Abstract Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions. 

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

The Botryosphaeriaceae family comprises numerous fungal pathogens capable of causing economically meaningful diseases in a wide range of crops. Many of its members can live as endophytes and turn into aggressive pathogens following the onset of environmental stress events. Their ability to cause disease may rely on the production of a broad set of effectors, such as cell wall-degrading enzymes, secondary metabolites, and peptidases. Here, we conducted comparative analyses of 41 genomes representing six Botryosphaeriaceae genera to provide insights into the genetic features linked to pathogenicity and virulence. We show that these Botryosphaeriaceae genomes possess a large diversity of carbohydrate-active enzymes (CAZymes; 128 families) and peptidases (45 families). Botryosphaeria, Neofusicoccum, and Lasiodiplodia presented the highest number of genes encoding CAZymes involved in the degradation of the plant cell wall components. The genus Botryosphaeria also exhibited the highest abundance of secreted CAZymes and peptidases. Generally, the secondary metabolites gene cluster profile was consistent in the Botryosphaeriaceae family, except for Diplodia and Neoscytalidium. At the strain level, Neofusicoccum parvum NpBt67 stood out among all the Botryosphaeriaceae genomes, presenting a higher number of secretome constituents. In contrast, the Diplodia strains showed the lowest richness of the pathogenicity- and virulence-related genes, which may correlate with their low virulence reported in previous studies. Overall, these results contribute to a better understanding of the mechanisms underlying pathogenicity and virulence in remarkable Botryosphaeriaceae species. Our results also support that Botryosphaeriaceae species could be used as an interesting biotechnological tool for lignocellulose fractionation and bioeconomy. 

Botryosphaeriaceae gene machinery: Correlation between diversity and virulence.

Archaeorhizomyces is a genus of the subphylum Taphrinomycotina, which contains soil-inhabiting/root-associated fungi. It is a diverse, ubiquitous, and sometimes dominant genus in the environment. Although ecological importance and root-associating lifestyles of Archaeorhizomyces can be postulated, morphological aspects of fungal body and root colonization is largely unknown due to the scarcity of cultures. We obtained three unidentified Archaeorhizomyces isolates from ericoid mycorrhizal (ErM) roots of Rhododendron scabrum and R. × obtusum collected in Japan. To advance our understanding of lifestyle of the genus, we investigated their general morphology, phylogeny, and in vitro root-colonizing ability in ericoid mycorrhizal hosts, Vaccinium virgatum and R. kaempferi. Some morphological characteristics, such as slow glowing white-to-creamy-colored colonies and formation of yeast-like or chlamydospore-like cells, were shared between our strains and two described species, A. finlayi and A. borealis, but they were phylogenetically distant. Our strains were clearly distinguished as two undescribed species based on morphology and phylogenetic relationship. As seen in typical ErM fungi, both species frequently formed hyphal coils within vital rhizodermal cells of ErM plants in vitro. The morphology of hyphal coils was also different between species. Consequently, two novel species, A. notokirishimae sp. nov. and A. ryukyuensis sp. nov., were described. 

Two novel Archaeorhizomyces species isolated from ericoid mycorrhizal roots and their association with ericaceous plants in vitro

ABSTRACT To determine the prevalence of the four major soilborne pathogens of strawberry in the Santa Maria growing district in California, symptomatic plant samples (n = 100) were collected from 68 fields between May and September 2022. Samples comprised 28.3% of 2021 fall-planted strawberry fields and 14.0% of 2022 summer-planted strawberry fields in the district. Recombinase polymerase amplification was used to detect Macrophomina phaseolina, Fusarium oxysporum f. sp. fragariae, Verticillium dahliae, and Phytophthora spp. in plant crown material. Macrophomina phaseolina was most prevalent, detected in 52 samples, followed by Verticillium dahliae in 17 samples, F. oxysporum f. sp. fragariae in 16 samples, and Phytophthora spp. in 14 samples. Macrophomina phaseolina was more likely in eastern field locations (P = .0159) and in instances where strawberries were planted consecutively (P = .0100). Disease incidence was more likely to be higher in samples from organic fields than conventional fields (P = .0304) and in samples from flat-fumigated fields than fields fumigated in-line (P = .0124).

Survey of Soilborne Pathogens Infecting Strawberry in Santa Maria, California

A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria.

Phenotypic Variability and Genetic Diversity of the Pathogenic Fungus Macrophomina phaseolina from Several Hosts and Host Specialization in Strawberry

Strawberry is a high-value crop in Spain, where fruits for fresh consumption are produced off-season and exported to central and northern European countries. Soil-borne pathogens (SBP), such as Macrophomina phaseolina and Meloidogyne hapla, are widely spread in strawberry crops in Spain. The prevalence of these pathogens is a significant barrier to producing strawberries of premium quality and at profitable yields. The current ban on fumigant pesticides drives the search for alternative SBP control methods that can simultaneously control both SBP. Twenty-nine bacterial strains were isolated and identified from strawberry and blueberry rhizospheres and screened for plant growth promotion activities as well as for biocontrol potential on M. phaseolina and M. hapla. Two of these bacterial strains (Bacillus velezensis FC37 and Pseudomonas aeruginosa AC17), together with Brevibacterium frigoritolerans Hvs8 coming from IFAPA’s bacterial collection, were selected and evaluated in planta for their biocontrol potential on strawberry SBP diseases caused by M. phaseolina and M. hapla. The three tested bacterial strains reduced charcoal rot disease severity, crown incidence and severity, and petiole colonization by M. phaseolina. Root-knot nematode (RKN) symptoms were reduced by P. aeruginosa AC17 and B. velezensis FC37, but RKN reproduction was only reduced in plants inoculated with P. aeruginosa AC17. Pseudomonas aeruginosa AC17 showed the greatest potential as a biocontrol agent candidate to be included in integrated disease management programs to control the two most prevalent soil-borne pathogens of strawberry in Spain.

/pdf/use-of-bacteria-isolated-from-berry-rhizospheres-as-213gxrzx.pdf

Use of Bacteria Isolated from Berry Rhizospheres as Biocontrol Agents for Charcoal Rot and Root-Knot Nematode Strawberry Diseases

Microbial interactions in agricultural soils can play important roles in the control of soil-borne phytopathogenic diseases. Yields from blueberry plantations from southern Spain have been impacted by the pathogenic fungus, Macrophomina phaseolina. The use of chemical fungicides has been the common method for preventing fungal infections, but due to their high environmental impact, legislation is increasingly restricting its use. Biocontrol alternatives based on the use of microorganisms is becoming increasingly important. Using the metabarcoding technique, fungi and bacteria were characterized (via 16S and ITS regions, respectively) from rhizosphere soils of healthy and dead blueberry plants infected by M. phaseolina, and which had undergone three different treatments: two biocontrol strategies—one of them a mix of Pseudomonas aeruginosa and Bacillus velezensis and the other one with Bacillus amyloliquefaciens—and a third treatment consisting of the application of a nutrient solution. The treatments produced changes in the bacterial microbiota and, to a lesser extent, in the fungi. The abundance of Fusarium was correlated with dead plants, likely favoring the infection by M. phaseolina. The presence of other microorganisms in the soil, such as the fungi Archaeorhizomyces or the bacteria Actinospica, were correlated with healthy plants and could promote their survival. The different genera detected between dead and healthy plants opens the possibility of studying new targets that can act against infection and identify potential microorganisms that can be used in biocontrol strategies.

/pdf/microbiota-modulation-in-blueberry-rhizosphere-by-biocontrol-3mkyf5xw.pdf

Microbiota Modulation in Blueberry Rhizosphere by Biocontrol Bacteria

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Papers

Phenotypic Variability and Genetic Diversity of the Pathogenic Fungus Macrophomina phaseolina from Several Hosts and Host Specialization in Strawberry

Use of Bacteria Isolated from Berry Rhizospheres as Biocontrol Agents for Charcoal Rot and Root-Knot Nematode Strawberry Diseases

Microbiota Modulation in Blueberry Rhizosphere by Biocontrol Bacteria