Biology subjects

Monard, C.

Publications and source records attributed to Monard, C..

5 recordsLinked to original sources

bioRxiv2026

T4-type phages diversity in wetland soils reveals their ubiquity and their likely host-dependent dynamics

Bacteriophages are abundant and diverse in soils, playing a major role in regulating bacterial communities and consequently affecting biogeochemical cycles. Such host-phage interactions may be influenced by fluctuations in soil moisture, as observed in wetlands soils which constitute a key feature of the ongoing climate change. Here, we investigated the spatial and temporal dynamics of both bacteria and T4-type bacteriophage community structures and diversities in soil of a freshwater wetland. Soil was sampled in three sites across a proximal soil transect presenting an increase moisture content at seven dates over an 18 months period with contrasted flooding periods. DNA was extracted and we applied amplicon sequencing of the bacterial 16S rRNA gene and viral g23 gene. Bacterial community composition varied across the proximal soil transect, with Methylomirabilia and Gammaproteobacteria being significantly enriched in the wettest site and comprising ASVs affiliated to methanotroph and denitrifying bacteria, respectively. We identified a large diversity of T4-type phages, among which a fraction was novel, while others were similar to phages previously sequenced from various biomes. These findings suggest that T4-type phages are capable of successfully colonizing diverse niches in the biosphere, contributing to their ubiquity and diversity. Viral community was however dominated by few vASVs, which were highly represented in one or two of the three studied sites supporting the Bank model. All together our results indicate that T4-type phages have broad host ranges and more likely follow bacterial population dynamics. The present study provides new insights into the role of phages in soil, highlighting their interactions with bacterial hosts involved in carbon and nitrogen cycles, interactions that are likely regulated by fluctuations in soil moisture, as observed in wetlands. HighlightsO_LIBoth bacterial and T4-type phages were structured across proximal sites C_LIO_LIBacterial 16S rRNA gene copy number was inversely correlated to the soil moisture C_LIO_LI26 viral ASVs did not cluster with reference sequences C_LIO_LIviral ASVs seem to be primarily controlled by host availability C_LIO_LISoil bacteria and phage diversities were significantly lower in the wettest site C_LI

ecology↗

bioRxiv2025

Hijacking host microPEP: pathogens modulate the microRNA-microPEP loop to promote infection

The partners of an ecological association tend to copy the biological system of their hosts. We hypothesized that microorganisms, particularly pathogens, have acquired the ability to express short peptides (pathoPEPs) homologous to host microPEPs (miPEPs) thus modulating the expression of the corresponding host microRNA (miRNA) and the function of miRNA-targeted genes. The pathosystem involving interactions between Brassica napus and its pathogen Plasmodiophora brassicae was studied. Using in silico analysis and ribosomal profiling, we identified three putative pathoPEPs produced by P. brassicae and their targeted plant miRNA genes. A link between the level of infection of B. napus by P. brassicae and the expression of pathoPEPs and their targeted miRNA genes was found, with the expression of the latter two being inversely related. Finally, we identified differential expression and translation of genes predicted to be targets of pathoPEP-regulated miRNAs. These genes, involved in auxin pathway, immune defense, root architecture or carbohydrate metabolism, are thought to enable P. brassicae, through its pathoPEPs, to hijack plants metabolic pathways (hormonal pathways, sugar synthesis, root morphology), thereby facilitating its invasion. Using computational in silico approaches, the involvement of miPEPs from plant pathogens as a host post-transcriptional regulatory pathway is described herein for the first time.

plant biology↗

bioRxiv2022

Plants release miRNAs in the rhizosphere, targeting microbial genes

Recently, small RNAs have been shown to play important roles in cross-kingdom communication, notably in plant-pathogen relationships. Plant miRNAs were even shown to regulate gene expression in the gut microbiota. But what impact do they have on the plant microbiota? Here we hypothesized that plant miRNAs can be found in the rhizosphere of plants, where they are taken up by rhizosphere bacteria, influencing their gene expression, thereby shaping the rhizosphere bacterial community. We found plant miRNAs in the rhizosphere of Arabidopsis thaliana and Brachypodium distachyon. These plant miRNAs were also found in rhizosphere bacteria, and fluorescent synthetic miRNAs were taken up by cultivated bacteria. A mixture of five plant miRNAs modulated the expression of more than a hundred genes in Variovorax paradoxus, whereas no effect was observed in Bacillus mycoides. Similarly, when V. paradoxus was grown in the rhizosphere of Arabidopsis that overexpressed a miRNA, it changed its gene expression profile. The rhizosphere bacterial communities of Arabidopsis mutants that were impaired in their miRNA or small RNA pathways differed from wildtype plants. Similarly, bacterial communities of Arabidopsis overexpressing specific miRNAs diverged from control plants. Finally, the growth and the abundance of specific ASVs of a simplified soil community were affected by exposure to a mixture of synthetic plant miRNAs. Taken together, our results support a paradigm shift in plant-bacteria interactions in the rhizosphere, adding miRNAs to the plant tools shaping microbial assembly.

plant biology↗

bioRxiv2019

Phenanthrene contamination and ploidy level influence the rhizosphere microbiome of Spartina

Spartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These evolutionary events have resulted in species with a heightened resilience to hydrocarbon contamination, which could make them an ideal model plant for the phytoremediation/reclamation of contaminated coastal ecosystems. However, it is still unknown if allopolyploidization events also resulted in differences in the plant rhizosphere-associated microbial communities, and if this could improve the plant phytoremediation potential. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene, a model tricyclic PAH. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene and ITS region were amplified and sequenced. Generally, both the presence of phenanthrene and the identity of the plant species had significant influences on the bacterial and fungal community structure, composition and diversity. In particular, the allopolyploid S. anglica, harbored a more diverse bacterial community in its rhizosphere, and relatively higher abundance of various bacterial and fungal taxa. Putative hydrocarbon degraders were significantly more abundant in the rhizosphere soil contaminated with phenanthrene, with the Nocardia genus being significantly more abundant in the rhizosphere of S. anglica. Overall our results are showing that the recent polyploidization events in the Spartina did influence the rhizosphere microbiome, both under normal and contaminated conditions, but more work will be necessary to confirm if these differences result in a higher phytoremediation potential.\n\nImportanceSalt marshes are at the forefront of coastal contamination events caused by marine oil spills. Microbes in these environments play a key role in the natural attenuation of these contamination events, often in association with plant roots. One such plant is the Spartina, which are widely distributed salt marsh plants. Intriguingly, some species of the Spartina show heightened resistance to contamination, which we hypothesized to be due to differences in their microbiota. This was indeed the case, with the most resistant Spartina also showing the most different microbiota. A better understanding of the relationships between the Spartina and their microbiota could improve the coastal oil spill clean-up strategies and provide green alternatives to more traditional physico-chemical approaches.

microbiology↗

bioRxiv2019

A core microbiota of the plant-earthworm interaction conserved across soils

Microorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively1. While effects of individual macroorganism on soil microbes are documented, no studies attempted to decipher how the mosaic of microhabitats built by multiple macroorganisms and their interaction determine the structure of microbial communities. Here we show a joint shaping of soil bacterial communities by these two macroorganisms, with a prevalent role of plants over earthworms. In a controlled microcosm experiment with three contrasted soils and meticulous microhabitat sampling, we found that the simultaneous presence of barley and endogeic earthworms resulted in non-additive effects on cast and rhizosphere bacterial communities. Using a source-sink approach derived from the meta-community theory2,3, we found specific cast and rhizosphere core microbiota4,5 of the plant-eartworm interaction, detected in all soils only when both macroorganisms are present. We also evidenced a core network of the plant-earthworm interaction, with cosmopolitan OTUs correlated both in cast and rhizosphere of all soils. Our study provides a new framework to explore aboveground-belowground interactions through the prism of microbial communities. This multiple-macroorganisms shaping of bacterial communities also affects fungi and archaea, while being strongly influenced by soil type. Further functional investigations are needed to understand how these core microbiota and core network contribute to the modulation of plant adaptive response to local abiotic and biotic conditions.

ecology↗