Biology subjects

Kotta-Loizou, I.

Publications and source records attributed to Kotta-Loizou, I..

7 recordsLinked to original sources

bioRxiv2026

Temperature-dependent biofilm and sublancin production immobilise arsenic and antibiotic resistance gene mobility in soil system

Climate change-induced warming and arsenic soil contamination synergistically threaten agricultural sustainability by restructuring microbial communities and accelerating antibiotic resistance evolution. Here, we demonstrate that Bacillus subtilis 168-derived sublancin, a temperature-optimised glycosylated antimicrobial peptide, simultaneously maximises microbial arsenic sequestration and suppresses antibiotic resistance gene (ARG) horizontal transfer. Temperature-dependent biofilm formation increased progressively from 25-35{degrees}C (absorbance: 0.37-1.2), correlating with enhanced arsenic accumulation within the extracellular polymeric substance matrix (74% increase in weight percentage). Time-of-flight secondary ion mass spectrometry confirmed maximum arsenic sequestration at 35{degrees}C (total counts: 4.725x10). Sublancin production peaked at 30.8{degrees}C (129.72 mg/L) and significantly reduced soil microbial biomass carbon by 33% (p < 0.001), with selective suppression of Gram-positive bacteria (42%-28% survival reduction). Conjugation assays revealed sublancin bio-amendment dramatically suppressed horizontal ARG transfer, reducing HGT frequency by 74.7% (6.64 x 10-3 to 1.68 x 10-3, p < 0.001) through dual mechanisms: decreased donor viability and reduced conjugation efficiency. Gene ontology enrichment identified coordinated upregulation of exopolysaccharide synthesis (FDR ~1.0x10-{superscript 2}), phosphotransferase systems, and arsenic resistance pathways, alongside downregulation of conventional antibiotic resistance genes. These findings establish sublancin as a dual-function soil amendment simultaneously addressing two critical agricultural threats: heavy metal bioaccumulation and antibiotic resistance dissemination under climate warming.

microbiology↗

bioRxiv2025

Molecular Insights Into PGPR-Biochar-Mediated Arsenic Detoxification and Nutritional Enhancement in Rice Rhizospheres

Arsenic (As) contamination in paddy soils threatens rice productivity and food safety through enhanced As(III) mobility under anaerobic conditions. This study evaluated the synergistic effects of rice biochar (RBC) and plant growth-promoting rhizobacteria (PGPR) on arsenic bioavailability and rice physiological responses under controlled and field conditions. Rice straw biochar pyrolyzed at 400 {degrees}C exhibited high porosity and surface functionality, while Metabacillus indicus AMB4 demonstrated arsenic tolerance ([≤]3500 mg kg-1) and multiple PGPR traits (IAA: 45.2 g mL-1, phosphate solubilization index: 2.8, ACC deaminase: 18.7 nmol -ketobutyrate mg-1 h-1). Combined RBC+PGPR treatment reduced soil arsenic bioavailability by 85% (p<0.001) and plant arsenic accumulation by 78% compared to controls, while significantly enhancing antioxidant enzyme activities (CAT: 4.2-fold, SOD: 3.7-fold, APX: 3.1-fold increase). Metagenomics revealed restructured microbial communities with increased Proteobacteria abundance and upregulated arsenic detoxification genes (arsC, arsB, aioA) coupled with enhanced nutrient cycling pathways (nifH, phoD, soxA). Network analysis demonstrated functional integration between As-transformation and nutrient metabolism, with coordinated expression of 47 arsenic-responsive and 126 nutrient-cycling genes. Field trials confirmed superior plant performance with RBC+PGPR treatment yielding 56% more tillers and 73% more panicles than controls, while maintaining enhanced soil nutrient status. This integrated biochar-PGPR system provides a mechanistically robust approach for simultaneous arsenic remediation and crop productivity enhancement in contaminated rice ecosystems, demonstrating practical applicability for sustainable paddy agriculture.

microbiology↗

bioRxiv2025

Furrow tillage reduces soil carbon loss and enhances microbial metabolism

With increasing global carbon loss from agricultural fields, agricultural practices should be monitored with proper regulatory measures. To address three problems of minimising carbon loss, optimising soil fertility and enhancing soil microbiota together, this study has developed a new innovative "Furrow tillage" approach that affords a balance between conventional and conservative tillage. Based on two years of trials in rice fields at multiple sites, this practice has justifications from agronomy, geochemistry, crop physiology, and molecular microbiology. Furrow tillage illustrated low carbon loss, similar to no-tillage, while retaining high nutrient bioavailability, similar to deep tillage. Microbial diversity, molecular responses and metabolic activities showed that furrow tillage induced microbial interactions while allowing a better entrapment of carbon dioxide in the soil. The study used CO2 flux, spatial distribution, total and available elemental analysis, plant ultra-structural observations, microbial metagenomics, high-throughput sequencing and molecular modelling to establish an optimal soil-crop quality, microbial maintenance and reduce carbon loss through furrow tillage practice.

ecology↗

bioRxiv2024

Pathogenic fungus expresses effector proteins in combination with a symbiotic virus to behaviourally manipulate housefly hosts

Host manipulation by pathogens and parasites is a widespread phenomenon, but the molecular mechanisms are poorly understood. We investigated the summiting disease caused by the fungus Entomophthora muscae in houseflies, where infected flies climb to elevated positions and die, releasing infectious conidia. We performed dual-RNA sequencing of fly heads at different time points and identified candidate genes from both the host and the pathogen that may be involved in this summiting phenotype. Surprisingly, we also detected a high abundance of a novel positive sense single-stranded (+ss-RNA iflavirus in infected fly heads. We show that the virus load increases over time and shows signs of accumulation in fly heads and thoraces. We also reveal predicted interactions between fungal secreted proteins and insect host proteins related to neurological and immune functions, suggesting a possible role of these proteins in host manipulation. Furthermore, we find that E. muscae encodes a homologue of ecdysteroid UDP-glucosyltransferase (egt), a gene that has been implicated in host manipulation by other pathogens. Our study reveals a complex interplay between a fungus, a virus and a fly, and suggests that convergent evolution of egt for host manipulation mechanisms may occur in different pathogens.

evolutionary biology↗

bioRxiv2022

Novel Viroid-like RNAs Naturally Infect a Filamentous Fungus

Viroids have been found to naturally infect only plants, resulting in big losses for some crops, but whether viroids or viroid-like RNAs naturally infect non-plant hosts remains unknown. Here we report the existence of a set of exogenous, single-stranded circular RNAs, ranging in size between 157-450 nucleotides (nt), isolated from the fungus Botryosphaeria dothidea and nominated Botryosphaeria dothidea circular RNAs (BdcRNAs). BdcRNA(s) replicate autonomously in the nucleus via a rolling-circle replication mechanism following symmetric pathways with distribution patterns depending on strand polarity and species. BdcRNAs can modulate to different degrees specific biological traits (e.g., alter morphology, decrease growth rate, attenuate virulence, and increase or decrease tolerance to osmotic stress and oxidative stress) of the host fungus by regulating related metabolic pathways. Overall, BdcRNA(s) have genome characteristics similar to those of viroids and exhibit pathogenic effects on the fungal hosts. These novel viroid-like RNAs infecting fungi are proposed to be termed as mycoviroids. BdcRNA(s) may be regarded as additional inhabitants at the frontier of life in terms of genomic complexity, and represent a new class of acellular entities endowed with regulatory functions, and novel epigenomic carriers of biological information. Significance statementSeveral viroids have been transfected into unicellular and filamentous fungi to assess whether they can replicate, but no natural infections of fungi with viroid or viroid-like RNAs have been reported before. Here we describe a set of exogenous circular RNAs (cRNAs) in a phytopathogenic fungus. These cRNAs display molecular and biological features which might represent a new class of viroid-like cRNAs endowed with regulatory functions, and novel epigenomic carriers of biological information. This is the first report of infectious viroid-like RNAs (or exogenous small cRNAs) in a life kingdom (fungi) other than plants. We also present a subcellular analysis of cRNAs in a fungus for the first time and provide useful understanding in how cRNAs replicate, move, and are distributed in fungal cells.

microbiology↗

bioRxiv2020

Molecular origins of transcriptional heterogeneity in diazotrophic K. oxytoca

Phenotypic heterogeneity in clonal bacterial batch cultures is an important adaptive strategy to changing environments, including in diazotrophs with the unique capacity to convert di-nitrogen into bio-available ammonium. In diazotrophic Klebsiella oxytoca we simultaneously measured mRNA levels of key regulatory (glnK-amtB, nifLA) and structural (nifHDK) operons required for establishing nitrogen fixation, using dual molecule, single cell RNA-FISH. Through stochastic transcription models and mutual information analysis we revealed likely molecular origins for heterogeneity in nitrogenase expression. In wildtype and regulatory variant strains we inferred contributions from intrinsic and extrinsic noise, finding that nifHDK transcription is inherently bursty, but that noise propagation through signalling is also significant. The regulatory gene glnK had the highest discernible effect on nifHDK variance, while noise from factors outside of the regulatory pathway were negligible. Results provide evidence that heterogeneity is a fundamental property of this regulatory system, indicating potential constraints for engineering homogeneous nitrogenase expression.

microbiology↗

bioRxiv2019

Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7

Bacteriophage T7 infects Escherichia coli and evades the host defence system. The Ocr protein of T7 was shown to exist as a dimer mimicking DNA and to bind to host restriction enzymes, thus preventing the degradation of the viral genome by the host. Here we report that Ocr can also inhibit host transcription by directly binding to bacterial RNA polymerase (RNAP) and competing with the recruitment of RNAP by sigma factors. Using cryo electron microscopy, we determined the structures of Ocr bound to RNAP. The structures show that an Ocr dimer binds to RNAP in the cleft, where key regions of sigma bind and where DNA resides during transcription synthesis, thus providing a structural basis for the transcription inhibition. Our results reveal the versatility of Ocr in interfering with host systems and suggest possible strategies that could be exploited in adopting DNA mimicry as a basis for forming novel antibiotics.\n\nImpact statementDNA mimicry Ocr protein, a well-studied T7 phage protein that inhibits host restriction enzymes, can also inhibit host transcription through competing with sigma factors in binding to RNA polymerase.

biophysics↗