioRxiv2022

Establishment of a transparent soil system to study Bacillus subtilis chemical ecology

Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.

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bioRxiv2021

Quorum sensing signal autoinducer-2 inhibits sporulation of Bacillus by interacting with RapC and functions across species

Collective behavior of bacteria is regulated by quorum sensing (QS). Bacterial cells sense the density of the population and induce corresponding traits and developmental processes. Autoinducer-2 (AI-2) is a common QS signal that regulates behavior of both Gram-positive and Gram-negative bacteria. In spite of the plethora of processes described to be influenced by AI-2 in diverse Gram-negative bacteria, the AI-2-regulated processes in Bacilli are relatively unexplored. Previously, we demonstrated that AI-2 regulates root colonization of Bacillus velezensis SQR9, a well-studied plant beneficial rhizobacterium. Here, we describe a novel function for AI-2 in B. velezensis SQR9 related to development of dormant spores. AI-2 inhibited the initiation of spore development throught the phosphatase RapC and the DNA binding regulator ComA. Using mutant strains and protein-protein interaction studies, we demonstrate that AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA. We further demonstrate that ComA is essential for Spo0A-regulated sporulation in B. velezensis SQR9. Finally, the AI-2 molecule could be shared cross species for inhibiting Bacillus sporulation. Our study revealed a novel function and regulation mechanism of AI-2 in sporulation inhibition of Bacilli that overall suggests sporulation to be a population-level decision process in Bacilli rather than just a individual cell behavior. Author summaryQuorum sensing (QS) regulates many bacterial social behavior. Bacteria cells could moniter and respond cell density by sensing the self produced QS signals. While most QS signals are unique for either Gram-positive or Gram-negative bacteria, autoinducer-2 (AI-2) is a QS signal that could produced by both bacteria groups. However, knowledge of the mechanism of AI-2 affecting bacterial behavior is poorly understood. Here, we found AI-2 inhibite Bacillus velezensis SQR9 sporulation, a generally known bacterial individual behavior. We further revealed the mechanism of AI-2 influencing sporulation of B. velezensis SQR9 was dependent on RapC and ComA. AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA, and then inhibited the Spo0A-regulated sporulation. Interestingly, we show B. velezensis SQR9 could also sense the AI-2 produced by other bacteria and reduce their own sporulation. Taken together we discovered the novel function of AI-2 in sporulation, which will expand the significance of QS signal that they regulate not only social behavior but also individual behavior of bacteria.

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bioRxiv2021

Adaptation and phenotypic diversification of Bacillus thuringiensis 407 biofilm are accompanied by a fuzzy spreader morphotype

Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enable the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry-during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407{Delta}rfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that adaptation process highly depends on the physical adhesive forces.

microbiology↗

bioRxiv2021

Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization in the presence of soil microbes

The soil ubiquitous Bacillus subtilis is known to promote plant growth and protect plants against disease. These characteristics make B. subtilis highly relevant in an agricultural perspective, fueling the interest in studying B. subtilis-plant interactions. Here, we employ an experimental evolution approach to explore adaptation of B. subtilis to Arabidopsis thaliana roots. We found that B. subtilis rapidly adapted to the plant root environment, as evidenced by improved root colonizers observed already after 12 consecutive transfers between seedlings in a hydroponic setup. In addition, two selected evolved isolates from independent populations from transfer 30 outcompeted the ancestor during root colonization. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits. Further, phenotypic characterization of evolved isolates from transfer 30 showed that increased root colonization was associated with robust biofilm formation in response to the plant polysaccharide xylan. Additionally, several evolved isolates across independent populations were impaired in motility, a redundant trait in the selective environment. Interestingly, two evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by a selected evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings provide novel insights into how a well-known plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.

microbiology↗

bioRxiv2021

Development of quantitative high-throughput screening methods for identification of antifungal biocontrol strains

Large screens of bacterial strain collections to identify potential biocontrol agents are often time consuming, costly, and fail to provide quantitative results. In this study, we present two quantitative and high-throughput methods to assess the inhibitory capacity of bacterial biocontrol candidates against fungal phytopathogens. One method measures the inhibitory effect of bacterial culture supernatant components on the fungal growth, while the other accounts for direct interaction between growing bacteria and the fungus by co-cultivating the two organisms. The antagonistic supernatant method quantifies the culture components antifungal activity by calculating the cumulative impact of supernatant addition relative to a non-treated fungal control, while the antagonistic co-cultivation method identifies the minimal bacterial cell concentration required to inhibit fungal growth by co-inoculating fungal spores with bacterial culture dilution series. Thereby, both methods provide quantitative measures of biocontrol efficiency and allow prominent fungal inhibitors to be distinguished from less effective strains. The combination of the two methods shed light on the type of inhibition mechanisms and provide the basis for further mode of action studies. We demonstrate the efficacy of the methods using Bacillus spp. with different levels of antifungal activities as model antagonists and quantify their inhibitory potency against classic plant pathogens. ImportanceFungal phytopathogens are responsible for tremendous agricultural losses on annual basis. While microbial biocontrol agents represent a promising solution to the problem, there is a growing need for high-throughput methods to evaluate and quantify inhibitory properties of new potential biocontrol agents for agricultural application. In this study, we present two high-throughput and quantitative fungal inhibition methods that are suitable for commercial biocontrol screening.

microbiology↗

bioRxiv2021

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization, however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathway involved in syntrophic cooperation when forming coculture biofilms. Assaying the metabolome further demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.

microbiology↗