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Abstract BackgroundArbuscular mycorrhizal fungi (AMF) are beneficial root symbionts contributing to improved plant growth and development and resistance to abiotic and biotic stresses. Commercial bioinoculants containing AMF are widely considered as an alternative to agrochemicals in vineyards. However, their effects on grapevine plants grown in soil containing native communities of AMF are still poorly understood. In a greenhouse experiment, we evaluated the influence of five different bioinoculants on the composition of native AMF communities of young Cabernet Sauvignon vines grown in a non-sterile soil. Root colonization, leaf nitrogen concentration, plant biomass and root morphology were assessed, and AMF communities of inoculated and non-inoculated grapevine roots were profiled using high-throughput sequencing. ResultsContrary to our predictions, no differences in the microbiome of plants exposed to native AMF communities versus commercial AMF bioinoculants + native AMF communities were detected in roots. However, inoculation induced positive changes in root traits as well as increased AMF colonization, plant biomass, and leaf nitrogen. Most of these desirable functional traits were positively correlated with the relative abundance of operational taxonomic units identified asGlomus,RhizophagusandClaroideoglomusgenera. ConclusionThese results suggest synergistic interactions between commercial AMF bioinoculants and native AMF communities of roots to promote grapevine growth. Long-term studies with further genomics, metabolomics and physiological research are needed to provide a deeper understanding of the symbiotic interaction among grapevine roots, bioinoculants and natural AMF communities and their role to promote plant adaptation to current environmental concerns. 

ABSTRACT Rhizopus microsporusis a necrotrophic post-harvest pathogen that causes significant economic losses in the agricultural sector. To explore alternatives to conventional management strategies for the mitigation of post-harvest infections, we investigated the potential of two previously identified endophyticBacillus velezensisstrains as biological control agents. Throughin vitroandin vivoexperiments, we examined the mechanisms of biocontrol displayed by twoB. velezensisstrains (KV10 and KV15) against threeR. microsporusstrains (W2-50, W2-51, and W2-58).In vitroassays assessed co-cultivability and the inhibitory effects ofB. velezensisagainstR. microsporus. The results demonstrated strain-specific antifungal activity with a reduction in fungal growth across treatments. Further analysis revealed that volatile organic compounds produced byB. velezensiscontributed to its antifungal properties. To evaluate the biocontrol efficacyin vivo, tomato fruits were inoculated withR. microsporusand subsequently treated withB. velezensis. The results support the strain-specific reduction in tomato spoilage, yielding various spoilage rates observed across treatments. Our findings highlight the potential ofB. velezensisas a promising biocontrol agent for the management ofR. microsporuspost-harvest infections in tomatoes. Further research is warranted to optimize the applicationof B. velezensisas a sustainable and environmentally friendly approach for controlling post-harvest diseases in tomatoes.IMPORTANCEOur study shows the significance of improving sustainable agriculture by offering an alternative to the use of chemical fungicides in post-harvest applications. Opportunistic fungal pathogens likeRhizopus microsporuscan have detrimental effects on post-harvest commodities like tomatoes. Post-harvest fungal infections are mainly controlled by chemical fungicides that pose health risks to humans and the environment. Utilizing biocontrol agents provides an environmentally safe alternative. Understanding the mechanisms of biocontrol employed by beneficial bacteria likeBacillus velezensison fungal pathogens gives insight into safer, more environmentally friendly alternatives to protect food crops. Our results suggest that targeted microbial solutions can mitigate post-harvest losses. 

Rhizopus rot is considered one of the most common diseases influencing global production and yield of horticulture commodities. However, the factors contributing to this pattern of prevalence are uncertain. Here, we focused on R. microsporus, which is known to rely on its endosymbiotic bacterium, Mycetohabitans, to produce toxins that interfere with plant development and inhibit the growth of other fungi. We assessed the impact of the symbiotic R. microsporus harboring its endosymbiont as well as the fungus cured of it on: (1) the magnitude of spoilage in tomato fruits, as evaluated by Koch's postulate for pathogenicity, (2) the shifts in native communities of endophytic fungi inhabiting these fruits, as examined by ITS rRNA gene metabarcoding and (3) secondary metabolites generated by these communities, as analyzed using multi-analyte LC-MS/MS. The pathogenicity test showed that the symbiotic endobacterium-containing R. microsporus W2-50 was able to cause tomato fruit spoilage. This was accompanied by decreased relative abundance of Alternaria spp. and an increase in the relative abundance of Penicillium spp. that may have facilitated the observed spoilage. In conclusion, symbiotic W2-50 appeared to facilitate fruit spoilage, possibly through successful colonization or toxin production by its endosymbiont. 

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

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades—primarily plant—associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.