The grapevine (Vitis vinifera) is a major fruit crop of economic importance worldwide. Commercial grapevine cultivars are susceptible to infection by pathogenic microorganisms that cause diseases both in leaves and fruits, and it is known that the leaf microbiome plays an important role in plant health and fitness. In this study, shotgun metagenomic sequencing was used to characterize the microbial communities associated with grapevine leaves in three commercial varieties, Cabernet Sauvignon, Garnacha, and Marselan, grown in the same biogeographical unit. Metagenomic data revealed a differential enrichment of the microbial communities living inside grapevine leaves or on the leaf surface in the three varieties. The most abundant fungal taxa associated with grapevine leaves belong to the phylum Ascomycota, which included relevant pathogenic fungi for grapevines, such as Botrytis cinerea, Sclerotinia sclerotium, and Alternaria alternata, as well as several fungal species potentially pathogenic for grapevines (e.g., members of the Colletotrichum, Aspergillus, and Penicillium genera). Basidiomycota constituted a minor fraction of the fungal microbial communities. Grapevine leaves also harbored a diversity of bacterial taxa. At the phylum level, bacterial communities in all three varieties were primarily composed of Pseudomonadata, Bacillota, Bacteroidota, and a lower proportion of Actinomycetota. Differences in the fungal and bacterial community structures were observed between varieties, although they were more important in fungi. In particular, S. sclerotiorum and B. cinerea were found to preferentially colonize leaves in the Marselan and Garnacha varieties, respectively. These findings further support that the host genotype can shape its own microbiome in grapevines. A better understanding of the leaf microbiome in grapevines will provide the basis for the development of tailored strategies to prevent diseases in vineyards while helping to increase sustainability in grapevine production.

It is normally supposed that populations of the same species should evolve shared mechanisms of adaptation to common stressors due to evolutionary constraint. Here, we describe a system of within-species local adaptation to coastal habitats, Brassica fruticulosa, and detail surprising strategic variability in adaptive responses to high salinity. These different adaptive responses in neighboring populations are evidenced by transcriptomes, diverse physiological outputs, and distinct genomic selective landscapes. In response to high salinity Northern Catalonian populations restrict root-to-shoot Na ⁺ transport, favoring K ⁺ uptake. Contrastingly, Central Catalonian populations accumulate Na ⁺ in leaves and compensate for the osmotic imbalance with compatible solutes such as proline. Despite contrasting responses, both metapopulations were salinity tolerant relative to all inland accessions. To characterize the genomic basis of these divergent adaptive strategies in an otherwise non-saline-tolerant species, we generate a long-read-based genome and population sequencing of 18 populations (nine inland, nine coastal) across the B. fruticulosa species range. Results of genomic and transcriptomic approaches support the physiological observations of distinct underlying mechanisms of adaptation to high salinity and reveal potential genetic targets of these two very recently evolved salinity adaptations. We therefore provide a model of within-species salinity adaptation and reveal cryptic variation in neighboring plant populations in the mechanisms of adaptation to an important natural stressor highly relevant to agriculture.

Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars.

Soil salinity inhibits germination and seedling establishment, causing patchy crop stands, uneven growth, and poor yields. This study aims to evaluate the early-stage salinity tolerance of Brassicaceae seeds inoculated with plant growth-promoting bacterial (PGPB) strains (E1 and T7) isolated from saline soils. Non-inoculated and inoculated seeds of Lobularia maritima, Sinapis alba, and Brassica napus were cultivated under control and salinity conditions, first in agar plates to assess a germination inhibitory concentration of salt for each species and later in soil irrigated with water containing 0 or 75 mM NaCl. Our results indicate that T7 was the only strain able to increase the germination of L. maritima under saline conditions. However, an increase in shoot biomass, root length, and number of branches was observed in L. maritima and S. alba plants inoculated with T7 and in B. napus with E1. Concomitantly, those seedlings exhibited less oxidative damage and greater capacity to balance plant reactive oxygen species production. This study suggests that inoculation of seeds with halotolerant PGPB strains is a suitable strategy for improving the negative effects of salinity in the early stages. Nonetheless, the observed specific plant–host interaction highlights the need for establishing tailored PGPB–crop associations for specific unfavourable environmental conditions.

Soil salinity is a major stress limiting agricultural productivity worldwide. To counteract the adverse effects of salinity, plants from coastal habitats may engage in positive interaction with microbial partners. We recently discovered inland and coastal populations of Brassica fruticulosa with contrasting salinity tolerance. Here we characterize the microbiomes of salt-tolerant (PST) and salt-sensitive (PSS) populations, analyzing the diversity and abundance of bacteria and fungi taxa in bulk soil, rhizosphere, roots, and leaves of eight populations. We tested in a reciprocal transplant experiment the effects of two salt-tolerant (MST) and two salt-sensitive (MSS) rhizospheric microbiomes on PST and PSS plants under high salinity. Inoculation with MST enhanced salinity tolerance, improved growth, nutritional status, and reduced oxidative stress of PSS plants. Later, we isolated 113 bacterial strains from MST, 26 of which grew in 150mM NaCl and exhibited phosphate solubilization and siderophore production mechanisms. Further screening for nitrogen fixation, auxin production, and ACC deaminase activity allowed us to select 15 top candidates for mediating tolerance. Only five strains significantly promoted salt-sensitive plants growth under saline conditions. These findings highlight that the microbiome of species adapted to harsh conditions harbor a reservoir of potentially beneficial microorganisms that may improve plant resilience to salinity.