A prophage tail-like protein is deployed by Burkholderia bacteria to feed on fungi

Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity

Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.

Microbial Diversity Associated with the Cabernet Sauvignon Carposphere (Fruit Surface) from Eight Vineyards in Henan Province, China

The microbial diversity on the carposphere (berry) surface of the grape cultivar Cabernet Sauvignon grown in eight different locations/vineyards of Henan Province was determined by high-throughput sequencing of the bacterial 16S rRNA gene and fungal 18S rRNA gene. The structure of bacterial and fungal communities varied according to the sampling sites, but with some common phyla. Proteobacteria and Ascomycota were dominant/common phyla for bacteria and fungi, respectively. A total of 27 and 20 bacterial and fungal families, respectively, and 39 and 20 bacterial and fungal genera, respectively, with statistically significant differences, were found among different sampling sites. The difference for metabolic pathways of bacteria among the sampling sites existed. In addition, various abundances of enzymes from different sites might indicate that different function patterns exist in microbiota from different sites. The results revealed that locations of grape vineyards might play a significant role in shaping the microbiome, as well as the fact that vineyards can be distinguished based on the abundance of several key bacterial and fungal taxa. Overall, these findings extend our understanding of the similarities and differences in microbial community and their metabolic function on Cabernet Sauvignon grape surfaces from different geographic locations.

Exploring the comparative genome of rice pathogen Burkholderia plantarii: unveiling virulence, fitness traits, and a potential type III secretion system effector

This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies.

Methionine biosynthetic genes and methionine sulfoxide reductase A are required for Rhizoctonia solani AG1-IA to cause sheath blight disease in rice

Rhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host tissues. Understanding R. solani ability to sustain growth under an oxidative-stress-enriched environment is important for developing disease control strategies. Here, we demonstrate that R. solani upregulates methionine biosynthetic genes, including Rs_MET13 during infection in rice, and double-stranded RNA-mediated silencing of these genes impairs the pathogen's ability to cause disease. Exogenous treatment with methionine restores the disease-causing ability of Rs_MET13-silenced R. solani and facilitates its growth on 10 mM H2O2-containing minimal-media. Notably, the Rs_MsrA gene that encodes methionine sulfoxide reductase A, an antioxidant enzyme involved in the repair of oxidative damage of methionine, is upregulated upon H2O2 treatment and also during infection in rice. Rs_MsrA-silenced R. solani is unable to cause disease, suggesting that it is important for the repair of oxidative damage in methionine during host colonization. We propose that spray-induced gene silencing of Rs_MsrA and designing of antagonistic molecules that block MsrA activity can be exploited as a drug target for effective control of sheath blight disease in rice.

Evaluation of Antibiotic Penicillin G Activities Based on Electrochemical Measurement of a Tetrazolium Salt

This study focused on the electrochemical properties of tetrazolium salts to develop a simple method for evaluating viable bacterial counts, which are indicators of drug susceptibility. Considering that the oxidized form of tetrazolium, which has excellent cell membrane permeability, changes to the insoluble reduced form formazan inside the cell, the number of viable cells was estimated based on the reduction current of the tetrazolium remaining in the bacterial suspension. Dissolved oxygen is an important component of bacterial activity. However, it interferes with the electrochemical response of tetrazolium. We estimated the number of viable bacteria in the suspension based on potential-selective current responses that were not affected by dissolved oxygen. Based on solubility, cell membrane permeability, and characteristic electrochemical properties of the tetrazolium salt 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium, we developed a method for rapidly measuring viable bacteria within one-fifth of the time required by conventional colorimetric methods for drug susceptibility testing.

Taxonomy-guided selection of Paraburkholderia busanensis sp. nov.: a versatile biocontrol agent with mycophagy against Colletotrichum scovillei causing pepper anthracnose

IMPORTANCE

Traditional control methods for postharvest diseases rely on fungicides, which cause human health and environmental concerns. This study introduces a taxonomy-guided strategy for selecting biocontrol agents. By focusing on Paraburkholderia group, which harbors diverse plant-beneficial strains, the inadvertent selection of harmful strains was circumvented, thereby obviating the need for laborious in vitro screening assays. A highly promising candidate, strain P39, has been identified, exhibiting remarkable biocontrol activity against Colletotrichum scovillei. Through comprehensive genomic, physiological, and biochemical analyses, P39 was characterized as a novel species within the Paraburkholderia genus and designated Paraburkholderia busanensis. Moreover, these findings deepen our understanding of bacterial-fungal interactions, as they elucidate a potential pathway for the utilization of fungal chitin, thereby enhancing our understanding of bacterial mycophagy. P. busanensis is a promising source of antifungal volatiles and putative novel secondary metabolites.

A prophage tail-like protein facilitates the endophytic growth of Burkholderia gladioli and mounting immunity in tomato

A prophage tail-like protein (Bg_9562) of Burkholderia gladioli strain NGJ1 possesses broad-spectrum antifungal activity, and it is required for the bacterial ability to forage over fungi. Here, we analyzed whether heterologous overexpression of Bg_9562 or exogenous treatment with purified protein can impart disease tolerance in tomato. The physiological relevance of Bg_9562 during endophytic growth of NGJ1 was also investigated. Bg_9562 overexpressing lines demonstrate fungal and bacterial disease tolerance. They exhibit enhanced expression of defense genes and activation of mitogen-activated protein kinases. Treatment with Bg_9562 protein induces defense responses and imparts immunity in wild-type tomato. The defense-inducing ability lies within 18-51 aa region of Bg_9562 and is due to sequence homology with the bacterial flagellin epitope. Interaction studies suggest that Bg_9562 is perceived by FLAGELLIN-SENSING 2 homologs in tomato. The silencing of SlSERK3s (BAK1 homologs) prevents Bg_9562-triggered immunity. Moreover, type III secretion system-dependent translocation of Bg_9562 into host apoplast is important for elicitation of immune responses during colonization of NGJ1. Our study emphasizes that Bg_9562 is important for the endophytic growth of B. gladioli, while the plant perceives it as an indirect indicator of the presence of bacteria to mount immune responses. The findings have practical implications for controlling plant diseases.

Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea)

Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.

Comprehensive Investigation of Die-Back Disease Caused by Fusarium in Durian

Durian (Durio zibethinus L.) is an economically important crop in the southern and eastern parts of Thailand. The occurrence of die-back disease caused by plant pathogenic fungi poses a serious threat to the quality and quantity of durian products. However, the identification of causal agents has been a subject of mixed information and uncertainty. In this research, we conducted a comprehensive investigation of die-back disease in nine durian plantations located in Thailand. By analyzing a total of 86 Fusarium isolates obtained from infected tissues, we aimed to provide clarity and a better understanding of the fungal pathogens responsible for this economically significant disease. Through a combination of colony characteristics, microscopic morphology, and a multilocus sequence analysis (MLSA) of the internal transcribed spacer (ITS) region, translation elongation factor 1-α (TEF1-α) gene, and RNA polymerase II gene (RPB2) sequences, we were able to identify and categorize the isolates into three distinct groups, namely, Fusarium incarnatum, F. solani, and F. mangiferae. Koch's postulates demonstrated that only F. incarnatum and F. solani were capable of causing die-back symptoms. This research represents the first report of F. incarnatum as a causal agent of die-back disease in durian in Thailand. Additionally, this study uncovers the association of ambrosia beetles and F. solani, highlighting the potential involvement of E. similia in facilitating the spread of die-back disease caused by Fusarium in durian.

Evaluation of Bacterial Activity Based on the Electrochemical Properties of Tetrazolium Salts

This study focused on the electrochemical properties of tetrazolium salts to develop a simple method for evaluating viable bacterial counts, which are indicators of hygiene control at food and pharmaceutical manufacturing sites. Given that the oxidized form of 3-(4,5-di-methylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), which has excellent cell membrane permeability, changes to the insoluble reduced form of formazan inside the cell, the number of viable cells was estimated by focusing on the reduction current of MTT remaining in the suspension. Dissolved oxygen is an important substance for bacterial activity; however, it interferes with the electrochemical response of MTT. We investigated the electrochemical properties of MTT to obtain a potential-selective current response that was not affected by dissolved oxygen. Real-time observation of viable bacteria in suspension revealed that uptake of MTT into bacteria was completed within 10 min, including the lag period. In addition, we observed that the current response depends on viable cell density regardless of the bacterial species present. Our method enables a rapid estimation of the number of viable bacteria, making it possible to confirm the safety of food products before they are shipped from the factory and thereby prevent food poisoning.

Nicotinic Acid Catabolism Modulates Bacterial Mycophagy in Burkholderia gladioli Strain NGJ1

Burkholderia gladioli strain NGJ1 exhibits mycophagous activity on a broad range of fungi, including Rhizoctonia solani, a devastating plant pathogen. Here, we demonstrate that the nicotinic acid (NA) catabolic pathway in NGJ1 is required for mycophagy. NGJ1 is auxotrophic to NA and it potentially senses R. solani as a NA source. Mutation in the nicC and nicX genes involved in NA catabolism renders defects in mycophagy and the mutant bacteria are unable to utilize R. solani extract as the sole nutrient source. As supplementation of NA, but not FA (fumaric acid, the end product of NA catabolism) restores the mycophagous ability of ΔnicC/ΔnicX mutants, we anticipate that NA is not required as a carbon source for the bacterium during mycophagy. Notably, nicR, a MarR-type of transcriptional regulator that functions as a negative regulator of the NA catabolic pathway is upregulated in ΔnicC/ΔnicX mutant and upon NA supplementation the nicR expression is reduced to the basal level in both the mutants. The ΔnicR mutant produces excessive biofilm and is completely defective in swimming motility. On the other hand, ΔnicC/ΔnicX mutants are compromised in swimming motility as well as biofilm formation, potentially due to the upregulation of nicR. Our data suggest that a defect in NA catabolism alters the NA pool in the bacterium and upregulates nicR which in turn suppresses bacterial motility as well as biofilm formation, leading to mycophagy defects. IMPORTANCE Mycophagy is an important trait through which certain bacteria forage over fungal mycelia and utilize fungal biomass as a nutrient source to thrive in hostile environments. The present study emphasizes that nicotinic acid (NA) is important for bacterial motility and biofilm formation during mycophagy by Burkholderia gladioli strain NGJ1. Defects in NA catabolism potentially alter the cellular NA pool, upregulate the expression of nicR, a negative regulator of biofilm, and therefore suppress bacterial motility as well as biofilm formation, leading to mycophagy defects.

RAV1 family members function as transcriptional regulators and play a positive role in plant disease resistance

Phytopathogens pose a severe threat to agriculture and strengthening the plant defense response is an important strategy for disease control. Here, we report that AtRAV1, an AP2 and B3 domain-containing transcription factor, is required for basal plant defense in Arabidopsis thaliana. The atrav1 mutant lines demonstrate hyper-susceptibility against fungal pathogens (Rhizoctonia solani and Botrytis cinerea), whereas AtRAV1 overexpressing lines exhibit disease resistance against them. Enhanced expression of various defense genes and activation of mitogen-activated protein kinases (AtMPK3 and AtMPK6) are observed in the R. solani infected overexpressing lines, but not in the atrav1 mutant plants. An in vitro phosphorylation assay suggests AtRAV1 to be a novel phosphorylation target of AtMPK3. Bimolecular fluorescence complementation and yeast two-hybrid assays support physical interactions between AtRAV1 and AtMPK3. Overexpression of the native as well as phospho-mimic but not the phospho-defective variant of AtRAV1 imparts disease resistance in the atrav1 mutant A. thaliana lines. On the other hand, overexpression of AtRAV1 fails to impart disease resistance in the atmpk3 mutant. These analyses emphasize that AtMPK3-mediated phosphorylation of AtRAV1 is important for the elaboration of the defense response in A. thaliana. Considering that RAV1 homologs are conserved in diverse plant species, we propose that they can be gainfully deployed to impart disease resistance in agriculturally important crop plants. Indeed, overexpression of SlRAV1 (a member of the RAV1 family) imparts disease tolerance against not only fungal (R. solani and B. cinerea), but also against bacterial (Ralstonia solanacearum) pathogens in tomato, whereas silencing of the gene enhances disease susceptibility.

Burkholderia gladioli strain KJ-34 exhibits broad-spectrum antifungal activity

INTRODUCTION

Plant pathogens are one of the major constraints on worldwide food production. The antibiotic properties of microbes identified as effective in managing plant pathogens are well documented.

METHODS

Here, we used antagonism experiments and untargeted metabolomics to isolate the potentially antifungal molecules produced by KJ-34.

RESULTS

KJ-34 is a potential biocontrol bacterium isolated from the rhizosphere soil of rice and can fight multiple fungal pathogens (i.e. Ustilaginoidea virens, Alternaria solani, Fusarium oxysporum, Phytophthora capsica, Corynespora cassiicola). The favoured fermentation conditions are determined and the fermentation broth treatment can significantly inhibit the infection of Magnaporthe oryzae and Botryis cinerea. The fermentation broth suppression ratio is 75% and 82%, respectively. Fermentation broth treatment disrupted the spore germination and led to malformation of hyphae. Additionally, we found that the molecular weight of antifungal products were less than 1000 Da through semipermeable membranes on solid medium assay. To search the potentially antifungal molecules that produce by KJ-34, we used comparative and bioinformatics analyses of fermentation broth before and after optimization by mass spectrometry. Untargeted metabolomics analyses are presumed to have a library of antifungal agents including benzoylstaurosporine, morellin and scopolamine.

DISCUSSION

These results suggest that KJ-34 produced various biological control agents to suppress multiple phytopathogenic fungi and showed a strong potential in the ecological technologies of prevention and protection.

Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto

Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.

Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome

Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.

The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability

Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.

N-Terminus Plays a Critical Role for Stabilizing the Filamentous Assembly and the Antifungal Activity of Bg_9562

Bg_9562, a prophage tail-like protein was earlier shown to be required for bacterial mycophagy by Burkholderia gladioli strain NGJ1. The purified protein exhibited broad-spectrum antifungal activity; however, the structural and mechanistic details vis-à-vis its activity remained elusive. In this study, we have structurally characterized the protein Bg_9562 using negatively stained transmission electron microscopy, molecular modeling and mutagenesis. We find that Bg_9562 shows structural similarity to Gp13, a tail assembly chaperone. The transmission electron microscopy revealed that, Bg_9562 forms long flexible tubular structures. Molecular modeling of the filament like structure divulges that the inter subunit contacts are meditated largely through hydrophobic interactions. Using mutagenesis, we demonstrate that the N-terminal residues of the protein when deleted results in reduced activity and destabilization of filament formation. Overall, structure-function analysis opens up avenues for further utilization of the protein as a potent antifungal molecule. IMPORTANCE Burkholderia gladioli strain NGJ1, isolated from healthy rice seedling, was earlier demonstrated to have mycophagous properties on a broad range of fungi, including Rhizoctonia solani, a causal agent of deadly sheath blight disease of rice. The purified Bg_9562 protein exerts broad-spectrum antifungal activity. The protein also inhibits the growth of laboratory strain of Candida, an opportunistic human pathogen. In this study, we structurally characterize Bg_9562 using a combination of negative staining transmission electron microscopy, molecular modeling, mutagenesis, and functional antifungal assay. We show that the protein assembles into long filament like structures stabilized by N-terminus residues and this region is important for its activity. Our study has implications in utilizing Bg_9562 or its derivatives as antifungal molecule(s) which will provide environmentally friendly control of fungal diseases of plants and animals.

Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations

Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network’s representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.

Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content

The study was undertaken to unravel the culturable endophytic bacterial microbiome of Crocus sativus L. (saffron crocus) and consequently obtain potential leads to develop plant growth-promoting and biocontrol agents for increased productivity and sustainable cultivation. The endophytes formed 47 different operational taxonomic units (OTUs), spanning over 28 genera. The host was preferentially colonized by the genus Bacillus, followed by Burkholderia and Pantoea, respectively. Several endophytes possessed potential plant growth-promoting properties and inhibitory activities against the specific fungal pathogens of saffron. The endophytes, except for Microbacterium oxydans, did not cause any disease symptoms in the pot experiments. The selected cultures, Burkholderia gladioli, Streptomyces achromogenes, and three species of Bacillus, enhanced the host plant growth significantly. Based on the pot experiment results, two isolates, Bacillus mojavensis CS4EB32 and Burkholderia gladioli E39CS3, were selected for the field experiments. We obtained an increase of 67.5%, 69.8%, and 68.3% in the production of flowers with the individual and collective treatments, respectively. The treatments also enhanced the biomass of the plant and the length and weight of stigmas significantly. The endophyte treatments induced the expression of the pathway genes, resulting in a marked increase in the concentration of apocarotenoids. The study indicates that the dominant endophytes support plant growth and development in nature and present an opportunity for developing microbial formulations for the sustainability of saffron cultivation.

Performance of Novel Antimicrobial Protein Bg_9562 and In Silico Predictions on Its Properties with Reference to Its Antimicrobial Efficiency against Rhizoctonia solani

Bg_9562 is a potential broad-spectrum antifungal effector protein derived from the bacteria Burkholderia gladioli strain NGJ1 and is effective against Rhizoctonia solani, the causal agent of sheath blight in rice. In the present study, in vitro antifungal assays showed that Bg_9562 was efficient at 35 °C and 45 °C and ineffective either at high acidic pH (3.0) or alkaline pH (9.5) conditions. Compatibility studies between the native bioagents Trichoderma asperellum TAIK1 and Bacillus subtilis BIK3 indicated that Bg_9562 was compatible with the bioagents. A field study using foliar spray of the Bg_9562 protein indicated the need of formulating the protein before its application. In silico analysis predicted that Bg_9562 possess 111 amino acid residues (46 hydrophobic residues, 12 positive and 8 negative residues) with the high aliphatic index of 89.92, attributing to its thermostability with a half-life of 30 h. Bg_9562 (C₄₉₁H₈₁₃N₁₃₇O₁₆₆S₅) possessed a protein binding potential of 1.27 kcal/mol with a better possibility of interacting and perturbing the membrane, the main target for antimicrobial proteins. The secondary structure revealed the predominance of random coils in its structure, and the best 3D model of Bg_9562 was predicted using an ab initio method with Robetta and AlphaFold 2. The predicted binding ligands were nucleic acids and zinc with confidence scores of 0.07 and 0.05, respectively. The N-terminal region (1–14 residues) and C-terminal region (101 to 111) of Bg_9562 residues were predicted to be disordered regions. Stability and binding properties of the protein from the above studies would help to encapsulate Bg_9562 using a suitable carrier to maintain efficiency and improve delivery against Rhizoctonia solani in the most challenging rice ecosphere.

The alternative sigma factors, rpoN1 and rpoN2 are required for mycophagous activity of Burkholderia gladioli strain NGJ1

Bacteria utilize RpoN, an alternative sigma factor (σ54) to grow in diverse habitats, including nitrogen-limiting conditions. Here, we report that a rice-associated mycophagous bacterium Burkholderia gladioli strain NGJ1 encodes two paralogues of rpoN viz. rpoN1 and rpoN2. Both of them are upregulated during 24 h of mycophagous interaction with Rhizoctonia solani, a polyphagous fungal pathogen. Disruption of either one of rpoNs renders the mutant NGJ1 bacterium defective in mycophagy, whereas ectopic expression of respective rpoN genes restores mycophagy in the complementing strains. NGJ1 requires rpoN1 and rpoN2 for efficient biocontrol to prevent R. solani to establish disease in rice and tomato. Further, we have identified 17 genes having RpoN regulatory motif in NGJ1, majority of them encode potential type III secretion system (T3SS) effectors, nitrogen assimilation, and cellular transport-related functions. Several of these RpoN regulated genes as well as certain previously reported T3SS apparatus (hrcC and hrcN) and effector (Bg_9562 and endo-β-1,3-glucanase) encoding genes are upregulated in NGJ1 but not in ΔrpoN1 or ΔrpoN2 mutant bacterium, during mycophagous interaction with R. solani. This highlights that RpoN1 and RpoN2 modulate T3SS, nitrogen assimilation as well as cellular transport systems in NGJ1 and thereby promote bacterial mycophagy.

Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation

Burkholderia sensu lato species are prominent for their diversity of hosts. The type 3 secretion system (T3SS) is a major mechanism impacting the interactions between bacteria and eukaryotic hosts. Besides the human pathogenic species Burkholderia pseudomallei and closely affiliated species, the T3SS has received little attention in this genus as in taxonomically and evolutionary close genera Paraburkholderia, Caballeronia, Trinickia, and Mycetohabitans. We proceeded to identify and characterize the diversity of T3SS types using the genomic data from a subset of 145 strains representative of the species diversity found in the Burkholderia s.l. group. Through an analysis of their phylogenetic distribution, we identified two new T3SS types with an atypical chromosomal organization and which we propose to name BCI (Burkholderia cepacia complex Injectisome) and PSI (Paraburkholderia Short Injectisome). BCI is the dominant T3SS type found in Burkholderia sensu stricto (s.s.) species and PSI is mostly restricted to the Paraburkholderia genus. By correlating their distribution with the ecology of their strains of origin, we propose a role in plant interaction for these T3SS types. Experimentally, we demonstrated that a BCI deficient B. vietnamiensis LMG10929 mutant was strongly affected in its rice colonization capacity.

Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites

Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.

Burkholderia gladioli E39CS3, an endophyte of Crocus sativus Linn., induces host resistance against corm-rot caused by Fusarium oxysporum

AIM

To investigate the role of the leading saffron endophyte Burkholderia gladioli strain E39CS3 (BG-E39) in the inhibition of corm-rot and induced systemic resistance (ISR) in the host against the saffron specific pathogen, Fusarium oxysporum.

METHODS AND RESULTS

We studied the interaction between BG-E39 and the corm-rot pathogen F. oxysporum in vitro and in vivo. BG-E39 strongly inhibited both the F. oxysporum strains and other saffron-specific and non-specific pathogens used in this study. Confrontation and microscopic analyses revealed that the endophyte possessed fungicidal activity against the pathogens and effectively induced cell death in the mycelia. The endophyte produced chitinases as well as β-1,3-glucanase that may be involved in the pathogen cell wall degradation. BG-E39 did not cause corm-rot in Crocus sativus and the closely related plant, Gladiolus, thus establishing that it is non-pathogenic to these plants. The endophyte reduced corm-rot through antibiosis and enhanced the endogenous jasmonic acid (JA) levels and expression of JA-regulated and other plant defence genes.

CONCLUSIONS

The bacterial endophyte BG-E39 provides resistance to the host plant against F. oxysporum corm-rot in nature.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current study discovers the role of the saffron endophyte BG-E39 in providing resistance to the host against corm-rot. Therefore, this endophyte is a potential candidate for developing a microbial formulation for the biocontrol of the most common disease of C. sativus.

Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors

Bacteria utilize type VI secretion system (T6SS) to deliver antibacterial toxins to target co-habiting bacteria. Here, we report that Burkholderia gladioli strain NGJ1 deploys certain T6SS effectors (TseTBg), having both DNase and RNase activities to kill target bacteria. RNase activity is prominent on NGJ1 as well as other bacterial RNA while DNase activity is pertinent to only other bacteria. The associated immunity (TsiTBg) proteins harbor non-canonical helix-turn-helix motifs and demonstrate transcriptional repression activity, similar to the antitoxins of type II toxin-antitoxin (TA) systems. Genome analysis reveals that homologs of TseTBg are either encoded as TA or T6SS effectors in diverse bacteria. Our results indicate that a new ORF (encoding a hypothetical protein) has evolved as a result of operonic fusion of TA type TseTBg homolog with certain T6SS-related genes by the action of IS3 transposable elements. This has potentially led to the conversion of a TA into T6SS effector in Burkholderia. Our study exemplifies that bacteria can recruit toxins of TA systems as T6SS weapons to diversify its arsenal to dominate during inter-bacterial competitions.

A β-lactamase gene of Fusarium oxysporum alters the rhizosphere microbiota of soybean

The rhizosphere is a multitrophic environment, and for soilborne pathogens such as Fusarium oxysporum, microbial competition in the rhizosphere is inevitable before reaching and infecting roots. This study established a tritrophic interaction among the plant growth-promoting rhizobacterium Burkholderia ambifaria, F. oxysporum and Glycine max (soybean) to study the effects of F. oxysporum genes on shaping the soybean microbiota. Although B. ambifaria inhibited mycelial growth and increased bacterial propagation in the presence of F. oxysporum, F. oxysporum still managed to infect soybean in the presence of B. ambifaria. RNA-Seq identified a putative F. oxysporum secretory β-lactamase-coding gene, FOXG_18438 (abbreviated as Fo18438), that is upregulated during soybean infection in the presence of B. ambifaria. The ∆Fo18438 mutants displayed reduced mycelial growth towards B. ambifaria, and the complementation of full Fo18438 and the Fo18438 β-lactamase domain restored mycelial growth. Using the F. oxysporum wild type, ∆Fo18438 mutants and complemented strains with full Fo18438, Fo18438 β-lactamase domain or Fo18438 RTA1-like domain for soil inoculation, 16S rRNA amplicon sequencing revealed that the abundance of a Burkholderia operational taxonomic unit (OTU) was increased in the rhizosphere microbiota infested by the strains with Fo18438 β-lactamase domain. Non-metric multidimensional scaling and PICRUSt2 functional analysis revealed differential abundance for the bacterial β-lactam-related functions when contrasting the genotypes of F. oxysporum. These results indicated that the Fo18438 β-lactamase domain provides F. oxysporum with the advantage of growing into the soybean rhizosphere, where β-lactam antibiosis is involved in microbial competition. Accordingly, this study highlights the capability of an F. oxysporum gene for altering the soybean rhizosphere and taproot microbiota.

Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils

Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.

Fungicidal Activity of Volatile Organic Compounds Emitted by Burkholderia gladioli Strain BBB-01

A Burkholderia gladioli strain, named BBB-01, was isolated from rice shoots based on the confrontation plate assay activity against several plant pathogenic fungi. The genome of this bacterial strain consists of two circular chromosomes and one plasmid with 8,201,484 base pairs in total. Pangenome analysis of 23 B. gladioli strains suggests that B. gladioli BBB-01 has the closest evolutionary relationship to B. gladioli pv. gladioli and B. gladioli pv. agaricicola. B. gladioli BBB-01 emitted dimethyl disulfide and 2,5-dimethylfuran when it was cultivated in lysogeny broth and potato dextrose broth, respectively. Dimethyl disulfide is a well-known pesticide, while the bioactivity of 2,5-dimethylfuran has not been reported. In this study, the inhibition activity of the vapor of these two compounds was examined against phytopathogenic fungi, including Magnaporthe oryzae, Gibberella fujikuroi, Sarocladium oryzae, Phellinus noxius and Colletotrichumfructicola, and human pathogen Candida albicans. In general, 2,5-dimethylfuran is more potent than dimethyl disulfide in suppressing the growth of the tested fungi, suggesting that 2,5-dimethylfuran is a potential fumigant to control plant fungal disease.

Enzymatic and non-enzymatic functional attributes of plant microbiome

Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.

Foliar Application or Seed Priming of Cholic Acid-Glycine Conjugates can Mitigate/Prevent the Rice Bacterial Leaf Blight Disease via Activating Plant Defense Genes

Xanthomonas Oryzae pv. oryzae (Xoo) causes bacterial blight and Rhizoctonia solani (R. solani) causes sheath blight in rice accounting for >75% of crop losses. Therefore, there is an urgent need to develop strategies for the mitigation of these pathogen infections. In this study, we report the antimicrobial efficacy of Cholic Acid-Glycine Conjugates (CAGCs) against Xoo and R. solani. We show that CAGC C6 is a broad-spectrum antimicrobial and is also able to degrade biofilms. The application of C6 did not hamper plant growth and showed minimal effect on the plant cell membranes. Exogenous application of C6 on pre-infection or post-infection of Xoo on rice susceptible genotype Taichung native (TN1) can mitigate the bacterial load and improve resistance through upregulation of plant defense genes. We further demonstrate that C6 can induce plant defense responses when seeds were primed with C6 CAGC. Therefore, this study demonstrates the potential of CAGCs as effective antimicrobials for crop protection that can be further explored for field applications.

Calcium regulates the mycophagous ability of Burkholderia gladioli strain NGJ1 in a type III secretion system-dependent manner

BACKGROUND

A rice associated bacterium Burkholderia gladioli strain NGJ1 demonstrates mycophagy, a phenomenon wherein bacteria feed on fungi. Previously, we have reported that NGJ1 utilizes type III secretion system (T3SS) to deliver a prophage tail-like protein (Bg_9562) into fungal cells to establish mycophagy.

RESULTS

In this study, we report that calcium ion concentration influences the mycophagous ability of NGJ1 on Rhizoctonia solani, an important fungal pathogen. The calcium limiting condition promotes mycophagy while high calcium environment prevents it. The expression of various T3SS apparatus encoding genes of NGJ1 was induced and secretion of several potential T3SS effector proteins (including Bg_9562) into extracellular milieu was triggered under calcium limiting condition. Using LC-MS/MS proteome analysis, we identified several calcium regulated T3SS effector proteins of NGJ1. The expression of genes encoding some of these effector proteins was upregulated during mycophagous interaction of NGJ1 with R. solani. Further, mutation of one of these genes (endo-β-1, 3- glucanase) rendered the mutant NGJ1 bacterium defective in mycophagy while complementation with full length copy of the gene restored its mycophagous activity.

CONCLUSION

Our study provides evidence that low calcium environment triggers secretion of various T3SS effectors proteins into the extracellular milieu and suggests the importance of cocktail of these proteins in promoting mycophagy.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community

BACKGROUND

Myxobacteria are micropredators in the soil ecosystem with the capacity to move and feed cooperatively. Some myxobacterial strains have been used to control soil-borne fungal phytopathogens. However, interactions among myxobacteria, plant pathogens, and the soil microbiome are largely unexplored. In this study, we aimed to investigate the behaviors of the myxobacterium Corallococcus sp. strain EGB in the soil and its effect on the soil microbiome after inoculation for controlling cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (FOC).

RESULTS

A greenhouse and a 2-year field experiment demonstrated that the solid-state fermented strain EGB significantly reduced the cucumber Fusarium wilt by 79.6% (greenhouse), 66.0% (2015, field), and 53.9% (2016, field). Strain EGB adapted to the soil environment well and decreased the abundance of soil-borne FOC efficiently. Spatiotemporal analysis of the soil microbial community showed that strain EGB migrated towards the roots and root exudates of the cucumber plants via chemotaxis. Cooccurrence network analysis of the soil microbiome indicated a decreased modularity and community number but an increased connection number per node after the application of strain EGB. Several predatory bacteria, such as Lysobacter, Microvirga, and Cupriavidus, appearing as hubs or indicators, showed intensive connections with other bacteria.

CONCLUSION

The predatory myxobacterium Corallococcus sp. strain EGB controlled cucumber Fusarium wilt by migrating to the plant root and regulating the soil microbial community. This strain has the potential to be developed as a novel biological control agent of soil-borne Fusarium wilt. Video abstract.

Proteome Analyses Reveal Macrophomina phaseolina's Survival Tools When Challenged by Burkholderia contaminans NZ

A phytopathogenic fungus, Macrophomina phaseolina, which infects a wide range of plants, is an important consideration in agronomy. A jute endophytic bacterium, Burkholderia contaminans NZ, was found to have a promising effect in controlling the fungus in in vitro culture conditions. Using the iTRAQ LC-MS/MS method for quantitative proteomics study, an analysis of the whole proteome of Macrophomina phaseolina with or without B. contaminans NZ challenge identified 2204 different proteins, of which 137 were found to have significant deviation in expression. Kyoto encyclopedia of genes and genomes pathway analysis identified most of the upregulated proteins to be functionally related to energy production (26.11%), as well as defense and stress response (23.45%), while there was significant downregulation in oxidative stress protection pathways (42.61%), growth and cell wall integrity (30.95%), and virulence (23.81%). Findings of this study suggest the development of a battle when the phytopathogen encounters the bacterium. B. contaminans NZ manages to arrest the growth of the fungus and decrease its pathogenicity, but the fungus apparently survives under "hibernating" conditions by upregulating its energy metabolism. This first ever proteomic study of M. phaseolina will go a long way in understanding and developing strategies for its effective control.

Morpho-Pathological and Global Transcriptomic Analysis Reveals the Robust Nonhost Resistance Responses in Chickpea Interaction with Alternaria brassicae

Alternaria blight, caused by Alternaria brassicae, causes considerable yield loss in Brassica crops. While several blight-resistant varieties have been developed using resistance sources from host germplasm, none of them are entirely successful in imparting durable resistance. This has prompted the exploration of novel gene pools of nonhost plant species. Nonhost resistance (NHR) is a durable form of resistance, comprising pre- and postinvasion layers of defense. We aimed to identify the molecular basis of NHR to A. brassicae and identify the layers of NHR operating in a nonhost, chickpea (Cicer arietinum). To elucidate the layers of NHR operating against A. brassicae, we compared the histopathology and infection patterns of A. brassicae in C. arietinum and Brassica juncea. Delayed conidial germination, impeded hyphal growth, suppressed appressorium formation, and limited hyphal penetration occurred in the nonhost plant compared with the host plant, implying the involvement of the preinvasion layer of NHR in C. arietinum. Next, we investigated the molecular basis of robust NHR, in C. arietinum challenged with A. brassicae, by microarray-based global transcriptome profiling. Genes involved in stomatal closure, cuticular wax biosynthesis, cell-wall modification, and secondary metabolite production (contributing to preinvasion NHR) as well as reactive oxygen species (ROS) and cell death (contributing to postinvasion NHR) were found to be upregulated. Consistent with transcriptomic analysis, the morpho-pathological analysis revealed stomatal closure, ROS accumulation, and localized cell death in C. arietinum as the defense strategies against A. brassicae. Thus, we identified NHR-contributing genes with potential applications in blight resistance gene transfer to B. juncea.

A novel outer membrane β-1,6-glucanase is deployed in the predation of fungi by myxobacteria

Myxobacterial predation on bacteria has been investigated for several decades. However, their predation on fungi has received less attention. Here, we show that a novel outer membrane β-1,6-glucanase GluM from Corallococcus sp. strain EGB is essential for initial sensing and efficient decomposition of fungi during predation. GluM belongs to an unstudied family of outer membrane β-barrel proteins with potent specific activity up to 24,000 U/mg, whose homologs extensively exist in myxobacteria. GluM was able to digest fungal cell walls efficiently and restrict Magnaporthe oryzae infection of rice plants. Genetic complementation with gluM restored the fungal predation ability of Myxococcus xanthus CL1001, which was abolished by the disruption of gluM homolog oar. The inability to prey on fungi with cell walls that lack β-1,6-glucans indicates that β-1,6-glucans are targeted by GluM. Our results demonstrate that GluM confers myxobacteria with the ability to feed on fungi, and provide new insights for understanding predator-prey interactions. Considering the attack mode of GluM, we suggest that β-1,6-glucan is a promising target for the development of novel broad-spectrum antifungal agents.

Bacteria-fungal Confrontation and Fungal Growth Prevention Assay

There are some bacteria which can grow and multiply at the cost of living fungal biomass. They can potentially utilize fungi as a source of nutrients to forage over them. Such phenomenon is known as bacterial mycophagy, however, its mechanistic insights need to be explored to identify the molecules involved in mycophagy for potential utilization in controlling various fungal diseases. Recently we have demonstrated that a rice-associated bacteria Burkholderia gladioli strain NGJ1 exhibits mycophagous ability on several fungi, including Rhizoctonia solani, the necrotrophic fungal pathogen causing sheath blight disease in rice. We hereby describe our validated and efficient methods used to study B. gladioli strain NGJ1-R. solani interactions. These methodologies would be useful for designing assays to study the confrontation between bacteria and fungi which in turn enable discovery of novel antifungal molecules from such bacteria.