Disease-Suppressive Soils-Beyond Food Production: a Critical Review

Biocontrol of Agroathelia rolfsii associated with stem rot disease in tomato (Solanum lycopersicum L.) and growth promotion using compost-associated actinobacteria

Stem rot disease (Agroathelia rolfsii) biocontrol is an environmentally safe alternative that could potentially decrease disease severity and limit plant and yield losses. In the present investigation, 11 actinomycetes isolates, recovered from disease-suppressive composts, were tested as whole cell suspensions and cell-free culture filtrates for their ability to suppress tomato stem rot and to stimulate plant growth. Five isolates (namely A5-3, A2-4, A3-4, A4-4 and A5-4), applied as cell suspensions, were found to be the most effective in suppressing disease severity by 37.5-56.2% compared to the untreated control and 25-56.2% using their cell-free culture filtrates. The in vitro antifungal activity of isolates tested and their filtrates were estimated at 58.8-88% and 59-91.3% decrease in fungus mycelial growth, respectively. As for their growth-promoting ability, tomato plants treated with A5-3, A2-4, A3-4, A4-4 and A5-4 isolates were 20-89.1% and 10.3-79% higher than A. rolfsii-inoculated and pathogen-free controls, respectively. Inoculated and uninoculated plants treated with filtrates showed significant increments in their growth parameters by 18.2-91.9% and 15.3-93.4% over control, respectively. The most bioactive isolates against target pathogen were affiliated, based on 16 S rDNA gene sequencing, to Streptomyces, Saccharomonospora and Micromonospora genera. All these isolates were shown able to produce indole-3-acetic acid. Streptomyces sp. (A5-3) and Streptomyces sp. (A5-4) displayed chitinase, protease and lipase activities together with phosphate solubilization and nitrogen-fixing abilities. Streptomyces sp. (A5-3) displayed the greatest amylolytic activity and ability to solubilize zinc and to produce siderophores and hydrogen cyanide. This investigation demonstrated that actinomycetes recovered from disease-suppressive composts can be explored as potential sources of bio-active compounds with antifungal and bio-fertilizing abilities useful for the improvement of tomato growth and health.

Plant Genetic Bases Associated With Microbiota Descriptors Shed Light Into a Novel Holobiont Generalist Genes Theory

Plants as animals are associated with a cortege of microbes influencing their health, fitness and evolution. Scientists refer to all living organisms as holobionts, complex genetic units that coevolve simultaneously. This is what has been recently proposed as the hologenome theory. This exciting theory has important implications on animal and plant health; however, it still needs consistent proof to be validated. Indeed, holobionts are still poorly studied in their natural habitats where coevolution processes occur. Compared to animals, wild plant populations are an excellent model to explore the hologenome theory. These sessile holobionts have coevolved with their microbiota for decades, and natural selection and adaptive processes acting on wild plants are likely to regulate the plant-microbe interactions. Here, we conducted a microbiota survey, plant genome sequencing and genome-environmental analysis (GEA) of 26 natural populations of the plant species Brassica rapa. We collected plants over two seasons in Italy and France and analysed the root and rhizosphere microbiota. When conducting GEA, we evidenced neat peaks of association correlating with both fungal and bacterial microbiota. Surprisingly, we found 13 common genes between fungal and bacterial diversity descriptors that we referred to under the name of holobiont generalist genes (HGGs).

Plant pathogens, microbiomes, and soil health

Healthy soil is vital for ecosystem sustainability and global food security. However, anthropogenic activities that promote intensive agriculture, landscape and biodiversity homogenization, and climate change disrupt soil health. The soil microbiome is a critical component of healthy soils, and increasing evidence suggests that soils with low diversity or homogenized microbial systems are more susceptible to soil pathogen invasion, but the extent and mechanisms that increase the threat of pathogen invasion (i.e., increase in prevalence of existing species and introduction of new species) remain unclear. This article aims to fill this knowledge gap by synthesizing the literature and providing novel insights for the scientific community and policy advisors. We also present the current and future global distribution of some dominant soil-borne pathogens. We argue that an improved understanding of the interplay between the soil microbiome, soil health, host, and pathogen distribution, and their responses to environmental changes is urgently needed to ensure the future of productive farms, safe food, sustainable environments, and holistic global well-being.

Incidence and Severity Distribution of Sweet Cherry (Prunus avium) and Their Influencing Factors in Southwest China

Root rot disease is a significant constraint to sweet cherry production in the highlands of southwest China, causing substantial yield losses. While the disease is prevalent, the complex interplay of climate, topography, soil, and management practices on its development remains poorly understood. To address this knowledge gap, a field survey encompassing 95 field sites was conducted to assess disease incidence (DI) and canopy damage index (CDI). Our results showed that the average DI and CDI were 27.04 and 20.52%, respectively. DI and CDI were influenced by management practices: they both increased with the number of planting years and were lower with Cerasus szechuanica rootstock and composted animal manures compared with Da-qingye rootstock and uncomposted animal manures. Climatic and topographic factors also played an important role in observing higher DI at higher altitudes and shady slopes (P < 0.05). Moreover, both DI and CDI demonstrated positive correlations with the aridity index and sunshine duration and negative correlations with mean annual temperature and mean annual precipitation (P < 0.05). Soil properties, including moisture content, bulk density, pH, and sand content, were positively associated with DI and CDI, while clay content and available potassium exhibited negative correlation. The present study emphasizes the combined impact of multiple factors on root rot disease in sweet cherry, with management practices and soil properties having a more decisive effect than climate and topography. These findings provide crucial insights for developing effective disease management strategies.

The relationship between pomegranate root collar rot and the diversity of fungal communities in its rhizosphere

Introduction

The pomegranate (Punica granatum) is a significant economic tree species. In recent years, the root collar rot has severely affected pomegranates in the dry-hot valley regions of Yunnan Province, China. The rhizosphere microbiome plays a crucial role in plant growth, development, and disease resistance.

Methods

This study utilized Illumina MiSeq sequencing to analyze the fungal communities in the roots and rhizosphere soils of healthy and diseased pomegranates, focusing on the impact of root collar rot disease on the diversity and structural composition of these communities.

Results

The results indicated that in the unique fungal communities of healthy plant roots, the relative abundance of ectomycorrhizal and arbuscular mycorrhizal functional (AMF) groups was 53.77%, including genera such as Glomus and Septoglomus. After infection with root collar rot disease, the rhizosphere fungal communities became more monotonous, with increased differentiation within sample groups. Fungal groups associated with plant diseases and soil nutrient structures underwent significant changes. The disease altered the composition and functional group proportions of rhizosphere fungal communities, a process linked to soil nutrient structures. And the balance between plant-pathogen-related and saprotrophic functional groups in the rhizosphere was disrupted. Through Koch's postulates verification, the pathogen was identified as Lauriomyces bellulus.

Discussion

This is the first report of collar rot of pomegranate caused by L. bellulus in China. Studying the differences in rhizosphere fungal community structures and quantities in response to new diseases aids in the rapid prediction of pathogens, effectively saving diagnostic time, and provides theoretical support for disease prediction, diagnosis, and control.

Sustainable Management of Major Fungal Phytopathogens in Sorghum (Sorghum bicolor L.) for Food Security: A Comprehensive Review

Sorghum (Sorghum bicolor L.) is a globally important energy and food crop that is becoming increasingly integral to food security and the environment. However, its production is significantly hampered by various fungal phytopathogens that affect its yield and quality. This review aimed to provide a comprehensive overview of the major fungal phytopathogens affecting sorghum, their impact, current management strategies, and potential future directions. The major diseases covered include anthracnose, grain mold complex, charcoal rot, downy mildew, and rust, with an emphasis on their pathogenesis, symptomatology, and overall economic, social, and environmental impacts. From the initial use of fungicides to the shift to biocontrol, crop rotation, intercropping, and modern tactics of breeding resistant cultivars against mentioned diseases are discussed. In addition, this review explores the future of disease management, with a particular focus on the role of technology, including digital agriculture, predictive modeling, remote sensing, and IoT devices, in early warning, detection, and disease management. It also provide key policy recommendations to support farmers and advance research on disease management, thus emphasizing the need for increased investment in research, strengthening extension services, facilitating access to necessary inputs, and implementing effective regulatory policies. The review concluded that although fungal phytopathogens pose significant challenges, a combined effort of technology, research, innovative disease management, and effective policies can significantly mitigate these issues, enhance the resilience of sorghum production to facilitate global food security issues.

The occurrence of wheat crown rot correlates with the microbial community and function in rhizosphere soil

Wheat crown rot (WCR) is a significant soil-borne disease affecting wheat production worldwide. Understanding the impact of wheat crown rot on the structure and function of microbial communities in the wheat rhizosphere soil can provide a theoretical basis for the mining biological control resources against WCR. In this study, rhizosphere soils with varying WCR severities (light, moderate, severe) were analyzed for chemical properties, microbial community composition and functions using high-throughput sequencing. The results revealed that WCR decreased rhizosphere soil pH, the content of available nitrogen and phosphorus, and the abundance of beneficial taxa such as Bacillus and Streptomyces. Additionally, functional predictions showed that microbial communities adapted to WCR by enhancing signaling pathways and reducing their anabolic activity. From soil with light WCR occurrence, we isolated Bacillus velezensis BF-237, whose abundance was reduced by WCR. Greenhouse experiments demonstrated that BF-237 achieved a control efficiency of 56.61% against WCR in artificially inoculated sterilized soil and 53.32% in natural soil. This study clarifies the impact of wheat crown rot on the community structure, and function of rhizosphere soil microorganisms, alongside identifying a promising biocontrol agent. These findings contribute to understanding WCR pathogenesis and offer practical resources for its management.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

The role of the rhizobiome recruited by root exudates in plant disease resistance: current status and future directions

Root exudates serve as a bridge connecting plant roots and rhizosphere microbes, playing a key role in influencing the assembly and function of the rhizobiome. Recent studies have fully elucidated the role of root exudates in recruiting rhizosphere microbes to enhance plant performance, particularly in terms of plant resistance to soil-borne pathogens; however, it should be noted that the composition and amount of root exudates are primarily quantitative traits regulated by a large number of genes in plants. As a result, there are knowledge gaps in understanding the contribution of the rhizobiome to soil-borne plant disease resistance and the ternary link of plant genes, root exudates, and disease resistance-associated microbes. Advancements in technologies such as quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) offer opportunities for the identification of genes associated with quantitative traits. In the present review, we summarize recent studies on the interactions of plant and rhizosphere microbes through root exudates to enhance soil-borne plant disease resistance and also highlight methods for quantifying the contribution of the rhizobiome to plant disease resistance and identifying the genes responsible for recruiting disease resistance-associated microbes through root exudates.

The Greening of One Health: Plants, Pathogens, and the Environment

One Health has an aspirational goal of ensuring the health of humans, animals, plants, and the environment through transdisciplinary, collaborative research. At its essence, One Health addresses the human clash with Nature by formulating strategies to repair and restore a (globally) perturbed ecosystem. A more nuanced evaluation of humankind's impact on the environment (Nature, Earth, Gaia) would fully intercalate plants, plant pathogens, and beneficial plant microbes into One Health. Here, several examples point out how plants and plant microbes are keystones of One Health. Meaningful cross-pollination between plant, animal, and human health practitioners can drive discovery and application of innovative tools to address the many complex problems within the One Health framework.

Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes

Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.

Phytocytokine StPep1-Secreting Bacteria Suppress Potato Powdery Scab Disease

Powdery scab is an important potato disease caused by the soilborne pathogen Spongospora subterranea f. sp. subterranea. Currently, reliable chemical control and resistant cultivars for powdery scab are unavailable. As an alternative control strategy, we propose a novel approach involving the effective delivery of a phytocytokine to plant roots by the rhizobacterium Bacillus subtilis. The modified strain is designed to secrete the plant elicitor peptide StPep1. In our experiments employing a hairy root system, we observed a significant reduction in powdery scab pathogen infection when we directly applied the StPep1 peptide. Furthermore, our pot assay, which involved pretreating potato roots with StPep1-secreting B. subtilis, demonstrated a substantial decrease in disease symptoms, including reduced root galling and fewer tuber lesions. These findings underscore the potential of engineered bacteria as a promising strategy for safeguarding plants against powdery scab.

Transplantation of soil from organic field confers disease suppressive ability to conducive soil

Organic agriculture is a sustainable method of farming, and confers disease-suppressing abilities to disease-conducive soils via specialized soil microbiomes. This study aimed at transforming a disease-conducive soil from a conventional field into disease-suppressive soil by inoculating soil from an organic field previously established as "disease-suppressive". The effectiveness of the transformed soil was established with the model plant wheat (Triticum aestivum) grown under natural conditions, with regard to its potential in inhibiting fungal phytopathogens, Rhizoctonia solani and Fusarium oxysporum. The conducive soil inoculated with the disease-suppressive soil performed better than the control conducive soil in terms of reduced disease severity in plants, improved soil nutrient content, increased activity of hydrolytic enzymes, and increased abundance of structural and functional microbial markers. The study demonstrates the efficacy of the soil microbiome under long-term organic agriculture in transforming disease-conducive soil into disease-suppressive soils. Such practises are simple and easy to implement, and could greatly improve the sustainability and crop yield in developing countries.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Recovery and utilization of waste filtrate from industrial biological fermentation: Development and metabolite profile of the Bacillus cereus liquid bio-fertilizer

Most fermentation waste filtrates can be used as raw materials for producing bio-fertilizers to reduce wastewater emissions and environmental pollution, but their bio-fertilizer utilization depends on the nutrients contained and their metabolized by functional microorganism. To achieve bio-fertilizer utilization of Acremonium terricola fermented waste filtrate, this study systematically explored the functional microbial species for making good use of waste liquid, optimized material process parameters for bio-fertilizer production based on D-optimal mixture design method, and analyzed the composition of the waste filtrate and its metabolism by functional microorganisms using a non-targeted LC-MS metagenomics technique. The results showed that Bacillus cereus was the functional microbial candidate for producing bio-fertilizer because of its more efficiently utilize the waste filtrate than other Bacillus sp. The optimal material process parameters of the liquid bio-fertilizer were the inoculum dose of 5% (v:v, %), 80% of waste filtrate, 0.25% of N, 3.5% of P2O5, 3.25% of K2O of mass percentage. Under these conditions, the colony forming unit (CFU) of Bacillus cereus could reach (1.59 ± 0.01) × 108 CFU/mL, which met the bio-fertilizer standard requirements of the People's Republic of China (NY/T798). Furthermore, the potential functions of bio-fertilizer were studied based on comparison of raw materials and production components: on the one hand, waste filtrate contained abundant of nitrogen and carbon sources, and bioactive substances secreted by Acremonium terricola, such as β-alanyl-L-lysine, anserine, UMP, L-lactic acid and etc., which could meet the nutrient requirements of the growth of Bacillus cereus; On the other hand, some compounds of waste filtrate with the potential to benefit the plant growth and defense, such as betaine aldehyde, (2E,6E)-farnesol, homogentisic acid and etc., were significantly up regulated by Bacillus cereus utilization of the filtrate. To sum up, this work highlighted that the waste filtrate could be efficiently developed into liquid bio-fertilizer by Bacillus cereus.

Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae

Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.

Siddique K, Li B. Nanobiotechnology to advance stress resilience in plants: Current opportunities and challenges

A sustainable and resilient crop production system is essential to meet the global food demands. Traditional chemical-based farming practices have become ineffective due to increased population pressures and extreme climate variations. Recently, nanobiotechnology is considered to be a promising approach for sustainable crop production by improving the targeted nutrient delivery, pest management efficacy, genome editing efficiency, and smart plant sensor implications. This review provides deeper mechanistic insights into the potential applications of engineered nanomaterials for improved crop stress resilience and productivity. We also have discussed the technology readiness level of nano-based strategies to provide a clear picture of our current perspectives of the field. Current challenges and implications in the way of upscaling nanobiotechnology in the crop production are discussed along with the regulatory requirements to mitigate associated risks and facilitate public acceptability in order to develop research objectives that facilitate a sustainable nano-enabled Agri-tech revolution. Conclusively, this review not only highlights the importance of nano-enabled approaches in improving crop health, but also demonstrated their roles to counter global food security concerns.

Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field

Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.

Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit

Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.

A Systematic Review on the Continuous Cropping Obstacles and Control Strategies in Medicinal Plants

Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and increased disease incidence, especially in medicinal plants. Continuous cropping obstacles (CCOs) are mainly due to changes in soil microbial communities, nutrient availability, and allelopathic effects. Recently, progressive studies have illustrated the molecular mechanisms of CCOs, and valid strategies to overcome them. Transcriptomic and metabolomics analyses revealed that identified DEGs (differently expressed genes) and metabolites involved in the response to CCOs are involved in various biological processes, including photosynthesis, carbon metabolism, secondary metabolite biosynthesis, and bioactive compounds. Soil improvement is an effective strategy to overcome this problem. Soil amendments can improve the microbial community by increasing the abundance of beneficial microorganisms, soil fertility, and nutrient availability. In this review, we sum up the recent status of the research on CCOs in medicinal plants, the combination of transcriptomic and metabolomics studies, and related control strategies, including uses of soil amendments, crop rotation, and intercropping. Finally, we propose future research trends for understanding CCOs, and strategies to overcome these obstacles and promote sustainable agriculture practices in medicinal plants.

Overview and Management of the Most Common Eukaryotic Diseases of Flax (Linum usitatissimum)

Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.

Changes in the Microbial Composition of the Rhizosphere of Hop Plants Affected by Verticillium Wilt Caused by Verticillium nonalfalfae

Verticillium wilt is a devastating disease affecting many crops, including hops. This study aims to describe fungal and bacterial populations associated with bulk and rhizosphere soils in a hop field cultivated in Slovenia with the Celeia variety, which is highly susceptible to Verticillium nonalfalfae. As both healthy and diseased plants coexist in the same field, we focused this study on the detection of putative differences in the microbial communities associated with the two types of plants. Bacterial communities were characterized by sequencing the V4 region of the 16S rRNA gene, whereas sequencing of the ITS2 region was performed for fungal communities. The bacterial community was dominated by phyla Proteobacteria, Acidobacteriota, Bacteroidota, Actinobacteriota, Planctomycetota, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota, which are typically found in crop soils throughout the world. At a fungal level, Fusarium sp. was the dominant taxon in both bulk and rhizosphere soils. Verticillium sp. levels were very low in all samples analyzed and could only be detected by qPCR in the rhizosphere of diseased plants. The rhizosphere of diseased plants underwent important changes with respect to the rhizosphere of healthy plants where significant increases in potentially beneficial fungi such as the basidiomycetes Ceratobasidium sp. and Mycena sp., the zygomycete Mortierella sp., and a member of Glomeralles were observed. However, the rhizosphere of diseased plants experienced a decrease in pathogenic basidiomycetes that can affect the root system, such as Thanatephorus cucumeris (the teleomorph of Rhizoctonia solani) and Calyptella sp.

The Golden Goal of Soil Management: Disease-Suppressive Soils

Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.

The socio-economic challenges of managing pathogen evolution in agriculture

Genetic resistance forms the foundation of infectious disease management in crops. However, rapid pathogen evolution is causing the breakdown of resistance and threatening disease control. Recent research efforts have identified strategies for resistance gene deployment that aim to disrupt pathogen adaptation and prevent breakdown. To date, there has been limited practical uptake of such strategies. In this paper, we focus on the socio-economic challenges associated with translating applied evolutionary research into scientifically informed management strategies to control pathogen adaptation. We develop a conceptual framework for the economic valuation of resistance and demonstrate that in addition to various direct benefits, resistance delivers considerable indirect and non-market value to farmers and society. Incentives for stakeholders to engage in stewardship strategies are complicated by the uncertain timeframes associated with evolutionary processes, difficulties in assigning ownership rights to genetic resources and lack of governance. These interacting biological, socio-economic and institutional complexities suggest that resistance breakdown should be viewed as a wicked problem, with often conflicting imperatives among stakeholders and no simple cause or solution. Promoting the uptake of scientific research outcomes that address complex issues in sustainable crop disease management will require a mix of education, incentives, legislation and social change. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Melanin Induction Restores the Pathogenicity of Gaeumannomyces graminis var. tritici in Wheat Plants

One of the most challenging aspects of long-term research based on microorganisms is the maintenance of isolates under ex situ conditions, particularly the conservation of phytopathological characteristics. Our research group has worked for more than 10 years with Gaumannomyces graminis var. tritici (Ggt), the main biotic factor affecting wheat. In this sense we preserved the microorganisms in oil overlaid. However, several strains preserved for a long time lost their pathogenicity. These strains show white and non-infective mycelia. In this sense, we hypothesized that this is attributable to low melanin content. Melanin is a natural pigment mainly involved in UV protection, desiccation, salinity, oxidation, and fungal pathogenicity. Therefore, understanding the melanin role on Ggt pathogenicity is fundamental to developing melanin activation strategies under laboratory studies. In this study, we induce melanin activation by UV-A light chamber, 320 to 400 nm (T1) and temperature changes of 30 °C, 15 °C, and 20 °C (T2). Fungal pathogenicity was evaluated by determination of blackening roots and Ggt was quantified by real-time PCR in inoculated wheat plants. Results revealed that Ggt grown under UV-A (T1) conditions showed around 40% higher melanin level with a concomitant effect on root infection (98% of blackened roots) and 4-fold more Ggt genome copy number compared with the control (non-infective mycelia) being T1, a more inductor factor compared with T2. These findings would support the role of melanin in pathogenicity in darkly pigmented fungi such as Ggt and could serve as a basis for activating pathogenicity under laboratory conditions.

Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies

Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.

Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem

Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO 3 - , total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.

Diversity, Ecological Characteristics and Identification of Some Problematic Phytopathogenic Fusarium in Soil: A Review

The genus Fusarium includes many pathogenic species causing a wide range of plant diseases that lead to high economic losses. In this review, we describe how the Fusarium taxonomy has changed with the development of microbiological methods. We specify the ecological traits of this genus and the methods of its identification in soils, particularly the detection of phytopathogenic representatives of Fusarium and the mycotoxins produced by them. The negative effects of soil-borne phytopathogenic Fusarium on agricultural plants and current methods for its control are discussed. Due to the high complexity and polymorphism of Fusarium species, integrated approaches for the risk assessment of Fusarium diseases are necessary.

A longitudinal study to examine the influence of farming practices and environmental factors on pathogen prevalence using structural equation modeling

The contamination of fresh produce with foodborne pathogens has been an on-going concern with outbreaks linked to these commodities. Evaluation of farm practices, such as use of manure, irrigation water source, and other factors that could influence pathogen prevalence in the farming environment could lead to improved mitigation strategies to reduce the potential for contamination events. Soil, water, manure, and compost were sampled from farms in Ohio and Georgia to identify the prevalence of Salmonella, Listeria monocytogenes (Lm), Campylobacter, and Shiga-toxin-producing Escherichia coli (STEC), as well as Arcobacter, an emerging human pathogen. This study investigated agricultural practices to determine which influenced pathogen prevalence, i.e., the percent positive samples. These efforts identified a low prevalence of Salmonella, STEC, and Campylobacter in soil and water (< 10%), preventing statistical modeling of these pathogens. However, Lm and Arcobacter were found in soil (13 and 7%, respectively), manure (49 and 32%, respectively), and water samples (18 and 39%, respectively) at a comparatively higher prevalence, suggesting different dynamics are involved in their survival in the farm environment. Lm and Arcobacter prevalence data, soil chemical characteristics, as well as farm practices and weather, were analyzed using structural equation modeling to identify which factors play a role, directly or indirectly, on the prevalence of these pathogens. These analyses identified an association between pathogen prevalence and weather, as well as biological soil amendments of animal origin. Increasing air temperature increased Arcobacter and decreased Lm. Lm prevalence was found to be inversely correlated with the use of surface water for irrigation, despite a high Lm prevalence in surface water suggesting other factors may play a role. Furthermore, Lm prevalence increased when the microbiome's Simpson's Diversity Index decreased, which occurred as soil fertility increased, leading to an indirect positive effect for soil fertility on Lm prevalence. These results suggest that pathogen, environment, and farm management practices, in addition to produce commodities, all need to be considered when developing mitigation strategies. The prevalence of Arcobacter and Lm versus the other pathogens suggests that multiple mitigation strategies may need to be employed to control these pathogens.

Plant Microbiome Engineering: Hopes or Hypes

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

Evaluation of Sulfur-Based Biostimulants for the Germination of Sclerotium cepivorum Sclerotia and Their Interaction with Soil

White rot is an economically significant disease of Allium crops. The pathogen Sclerotium cepivorum produces long-lived sclerotia that germinate in response to sulfur-containing compounds released from Allium roots. Diallyl disulfide (DADS) was the primary organic sulfur compound detected in the rhizosphere soil of two garlic cultivars, "California Early and Late", growing in greenhouse conditions. DADS, dimethyl trisulfide (DMTS), dimethyl disulfide (DMDS), isopropyl disulfide (IPDS), dipropyl disulfide (DPDS), diethyl disulfide (DEDS), together with garlic oil, garlic juice, garlic powder, raw onion pieces, cabbage pieces, and Chinese cabbage pieces were investigated for their activities toward germinating dormant sclerotia. Results showed that DADS and other volatile sulfur compounds could stimulate sclerotial germination, and a dose-response was observed. In addition, garlic juice, powder, raw onion, and the two cabbages could stimulate sclerotial germination. Furthermore, the laboratory soil incubation experiments demonstrated the strong interaction of organic sulfur compounds with soil.

Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States

In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

BACKGROUND

Organic mulch is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulch and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulch on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulch.

RESULTS

Organic mulch could significantly suppress the disease incidence in the litchi plantation, and with a reduction of 37.74% to 85.66%. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, significantly higher bacterial and fungal community diversity indexes were found in organic mulch soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils.

CONCLUSIONS

Thus, we believe that organic mulch has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Soil Sterilization Eliminates Beneficial Microbes That Provide Natural Pest Suppression Ecosystem Services Against Radopholus similis and Fusarium Oxysporum V5w2 in the Endosphere and Rhizosphere of Tissue Culture Banana Plants

Endosphere and rhizosphere microbes offer plant growth promotion and pest suppression ecosystem services in banana-based agroecosystems. Interest has been growing towards the use of such beneficial microbes in protecting vulnerable tissue culture banana plants against pathogens such as Radopholus similis and Fusarium oxysporum. A screenhouse experiment with potted tissue culture banana plants was conducted using sterile and non-sterile soil to investigate the effect of soil biota on R. similis and F. oxysporum strain V5w2. Plants grown in non-sterile soil had lower damage and R. similis density in roots and rhizosphere, while most plant growth-related parameters including root freshweight, shoot freshweight, total freshweight, plant height, and leaf size were larger compared to those from sterile soil. Shoot dryweight and Mg content were higher in plants from sterile soil, while their leaves developed discolored margins. R. similis-inoculated plants in sterile soil were smaller, had more dead roots, higher nematode density, and produced fewer and smaller leaves, than those from non-sterile soil. For all plant growth-related parameters, nematode density and root damage, no differences were recorded between controls and F. oxysporum V5w2-inoculated plants; and no differences between those inoculated with R. similis only and the ones co-inoculated with the nematode and F. oxysporum V5w2. Banana roots inoculated with F. oxysporum V5w2 were lighter in color than those without the fungus. Independent or combined inoculation of banana plants with F. oxysporum V5w2 and R. similis resulted in lower optical density of root extracts. In vitro assays indicated the presence of Fusarium spp. and other root endophytic microbes that interacted antagonistically with the inoculated strain of F. oxysporum V5w2. It is concluded that, soil sterilization eliminates beneficial microbes that provide natural pest suppression ecosystem services against R. similis and F. oxysporum in the endosphere and rhizosphere of tissue culture banana plants. I recommend the integration of microbiome conservation into tissue culture technology through the proposed “Tissue Culture Microbiome Conservation Technology.”

Soil Microbes Determine Outcomes of Pathogenic Interactions Between Radopholus similis and Fusarium oxysporum V5w2 in Tissue Culture Banana Rhizospheres Starved of Nitrogen, Phosphorus, and Potassium

The contributions of soil biota toward outcomes of pathogenic interactions between Radopholus similis and Fusarium oxysporum V5w2 in tissue culture banana plants starved of nitrogen (N), phosphorus (P), and potassium (K) were investigated. The study was based on three screenhouse factorial experiments (2 × 2 × 2) comprising of potted banana plants with or without R. similis, with or without F. oxysporum V5w2, and either grown in sterile or non-sterile soil. All plants in each of the three experiments received nutrient solutions that were deficient in N, P, or K, respectively. In all the three nutritional regimes, plants inoculated with R. similis were heavily colonized by the nematode with high percentage dead roots and necrosis, while their root biomasses were low. N-starved plants co-inoculated with R. similis and F. oxysporum V5w2 had lower percentage dead roots and tended to have numerically lower nematode density compared to those treated with R. similis only, especially in non-sterile soil. N-starved plants inoculated with R. similis had higher shoot dry weight, were taller with more leaves that were larger, compared to those not inoculated with the nematode. Plants grown in non-sterile soil had lower percentage dead roots, necrosis and R. similis density than those from sterile soil, regardless of the nutrient regime. N-starved plants from non-sterile soil were shorter with smaller leaves having decreased chlorophyll content and lower biomass, compared to those from sterile soil. By contrast, P and K starved plants from non-sterile soil were taller with larger leaves and more biomass, compared to those from sterile soil. Roots inoculated with R. similis had higher endophytic colonization by Fusarium spp., especially when co-inoculated with F. oxysporum V5w2 and grown in sterile soil among the N and K-starved plants. In conclusion, pathogenic interactions between R. similis and F. oxysporum V5w2 are predominantly suppressed by a complex of soil microbes that exert plant growth promoting effects in tissue culture banana plants through N, P, and K dependent processes. Nitrogen is the most important limiting factor in rhizosphere interactions between banana roots, beneficial microbes and the pathogens. Soil sterilization and the stringent aseptic tissue culture techniques still require the development of alternative innovative ways of conserving microbial services for sustainable agriculture.

Predicting global numbers of teleomorphic ascomycetes

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.

Evaluation of Pseudomonas fulva PS9.1 and Bacillus velezensis NWUMFkBS10.5 as Candidate Plant Growth Promoters during Maize-Fusarium Interaction

Based on in vitro assessments, molecular and chemical analysis, Pseudomonas fulva PS9.1 and Bacillus velezensis NWUMFkBS10.5 are candidate biocontrol agents for plant disease management including maize fusariosis, a disease caused by members of the Fusarium species. This in vivo study evaluated the bio-protective potential of the aforementioned rhizobacteria strains on maize against the proliferation of the pathogenic fungus Fusarium graminearum (Fg). The study results show that the bacterized plants were not susceptible to Fg aggression and the antagonists displayed the capability to proliferate in the presence of other likely competing microflora. The screen-house data also suggest that the presence of resident soil microbiota impacted the activity of antagonists (PS9.1 and NWUMFkBS10.5). This variation was recorded in the soil treatments (sterilized and unsterilized soil). In all the experimental periods, bacterized maize plants with or without Fg inoculation significantly (p = 0.05) grew better in unsterilized soil. Besides, during the experimental periods, all the consortia treatments with or without Fg infection regardless of the soil used demonstrated appreciable performance. The result of this study suggests that the microbial agents can actively colonize the surface of their maize plant host, improve plant growth, and suppress the growth of phytopathogens. Considering their overall performance in this screen-house evaluation, P. fulva PS9.1 and B. velezensis NWUMFkBS10.5 have potential for field applications. All safety issues regarding their use under field conditions and risks associated with their extended-release into the environmental will, however, be assessed prior to further bioformulation, field investigation, and scale-up.

Evaluation of Disease Suppressiveness of Soils in Croplands by Co-Cultivation of Pathogenic Fusarium oxysporum and Indigenous Soil Microorganisms

An evaluation of suppressiveness against soil-borne diseases is important for their control. We herein assessed disease suppression against F. oxysporum f. sp. spinaciae using the Fusarium co-cultivation method in 75 soils collected from croplands around the country. The suppressive effects of soil microbes against F. oxysporum growth were examined by simultaneously culturing soil suspensions and F. oxysporum f. sp. spinaciae on a culture medium. The growth degree of F. oxysporum on the medium varied among the 75 soils tested, and 14 soils showing different degrees of growth were selected to investigate the incidence of spinach wilt by cultivating spinach inoculated with the pathogenic F. oxysporum strain. A correlation (r=0.831, P<0.001) was observed between the disease incidence of spinach wilt and the growth degree of F. oxysporum using the co-cultivation method in the 14 selected soils. No correlations were noted between chemical and biological parameters (including pH and the population density of microbes, except for the growth degree of F. oxysporum) and the growth degree of F. oxysporum and incidence of spinach wilt, indicating that it was not possible to predict the degree of growth or disease incidence based on specific chemical and biological characteristics or their combination. The present results suggest that an evaluation of the growth degree of F. oxysporum by the Fusarium co-cultivation will be useful for diagnosing the disease suppressiveness of soil against pathogenic F. oxysporum in croplands.

Role of pollution on the selection of antibiotic resistance and bacterial pathogens in the environment

There is evidence that human activity causes pollution that contributes to an enhanced selection of bacterial pathogens in the environment. In this review, we consider how environmental pollution can favour the selection of bacterial pathogens in the environment. We specifically discuss pollutants released into the environment by human activities (mainly human waste) that are associated with the selection for genetic features in environmental bacterial populations that lead to the emergence of bacterial pathogens. Finally, we also identify key pollutants that are associated with antibiotic resistance and discuss possibilities of how to prevent their release into the environment.