Biology subjects

Babin, D.

Publications and source records attributed to Babin, D..

4 recordsLinked to original sources

bioRxiv2026

Assembly of plant holobionts is governed by nematode communities and their associated microbiota, conditioned by preceding plants

Plants form holobionts by associating with diverse microbiota. Self-organization gives rise to emergent properties of the holobiont, such as increased resistance to pathogens. However, the local factors contributing to the self-organization are not well understood. We hypothesized that nematode communities and their associated microbiota govern the rhizobiome of the model plant holobiont tomato in terms of its suppression of root invasion by the parasite Meloidogyne hapla, and that the soil legacy influences the suppressive potential mediated by these biota. In pot experiments, a resistant tomato holobiont was favored by assembly in the presence of a nematode community conditioned by tomato plants, compared to oilseed rape or fallow soil. Nematode communities conditioned by tagetes could enhance resistance even better than tomato. Microbiota from crushed tomato-conditioned nematode communities increased resistance of the tomato holobiont, compared to microbiota of nematode communities conditioned by maize, or heat-inactivated microbiota. The 0.2 {micro}m-filtered microbiota from crushed nematodes had the same effect, suggesting a role of nematode-associated bacteriophages in holobiont assembly. The results indicate that soil nematodes and their associated microbiota play a role in the local organization and stabilization of plant holobionts. They can influence the resistance of plants that subsequently grow in the same soil. From an applied perspective, crop rotation schemes that alter nematode-microbiota communities could be harnessed to engineer crop holobionts. SUMMARY STATEMENTDepending on plant-specific soil legacies, nematode communities and their associated phages govern holobiont assembly leading to increased resistance against pathogen invasion.

ecology↗

bioRxiv2026

Genome-resolved metagenomics reveals the potential for selection for antibiotic resistance due to metal pollution in soil microbial communities near a copper-nickel mine site in Botswana

Waste mismanagement and metal pollution are high in countries in the global south and often create challenging, extreme conditions for soil microbial communities, which might lead to selection for antibiotic resistance. However, soils from polluted sites in Sub-Saharan areas are rarely sampled. Thus, it remains unclear whether the potential for dissemination of antibiotic resistance exists in these areas. In the present study, we performed genome-resolved metagenomics on samples across a gradient around an area impacted by a copper-nickel mine in Botswana to identify the potential for co-selection for antibiotic resistance due to mine pollution. Specifically, we sampled over a gradient across a mine area in Botswana and performed genome-resolved metagenomics. In general, pollution increased with proximity to the mine, while prokaryotic diversity increased with increasing distance from the mine, and we could identify a few taxa that significantly correlated with the metal concentrations. Moreover, our assembled contigs indicate a potential for co-selection due to the dual function of these genes as both antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), as they act as multidrug efflux pumps. In contrast, some ARGs co-occurred in the same region as MRGs, indicating the potential for co-selection due to co-localization. However, we could not detect any co-localization of ARGs/MRGs with horizontal gene transfer (HGT) markers at the contig level. We binned the contigs to MAGs, and we found several MAGs of high quality and completeness, belonging to taxa such as Actinobacteriota, Chloroflexota, Acidobacteriota, and Dormibacterota, that possess ARGs, MRGs, and HGT-markers. Moreover, we found ARGs, MRGs, and HGT-markers in eight MAGs, after binning, indicating no direct association of HGT-markers with ARG and MRG occurrence. In summary, our metagenomic analysis indicates that pollution in mines can lead to co-selection of AMR, specifically ARGs with a broad spectrum of substrates (e.g., efflux pumps) that can act as MRGs, in an under-sampled location such as Sub-Saharan countries. IMPORTANCEThis study indicates the potential role of metal pollution from mismanaged mining activities in facilitating the selection for antibiotic resistance in soil microbial communities in a Sub-Saharan area located in Botswana. In combination with the lower amount of health regulations and hygiene standards, the dissemination of antibiotic resistance poses risks to human health through the environment in many Sub-Saharan countries. By performing genome-resolved metagenomics and identifying antibiotic resistance genes (ARGs) as metal resistance genes (MRGs) across diverse assembled genomes or co-localization, this work highlights the potential for antimicrobial resistance dissemination due to mine activities. Thus, these findings underscore the urgent need to understand the potential side effects of mine pollution on the spread of antimicrobial-resistant bacteria (ARB) and associated ARGs in Sub-Saharan countries.

microbiology↗

bioRxiv2025

Novel insights into the genome organization of Rhizobiaceae: identification of linear plasmids

2.Members of the family Rhizobiaceae typically have multipartite genomes, that are split between two or more replicons, including the chromosome and a variable number of extrachromosomal replicons (chromids and plasmids). Nearly all Rhizobiaceae replicons sequenced and described to date have a circular topology, with the exception of the linear chromid found in the genomes of most Agrobacterium spp. In this study, genomes of five nonpathogenic Agrobacterium strains and one plant tumorigenic Allorhizobium strain were fully sequenced. Surprisingly, genome analysis revealed that these six strains each carry an 80-kbp linear plasmid. Linear plasmids were so far not identified in this bacterial family or other bacteria within the class Alphaproteobacteria. The ends of all six plasmids identified in this study have a hairpin structure with covalently closed ends. The plasmid sequences showed a high degree of homology, clearly indicating their common ancestry. Database searches led to the identification of additional linear plasmids in previously published Rhizobiaceae genome assemblies that were not previously recognized to have linear plasmids, suggesting that these replicons may be more widespread. Most likely, linear plasmids may be even more widely distributed than anticipated. Although the biological functions of the linear plasmids identified in this study remain unknown, they are associated with both nonpathogenic and plant tumorigenic Rhizobiaceae strains. 3. Impact statementThe family Rhizobiaceae includes some remarkable and important representatives, such as plant symbiotic bacteria (rhizobia) and plant pathogenic bacteria associated with neoplasia (agrobacteria). In this study, the complete genome sequences of six Rhizobiaceae strains were generated and their genome organizations were examined. Strikingly, our results showed that these six strains harbor a linear plasmid. Moreover, GenBank searches suggested that linear plasmids may be even more widespread in the family Rhizobiaceae. Linear plasmids may go undetected in genome sequencing studies if the assemblies are not specifically examined for linear plasmid. Overall, this study provides further evidence for the extraordinary genome plasticity of members of the family Rhizobiaceae and expands the taxonomic range in which linear plasmids have been identified. To the best of our knowledge, this is the first report of linear plasmids in the family Rhizobiaceae or the class Alphaproteobacteria. 4. Data summaryThe whole-genome sequences have been deposited at DDBJ/ENA/GenBank under the accessions CP192696-CP192701 (Av2), CP000000-CP000000 (rho-7.1), CP000000-CP000000 (rho-8.1), CP000000-CP000000 (rho-11.1), CP000000-CP000000 (rho-13.3), and CP000000-CP000000 (rho-14.1), within the BioProjects PRJNA557463 and PRJNA1009994. The raw sequencing reads were deposited in the Sequence Read Archive (SRA) under the same BioProjects PRJNA557463 and PRJNA1009994: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA557463 and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1009994. NCBI submission for five genome sequences is undergoing processing and accession numbers will be added when available; in https://figshare.com/s/29a9e621adc1b66d0957

genomics↗

bioRxiv2022

Large scale in vivo acquisition, segmentation and 3D reconstruction of cortical vasculature using functional ultrasound imaging.

The brain is composed of a dense and ramified vascular network comprising various sizes of arteries, veins, and capillaries. One way to assess the risk of cerebrovascular pathologies is to use computational models to predict the physiological effects of a reduction of blood supply and correlate these responses with observations of brain damage. Therefore, it is crucial to establish a detailed 3D organization of the brain vasculature, which could be used to develop more accurate in silico models. For this purpose, we have adapted our open-access functional ultrasound imaging platform previously designed for recording brain-wide activity that is now capable of fast and reproducible acquisition, segmentation, and reconstruction of the cortical vasculature. For the first time, it allows us to digitize the cortical vasculature in awake rodents with a [~]100 {micro}m3 spatial resolution. Contrary to most available strategies, our approach can be performed in vivo within minutes. Moreover, it is easy to implement since it neither requires exogenous contrast agents nor long post-processing time. Hence, we performed a cortex-wide reconstruction of the vasculature and its quantitative analysis, including i) classification of descending arteries versus ascending veins in more than 1500 vessels/animal, ii) quick estimation of their length. Importantly, we confirmed the relevance of our approach in a model of cortical stroke, which enables quick visualization of the ischemic lesion. This development contributes to extending the capabilities of ultrasound neuroimaging to understand better cerebrovascular pathologies such as stroke, vascular cognitive impairment, and brain tumors and is highly scalable for the clinic.

neuroscience↗