Microbial Consortia for Effective Biocontrol of Root and Foliar Diseases in Tomato

One stone two birds: Endophytes alleviating trace elements accumulation and suppressing soilborne pathogen by stimulating plant growth, photosynthetic potential and defense related gene expression

In the present investigation, we utilized zinc nanoparticles (Zn-NPs) and bacterial endophytes to address the dual challenge of heavy metal (HM) toxicity in soil and Rhizoctonia solani causing root rot disease of tomato. The biocontrol potential of Bacillus subtilis and Bacillus amyloliquefaciens was harnessed, resulting in profound inhibition of R. solani mycelial growth and efficient detoxification of HM through strong production of various hydrolytic enzymes and metabolites. Surprisingly, Zn-NPs exhibited notable efficacy in suppressing mycelial growth and enhancing the seed germination (%) while Gas chromatography-mass spectrometry (GC-MS) analysis unveiled key volatile compounds (VOCs) crucial for the inhibition of pathogen. Greenhouse trials underscored significant reduction in the disease severity (%) and augmented biomass in biocontrol-mediated plants by improving photosynthesis-related attributes. Interestingly, Zn-NPs and biocontrol treatments enhanced the antioxidant enzymes and mitigate oxidative stress indicator by increasing H2O2 concentration. Field experiments corroborated these findings, with biocontrol-treated plants, particularly those receiving consortia-mediated treatments, displayed significant reduction in disease severity (%) and enhanced the fruit yield under field conditions. Root analysis confirmed the effective detoxification of HM, highlighting the eco-friendly potential of these endophytes and Zn-NPs as fungicide alternative for sustainable production that foster soil structure, biodiversity and promote plant health.

Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests

Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.

Development of a Pseudomonas-based biocontrol consortium with effective root colonization and extended beneficial side effects for plants under high-temperature stress

The root microbiota plays a crucial role in plant performance. The use of microbial consortia is considered a very useful tool for studying microbial interactions in the rhizosphere of different agricultural crop plants. Thus, a consortium of 3 compatible beneficial rhizospheric Pseudomonas strains previously isolated from the avocado rhizosphere, was constructed. The consortium is composed of two compatible biocontrol P. chlororaphis strains (PCL1601 and PCL1606), and the biocontrol rhizobacterium Pseudomonas alcaligenes AVO110, which are all efficient root colonizers of avocado and tomato plants. These three strains were compatible with each other and reached stable levels both in liquid media and on plant roots. Bacterial strains were fluorescent tagged, and colonization-related traits were analyzed in vitro, revealing formation of mixed biofilm networks without exclusion of any of the strains. Additionally, bacterial colonization patterns compatible with the different strains were observed, with high survival traits on avocado and tomato roots. The bacteria composing the consortium shared the same root habitat and exhibited biocontrol activity against soil-borne fungal pathogens at similar levels to those displayed by the individual strains. As expected, because these strains were isolated from avocado roots, this Pseudomonas-based consortium had more stable bacterial counts on avocado roots than on tomato roots; however, inoculation of tomato roots with this consortium was shown to protect tomato plants under high-temperature stress. The results revealed that this consortium has side beneficial effect for tomato plants under high-temperature stress, thus improving the potential performance of the individual strains. We concluded that this rhizobacterial consortium do not improve the plant protection against soil-borne phytopathogenic fungi displayed by the single strains; however, its inoculation can show an specific improvement of plant performance on a horticultural non-host plant (such as tomato) when the plant was challenged by high temperature stress, thus extending the beneficial role of this bacterial consortium.

Recent advances in the use of Trichoderma-containing multicomponent microbial inoculants for pathogen control and plant growth promotion

Chemical pesticides and fertilizers are used in agricultural production worldwide to prevent damage from plant pathogenic microorganisms, insects, and nematodes, to minimize crop losses and to preserve crop quality. However, the use of chemical pesticides and fertilizers can severely pollute soil, water, and air, posing risks to the environment and human health. Consequently, developing new, alternative, environment-friendly microbial soil treatment interventions for plant protection and crop yield increase has become indispensable. Members of the filamentous fungal genus Trichoderma (Ascomycota, Sordariomycetes, Hypocreales) have long been known as efficient antagonists of plant pathogenic microorganisms based on various beneficial traits and abilities of these fungi. This minireview aims to discuss the advances in the field of Trichoderma-containing multicomponent microbiological inoculants based on recent experimental updates. Trichoderma strains can be combined with each other, with other fungi and/or with beneficial bacteria. The development and field performance of such inoculants will be addressed, focusing on the complementarity, synergy, and compatibility of their microbial components.

Plant growth-promoting bacteria potentiate antifungal and plant-beneficial responses of Trichoderma atroviride by upregulating its effector functions

Trichoderma uses different molecules to establish communication during its interactions with other organisms, such as effector proteins. Effectors modulate plant physiology to colonize plant roots or improve Trichoderma's mycoparasitic capacity. In the soil, these fungi can establish relationships with plant growth-promoting bacteria (PGPBs), thus affecting their overall benefits on the plant or its fungal prey, and possibly, the role of effector proteins. The aim of this study was to determine the induction of Trichoderma atroviride gene expression coding for effector proteins during the interaction with different PGPBs, Arabidopsis or the phytopathogen Fusarium brachygibbosum, and to determine whether PGPBs potentiates the beneficial effects of T. atroviride. During the interaction with F. brachygibbosum and PGPBs, the effector coding genes epl1, tatrx2 and tacfem1 increased their expression, especially during the consortia with the bacteria. During the interaction of T. atroviride with the plant and PGPBs, the expression of epl1 and tatrx2 increased, mainly with the consortium formed with Pseudomonas fluorescens UM270, Bacillus velezensis AF12, or B. halotolerans AF23. Additionally, the consortium formed by T. atroviride and R. badensis SER3 stimulated A. thaliana PR1:GUS and LOX2:GUS for SA- and JA-mediated defence responses. Finally, the consortium of T. atroviride with SER3 was better at inhibiting pathogen growth, but the consortium of T. atroviride with UM270 was better at promoting Arabidopsis growth. These results showed that the biocontrol capacity and plant growth-promoting traits of Trichoderma spp. can be potentiated by PGPBs by stimulating its effector functions.

Bacillus species as tools for biocontrol of plant diseases: A meta-analysis of twenty-two years of research, 2000-2021

The traditional way of dealing with plant diseases has been the use of chemical products, but these harm the environment and are incompatible with the global effort for sustainable development. The use of Bacillus and related species in the biological control of plant diseases is a trend in green agriculture. Many studies report the positive effect of these bacteria, but a synthesis is still necessary. So, the objective of this work is to perform a meta-analysis of Bacillus biocontrol potential and identify factors that drive its efficacy. Data were compiled from articles published in journals listed in two of the main scientific databases between 2000 and 2021. Among 6159 articles retrieved, 399 research papers met the inclusion criteria for a systematic review. Overall, Bacilli biocontrol agents reduced disease by 60% compared to control groups. Furthermore, experimental tests with higher concentrations show a strong protective effect, unlike low and single concentration essays. Biocontrol efficacy also increased when used as a protective inoculation rather than therapeutic inoculation. Inoculation directly in the fruit has a greater effect than soil drenching. The size of the effect of Bacillus-based commercial products is lower than the newly tested strains. The findings presented in this study confirm the power of Bacillus-based bioinoculants and provide valuable guidance for practitioners, researchers, and policymakers seeking effective and sustainable solutions in plant disease management.

Crop residue heterogeneity: Decomposition by potential indigenous ligno-cellulolytic microbes and enzymatic profiling

The continuous depletion of fossil resources, energy-crisis and environmental pollution has gained popularity for careful selection of suitable microbial consortium to efficiently decompose crop residue and facilitate nutrient cycling. While crop residue is commonly incorporated into soil, the impact of the heterogeneity of residue on decomposition and biological mechanisms involved in extracellular carbon (C) cycle related enzyme activities remain not fully understood. To address this problem, an incubation study was conducted on chemical heterogeneity of straw and root residue with indigenous ligno-cellulolytic microbial consortium on extracellular enzymes as their activity is crucial for making in-situ residue management decisions under field condition. The activity of extracellular enzymes in different substrates showed differential variation with the type of enzyme and ranged from 16.9 to 77.6 µg mL-1, 135.7 to 410.8 µg mL-1, 66.9 to 177.1 µg mL-1 and 42.1 to 160.9 µg mL-1 for cellulase, xylanase, laccase and lignin peroxidase, respectively. Extracellular enzyme activities were sensitive to heterogeneity of biochemical constituent's present in straw and root residues and enhanced the decomposition processes with indigenous ligno-cellulolytic microbial consortium (Bacillus altitudinis, Streptomyces flavomacrosporus and Aspergillus terreus). Correlation matrix elucidated A. terreus and B. altitudinis as potential indigenous ligno-cellulolytic microbial inoculant influencing soil enzymatic activity (p < 0.001). This research work demonstrates a substantial impact of chemically diverse crop residues on the decomposition of both straw and root. It also highlights the pivotal role played by key indigenous decomposers and interactions between different microorganisms in governing the decomposition of straw and root primarily through release of extracellular enzyme. Consequently, it is novel bio-emerging strategy suggested that incorporation of the crop residues under field conditions should be carried out in conjunction with the potential indigenous ligno-cellulolytic microbial consortium for efficient decomposition in the short period of time under sustainable agriculture system.

Use of ginger extract and bacterial inoculants for the suppression of Alternaria solani causing early blight disease in Tomato

Early blight (EB), caused by Alternaria solani, is a serious problem in tomato production. Plant growth-promoting rhizobacteria promote plant growth and inhibit plant disease. The present study explored the bio-efficacy of synergistic effect of rhizobacterial isolates and ginger powder extract (GPE) against tomato EB disease, singly and in combination. Six fungal isolates from symptomatic tomato plants were identified as A. solani on the basis of morphological features i.e., horizontal septation (6.96 to 7.93 µm), vertical septation (1.50 to 2.22 µm), conidia length (174.2 to 187.6 µm), conidial width (14.09 to 16.52 µm), beak length (93.06 to 102.26 µm), and sporulation. Five of the twenty-three bacterial isolates recovered from tomato rhizosphere soil were nonpathogenic to tomato seedlings and were compatible with each other and with GPE. Out of five isolates tested individually, three isolates (St-149D, Hyd-13Z, and Gb-T23) showed maximum inhibition (56.3%, 48.3%, and 42.0% respectively) against mycelial growth of A. solani. Among combinations, St-149D + GPE had the highest mycelial growth inhibition (76.9%) over the untreated control. Bacterial strains molecularly characterized as Pseudomonas putida, Bacillus subtilis, and Bacillus cereus and were further tested in pot trials through seed bacterization for disease control. Seeds treated with bacterial consortia + GPE had the highest disease suppression percentage (78.1%), followed by St-149D + GPE (72.2%) and Hyd-13Z + GPE (67.5%). Maximum seed germination was obtained in the bacterial consortia + GPE (95.0 ± 2.04) followed by St-149D + GPE (92.5 ± 1.44) and Hyd-13Z + GPE (90.0 ± 2.04) over control (73.8 ± 2.39) and chemical control as standard treatment (90.0 ± 2). Ginger powder extracts also induce the activation of defence-related enzymes (TPC, PO, PPO, PAL, and CAT) activity in tomato plants. These were highly significant in the testing bacterial inoculants against A. solani infection in tomato crops.

Applied microbiology of the phyllosphere

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.

Identification of synthetic consortia from a set of plant-beneficial bacteria

The use of microbial inoculants in agriculture as biofertilisers and/or biopesticides is an appealing alternative to replace or reduce the practice of agrochemicals. Plant microbiota studies are revealing the different bacterial groups which are populating plant microbiomes re-energising the plant probiotic bacteria (PPB) translational research sector. Some single-microbial strain bioinoculants have proven valid in agriculture (e.g., based on Trichoderma, mycorrhiza or rhizobia); however, it is now recommended to consider multistrain consortia since plant-beneficial effects are often a result of community-level interactions in plant microbiomes. A limiting step is the selection of a fitting combination of microbial strains in order to accomplish the best beneficial effect upon plant inoculation. In this study, we have used a subset of 23 previously identified and characterised rice-beneficial bacterial colonisers to design and test a series of associated experiments aimed to identify potential PPB consortia which are able to co-colonise and induce plant growth promotion. Bacterial strains were co-inoculated in vitro and in planta using several different methods and their co-colonisation and co-persistence monitored. Results include the identification of two 5-strain and one 2-strain consortia which displayed plant growth-promoting features. Future practical applications of microbiome research must include experiments aimed at identifying consortia of bacteria which can be most effective as crop amendments.

Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato

The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.

Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress

Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.

Biocontrol mechanisms of Bacillus: Improving the efficiency of green agriculture

Species of the genus Bacillus have been widely used for the biocontrol of plant diseases in the demand for sustainable agricultural development. New mechanisms underlying Bacillus biocontrol activity have been revealed with the development of microbiome and microbe-plant interaction research. In this review, we first briefly introduce the typical Bacillus biocontrol mechanisms, such as the production of antimicrobial compounds, competition for niches/nutrients, and induction of systemic resistance. Then, we discussed in detail the new mechanisms of pathogen quorum sensing interference and reshaping of the soil microbiota. The "cry for help" mechanism was also introduced, in which plants can release specific signals under pathogen attack to recruit biocontrol Bacillus for root colonization against invasion. Finally, two emerging strategies for enhancing the biocontrol efficacy of Bacillus agents, including the construction of synthetic microbial consortia and the application of rhizosphere-derived prebiotics, were proposed.

Interactions between plant-beneficial microorganisms in a consortium: Streptomyces microflavus and Trichoderma harzianum

The construction of microbial consortia is challenging due to many variables to be controlled, including the cross-compatibility of the selected strains and their additive or synergistic effects on plants. In this work, we investigated the interactions in vitro, in planta, and at the molecular level of two elite biological control agents (BCAs), that is Streptomyces microflavus strain AtB-42 and Trichoderma harzianum strain M10, to understand their attitude to cooperate in a consortium. In vitro, we observed a strong cross-antagonism between AtB-42 and M10 in agar plates due to diffusible metabolites and volatile organic compounds. In liquid co-cultures, M10 hindered the growth of AtB-42 very likely because of secondary metabolites and strong competition for the nutrients. The interaction in the co-culture induced extensive transcriptional reprogramming in both strains, especially in the pathways related to ribosomes, protein synthesis, and oxidoreductase activity, suggesting that each strain recognized the counterpart and activated its defence responses. The metabolome of both strains was also significantly affected. In contrast, in the soil, M10 growth was partially contrasted by AtB-42. The roots of tomato seedlings inoculated with the consortium appeared smaller than the control and single-strain-inoculated plants, indicating that plants diverted some energy from the development to defence activation, as evidenced by the leaf transcriptome. The consortium induced a stronger transcriptional change compared to the single inoculants, as demonstrated by a higher number of differentially expressed genes. Although the cross-antagonism observed in vitro, the two strains exerted a synergistic effect on tomato seedlings by inducing resistance responses stronger than the single inoculants. Our observations pose a question on the usefulness of the sole in vitro assays for selecting BCAs to construct a consortium. In vivo experiments should be preferred, and transcriptomics may greatly help to elucidate the activity of the BCAs beyond the phenotypic effects on the plant.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation

Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.

Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure

Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach is the investigation of disease escape plants, which remain healthy under high disease pressure, likely due to their microbiome function. This study explored the microbiome of grapevines with the disease escape phenotype. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was applied to trunk tissues of GTD escape and adjacent diseased vines. Our findings showed that the GTD escape vines had a significantly different microbiome compared with diseased vines. The GTD escape vines consistently harbored a higher relative abundance of the bacterial taxa Pseudomonas and Hymenobacter. Among fungi, Aureobasidium and Rhodotorula were differentially associated with GTD escape vines, while the GTD pathogen, Eutypa, was associated with the diseased vines. This is the first report of the link between the GTD escape phenotype and the grapevine microbiome.

Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato

Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant-fungus relationship. In the early stages of colonization (5-7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12-19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.

Streptomyces and their specialised metabolites for phytopathogen control - comparative in vitro and in planta metabolic approaches

In the search for new crop protection microbial biocontrol agents, isolates from the genus Streptomyces are commonly found with promising attributes. Streptomyces are natural soil dwellers and have evolved as plant symbionts producing specialised metabolites with antibiotic and antifungal activities. Streptomyces biocontrol strains can effectively suppress plant pathogens via direct antimicrobial activity, but also induce plant resistance through indirect biosynthetic pathways. The investigation of factors stimulating the production and release of Streptomyces bioactive compounds is commonly conducted in vitro, between Streptomyces sp. and a plant pathogen. However, recent research is starting to shed light on the behaviour of these biocontrol agents in planta, where the biotic and abiotic conditions share little similarity to those of controlled laboratory conditions. With a focus on specialised metabolites, this review details (i) the various methods by which Streptomyces biocontrol agents employ specialised metabolites as an additional line of defence against plant pathogens, (ii) the signals shared in the tripartite system of plant, pathogen and biocontrol agent, and (iii) an outlook on new approaches to expedite the identification and ecological understanding of these metabolites under a crop protection lens.

Developing rumen mimicry process for biological ammonia synthesis

The ruminant rumen houses hyper-ammonia-producing bacteria (HAB) that produce ammonia with minimal energy use. Here we developed a mimicry process to produce bio-ammonia, a solution of ammonia and ammonium. The rumen microbes were used to ferment soybean (SYB), soybean protein isolate (SPI), and pepsin-hydrolysate (HP) for bio-ammonia production. The maximum bio-ammonia produced from SYB, SPI, and HP were 0.65, 1.2_, and 1.1 g/L, respectively. The presence of non-protein in SYB hindered bio-ammonia production and the processing of SYB to SPI and HP significantly (p < 0.05) increased bio-ammonia production. HP was converted to bio-ammonia quicker than SPI suggesting that enzymatic hydrolysis increases bioprocessing efficiency. Metagenomic analysis of a sample culture revealed that the HAB population is predominantly Klebsiella quasivariicola (73%), Escherichia coli (6%), and Enterobacter cloacae (6%). The bioprocessing steps developed would enable industrial ammonia production to achieve a low CO₂ footprint.

Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture

Trichoderma is a cosmopolitan and opportunistic ascomycete fungal genus including species that are of interest to agriculture as direct biological control agents of phytopathogens. Trichoderma utilizes direct antagonism and competition, particularly in the rhizosphere, where it modulates the composition of and interactions with other microorganisms. In its colonization of plants, on the roots or as an endophyte, Trichoderma has evolved the capacity to communicate with the plant and produce numerous multifaceted benefits to its host. The intricacy of this plant-microorganism association has stimulated a marked interest in research on Trichoderma, ranging from its capacity as a plant growth promoter to its ability to prime local and systemic defence responses against biotic and abiotic stresses and to activate transcriptional memory affecting plant responses to future stresses. This Review discusses the ecophysiology and diversity of Trichoderma and the complexity of its relationships in the agroecosystem, highlighting its potential as a direct and indirect biological control agent, biostimulant and biofertilizer, which are useful multipurpose properties for agricultural applications. We also highlight how the present legislative framework might accommodate the demonstrated evidence of Trichoderma proficiency as a plant-beneficial microorganism contributing towards eco-sustainable agriculture.

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.

Diversity and Exploration of Endophytic Bacilli for the Management of Head Scab (Fusarium graminearum) of Wheat

Fusarium graminearum causing head scab (HS) or head blight (HB) disease in wheat is one of the nasty fungi reported to cause significant grain quality and yield loss. Biological control using endophytic bacteria has emerged as a prospective option for containing fungal diseases in an environmentally benevolent, durable, and sustainable manner. In this regard, 112 endophytic bacilli were isolated from the anthesis stage (Zadok’s growth stage 65) from five different wheat genotypes with an aim to identify prospective antagonistic strains against F. graminearum. The molecular identity of the strains was confirmed by matching 16S rRNA sequences of bacterial strains with the gene sequences of type strains available in the National Center for Biotechnology Information database and reported 38 different species of Bacillus in all the five wheat cultivars. Further, it has been observed that only fourteen strains (B. clarus NOK09, B. mojavensis NOK16, B. subtilis NOK33, B. rugosus NOK47, B. mojavensis NOK52, B. clarus NOK59, B. coahuilensis NOK72, B. cabrialesii NOK78, B. cabrialesii NOK82, B. rugosus NOK85, B. amyloliquefaciens NOK89, B. australimaris NOK95, B. pumilus NOK103, and B. amyloliquefaciens NOK109) displayed in-vitro antagonistic effect against Fusarium graminearum fungus. Furthermore, the three endophytic Bacillus strains showing the strongest antagonistic effect (>70% of growth inhibition of fungal mycelium) under in-vitro antagonistic assay were selected for field experiments. In a two-year consecutive field study, a combination of three strains (B. clarus NOK09 + B. subtilis NOK33 + B. amyloliquefaciens NOK109) displayed a remarkable reduction in HS disease index by 81.47% and 77.85%, respectively. Polymerase chain reaction assay detected three genes (ituD, bmyC, and srfA) involved in antibiotic biosynthesis pathways. Additional attributes such as potassium solubilization, siderophore release, and hydrolytic enzyme (protease, lipase, amylase, chitinase, and pectinase) synthesis have been observed in these strains. Overall, the present study was successful in profiling endophytic bacilli and selecting the combination of effective antagonistic endophytic Bacillus strains that could be the best alternative for the sustainable and ecological sound management of HS disease in wheat under field conditions.

Metabolites derived from fungi and bacteria suppress in vitro growth of Gnomoniopsis smithogilvyi, a major threat to the global chestnut industry

INTRODUCTION

Chestnut rot caused by the fungus Gnomoniopsis smithogilvyi is a disease present in the world's major chestnut growing regions. The disease is considered a significant threat to the global production of nuts from the sweet chestnut (Castanea sativa). Conventional fungicides provide some control, but little is known about the potential of biological control agents (BCAs) as alternatives to manage the disease.

OBJECTIVE

Evaluate whether formulated BCAs and their secreted metabolites inhibit the in vitro growth of G. smithogilvyi.

METHODS

The antifungal potential of BCAs was assessed against the pathogen through an inverted plate assay for volatile compounds (VOCs), a diffusion assay for non-volatile compounds (nVOCs) and in dual culture. Methanolic extracts of nVOCs from the solid medium were further evaluated for their effect on conidia germination and were screened through an LC-MS-based approach for antifungal metabolites.

RESULTS

Isolates of Trichoderma spp., derived from the BCAs, significantly suppressed the pathogen through the production of VOCs and nVOCs. The BCA from which Bacillus subtilis was isolated was more effective in growth inhibition through the production of nVOCs. The LC-MS based metabolomics on the nVOCs derived from the BCAs showed the presence of several antifungal compounds.

CONCLUSION

The results show that G. smithogilvyi can be effectively controlled by the BCAs tested and that their use may provide a more ecological alternative for managing chestnut rot. The in vitro analysis should now be expanded to the field to assess the effectiveness of these alternatives for chestnut rot management.

Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen

Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from Rhizoctonia solani AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of Arabidopsis. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.

Designing a synthetic microbial community devoted to biological control: The case study of Fusarium wilt of banana

Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4) is threatening banana production because of its increasing spread. Biological control approaches have been widely studied and constitute interesting complementary measures to integrated disease management strategies. They have been based mainly on the use of single biological control agents (BCAs). In this study, we moved a step forward by designing a synthetic microbial community (SynCom) for the control of Fusarium wilt of banana (FWB). Ninety-six isolates of Pseudomonas spp., Bacillus spp., Streptomyces spp., and Trichoderma spp. were obtained from the banana rhizosphere and selected in vitro for the antagonism against Foc TR4. In pot experiments, a large community such as SynCom 1.0 (44 isolates with moderate to high antagonistic activity) or a small one such as SynCom 1.1 (seven highly effective isolates) provided similar disease control (35% symptom severity reduction). An in vitro study of the interactions among SynCom 1.1 isolates and between them and Foc revealed that beneficial microorganisms not only antagonized the pathogen but also some of the SynCom constituents. Furthermore, Foc defended itself by antagonizing the beneficial microbes. We also demonstrated that fusaric acid, known as one of the secondary metabolites of Fusarium species, might be involved in such an interaction. With this knowledge, SynCom 1.2 was then designed with three isolates: Pseudomonas chlororaphis subsp. piscium PS5, Bacillus velezensis BN8.2, and Trichoderma virens T2C1.4. A non-simultaneous soil application of these isolates (to diminish cross-inhibition) delayed FWB progress over time, with significant reductions in incidence and severity. SynCom 1.2 also performed better than two commercial BCAs, BioPak® and T-Gro. Eventually, SynCom 1.2 isolates were characterized for several biocontrol traits and their genome was sequenced. Our data showed that assembling a SynCom for biocontrol is not an easy task. The mere mixtures of antagonists (e.g., SynCom 1.0 and 1.1) might provide effective biocontrol, but an accurate investigation of the interactions among beneficial microorganisms is needed to improve the results (e.g., SynCom 1.2). SynCom 1.2 is a valuable tool to be further developed for the biological control of FWB.

Epiphytic Yeasts and Bacteria as Candidate Biocontrol Agents of Green and Blue Molds of Citrus Fruits

Overall, 180 yeasts and bacteria isolated from the peel of citrus fruits were screened for their in vitro antagonistic activity against Penicillium digitatum and P. italicum, causative agents of green and blue mold of citrus fruits, respectively. Two yeast and three bacterial isolates were selected for their inhibitory activity on mycelium growth. Based on the phylogenetic analysis of 16S rDNA and ITS rDNA sequences, the yeast isolates were identified as Candida oleophila and Debaryomyces hansenii while the bacterial isolates were identified as Bacillus amyloliquefaciens, B. pumilus and B. subtilis. All five selected isolates significantly reduced the incidence of decay incited by P. digitatum and P. italicum on ‘Valencia’ orange and ‘Eureka’ lemon fruits. Moreover, they were effective in preventing natural infections of green and blue mold of fruits stored at 4 °C. Treatments with antagonistic yeasts and bacteria did not negatively affect the quality and shelf life of fruits. The antagonistic efficacy of the five isolates depended on multiple modes of action, including the ability to form biofilms and produce antifungal lipopeptides, lytic enzymes and volatile compounds. The selected isolates are promising as biocontrol agents of postharvest green and blue molds of citrus fruits.

Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes

Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.