Biology subjects

Vasileiadis, S.

Publications and source records attributed to Vasileiadis, S..

5 recordsLinked to original sources

bioRxiv2026

A new automated pipeline for whole genome shotgun sequencing analysis and hazard characterization of microbial pesticides

Microbial pesticides are increasingly important for sustainable crop protection, yet hazard analysis and risk assessment remain challenging and require specific characterization of properties relevant to both safety and biological activity. Whole-genome sequencing (WGS) can support the identification of microorganisms at high resolution and characterize potential hazards associated with infectivity, pathogenicity, antimicrobial resistance, and toxic metabolite production. However, the routine use of WGS in this context requires accessible, reproducible, and interpretable workflows. Here, we present a publicly available web-based workflow for WGS-supported hazard analysis of microbial biocontrol agents. The workflow accepts assembled genomes as well as short-read, long-read and hybrid sequencing data, and performs genome quality assessment, taxonomic assignment, genome annotation, AMR detection, mobile-element screening, pathogenicity prediction and secondary-metabolite analysis, and compiles the results into an HTML report. For bacterial agents, we implement a transparent rule-based risk-classification module integrating taxonomic identity, PathogenFinder2 predictions, CARD/RGI resistance evidence, WHO priority taxa, and medically important antimicrobial categories. Secondary-metabolite assessment combines antiSMASH with local BLAST searches and EFSA-aligned identity/coverage thresholds to support product-level interpretation of biosynthetic gene clusters. Comparison with the currently used MOpS workflow developed by EFSA demonstrates the added benefits of the proposed workflow for a guided hazard analysis of microbial pesticides. The workflow is intended as a community-accessible pre-assessment tool that complements regulatory platforms by improving transparency, reproducibility, and early identification of potential hazards in microbial biocontrol candidates, envisioned to make WGS an integral part of the risk assessment of microbial pesticides. Key pointsO_LIThe RATION-GUI provides a public, reproducible workflow for whole-genome sequencing- supported hazard characterization of bacterial and fungal microbial pesticides. C_LIO_LIThe workflow integrates genome quality, taxonomy, annotation, antimicrobial resistance, pathogenicity-related evidence, mobile elements, and secondary-metabolite potential. C_LIO_LIDomain-specific outputs are translated into structured hazard indicators, evidence summaries, and recommended follow-up actions without replacing expert regulatory judgment. C_LIO_LICase studies demonstrate how the workflow improves transparency, traceability, and interpretation of genomic evidence for microbial pesticide risk assessment. C_LI

bioinformatics↗

bioRxiv2024

Isolation of a novel Sphingomonas strain able to degrade the pleuromutilin tiamulin: omic analysis reveals its transformation pathway

Tiamulin (TIA) is a commonly used veterinary antibiotic, persistent in the animal digestive system and downstream receiving environments like soil after manuring. We aimed to isolate and characterize TIA-degrading bacteria for bioaugmentation strategies towards mitigating TIA environmental pressure. A strain able to degrade TIA and use it as sole C source was isolated from a soil exhibiting enhanced biodegradation of the antibiotic. The isolate degraded TIA at concentrations up to 100 {micro}g ml-1, with pH and temperature optima of 6.5-7.5 and 16-25{degrees}C respectively. Phylogenomic analysis deemed the isolate to be a new Sphingomonas species (83.87 % ANI with S. laterariae, [≤] 95 %), which was named Candidatus Sphingomonas perruchonii. Genomics and transcriptomics revealed the TIA-driven induction of features conducive with its antiotrophic character; genes encoding for drug efflux pumps and the catabolism of xenobiotics. These included ribosome protective ABC-F transporters and efflux pumps able to protect the ribosome and microbial cells from TIA, oxygenases (e.g. P450 cytochrome) and hydrolases (e.g. alpha/beta hydrolases and amidohydrolases) possibly contributing to its degradation. LC-MS/MS analysis detected putative transformation products (TPs) of TIA, leading us to propose a transformation pathway. This involved a primary oxidation of the tricyclic moiety of TIA to a mono-hydroxylated derivative (TIA-O), potentially mediated by the highly upregulated monoxygenases, which was either further oxidized to TIA-O2 or hydrolysed, by the upregulated hydrolase or amidohydrolases, to 2-diethylamino-ethyl-thio acetic acid, both not degrading further. Further tests and in vitro functional analysis will verify the role of these genes in the transformation of TIA. IMPORTANCEAnthropogenic antibiotic pressure in environmental settings has been acknowledged as a major threat for the public health and the environment, through the: (i) associated ecotoxicological impact; and (ii) the increase of antibiotic resistance dispersal among non-pathogenic and pathogenic bacteria, restricting available choices for treating infections in health care. In situ microbial biotransformation of antibiotics and eventual removal is an environmentally friendly method currently under intense investigation, which was recently proposed for the reduction of antibiotic selective pressure. The present study provides mechanistic insights on the genomic constituents of antibiotrophy, namely, the tolerance against and the biodegradation/transformation of the antibiotic in question. We characterize the capacity of a bacterial isolate to transform tiamulin, a heavily used antibiotic in pig farming, and propose associated biotransformation mechanisms, through an integrated approach of standard microbiological methods combined with and multi-omics (genomics, transcriptomics, metabolomics).

genomics↗

bioRxiv2022

Systemic silencing and DNA methylation of a host reporter gene induced by a beneficial fungal root endophyte

A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional cross-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms have been elusive to this date. Here, we report on an RNAi-based mechanism of communication between a beneficial fungal endophyte, Fusarium solani strain K (FsK) and its host plants. This soil-borne endophyte that confers resistance and/or tolerance to biotic and abiotic stress in tomato and, as shown in this study, promotes plant growth in Nicotiana benthamiana, is restricted to the root system in both host plants. We first showed that the fungus has a functional core RNAi machinery; double stranded RNAs (dsRNAs) are processed into short interfering RNAs (siRNAs) of predominantly 21-nt in size, which lead to the degradation of homologous mRNAs. Importantly, by using an RNAi sensor system, we demonstrated that root colonization of N. benthamiana by FsK led to the induction of systemic silencing and DNA methylation of a host reporter gene.. These data reflect a more general but so far unrecognized mechanism wherein root endophytes systemically translocate RNAi signals to the aboveground tissues of their hosts to modulate gene expression during symbiosis, which may be translated to the beneficial phenotypes. HighlightA root-restricted, beneficial fungal endophyte can induce systemic silencing and epigenetic modifications to its host plant.

plant biology↗

bioRxiv2020

Comparison of the in vitro activity of novel and established nitrification inhibitorsapplied in agriculture: challenging the effectiveness of the currently availablecompounds

Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agricultural ecosystems. Currently available NIs appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other groups of nitrifiers is limited. Ethoxyquin (EQ), a preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI) and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives in vitro with other established NIs that have been applied in an agricultural setting (dicyandiamide (DCD), nitrapyrin (NP), 3,4-dimethylpyrazole phosphate (DMPP)) by evaluating their impact on the activity and growth of five soil-derived strains (two AOB (Nitrosomonas europaea, Nitrosospira multiformis), two ammonia-oxidizing archaea (AOA) ("Candidatus Nitrosocosmicus franklandus", "Candidatus Nitrosotalea sinensis"), and one nitrite-oxidizing bacterium (NOB) (Nitrobacter sp.)). NIs degradation was also determined. AOA were more sensitive than AOB or NOB to EQ and its derivatives. Despite its transient character, QI was primarily responsible for AO inhibition by EQ, and the most potent NI against AOA. For AOB, QI was more potent than DCD but less than nitrapyrin and DMPP. AOA and NOB showed higher tolerance to the persistent compounds DCD and DMPP. Our findings benchmark the activity range of known and novel NIs with practical implications for their use, and the development of novel NIs with broad or complementary activity against all AO.

microbiology↗

bioRxiv2020

Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazol

BackgroundThiabendazole (TBZ), is a benzimidazole fungicide and anthelminthic whose high persistence and toxicity pose a serious environmental threat. In our quest for environmental mitigation we previously isolated the first TBZ-degrading bacterial consortium and provided preliminary evidence for its composition and the degrading role of a Sphingomonas. Here, we employed a multi-omic approach combined with DNA-stable isotope probing (SIP) to determine the genetic make-up of the key consortium members, to disentangle nutritional and metabolic interdependencies, to identify the transformation pathway of TBZ and to understand the genetic network driving its transformation. ResultsTime-series SIP in combination with amplicon sequencing analysis verified the key role of Sphingomonas in TBZ degradation by assimilating over 80% of the 13C-labelled phenyl moiety of TBZ. Non-target mass spectroscopy (MS) analysis showed the accumulation of thiazole-4-carboxamidine as a single dead-end transformation product and no phenyl-containing derivative, in line with the phenyl moiety assimilation in the SIP analysis. Time series metagenomic analysis of the consortium supplemented with TBZ or succinate led to the assembly of 18 metagenome-assembled genomes (MAGs) with >80% completeness, six (Sphingomonas 3X21F,{gamma} -Proteobacterium 34A, Bradyrhizobiaceae 9B and Hydrogenophaga 19A, 13A, and 23F) being dominant. Meta-transcriptomic and -proteomic analysis suggested that Sphingomonas mobilize a carbazole dioxygenase (car) operon during the initial cleavage of TBZ to thiazole-4-carboxamidine and catechol, the latter is further transformed by enzymes encoded in a catechol ortho-cleavage (cat) operon; both operons being up-regulated during TBZ degradation. Computational docking analysis of the terminal oxygenase component of car, CarAa, showed high affinity to TBZ, comparable to carbazole, reinforcing its high potency for TBZ transformation. These results suggest no interactions between consortium members in TBZ transformation, performed solely by Sphingomonas. In contrast, gene expression network analysis revealed strong interactions between Sphingomonas MAG 3X12F and Hydrogenophaga MAG 23F, with Hydrogenophaga activating its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway along TBZ degradation. ConclusionsOur findings suggest interactions between consortium members which align with the "black queen hypothesis": Sphingomonas detoxifies TBZ, releasing consortium members by a toxicant; in return for this, Hydrogenophaga 23F provides cobalamin to the auxotrophic Sphingomonas.

systems biology↗