Biology subjects

Sarris, P. F.

Publications and source records attributed to Sarris, P. F..

13 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↗

bioRxiv2024

Os-circANK negatively regulates resistance to bacterial blight in rice via Osa-miR398b/OsCSD1/OsCSD2 pathways

CircRNAs are widely present in plants, yet there have been no reports on the role of circRNA in the regulatory mechanisms of interactions between rice and pathogenic bacteria. As the sequence of circRNAs matches the parent gene except for the back splicing site, there is no feasible way to specifically knockdown circRNAs in plants. We identified a circRNA, named Os-circANK, derived from an ankyrin repeat protein, which was significantly downregulated post Xanthomonas oryzae pv. oryzae (Xoo) inoculation. We have created a CRISPR-Cas13d system to specifically knockdown a plant circular RNA, resulting in genetically edited rice with a targeted decrease in Os-circANK expression. Os-circANK was found to function as a sponge for Osa-miR398b, suppressing the cleavage of OsCSD1/OsCSD2 by Osa-miR398b, leading to a reduction in ROS levels following Xoo infection and a negative regulation of resistance to bacterial blight in rice. Our findings demonstrate that Os-circANK inhibits the resistance to bacterial blight in rice via the Osa-miR398b/OsCSD1/OsCSD2 pathways.

microbiology↗

bioRxiv2023

A Proxitome-RNA-capture Approach Reveals that Processing Bodies Repress Co-Regulated Hubs

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because they lack a delineating membrane, the compositional determination of condensates is laborious. Here we set up a pipeline for proximity-biotinylation-dependent capture of RNA to investigate the RNA composition of the condensate in Arabidopsis known as the processing bodies (PBs). Using this pipeline together with in situ protein-protein interaction and RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal and heat stress conditions. The composition of PBs in RNAs is much more dynamic than that of the total transcriptome. RNAs involved in cell wall development and regeneration, hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA binding proteins and liquid-to-solid phase transitions modulated specificity of RNA recruitment in PBs. Surprisingly, RNAs were sometimes recruited together with their encoded proteins. In PBs RNAs follow distinct fates, with small liquid-like PBs modulating RNA decay while larger ones storage. The size and properties of PBs are regulated by the actin polymerization cAMP receptor (SCAR)-WASP family verprolin homologous (WAVE) complex. SCAR/WAVE modulates signaling by shuttling RNAs between PBs and the translational machinery adjusting the ethylene signaling pathway. Heat stress leads to the storage of immunity-related RNAs in PBs by reducing PBs dynamics, suggesting why processes such as immunity malfunction under heat stress. In summary, we provide a method to identify RNAs in condensates which allowed us to reveal a mechanism for RNA fate regulation.

plant biology↗

bioRxiv2022

The functional and structural characterization of Xanthomonas campestris pv. campestris core effector XopP revealed a new kinase activity

The exocyst complex subunit protein Exo70B1 plays a crucial role in a variety of cell mechanisms including immune responses against pathogens. The calcium dependent kinase 5 (CPK5) of Arapidopsis thaliana, phosphorylates AtExo70B1 upon functional disruption. We previously reported that, the Xanthomonas campestris pv. campestis effector XopP, compromises Exo70B1 and bypasses the hosts hypersensitive response (HR), in a way that is still unclear. Herein we designed an experimental approach based on biophysical, biochemical and molecular assays, based on structural and functional predictions, as well as, utilizing Aplhafold and DALI online servers respectively, in order to characterize the in vivo XccXopP function. The interaction between AtExo70B1 and XccXopP is very stable in high temperatures, while the AtExo70B1 appeared to be phosphorylated at XccXopP expressing transgenic Arabidopsis. XccXopP reveals similarities with known mammalian kinases, and phosphorylates AtExo70B1 at Ser107, Ser111, Ser248, Thr309 and Thr364. Furthermore, XccXopP protects AtExo70B1 from AtCPK5 phosphorylation. Together these findings show that, XccXopP is an effector, which not only functions as a novel serine/threonine kinase upon its hosts protein target AtExo70B1, but also protects the latter from the innate AtCPK5 phosphorylation, to bypass the hosts immune responses.

microbiology↗

bioRxiv2022

Atmospheric nitrogen fixation by eukaryotes: Should we reconsider the nitrogen cycle in nature?

Nitrogen is the most abundant element in our planets atmosphere. Approximately 78% of the atmosphere is made up of nitrogen gas (N2). It is essential for organisms, as a major component of biomolecules and cellular biochemistry. Until today, atmospheric N2 assimilation in eukaryotic organisms has been reported to occur only through specific symbiotic N2-fixing bacterial groups that make it available to plants, the base of the food chain. In this work, using Gas Chromatography with Thermal Conductivity Detection, we proved the direct consumption of atmospheric N2 by eukaryotic organisms. Three yeast species: Debaryomyces hansenii, Metschnikowia reukaufii and model-species Saccharomyces cerevisiae are able to directly assimilate atmospheric nitrogen in various conditions, with a yet unknown mechanisms that are not based on the presence of known N2-fixation enzymes. Our findings could change the way we consider the N2-assimilation in nature, laying the basis for future focused studies on the molecular mechanism underling the biological phenomenon of eukaryotic N2-assimilation.

microbiology↗

bioRxiv2022

Ralstonia solanacearum core effector RipE1 interacts and cleaves the Arabidopsis exocyst component Exo70B1

Ralstonia solanacearum depends on numerous virulence factors, also known as effectors, to promote disease in a wide range of economically important host plants. Although some of these effectors have been characterized, none have yet been shown to target the hosts secretion machinery. Here, we used an extended library of NLR plant immune receptor integrated domains (IDs), to identify new effector targets. The screen uncovered that the core effector RipE1, of the R. solanacearum species complex, among other targets, associates with Arabidopsis exocyst component Exo70B1. RipE1, in accordance with its predicted cysteine protease activity, cleaves Exo70B1 in vitro and also promotes Exo70B1 degradation in planta. RipE1 enzymatic activity additionally results in the activation of TN2-dependent ectopic cell death. TN2 is an atypical NLR that has been proposed to guard Exo70B1. Despite the fact that RipE1 has been previously reported to activate defense responses in model plant species, we present here a Nicotiana species, in which RipE1 expression does not activate cell death. In addition, we discovered that RipE1 is recognized by Ptr1, a Nicotiana benthamiana CC-NLR, via its cysteine protease activity. Overall, this study uncovers a new RipE1 host target and a new RipE1-activated NLR while providing evidence and novel tools to advance in-depth studies of RipE1 and homologous effectors. Author SummaryBacterial wilt disease caused by Ralstonia solanacearum, poses a serious global threat for a wide range of agriculturally important plant species. This Gram-negative bacterium utilizes a collection of Type III Secretion System (T3SS) effectors to manipulate host cell defense and physiology. In this study, we searched for new subcellular plant targets of the core R. solanacearum effector RipE1, a cysteine protease. We discovered that RipE1 has multiple potential eukaryotic targets and further elucidated its association with the host exocyst complex. Using Artificial Intelligence (AI)-based predictions and performing both in vitro and in planta assays, we found that RipE1 promotes the degradation of plant exocyst component Exo70B1 through its enzymatic activity. Apart from being the first report of a R. solanacearum effector targeting a component of the host secretion machinery, our findings also identify an NLR from a model plant species that is able to recognize RipE1 protease activity and provide evidence that can lead to the discovery of additional RipE1 targets inside the host cell.

microbiology↗

bioRxiv2021

Assassination Tango: An NLR/NLR-ID immune receptors pair of rapeseed co-operates inside the nucleus to activate cell death

Plant immunity relies on cell-surface receptors and intracellular NLR immune receptors. Some plant NLRs carry integrated domains (IDs) that that mimic authentic pathogens effector targets. We report here the identification in Brassica napus of the genetically linked NLR/NLR-ID pair, BnRPR1 and BnRPR2. The NLR-ID carries two ID fusions and their mode of action conforms to the proposed "integrated sensor/decoy" model. The two NLRs interact and the heterocomplex localizes in the plant-cell nucleus and nucleolus. However, the BnRPRs pair does not operate through a negative regulation as it was previously reported for other NLR-IDs. Cell death is induced only upon co-expression of the two proteins and it is dependent on the helper genes EDS1 and NRG1. Truncations of the IDs of BnRPR1 results in cytoplasmic localization and compromises cell death activation. Expression, using the native promoter in Nicotiana species, led to a conditional cell death induction. However, this was not the case for the transgenic Arabidopsis, where no cell death was observed. In summary, we describe a new pair of NLR-IDs with interesting features in relation to its regulation and the cell death activation.

immunology↗

bioRxiv2021

Expression of putative effectors of different Xylella fastidiosa subspecies/strains reveals recognition and defense activation in various model plants

The re-emergence of Gram-negative bacterium Xylella fastidiosa in Europe in 2013 impelled the scientific community to discover novel strategies for crop protection. The wide host range of Xylella indicates the existence of yet not characterized pathogenic mechanisms to overcome plant defenses. The recent uprising accuracy of a variety of bioinformatics tools, with the ability to predict the function of putative microbial protein represent a useful approach for understanding which of these proteins are associated with pathogens virulence. In this study we collected a number of putative effectors from two X. fastidiosa strains: Temecula1 and CoDiRo and the subspecies (ssp.) Sandyi Ann-1. We designed an in-planta Agrobacterium based expression system that drives the expressed proteins to the cell apoplast, in order to investigate their ability to activate defense in various model plants. Furthermore, we organized the resulted proteins according to their sequential and structural similarities via the I-TASSER online tool. We identified that various X. fastidiosa proteins were able to differentially elicit cell death-like phenotypes in Nicotiana tabacum, N. sylvestris and N. benthamiana. These proteins are members of different enzymatic groups: a) hydrolases/hydrolases inhibitors, b) serine proteases and c) metal transferases. Collectively, we identified structurally similar proteins that were able to differentially elicit cell death-like phenotypes in different cultivars of the same species. Our findings provide the bases for further studies on the mechanisms that underlie host-defense activation by X. fastidiosa putative effectors, as well as, pathogens adaptation in susceptible hosts.

microbiology↗

bioRxiv2020

The host exocyst complex is targeted by a conserved bacterial type III effector protein that promotes virulence

For most Gram-negative bacteria, pathogenicity largely depends on the type-III secretion system that delivers virulence effectors into eukaryotic cells. The subcellular targets for the majority of these effectors remain unknown. Here, we show that Xanthomonas campestris, the causal agent of black rot disease, delivers the highly conserved effector XopP that interacts with hosts EXO70 protein. EXO70 is an essential component of the exocyst complex with a role in plant immunity. The XopP/EXO70 interaction is specific and inhibits exocyst-dependent exocytosis without activating a specific plant NLR receptor that guards EXO70. In this way, Xanthomonas efficiently inhibits the hosts PAMP-triggered immunity (PTI) by blocking exocytosis of PR1, callose deposition and the FLS2 immunity-receptor translocation to the plasma membrane, promoting successful infection.

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↗

bioRxiv2019

Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

Crop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.\n\nThe genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.\n\nBrassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.\n\nHere, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica.\n\nDe novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins.\n\nFurthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.

genomics↗