Root Exudates of Stressed Plants Stimulate and Attract Trichoderma Soil Fungi

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Exploitation of rhizosphere microbiome biodiversity in plant breeding

Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.

Urban soils immobilize harmful microbes and antibiotic resistance genes

Exposure to harmful microbiomes and antibiotic resistance genes (ARGs) can negatively affect human health. However, the contribution of vegetation and soils to the airborne microbiota transferred indoors (AMTI) remains unclear. We used our newly-developed airborne microbial sampler (VenTube) to collect AMTI samples from 72 neighborhoods in Shanghai. The AMTI sampling coincided with simultaneous adjacent phyllosphere and soil microbes. We characterized the microbial communities using next-generation sequencing and quantitative PCR, and employed traceability analysis to identify the sources of AMTI. Our findings revealed that both bacterial and fungal communities in AMTI predominantly originated from phyllosphere, which was estimated to contribute up to 52.3 % and 67.2 % of the bacterial and fungal communities, respectively. Notably, there was extensive co-transfer of potential human pathogens (PHP) between phyllosphere microbes and AMTI. Surprisingly, although the soil harbored higher levels of PHP and respiratory diseases (RDs)-associated ARGs than AMTI, it contained fewer RDs-associated microbes overall. Furthermore, soil sulfur enrichment due to an increase in Ligustrum trees influenced the release of RDs-associated microorganisms from the soil. Collectively, our study emphasizes that the elevated levels of RDs-associated microbes in AMTI primarily derived from phyllosphere microbes. We also highlight that soils may limit the spread of RDs-associated microbes and ARGs.

Deciphering metabolite signalling between plant roots and soil pathogens to design resistance

Metabolites are important signaling molecules mediating plant-microbe interaction in soil. Plant root exudates are composed of primary metabolites, secondary metabolites, and macro-molecules such as organic acids. Certain organic acids in root exudates can attract pathogenic microbes in soil and promote infection. Meanwhile, secretions from soil microbes can also alter the compositions of root exudates and enhance the pathogenicity towards the target host plant. Examples of toxins in microbial secretions include polyketides and thaxtomins. The pathogenicity of plant microbes is mediated by the dynamic exchange of metabolites between the pathogen and the host plant. By deciphering this metabolite-mediated infection process, targeted strategies can be developed to promote plant resistance to soil pathogens. Examples of the strategies include the manipulation of root exudate composition and the blocking of metabolite signals that promote microbial infection. Other possibilities include minimizing the harmfulness of pathogenic microbial secretions to plants by habituating the plants to the toxin, genetically engineering plants to enhance their pathogen resistance, and treating plants with beneficial hormones and microbes. In this review, we summarized the current understanding of root exudates and soil microbe secretions that promote infection. We also discussed the strategies for promoting pathogen resistance in plants by focusing on the metabolite signaling between plants and pathogenic soil microbes.

Endophytes as bioenhancers of plant growth: An overview

The need for food production rises with the era of expanding population. As a result, there is more indirect demand for chemical pesticides and fertilizers. Serious environmental concerns result from the continuous and careless usage of chemicals. Additionally, they could make the land infertile. One of the finest substitutes for chemicals is to use microorganisms, particularly endophytes. Endophytes uses both direct and indirect mechanisms to encourage plant growth by increased mineral availability, resilience to biotic and abiotic stresses, synthesis of significant phytohormones. This review is focused on exploring the plant growth promoting effect of endophytes and its potential implications in the crop production.

Trichoderma Species from Semiarid Regions and Their Antagonism Against the Microorganisms That Cause Pepper Wilt

Chili wilt is a significant challenge in producing jalapeño peppers, which has led to the implementation of strategies to help counteract or combat the microorganisms responsible for it. One of these strategies is the use of biological control microorganisms, such as Trichoderma, a fungus recognized as a natural enemy of the microorganisms that cause chili wilt. Therefore, this study aimed to isolate and identify Trichoderma species from the soils and roots of different plants, and evaluate their antagonism against Rhizoctonia solani, Phytophthora capsici, and Fusarium sp. Due to the complexity in identifying Trichoderma at the species level, performing a multilocus phylogenetic analysis was necessary, using the ITS, RPB2, and TEF1 regions. The species isolated were T. afroharzianum, T. lentiforme, T. rifaii, T. brevicompactum, T. arundinaceum, and T. longibrachiatum. Subsequently, they were used in three antagonism tests (dual culture, non-volatile organic compounds, and volatile organic compounds) against the phytopathogenic microorganisms. The tests demonstrated that the Trichoderma isolates could inhibit the mycelial growth of all three tested pathogens, obtaining the best results with the strains T. brevicompactum (19RCS), T. lentiforme (63DPS), T. longibrachiatum (71JES), T. rifaii (77JCR), and T. afroharzianum (24RQS, 87CCS, 88CCS and 17RCS). The strain with the best results in all three tests was 17RCS.

Industrial hemp (Cannabis sativa L.) adapts to cadmium stress by reshaping rhizosphere fungal community

Increasing evidence indicates that plants under environmental stress can actively seek the help of microbes ('cry-for-help' hypothesis). However, empirical evidence underlying this strategy is limited under metal-stress conditions. Here, we employed integrated microbial community profiling in cadmium (Cd) polluted soil and culture-based methods to investigate the three-way interactions between the industrial hemp (Cannabis Sativa L.), rhizospheric microbes, and Cd stress. Results from the pot and three cycles of the successful hemp planting experiments showed that Cd stress significantly affected the composition of rhizosphere fungi in industrial hemp and induced enrichment of the fungal operational taxonomic unit (OTU)3 (Cladosporium). A representative of OTU3 (strain DM-2) was successfully isolated. In a hydroponic experiment, inoculation of DM-2 significantly increased the shoot length (by 25.84 %) and fresh weight (by 92.66 %) of hemp seedlings when compared to the absence of DM-2 under the Cd stress. The findings indicate that DM-2 inoculation could effectively alleviate the Cd stress in hemp seedlings. Metabolomic analysis of spent media with or without DM-2 revealed the association of DM-2 with the transformation of root exudates to melatonin, which may be a key chemical in plant-microbe interactions against abiotic stresses. The findings will inform efforts to manipulate the root microbiome to enhance plant growth in polluted environments.

Meddling with the microbiota: Fungal tricks to infect plant hosts

Plants associate with a wealth of microbes, collectively referred to as the plant microbiota, whose composition is determined by host plant genetics, immune responses, environmental factors and intermicrobial relations. Unsurprisingly, microbiota compositions change during disease development. Recent evidence revealed that some of these changes can be attributed to effector proteins with antimicrobial activities that are secreted by plant pathogens to manipulate host microbiota to their advantage. Intriguingly, many of these effectors have ancient origins, predating land plant emergence, and evolved over long evolutionary trajectories to acquire selective antimicrobial activities to target microbial antagonists in host plant microbiota. Thus, we argue that host-pathogen co-evolution likely involved arms races within the host-associated microbiota.

Trichoderma and Bacillus multifunctional allies for plant growth and health in saline soils: recent advances and future challenges

Saline soils pose significant challenges to global agricultural productivity, hindering crop growth and efficiency. Despite various mitigation strategies, the issue persists, underscoring the need for innovative and sustainable solutions. One promising approach involves leveraging microorganisms and their plant interactions to reclaim saline soils and bolster crop yields. This review highlights pioneering and recent advancements in utilizing multi-traits Trichoderma and Bacillus species as potent promoters of plant growth and health. It examines the multifaceted impacts of saline stress on plants and microbes, elucidating their physiological and molecular responses. Additionally, it delves into the role of ACC deaminase in mitigating plant ethylene levels by Trichoderma and Bacillus species. Although there are several studies on Trichoderma-Bacillus, much remains to be understood about their synergistic relationships and their potential as auxiliaries in the phytoremediation of saline soils, which is why this work addresses these challenges.

Native and Alien Antarctic Grasses as a Habitat for Fungi

Biological invasions are now seen as one of the main threats to the Antarctic ecosystem. An example of such an invasion is the recent colonization of the H. Arctowski Polish Antarctic Station area by the non-native grass Poa annua. This site was previously occupied only by native plants like the Antarctic hair grass Deschampsia antarctica. To adapt successfully to new conditions, plants interact with soil microorganisms, including fungi. The aim of this study was to determine how the newly introduced grass P. annua established an interaction with fungi compared to resident grass D. antarctica. We found that fungal diversity in D. antarctica roots was significantly higher compared with P. annua roots. D. antarctica managed a biodiverse microbiome because of its ability to recruit fungal biocontrol agents from the soil, thus maintaining a beneficial nature of the endophyte community. P. annua relied on a set of specific fungal taxa, which likely modulated its cold response, increasing its competitiveness in Antarctic conditions. Cultivated endophytic fungi displayed strong chitinolysis, pointing towards their role as phytopathogenic fungi, nematode, and insect antagonists. This is the first study to compare the root mycobiomes of both grass species by direct culture-independent techniques as well as culture-based methods.

Shifts in fungal community diversity and potential function under natural forest succession and planted forest restoration in the Kunyu Mountains, East China

Soil fungi participate in various ecosystem processes and are important factors driving the restoration of degraded forests. However, little is known about the changes in fungal diversity and potential functions under the development of different vegetation types during natural (secondary forest succession) and anthropogenic (reforestation) forest restoration. In this study, we selected typical forest succession sequences (including Pinus densiflora Siebold & Zucc., pine-broadleaf mixed forest of P. densiflora and Quercus acutissima Carruth., and Q. acutissima), as well as natural secondary deciduous broadleaved mixed forests and planted forests of Robinia pseudoacacia on Kunyu Mountain for analysis. We used ITS rRNA gene sequencing to characterize fungal communities and used the FUNGuild database to predict fungal functional groups. The results showed that forest succession affected fungal β-diversity, but not the α-diversity. There was a significant increase in Basidiomycota and a decrease in Ascomycota in the later successional stage, accompanied by an increase in the functional groups of ectomycorrhizal fungi (ECM). Conversely, planted forests exhibited decreased fungal α-diversity and altered community compositions, characterized by fewer Basidiomycota and more Ascomycota and Mucoromycota. Planted forests led to a decrease in the relative abundances of ECM and an increase in animal pathogens. The TK content was the major factor explaining the distinction in fungal communities among the three successional stages, whereas pH, AP, and NH4 + were the major factors explaining community variations between natural and planted forests. Changes in vegetation types significantly affected the diversity and functional groups of soil fungal communities during forest succession and reforestation, providing key insights for forest ecosystem management in temperate forests.

Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates

The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.

Wearable sensor supports in-situ and continuous monitoring of plant health in precision agriculture era

Plant health is intricately linked to crop quality, food security and agricultural productivity. Obtaining accurate plant health information is of paramount importance in the realm of precision agriculture. Wearable sensors offer an exceptional avenue for investigating plant health status and fundamental plant science, as they enable real-time and continuous in-situ monitoring of physiological biomarkers. However, a comprehensive overview that integrates and critically assesses wearable plant sensors across various facets, including their fundamental elements, classification, design, sensing mechanism, fabrication, characterization and application, remains elusive. In this study, we provide a meticulous description and systematic synthesis of recent research progress in wearable sensor properties, technology and their application in monitoring plant health information. This work endeavours to serve as a guiding resource for the utilization of wearable plant sensors, empowering the advancement of plant health within the precision agriculture paradigm.

Genetic diversity and antagonistic properties of Trichoderma strains from the crop rhizospheres in southern Rajasthan, India

There are fewer studies on Trichoderma diversity in agricultural fields. The rhizosphere of 16 crops was analyzed for Trichoderma species in 7 districts of Rajasthan state of India. Based on DNA sequence of translation elongation factor 1α (tef-1α), and morphological characteristics, 60 isolates were identified as 11 species: Trichoderma brevicompactum, species in Harzianum clade identified as T. afroharzianum, T. inhamatum, T. lentiforme, T. camerunense, T. asperellum, T. asperelloides, T. erinaceum, T. atroviride, T. ghanense, and T. longibrachiatum. T. brevicompactum is the most commonly occurring strain followed by T. afroharzianum. No new species were described in this study. T. lentiforme, showed its first occurrence outside the South American continent. The morphological and cultural characteristics of the major species were observed, described, and illustrated in detail. The isolates were tested for their antagonistic effect against three soilborne plant pathogens fungi: Sclerotium rolfsii, Rhizoctonia solani, and Fusarium verticillioides in plate culture assays. One of the most potent strains was T. afroharzianum BThr29 having a maximum in vitro inhibition of S. rolfsii (76.6%), R. solani (84.8%), and F. verticillioides (85.7%). The potential strain T. afroharzianum BThr29 was also found to be efficient antagonists against soil borne pathogens in in vivo experiment. Such information on crop selectivity, antagonistic properties, and geographic distribution of Trichoderma species will be beneficial for developing efficient Trichoderma-based biocontrol agents.

Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems

Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.

MAPK Cascades in Plant Microbiota Structure and Functioning

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

Nonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant "cry for help" response to assemble disease suppressing and growth promoting rhizomicrobiome

Plants are capable of assembling beneficial rhizomicrobiomes through a "cry for help" mechanism upon pathogen infestation; however, it remains unknown whether we can use nonpathogenic strains to induce plants to assemble a rhizomicrobiome against pathogen invasion. Here, we used a series of derivatives of Pseudomonas syringae pv. tomato DC3000 to elicit different levels of the immune response to Arabidopsis and revealed that two nonpathogenic DC3000 derivatives induced the beneficial soil-borne legacy, demonstrating a similar "cry for help" triggering effect as the wild-type DC3000. In addition, an increase in the abundance of Devosia in the rhizosphere induced by the decreased root exudation of myristic acid was confirmed to be responsible for growth promotion and disease suppression of the soil-borne legacy. Furthermore, the "cry for help" response could be induced by heat-killed DC3000 and flg22 and blocked by an effector triggered immunity (ETI) -eliciting derivative of DC3000. In conclusion, we demonstrate the potential of nonpathogenic bacteria and bacterial elicitors to promote the generation of disease-suppressive soils.

Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes

Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Exploiting root exudates to manage soil-borne disease complexes in a changing climate

Ongoing climate change will both profoundly impact land-use (e.g., changes in crop species or cultivar and cropping practices) and abiotic factors (e.g., moisture and temperature), which will in turn alter plant-microorganism interactions in soils, including soil-borne pathogens (i.e., plant pathogenic bacteria, fungi, oomycetes, viruses, and nematodes). These pathogens often cause soil-borne disease complexes, which, due to their complexity, frequently remain undiagnosed and unmanaged, leading to chronic yield and quality losses. Root exudates are a complex group of organic substances released in the rhizosphere with potential to recruit, repel, stimulate, inhibit, or kill other organisms, including the detrimental ones. An improved understanding of how root exudates affect interspecies and/or interkingdom interactions in the rhizosphere under ongoing climate change is a prerequisite to effectively manage plant-associated microbes, including those causing diseases.

Insights into the molecular mechanism of Trichoderma stimulating plant growth and immunity against phytopathogens

Trichoderma species have received significant interest as beneficial fungi for boosting plant growth and immunity against phytopathogens. By establishing a mutualistic relationship with plants, Trichoderma causes a series of intricate signaling events that eventually promote plant growth and improve disease resistance. The mechanisms contain the indirect or direct involvement of Trichoderma in enhancing plant growth by modulating phytohormones signaling pathways, improving uptake and accumulation of nutrients, and increasing soil bioavailability of nutrients. They contribute to plant resistance by stimulating systemic acquired resistance through salicylic acid, jasmonic acid, and ethylene signaling. A cascade of signal transduction processes initiated by the interaction of Trichoderma and plants regulate the expression of defense-related genes, resulting in the synthesis of defense hormones and pathogenesis-related proteins (PRPs), which collectively improve plant resistance. Additionally, advancements in omics technologies has led to the identification of key pathways, their regulating genes, and molecular interactions in the plant defense and growth promotion responses induced by Trichoderma. Deciphering the molecular mechanism behind Trichoderma's induction of plant defense and immunity is essential for harnessing the full plant beneficial potential of Trichoderma. This review article sheds light on the molecular mechanisms that underlie the positive effects of Trichoderma-induced plant immunity and growth and opens new opportunities for developing environmentally friendly and innovative approaches to improve plant immunity and growth.

Diversity of bioprotective microbial organisms in Upper Region of Assam and its efficacy against Meloidogyne graminicola

Meloidogyne graminicola has a well-established negative impact on rice yield in transplanted and direct-seeded rice, resulting in yield losses of up to 20 to 90 percent. Studies were undertaken to isolate potential native strains of bio-control agents to manage the devastating Rice Root Knot Nematode (M. graminicola). Eighteen bacterial strains and eleven fungal strains were isolated from the rhizosphere of crops like rice, okra, ash gourd, chili, beans and cucumber, enveloping diverse soil types from the Upper Brahmaputra Valley region of Assam. Six bacterial strains were gram-positive according to morphological results, while twelve others stained negatively. Fifteen bacteria were rod-shaped, two were coccus and one was diplococcus, and all the bacterial isolates showed signs of movement. All the bacterial strains exhibited positivity for gelatin hydrolysis and catalase test. Seven bacteria showed positive, while eleven showed negative reactions to possess the ability to deduce carbon and energy from citrate. The study of the in vitro efficacy of the twenty-nine bacterial and fungal isolates tested against second-stage juveniles (J₂) of Meloidogyne graminicola revealed that all the bacterial and fungal isolates potentially inhibited the test organism and caused significant mortality over sterile water treatment. The promising bacterial and fungal isolates that exhibited mortality above 50% were identified as BSH8, BTS4, BTS5, BJA15, FJB 11 and FSH5. The strain BSH8 exhibited the best result of mortality, with 80.79% mortality against J₂ of M. graminicola. The strain BTS4 and BTS5 expressed mortality of 71.29% and 68.75% under in-vitro conditions and were significant. The effective and promising bioagents were identified using the 16 S rRNA sequencing as Bacillis subtilis (BSH8), Bacillus velezensis (BTS4), Alcaligenes faecalis (BTS5), Rhizobium pusense (BJA15), Talaromyces allahabadensis (FSH5) and Trichoderma asperellum (FJB11). These results indicated the microorganism's potential against M. graminicola and its potential for successful biological implementation. Further, the native strains could be tested against various nematode pests of rice in field conditions. Its compatibility with various pesticides and the implication of the potential strains in integrated pest management can be assessed.

Light-Induced Changes in Secondary Metabolite Production of Trichoderma atroviride

Many studies aim at maximizing fungal secondary metabolite production but the influence of light during cultivation has often been neglected. Here, we combined an untargeted isotope-assisted liquid chromatography-high-resolution mass spectrometry-based metabolomics approach with standardized cultivation of Trichoderma atroviride under three defined light regimes (darkness (PD), reduced light (RL) exposure, and 12/12 h light/dark cycle (LD)) to systematically determine the effect of light on secondary metabolite production. Comparative analyses revealed a similar metabolite profile upon cultivation in PD and RL, whereas LD treatment had an inhibiting effect on both the number and abundance of metabolites. Additionally, the spatial distribution of the detected metabolites for PD and RL was analyzed. From the more than 500 detected metabolites, only 25 were exclusively produced upon fungal growth in darkness and 85 were significantly more abundant in darkness. The majority were detected under both cultivation conditions and annotation revealed a cluster of substances whose production followed the pattern observed for the well-known T. atroviride metabolite 6-pentyl-alpha-pyrone. We conclude that cultivation of T. atroviride under RL can be used to maximize secondary metabolite production.

The Microbial Connection to Sustainable Agriculture

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings

BACKGROUND

The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota.

RESULTS

The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant.

CONCLUSIONS

Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.

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.

Grapefruit Root and Rhizosphere Responses to Varying Planting Densities, Fertilizer Concentrations and Application Methods

Huanglongbing (HLB) disease has caused a severe decline in citrus production globally over the past decade. There is a need for improved nutrient regimens to better manage the productivity of HLB-affected trees, as current guidelines are based on healthy trees. The aim of this study was to evaluate the effects of different fertilizer application methods and rates with different planting densities on HLB-affected citrus root and soil health. Plant material consisted of 'Ray Ruby' (Citrus × paradisi) grapefruit trees grafted on 'Kuharske' citrange (Citrus × sinensis × Citrus trifoliata). The study consisted of 4 foliar fertilizer treatments, which included 0×, 1.5×, 3× and 6× the University of Florida Institute of Food and Agriculture (UF/IFAS) recommended guidelines for B, Mn and Zn. Additionally, 2 ground-applied fertilizer treatments were used, specifically controlled-release fertilizer (CRF1): 12-3-14 + B, Fe, Mn and Zn micronutrients at 1× UF/IFAS recommendation, and (CRF2): 12-3-14 + 2× Mg + 3× B, Fe, Mn and Zn micronutrients, with micronutrients applied as sulfur-coated products. The planting densities implemented were low (300 trees ha-1), medium (440 trees ha-1) and high (975 trees ha-1). The CRF fertilizer resulted in greater soil nutrient concentrations through all of the time sampling points, with significant differences in soil Zn and Mn. Grapefruit treated with ground-applied CRF2 and 3× foliar fertilizers resulted in the greatest bacterial alpha and beta diversity in the rhizosphere. Significantly greater abundances of Rhizobiales and Vicinamibacterales were found in the grapefruit rhizosphere of trees treated with 0× UF/IFAS foliar fertilizer compared to higher doses of foliar fertilizers.

Plant-microbiome crosstalk and disease development

Plants harbor a complex immune system to fight off invaders and prevent diseases. For decades, the interactions between plants and pathogens have been investigated primarily through the lens of binary interactions, largely neglecting the diversity of microbes that naturally inhabit plant tissues. Recent research, however, demonstrates that resident microbes are more than mere spectators. Instead, the plant microbiome extends host immune function and influences the outcome of a pathogen infection. Both plants and the interacting microbes produce a large diversity of metabolites that form an intricate chemical network of nutrients, signals, and antimicrobial molecules. In this review, we discuss the involvement of the plant microbiome in disease development, focusing on the biochemical conversation that occurs between plants and their associated microbiota before, during and after infection. We also highlight outstanding questions and possible directions for future research.

Components of TOR and MAP kinase signaling control chemotropism and pathogenicity in the fungal pathogen Verticillium dahliae

Filamentous fungi can sense useful resources and hazards in their environment and direct growth of their hyphae accordingly. Chemotropism ensures access to nutrients, contact with other individuals (e.g., for mating), and interaction with hosts in the case of pathogens. Previous studies have revealed a complex chemotropic sensing landscape during host-pathogen interactions, but the underlying molecular machinery remains poorly characterized. Here we studied mechanisms controlling directed hyphal growth of the important plant-pathogenic fungus Verticillium dahliae towards different chemoattractants. We found that the homologs of the Rag GTPase Gtr1 and the GTPase-activating protein Tsc2, an activator and a repressor of the TOR kinase respectively, play important roles in hyphal chemotropism towards nutrients, plant-derived signals, and heterologous α-pheromone of Fusarium oxysporum. Furthermore, important roles of these regulators were identified in fungal development and pathogenicity. We also found that the mitogen-activated protein kinase (MAPK) Fus3 is required for chemotropism towards nutrients, while the G protein-coupled receptor (GPCR) Ste2 and the MAPK Slt2 control chemosensing of plant-derived signals and α-pheromone. Our study establishes V. dahliae as a suitable model system for the analysis of fungal chemotropism and discovers new components of chemotropic signaling during growth and host-pathogen interactions of V. dahliae.

Changes in Metal-Chelating Metabolites Induced by Drought and a Root Microbiome in Wheat

The essential metals Cu, Zn, and Fe are involved in many activities required for normal and stress responses in plants and their microbiomes. This paper focuses on how drought and microbial root colonization influence shoot and rhizosphere metabolites with metal-chelation properties. Wheat seedlings, with and without a pseudomonad microbiome, were grown with normal watering or under water-deficit conditions. At harvest, metal-chelating metabolites (amino acids, low molecular weight organic acids (LMWOAs), phenolic acids, and the wheat siderophore) were assessed in shoots and rhizosphere solutions. Shoots accumulated amino acids with drought, but metabolites changed little due to microbial colonization, whereas the active microbiome generally reduced the metabolites in the rhizosphere solutions, a possible factor in the biocontrol of pathogen growth. Geochemical modeling with the rhizosphere metabolites predicted Fe formed Fe-Ca-gluconates, Zn was mainly present as ions, and Cu was chelated with the siderophore 2'-deoxymugineic acid, LMWOAs, and amino acids. Thus, changes in shoot and rhizosphere metabolites caused by drought and microbial root colonization have potential impacts on plant vigor and metal bioavailability.

Microbiome engineering for bioremediation of emerging pollutants

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes

This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.

Metabolic Profiling Identifies Changes in the Winter Wheat Grains Following Fusarium Treatment at Two Locations in Croatia

Fusarium head blight (FHB) is one of the most dangerous diseases of winter wheat, resulting in reduced grain yield and quality, and production of mycotoxins by the Fusarium fungi. In the present study, changes in the grain metabolomics of winter wheat samples infected with Fusarium spp. and corresponding non-infected samples from two locations in Croatia were investigated by GC-MS. A Mann-Whitney test revealed that 24 metabolites detected were significantly separated between Fusarium-inoculated and non-infected samples during the variety by treatment interactions. The results confirmed that in grains of six FHB-resistant varieties, ten metabolites were identified as possible resistance-related metabolites. These metabolites included heptadecanoic acid, 9-(Z)-hexadecenoic acid, sophorose, and secolaganin in grains of FHB-resistant varieties at the Osijek location, as well as 2-methylaminomethyltartronic acid, maleamic acid, 4-hydroxyphenylacetonitrile, 1,4-lactonearabinonic acid, secolaganin, and alanine in grains of FHB-resistant varieties at the Tovarnik location. Moreover, on the PCA bi-plot, FHB-susceptible wheat varieties were closer to glycyl proline, decanoic acid, and lactic acid dimer that could have affected other metabolites, and thus, suppressed resistance to FHB. Although defense reactions were genetically conditioned and variety specific, resulting metabolomics changes may give insight into defense-related pathways that could be manipulated to engineer plants with improved resistance to the pathogen.

Plant Disease Resistance-Related Pathways Recruit Beneficial Bacteria by Remodeling Root Exudates upon Bacillus cereus AR156 Treatment

The environmentally friendly biological control strategy that relies on beneficial bacterial inoculants to improve plant disease resistance is a promising strategy. Previously, it has been demonstrated that biocontrol bacteria treatments can change the plant rhizosphere microbiota but whether plant signaling pathways, especially those related to disease resistance, mediate the changes in rhizosphere microbiota has not been explored. Here, we investigated the complex interplay among biocontrol strains, plant disease resistance-related pathways, root exudates, rhizosphere microorganisms, and pathogens to further clarify the biocontrol mechanism of biocontrol bacteria by using plant signaling pathway mutants. Bacillus cereus AR156, which was previously isolated from forest soil by our laboratory, can significantly control tomato bacterial wilt disease in greenhouse and field experiments. Moreover, compared with the control treatment, the B. cereus AR156 treatment had a significant effect on the soil microbiome and recruited 35 genera of bacteria to enrich the rhizosphere of tomato. Among them, the relative rhizosphere abundance of nine genera, including Ammoniphilus, Bacillus, Bosea, Candidimonas, Flexivirga, Brevundimonas, Bordetella, Dyella, and Candidatus_Berkiella, was regulated by plant disease resistance-related signaling pathways and B. cereus AR156. Linear correlation analysis showed that the relative abundances of six genera in the rhizosphere were significantly negatively correlated with pathogen colonization in roots. These rhizosphere bacteria were affected by plant root exudates that are regulated by signaling pathways. IMPORTANCE Our data suggest that B. cereus AR156 can promote the enrichment of beneficial microorganisms in the plant rhizosphere by regulating salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) signaling pathways in plants, thereby playing a role in controlling bacterial wilt disease. Meanwhile, Spearman correlation analysis showed that the relative abundances of these beneficial bacteria were correlated with the secretion of root exudates. Our study reveals a new mechanism for SA and JA/ET signals to participate in the adjustment of plant resistance whereby the signaling pathways adjust the rhizosphere microecology by changing the root exudates and thus change plant resistance. On the other hand, biocontrol strains can utilize this mechanism to recruit beneficial bacteria by activating disease resistance-related signaling pathways to confine the infection and spread of pathogens. Finally, our data also provide a new idea for the in-depth study of biocontrol mechanisms.

Regulation mechanism of plant response to heavy metal stress mediated by endophytic fungi

Endophytic fungi exist widely in plants and play an important role in the growth and adaptation of plants. They could be used in phytoremediation techniques against heavy metal contaminated soil since beneficial microbial symbionts can endow plants with resistance to external heavy metal stresses. This review summarized the regulation mechanism of plant response to heavy metal stress mediated by endophytic fungi. Potential endophytic fungi in enhancing plant's adaption to heavy metal stresses include arbuscular mycorrhizal fungi, dark septate endophytic fungi, plant growth promoting endophytic fungi. The mechanisms involve coevolution strategy, immune regulation and detoxification transport to improve the ability of plants to adapt to heavy metal stress. They can increase the synthesis of host hormones and maintaining the balance of endogenous hormones, strengthen osmotic regulation, regulate carbon and nitrogen metabolism, and increase immune activity, antioxidant enzyme and glutathione activity. They also help to improve the detoxification transport and heavy metal emission capacity of the host by significantly producing iron carrier, metallothionein and 1-aminocyclopropane-1-carboxylic acid deaminase. The combination of endophytic fungi and hyperaccumulation plants provides a promising technology for the ecological restoration of heavy metal contaminated soil. Endophytic fungi reserves further development on enhancing host plant's adaptability to heavy metal stresses.

Plant Microbiome: An Ocean of Possibilities for Improving Disease Resistance in Plants

Plant diseases pose a serious threat to crop production and the agricultural economy across the globe. Currently, chemical pesticides are frequently employed to combat these infections, which cause environmental toxicity and the emergence of resistant pathogens. Moreover, the genetic manipulation of plant defense pathways and the breeding of resistant genes has attained limited success due to the rapid evolution of pathogen virulence and resistance, together with host range expansion. Additionally, due to climate change and global warming, the occurrence of multiple stresses during disease outbreak has further impacted overall crop growth and productivity, posing a serious threat to food security. In this regard, harnessing the plant beneficial microbiome and its products can provide novel avenues for disease resistance in addition to boosting agricultural output, soil fertility and environmental sustainability. In plant-beneficial microbiome interactions, induced systemic resistance (ISR) has emerged as a key mechanism by which a beneficial microbiome primes the entire plant system for better defense against a wide range of phytopathogens and pests. In this review, we provide the recent developments on the role of plant beneficial microbiomes in disease resistance. We also highlight knowledge gaps and discuss how the plant immune system distinguishes pathogens and beneficial microbiota. Furthermore, we provide an overview on how immune signature hormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), shape plant beneficial microbiome. We also discuss the importance of various high-throughput tools and their integration with synthetic biology to design tailored microbial communities for disease resistance. Finally, we conclude by highlighting important themes that need future attention in order to fill the knowledge gaps regarding the plant immune system and plant-beneficial-microbiome-mediated disease resistance.

Root Exudates of Ginger Induced by Ralstonia solanacearum Infection Could Inhibit Bacterial Wilt

Bacterial wilt caused by Ralstonia solanacearum (Rs) is one of the most important diseases found in ginger; however, the disease resistance mechanisms dependent on root bacteria and exudates are unclear. In the present study, we analyzed the changes in the composition of rhizobacteria, endobacteria, and root exudates during the pathogenesis of bacterial wilt using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS). Rs caused bacterial wilt in ginger with an incidence of 50.00% and changed the bacterial community composition in both endosphere and rhizosphere. It significantly reduced bacterial α-diversity but increased the abundance of beneficial and stress-tolerant bacteria, such as Lysobacter, Ramlibacter, Pseudomonas, and Azospirillum. Moreover, the change in rhizobacterial composition induced the changes in endobacterial and root exudate compositions. Moreover, the upregulated exudates inhibited ginger bacterial wilt, with the initial disease index (77.50%) being reduced to 40.00%, suggesting that ginger secretes antibacterial compounds for defense against bacterial pathogens.

Foliar Pathogen Infection Manipulates Soil Health through Root Exudate-Modified Rhizosphere Microbiome

Negative plant-soil feedback (NPSF) due to the buildup of soilborne pathogens in soil is a major obstacle in sustainable agricultural systems. Beneficial rhizosphere microfloras are recruited by plants, and mediating this has become a strategic priority to manipulate plant health. Here, we found that foliar infection of Panax notoginseng by Alternaria panax changed plant-soil feedback from negative to positive. Foliar infection modified the rhizosphere soil microbial community and reversed the direction of the buildup of the soilborne pathogen Ilyonectria destructans and beneficial microbes, including Trichoderma, Bacillus, and Streptomyces, in rhizosphere soil. These beneficial microbes not only showed antagonistic ability against the pathogen I. destructans but also enhanced the resistance of plants to A. panax. Foliar infection enhanced the exudation of short- and long-chain organic acids, sugars, and amino acids from roots. In vitro and in vivo experiments validated that short- and long-chain organic acids and sugars play dual roles in simultaneously suppressing pathogens but enriching beneficial microbes. In summary, foliar infection could change root secretion to drive shifts in the rhizosphere microbial community to enhance soil health, providing a new strategy to alleviate belowground disease in plants through aboveground inducement. IMPORTANCE Belowground soilborne disease is the main factor limiting sustainable agricultural production and is difficult to manage due to the complexity of the soil environment. Here, we found that aboveground parts of plants infected by foliar pathogens could enhance the secretion of organic acids, sugars, and amino acids in root exudates to suppress soilborne pathogens and enrich beneficial microbes, eventually changing the plant and soil feedback from negative to positive and alleviating belowground soilborne disease. This is an exciting strategy by which to achieve belowground soilborne disease management by manipulating the aboveground state through aboveground stimulation.

Phytomicrobiome communications: Novel implications for stress resistance in plants

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.

The Role of Endophytes in Combating Fungal- and Bacterial-Induced Stress in Plants

Plants are subjected to multifaceted stresses that significantly jeopardize crop production. Pathogenic microbes influence biotic stress in plants, which ultimately causes annual crop loss worldwide. Although the use of pesticides and fungicides can curb the proliferation of pathogens in plants and enhance crop production, they pollute the environment and cause several health issues in humans and animals. Hence, there is a need for alternative biocontrol agents that offer an eco-friendly mode of controlling plant diseases. This review discusses fungal- and bacterial-induced stress in plants, which causes various plant diseases, and the role of biocontrol defense mechanisms, for example, the production of hydrolytic enzymes, secondary metabolites, and siderophores by stress-tolerant fungi and bacteria to combat plant pathogens. It is observed that beneficial endophytes could sustain crop production and resolve the issues regarding crop yield caused by bacterial and fungal pathogens. The collated literature review indicates that future research is necessary to identify potential biocontrol agents that can minimize the utility of synthetic pesticides and increase the tenable agricultural production.

Fungal and bacterial oxylipins are signals for intra- and inter-cellular communication within plant disease

Lipids are central at various stages of host-pathogen interactions in determining virulence and modulating plant defense. Free fatty acids may act as substrates for oxidizing enzymes [e.g., lipoxygenases (LOXs) and dioxygenases (DOXs)] that synthesize oxylipins. Fatty acids and oxylipins function as modulators of several pathways in cell-to-cell communication; their structural similarity among plant, fungal, and bacterial taxa suggests potential in cross-kingdom communication. We provide a prospect of the known role of fatty acids and oxylipins in fungi and bacteria during plant-pathogen interactions. In the pathogens, oxylipin-mediated signaling pathways are crucial both in development and host infection. Here, we report on case studies suggesting that oxylipins derived from oleic, linoleic, and linolenic acids are crucial in modulating the pathogenic lifestyle in the host plant. Intriguingly, overlapping (fungi-plant/bacteria-plant) results suggest that different inter-kingdom pathosystems use similar lipid signals to reshape the lifestyle of the contenders and occasionally determine the outcome of the challenge.

Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom

Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.

Hybridization affects the structure and function of root microbiome by altering gene expression in roots of wheat introgression line under saline-alkali stress

The mutually beneficial relationship between plants and their root microbiota is essential for plants to adapt to unfavorable environments. However, the molecular mechanism of wheat regulating the structure of root microbiome and the influence of distant hybridization on this process are poorly understood. In this study, we systematically compared the root transcriptome and microbiome between a saline-alkali tolerant wheat introgression line SR4 (derived from somatic hybridization between wheat and tall wheatgrass) and its parent wheat variety JN177. The results indicated that root microorganisms were key factor maintaining better homeostasis of the sodium and potassium ion contents in SR4 than in JN177 under saline-alkali stress. Through systematic comparisons, we identified SR4-specific root bacterial and fungal taxa under saline-alkali stress. Through a weighted gene correlation network analysis (WGCNA) combining microbiome and transcriptome data, key functional genes and pathways, which were strongly related to root bacteria and fungi with differential abundance between JN177 and SR4, were identified. These results suggest that somatic hybridization has altered the key genes regulating root microbiome in wheat, further improving the saline-alkali tolerance of wheat introgression line. These findings provide the key bacterial and fungal taxa and functional target genes for wheat root microbiome engineering under saline-alkali stress.

Identification of Non-Volatile Compounds That Impact Flavor Disliking of Whole Wheat Bread Made with Aged Flours

Whole wheat flour has a shorter shelf life than refined wheat flour due to off-flavor development. An untargeted liquid chromatography/mass spectrometry (LC/MS) flavoromics approach was applied to identify compounds that negatively impact the flavor liking in whole wheat bread made from aged flours. The chemical profiles of thirteen breads made from aged flours were obtained using LC/MS and modeled by orthogonal partial least squares (OPLS) to predict flavor liking. Top predictive chemical features (negatively correlated) were identified as pinellic acid (9S,12S,13S-trihydroxy-10E-octadecenoic acid), 12,13-dihydroxy-9Z-octadecenoic acid, and 1-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine. The sensory analysis confirmed the three compounds increased the bitterness intensity of the bread samples. The formation of the trihydroxy fatty acid bitter compound, pinellic acid (9S,12S,13S-trihydroxy-10E-octadecenoic acid), was impacted by the lipoxygenase activity of the flour; however, there was no influence on the formation of 12,13-dihydroxy-9Z-octadecenoic acid or 1-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine. Additionally, the concentrations of all bitter compounds were significantly higher in bread made from aged flour versus non-aged flour.

Novel Trichoderma Isolates Alleviate Water Deficit Stress in Susceptible Tomato Genotypes

Symbiotic fungi in the genus Trichoderma can induce abiotic stress tolerance in crops. The beneficial effects of Trichoderma on water deficit stress are poorly understood and may be isolate-specific. Our objective was to evaluate a collection of Nepalese Trichoderma isolates and their efficacy to improve tomato (Solanum lycopersicum) growth under water deficit. Variable growth in low moisture environments was observed among Trichoderma isolates from Nepal, Ohio, and commercial sources using in vitro assays. The overall performance of the population decreased when cultured under conditions of decreasing matric water potential (0.0, -2.8, -4.8, and -8.5 Ψ). Twelve isolates were selected for evaluation for their potential to elicit drought tolerance in greenhouse-grown 'Roma Organic' tomatoes. Plants treated with T. asperelloides-NT33 had higher shoot weight than the non-inoculated control (T0) under water deficit stress conditions. Further, the stress-reducing efficacy of isolates T. asperelloides-NT33, T. asperellum-NT16, T. asperelloides-NT3, and commercial T. harzianum-T22 were tested on tomato genotypes with differing tolerance to drought ['Roma Organic,' 'Jaune Flamme,' and 'Punta Banda']. The water deficit susceptible genotypes 'Roma Organic' and 'Jaune Flamme' inoculated with isolate NT33 had significantly higher shoot weight (37 and 30% respectively; p < 0.05) compared to the non-inoculated control under water deficit stress conditions. In drought tolerant 'Punta Banda,' shoot weight was also significantly greater in NT33 inoculated plants under water deficit stress conditions, but with lower magnitude difference (8%; p < 0.05). Our results demonstrate differences in the ability of Trichoderma isolates to confer tolerance to water deficit in tomato with NT33 potentially relieving stress. Tomato genotypes also play a role in the outcome of interactions with the Trichoderma isolates we tested.

How do plants sense volatiles sent by other plants?

Plants communicate via the emission of volatile organic compounds (VOCs) with many animals as well as other plants. We still know little about how VOCs are perceived by receiving (eavesdropping) plants. Here we propose a multiple system of VOC perception, where stress-induced VOCs dock on odorant-binding proteins (OBPs) like in animals and are transported to as-yet-unknown receptors mediating downstream metabolic and/or behavioral changes. Constitutive VOCs that are broadly and lifelong emitted by plants do not bind OBPs but may directly change the metabolism of eavesdropping plants. Deciphering how plants listen to their talking neighbors could empower VOCs as a tool for bioinspired strategies of plant defense when challenged by abiotic and biotic stresses.