Biology subjects

Christakis, C. A.

Publications and source records attributed to Christakis, C. A..

4 recordsLinked to original sources

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

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↗

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↗