Halophytic microbiomes represent an untapped reservoir of stress-adapted microbial functions, yet whether these functions can be transferred across ecological boundaries to enhance crop immune resilience remains unknown. Here we show that Kushneria , a halophyte-associated genus with broad environmental resilience, confers robust disease protection in tomato and cucumber plants against fungal and oomycete pathogens despite lacking direct antagonistic activity. Comparative genomics across 26 genomes revealed extensive biosynthetic novelty and conserved catabolic clusters associated with rhizosphere competence, providing a genomic framework for persistence of Kushneria in saline environments. Multi-omics profiling associated protection with a distinct host immune regulatory response, characterized by strong induction of core NLR receptors, including a ZAR1 paralogue. This response was further linked to a previously uncharacterized long noncoding RNA, Solyc10r048010.1, connected to the induced NLR network. Our findings establish halophytic endophytes as field-validated and transferable modulators of crop immunity and identify a candidate regulatory RNA–NLR axis associated with Kushneria -induced disease resistance.

In the present study, a novel method was developed and validated for the early, rapid and on-site detection of Botrytis cinerea in crude tomato samples using a newly designed loop-mediated isothermal amplification (LAMP) assay and the portable device PEBBLE. LAMP primers (targeting the IGS region of rDNA gene) were designed, and the sensitivity, specificity and accuracy of the developed method were determined (97.96%, 100% and 98.70%, respectively). The LAMP assay, combined with the portable device, enabled real-time quantitative colorimetric (qcLAMP) detection of B. cinerea in less than 30 min. The limit of detection (LoD) of the qcLAMP assay was 1 pg genomic DNA (≈20 genome copies) per reaction, whereas conventional PCR (utilized as the gold standard method) detected no less than 100 pg of genomic DNA per reaction. In terms of B. cinerea infective propagules, qcLAMP could detect as few as 10² spores in both pure and crude DNA samples extracted from artificially inoculated tomato leaves, whereas PCR detected no fewer than 10⁴ spores in pure DNA samples, failing to achieve detection in crude extracts. In in-vivo bioassays, qcLAMP successfully detected B. cinerea immediately following spore deposition on leaf tissues (0 hours post inoculation) in both pure and crude DNA extracts. In contrast, conventional PCR was successful only in pure DNA samples from leaves collected 2 days post inoculation (dpi) and in crude extracts at 3 dpi, when symptoms were already evident. Evaluations in field samples demonstrated that qcLAMP detected B. cinerea in 100% of crude extracts from symptomatic tissues and in 45% of asymptomatic (latently infected) samples. Conversely, conventional PCR failed to detect the pathogen in crude extracts, regardless of the disease status (symptomatic or asymptomatic). The developed method can serve as a rapid, reliable, and user-friendly tool for the early detection of B. cinerea in the field, enabling prompt assessment of inoculum pressure, thereby facilitating timely management interventions.

Introduction: Caves represent unique, nutrient-limited windows into the deep biosphere, yet the microbiology of the deep terrestrial subsurface remains remarkably under-explored. In this work, we conducted a rare expedition into Gourgouthakas Cave (Crete, Greece), one of the world’s deepest vertical systems, which had remained untouched by humans for 19 years. Methods: We performed a high-resolution vertical profiling of the cavès microbes by sampling rock surfaces across nine different depths down to 1,100 meters. Through extensive cultivation on various media and at different temperatures, we established a biobank of 820 bacterial isolates. Results: Taxonomic identification of a 374-isolate subset revealed a diverse community spanning 35 genera and 4 phyla, dominated by Pseudomonas , Aquipseudomonas , Bacillus , and Stenotrophomonas . Beyond characterizing this taxonomic diversity, we explored the biotechnological potential of these subterranean microbes against major agricultural threats. Screening 70 representative isolates against six key pathogens, including Ralstonia solanacearum , Verticillium dahliae , and Phytophthora nicotianae , uncovered a notable group of strains with potent antagonistic activity, particularly within the Pseudomonas and Brevibacillus groups. Genomic sequencing of cave-derived Actinobacteria ( Streptomyces and Nocardiopsis isolates) further highlighted this potential, revealing 142 biosynthetic gene clusters (BGCs), over half of which showed little to no similarity to known clusters, suggesting a hidden reservoir of novel secondary metabolites. Pangenomic analysis of Streptomyces revealed 1,497 unique gene clusters. Finally, ex vivo trials showed that the Aquipseudomonas paracarnis (formerly Pseudomonas sp. ) isolate SRL917 significantly reduced Botrytis cinerea infections on tomato leaves, even surpassing the performance of a commercial biocontrol agent. Discussion: Collectively, our results demonstrate that deep karstic systems are not merely geological wonders but vital hotspots for microbial innovation with tangible applications for sustainable agriculture.

Endophytic microbiomes of c rop w ild r elatives (CWRs) adapted to extreme environments, such as halophytes, are promising sources of plant-beneficial bacteria and secondary metabolites for sustainable food production. Here, we analysed 25 Bacilli isolates obtained from CWRs, halophytes and other plant species in Crete, Greece. Using a hybrid Illumina–PacBio sequencing approach, we generated high-quality genomes and performed comparative genomics, phylogenetic and pangenome analyses, complemented by in vitro assays. We identified 312 b iosynthetic g ene c lusters (BGCs), nearly 60% of which showed no similarity to known clusters, revealing extensive unexplored biosynthetic potential. These unique BGCs may constitute an adaptive feature enabling endophytic Bacilli to colonize and interact with host plants. The isolates spanned diverse genera ( Bacillus , Paenibacillus , Peribacillus , Neobacillus , Cytobacillus and Rossellomorea ), including three novel species. Phenotypic assays of our isolates demonstrated high salinity tolerance (up to 17.5% wt/v NaCl) and strong antagonism against major bacterial and fungal phytopathogens. Genome mining further revealed a broad array of putatively plant-beneficial traits related to growth promotion, stress adaptation, host interaction and inhibition of pathogens. Together, these findings show that Bacilli endophytes from wild and halophytic plants possess exceptional phylogenetic novelty, functional diversity and biosynthetic capacity, providing new genomic and ecological insights into Bacilli associated with plants inhabiting extreme environments.