Biology subjects

Moulin, L.

Publications and source records attributed to Moulin, L..

13 recordsLinked to original sources

bioRxiv2026

Drinking water treatment drastically modifies multi-kingdom water communities, but clinically relevant opportunistic bacterial pathogens persist

Controlling pathogenic microorganisms during water treatment processes is a major public health concern. However, the impact of different water sources and treatment processes on the drinking water microbiome and opportunistic bacterial pathogens remains poorly understood. Here, we report the analyses of two water systems: a river and groundwater source, and their corresponding treated waters, sampled bi-weekly for 6 months. Microbial communities were analysed through a metabarcoding and dPCR workflow coupling universal prokaryotic and eukaryotic primers with genus-targeting primers for Legionella and Pseudomonas to achieve a deep taxonomic resolution. We show that microbial communities in groundwater were more diverse than those in river water and that water treatment affected -diversity. Water treatment had a stronger influence on community composition than water system or seasonal variation. Despite lower bacterial loads, the relative abundance of Legionella, Pseudomonas, and non-tuberculous Mycobacteria (NTM) remained stable or even increased after water treatment, suggesting that conventional treatment processes promote enrichment of specific taxa. Excitingly, the genus-targeting analyses revealed a remarkable and previously uncharacterized diversity of Legionella species. L.pneumophila, pathogenic Pseudomonas clades and P. aeruginosa were detected in all environments, emphasizing their ability to adapt to diverse ecological conditions. Analysis of the eukaryotic fraction emphasized the persistence and emergence of eukaryotic hosts associated with these waterborne opportunistic pathogens. Our findings offer important insights into how water source characteristics and treatment processes influence the composition of the drinking water microbiome, while the high taxonomic resolution achieved for waterborne opportunistic bacterial pathogens underscores their ecological adaptability.

microbiology↗

bioRxiv2026

Lytic bacteriophages active in urine against multi-drug resistant clinically derived Klebsiella pneumoniae causing urinary tract infection

ObjectivesMultidrug-resistant (MDR) Klebsiella pneumoniae is an increasingly important cause of recurrent urinary tract infections (UTIs), particularly in high-risk patients such as those with neurogenic bladder, where therapeutic options are limited. Bacteriophage therapy represents a promising alternative, but pre-clinical models and characterization of phages active against UTI-derived strains remain scarce. We therefore aimed to isolate and characterize bacteriophages targeting a clinical MDR K. pneumoniae strain causing recurrent UTI and evaluate their activity under urinary conditions. MethodsThree bacteriophages were isolated from environmental samples using an ESBL-producing K. pneumoniae clinical isolate obtained from a neurogenic bladder patient. Phages were characterized by genome sequencing, electron microscopy, stability assays, one-step growth curves, and host-range analysis across 79 clinical UTI isolates. Phage activity was quantified in LB medium and human urine using bacterial growth kinetics and a lytic activity score. ResultsThree lytic phages from the former siphoviridae family (EDIRA083, EDIRA088, and EDIRA092) belonging to distinct genera were identified. Genomic analysis confirmed the absence of lysogeny-associated, virulence, or antibiotic-resistance genes. Latent periods ranged from 8 to 40 minutes and burst sizes from 38 to 170 virions per infected bacterium. Host-range analysis revealed narrow activity for EDIRA083 and EDIRA088, whereas EDIRA092 infected 29% of the 79 clinical isolates tested. In liquid phage infection assays, overall lytic activity was consistently higher and more sustained in human urine than in LB, suggesting reduced fitness of resistant mutants under urinary conditions. ConclusionsThese results identify three genetically distinct lytic phages targeting MDR K. pneumoniae and highlight the importance of testing phage activity under infection-relevant conditions. Their activity in urine supports further evaluation of these phages as candidates for therapeutic development against MDR Klebsiella UTI.

microbiology↗

bioRxiv2025

Re-evaluation of the nodulation capacity of Sphingomonas sediminicola DSM 18106T indicates that this strain is not capable of inducing root nodule formation on Pisum sativum (pea)

Rhizobia are soil-dwelling proteobacteria that can enter into symbiotic nitrogen-fixing relationships with compatible leguminous plants. Taxonomically, rhizobia are divided into alpha-rhizobia, which belong to the class Alpharoteobacteria, and beta-rhizobia, which belong to the class Betaproteobacteria. To date, all bona fide alpha-rhizobia belong to the order Hyphomicrobiales. However, a recent study suggested that Sphingomonas sediminicola DSM 18106T is also a rhizobium and is capable of nodulating pea plants (Pisum sativum), which would expand the known taxonomic distribution of alpha-rhizobia to include the order Sphingomonadales. Here, we attempted to replicate the results of that previous study. Resequencing and computational analysis of the genome of S. sediminicola DSM 18106T failed to identify genes encoding proteins involved in legume nodulation or nitrogen fixation. In addition, experimental plant assays indicated that S. sediminicola DSM 18106T is unable to nodulate the two cultivars of pea tested in our study, unlike the rhizobium Rhizobium johnstonii 3841T. Taken together, and in contrast to the previous study, these results suggest that S. sediminicola DSM 18106T is not capable of inducing root nodule formation on pea, meaning that the taxonomic distribution of all known alpha-rhizobia remains limited to the class Hyphomicrobiales.

microbiology↗

bioRxiv2024

Analysis of the potential of environmental Burkholderia sensu lato isolates to cause infection in a zebrafish embryo model

Burkholderia sensu lato (s.l.) regroups several genera of closely related bacterial species with remarkable diversity in metabolic features. They can be free-living or have mutualistic or pathogenic interactions with different host organisms, including insects, plants and animals. Burkholderia s.l. species display numerous characteristics that can be beneficial for agronomical and biotechnological applications, including promotion of plant growth and bioremediation; however, many of the species are known human pathogens. Several recent taxonomical reclassifications of the Burkholderia genus resulted in its separation into 7 distinct genera. Burkholderia sensu stricto (s.s.), which includes the Burkholderia cepacia complex and the pseudomallei group, regroups most of the species that have been shown to cause infection in humans and plants. Little is known about the pathogenic potential of species belonging to the other 6 genera; however there have been occasional reports of human infections. Here, the vertebrate zebrafish embryo was used to analyse the behaviour of a panel of environmental isolates belonging to different species of the Burkholderia cepacia complex (5), Paraburkholderia (5) and Caballeronia (1). Burkholderia cepacia P14-NS, Burkholderia orbicola P21-NS, and Paraburkholderia sp. ABIP659 (closest to P. tropica, and further named tropica-like) each caused a low percentage (2%) of embryo mortality. While the other strains had not killed the embryos during the 4-day time span of the experiments, overall, Paraburkholderia and Burkholderia s.s. strains persisted equally well in this vertebrate host. Unexpectedly, P. tropica-like showed the highest increase in bacterial burden during infection, and induced the strongest pro-inflammatory response, including abscess formation, and poor prognosis at the endpoint of the experiment. Our study emphasizes that in vivo infection studies are needed to gain more insight into potential pathogenicity of the different Burkholderia s.l. species.

microbiology↗

bioRxiv2023

Culturable approach to rice-root associated bacteria in Burkina Faso: diversity, plant growth-promoting rhizobacteria properties and cross-comparison with metabarcoding data.

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity so as, to be able to assess the diversity of the collection based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected working collection isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the functional description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

microbiology↗

bioRxiv2022

Quantification of the diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media, using 16S amplicon barcoding

Culturing bacteria from plant material is well known to introduce a strong bias compared to the real diversity present in the original samples. This bias is related to cultivability of bacteria, the chemical composition of media and culture conditions. The bias of recovery is often observed but was never quantified on different media using an amplicon barcoding approach comparing plant microbiota DNA extractions versus DNA extracted from serial dilutions of the same plant tissues grown on bacterial culture media. In this study, we i) quantified the culturing diversity bias using 16S amplicon barcode sequencing by comparing a culture-dependent approach (CDA) on rice roots on four popular bacterial media (Tryptone Soybean Agar-TSA-at two concentrations, 10% and 50%; a plant-based media with rice flour; Norris Glucose Nitrogen Free Medium-NGN; and Nitrogen Free -NFb) versus a culture-independent approach (CIA) assessed from DNA extracted directly on root and rhizosphere samples; ii) assessed enriched and missing taxa detected on the different media; iii) use biostatistics functional predictions to predict which metabolic profiles are enriched in the CDA and CIA. A comparative analysis of the two approaches revealed that among the 22 phyla present in the microbiota of the studied rice root samples, only five were present on the culture media approach (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia). The Proteobacteria phylum was the most abundant in all cultured media samples, showing a high enrichment of gamma-Proteobacteria. The diversity of the combined culture media represented about 1/3 of the diversity of the total microbiota, and its genus diversity and frequency was documented. The functional prediction tool (PiCrust2) detected an enrichment of nitrogenase enzyme in bacterial taxa sampled from Nitrogen-free media, validating its predictive capacity. Further functional predictions also showed that the CDA missed mostly anaerobic, methylotrophic, methanotrophic and photosynthetic bacteria compared to the culture independent approach, delivering valuable insights to design ad-hoc culture media and conditions to increase cultivability of the rice-associated microbiota.

microbiology↗

bioRxiv2022

Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species

Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.

microbiology↗

bioRxiv2022

Differential genetic strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for root colonization of Oryza sativa ssp. japonica and ssp. indica, as revealed by Tn-seq

Burkholderia vietnamiensis LMG10929 (Bv) and Paraburkholderia kururiensis M130 (Pk) are bacterial rice growth-promoting models. Besides this common ecological niche, species of the Burkholderia genus are also found as opportunistic human pathogens while Paraburkholderia are mostly environmental and plant-associated species. Here, we compared the genetic strategies used by Bv and Pk to colonize two subspecies of their common host, Oryza sativa ssp. japonica (cv. Nipponbare) and ssp. indica (cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes in Bv involved in rice roots colonization compared to Pk, including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towards Bv compared to Pk. For both strains, the bacterial fitness depends on a higher number of genes when colonizing indica rice compared to japonica. These divergences in host pressure on bacterial adaptation could be partly linked to the cultivars differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production in Bv and quorum sensing in Pk. The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays. ImportanceBurkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. However, the closely related Burkholderia genus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits in Burkholderia vietnamiensis and Paraburkholderia kururiensis that contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.

microbiology↗

bioRxiv2022

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

As a consequence of its potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmers fields from irrigated and rainfed lowlands in western Burkina Faso, using an amplicon metabarcoding approach 16S (Prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure according to the root compartment (root vs. rhizosphere) and geographical zones, we show that the rice production system is a major driver of microbiome structure, both for prokaryotes and fungi. In irrigated systems, we found a higher diversity of prokaryotic communities from rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands. Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae and Bradyrhizobiaceae families in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, phylotypes assigned to putative phytobeneficial and pathogen species were found. Mycorrhizal fungi Glomeromycetes abundance was higher in rainfed lowlands. Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for potential microbial engineering applications.

microbiology↗

bioRxiv2021

First evidence of SARS-CoV-2 genome detection in zebra mussel (Dreissena polymorpha).

The uses of bivalve molluscs in environmental biomonitoring have recently gained momentum due to their ability to indicate and concentrate human pathogenic microorganisms. In the context of the health crisis caused by the COVID-19 epidemic, the objective of this study was to determine if the SARS-CoV-2 ribonucleic acid genome can be detected in zebra mussels (Dreissena polymorpha) exposed to raw and treated urban wastewaters from two separate plants to support its interest as bioindicator of the SARS-CoV-2 genome contamination in water. The zebra mussels were exposed to treated wastewater through caging at the outlet of two plants located in France, as well as to raw wastewater at laboratory scale in controlled conditions. Within their digestive tissues, our results showed that SARS-CoV-2 genome was detected in zebra mussels, whether in raw and treated wastewaters. Moreover, the detection of the SARS-CoV-2 genome in such bivalve molluscans appeared even with low concentrations in raw wastewaters. This is the first detection of the SARS-CoV-2 genome in the tissues of a sentinel species exposed to raw and treated urban wastewaters. Despite the need for development for quantitative approaches, these results support the importance of such invertebrate organisms, especially zebra mussel, for the active surveillance of pathogenic microorganisms and their indicators in environmental waters. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/446136v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@781087org.highwire.dtl.DTLVardef@853128org.highwire.dtl.DTLVardef@5e667forg.highwire.dtl.DTLVardef@19b243e_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2019

Influence of plant genotype and soil on the wheat rhizosphere microbiome: identification of a core microbiome across eight African and European soils

Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our dataset. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/777383v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@dd56a6org.highwire.dtl.DTLVardef@163b5f7org.highwire.dtl.DTLVardef@13f6bd7org.highwire.dtl.DTLVardef@c10d9d_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2018

A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses

SUMMARYO_LISome Aeschynomene legume species have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes. Knowledge of this unique Nod (factor)-independent symbiosis has been gained from the model A. evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod-dependent process.\nC_LIO_LITo fill this gap, this study significantly broadened previous taxon sampling, including in allied genera, to construct a comprehensive phylogeny. This backbone tree was matched with data on chromosome number, genome size, low-copy nuclear genes and strengthened by nodulation tests and a comparison of the diploid species.\nC_LIO_LIThe phylogeny delineated five main lineages that all contained diploid species while polyploid groups were clustered in a polytomy and were found to originate from a single paleo-allopolyploid event. In addition, new nodulation behaviours were revealed and Nod-dependent diploid species were shown to be tractable.\nC_LIO_LIThe extended knowledge of the genetics and biology of the different lineages in the legume genus Aeschynomene provides a solid research framework. Notably, it enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.\nC_LI

plant biology↗

bioRxiv2018

Parallels between experimental and natural evolution of legume symbionts

The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. We compared the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time-span, environment, genetic background and phenotypic achievement, both processes resulted in rapid diversification dominated by purifying selection concomitant with acquisition of positively selected mutations. The latter were lacking in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation targeted the same set of genes leading to the cooption of the same quorum-sensing system. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis.

evolutionary biology↗