Biology subjects

Markakis, E. A.

Publications and source records attributed to Markakis, E. A..

7 recordsLinked to original sources

bioRxiv2026

Halophytic endophytes provide transferable immune functions for crop resilience

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.

microbiology↗

bioRxiv2026

A Thousand Meters Deep: Vertical Profiling of the Subterranean Microbiome of Gourgouthakas Cave

IntroductionCaves 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 worlds deepest vertical systems, which had remained untouched by humans for 19 years. MethodsWe performed a high-resolution vertical profiling of the caves 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. ResultsTaxonomic 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. DiscussionCollectively, our results demonstrate that deep karstic systems are not merely geological wonders but vital hotspots for microbial innovation with tangible applications for sustainable agriculture.

microbiology↗

bioRxiv2026

Unravelling the genomic and functional arsenal of Bacilli endophytes from plants with different lifestyles

Endophytic microbiomes of crop wild relatives (CWRs) adapted to extreme environments, such as halophytes, are promising sources of plant-beneficial bacteria and secondary metabolites for sustainable food production. Here, we analyzed 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 biosynthetic gene clusters (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, Rossellomorea), including three novel species. Phenotypic assays of our isolates demonstrated high salinity tolerance (up to 17.5% w/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.

microbiology↗

bioRxiv2022

Components of TOR and MAP kinase signaling control chemotropism and pathogenicity in a fungal pathogen

Filamentous fungi can sense useful resources and hazards in their environment and direct growth of their hyphae accordingly. Chemotropism ensures access to nutrients, contact with other individuals (e.g., for mating), and interaction with hosts in the case of pathogens. Previous studies have revealed a complex chemotropic sensing landscape during host-pathogen interactions, but the underlying molecular machinery remains poorly characterized. Here we studied mechanisms controlling directed hyphal growth of the important plant-pathogenic fungus Verticillium dahliae towards different chemoattractants. We found that the homologs of the Rag GTPase Gtr1 and the GTPase-activating protein Tsc2, an activator and a repressor of the TOR kinase respectively, play important roles in hyphal chemotropism towards nutrients, plant-derived signals, and heterologous -pheromone of Fusarium oxysporum. Furthermore, important roles of these regulators were identified in fungal development and pathogenicity. We also found that the mitogen-activated protein kinase (MAPK) Fus3 is required for chemotropism towards nutrients, while the G protein-coupled receptor (GPCR) Ste2 and the MAPK Slt2 control chemosensing of plant-derived signals and -pheromone. Our study establishes V. dahliae as a suitable model for the analysis of fungal chemotropism and discovers new components of chemotropic signaling, during growth and host-pathogen interactions of V. dahliae.

microbiology↗

bioRxiv2021

The NADPH Oxidase A of Verticillium dahliae is Essential for Pathogenicity, Normal Development, and Stress Tolerance, and it Interacts with Yap1 to Regulate Redox Homeostasis

Maintenance of redox homeostasis is vital for aerobic organisms and particularly relevant to plant pathogens. These need to balance between endogenous ROS production that is required for their development and pathogenicity, and host-derived oxidative stress. Endogenous ROS in fungi are generated by the membrane-bound NADPH oxidase (NOX) complexes and the mitochondrial respiratory chain, while the transcription factor Yap1 is a major regulator of the antioxidant response. Here we investigated the roles of NoxA and Yap1 in fundamental biological processes of the important plant pathogen Verticillium dahliae. Deletion of noxA impaired growth and morphogenesis, compromised formation of hyphopodia, diminished penetration ability and pathogenicity, increased sensitivity against antifungal agents, and dysregulated expression of antioxidant genes. On the other hand, deletion of yap1 resulted in defects in conidial and microsclerotia formation, increased sensitivity against oxidative stress, and down-regulated antioxidant genes. Localized accumulation of ROS was observed before conidial fusion and during the heterokaryon incompatibility reaction upon nonself fusion. The frequency of inviable fusions was not affected by deletion of Yap1. Analysis of a double knockout mutant revealed an epistatic relationship between noxA and yap1. Our results collectively reveal instrumental roles of NoxA and ROS homeostasis in the biology of V. dahliae.

genetics↗

bioRxiv2020

Hex1, the Major Component of Woronin Bodies, is Required for Normal Development, Pathogenicity and Stress Response in the Plant Pathogenic Fungus Verticillium dahliae

Woronin bodies are membrane-bound organelles of filamentous ascomycetes that mediate hyphal compartmentalization by plugging septal pores upon hyphal damage. Their major component is the peroxisomal protein Hex1, which has also been implicated in additional cellular processes in fungi. Here, we analyzed the Hex1 homolog of Verticillium dahliae, an important asexual plant pathogen, and we report its pleiotropic involvement in fungal growth, physiology, stress response and pathogenicity. Alternative splicing of the Vdhex1 gene can lead to the production of two Hex1 isoforms, which are structurally similar to their Neurospora crassa homolog. We show that VdHex1 is targeted to the septum, consistently with its demonstrated function in sealing hyphal compartments to prevent excessive cytoplasmic bleeding upon injury. Furthermore, our investigation provides direct evidence for significant contributions of Hex1 in growth and morphogenesis, as well as in asexual reproduction capacity. We discovered that Hex1 is required both for normal responses to osmotic stress and factors that affect the cell wall and plasma membrane integrity, and for normal resistance to oxidative stress and ROS homeostasis. The Vdhex1 mutant exhibited diminished ability to colonize and cause disease on eggplant. Overall, we show that Hex1 has fundamentally important multifaceted roles in the biology of V. dahliae.

microbiology↗

bioRxiv2020

Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture

Halophytes have evolved several strategies to survive in saline environments; however, additional support from their associated microbiota could help combat adverse conditions. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the hosts adaptation to adverse environmental conditions and can improve host tolerance against various biotic and abiotic stresses, which may be of importance in modern and sustainable agriculture. In this study the culturable endophytic bacteria of three halophytic species Cakile maritima, Matthiola tricuspidata and Crithmum maritimum were isolated and identified. Endophytic bacteria were isolated from roots and leaves of the sampled plants. Significant differences were observed in bacterial species abundance among different plant species and tissue from which the isolates were obtained. In total, 115 strains were identified by analysis of complete 16S rDNA sequences, while the majority of these isolates were derived from the root samples. The strains were evaluated for their ability to: 1) grow in-vitro in high levels of NaCl; 2) inhibit the growth of the economically important plant pathogenic fungus Verticillium dahliae in vitro and in planta, the human pathogenic fungus Aspergillus fumigatus in vitro, as well as, the economically important plant bacterial pathogens Ralstonia solanacearum and Clavibacter michiganensis in vitro; 3) provide salt tolerance in planta; 4) provide growth promoting effect in planta. Additionally, the genomes of twelve selected isolates, exhibiting interesting features, were sequenced and analysed. Three novel bacterial species were identified that belong to the genus Pseudomonas (two strains) and Arthrobacter (one strain). The outcome of our study is the proof-of-concept that the crop wild relatives (CWR) halophytic microbiome could potentially serve as a source of beneficial microorganisms that could be used (as unique species or as artificial communities) as Bio-Inoculants, for the enhancement of plant growth and stress tolerance in crops, including the high-salinity stress. This is very important in the era of ecosystem degradation and climate change, where the maximizing microbial functions in agroecosystems could be a prerequisite for the future of global sustainable agriculture. Globally, there is a strong need for the identification and bio-banking of novel beneficial endophytic microbes with as many desirable characters, for the development of a new environmentally friendly global strategy in food production that will be based in the sustainable agriculture with low chemical inputs and a low environmental impact.

microbiology↗