Biology subjects

Bonin, A.

Publications and source records attributed to Bonin, A..

5 recordsLinked to original sources

bioRxiv2024

Plants reverse the positive effect of nutrient addition on the drought resistance of soil multifunctionality

Increasing droughts threaten soil microbial communities and the multiple functions they control in agricultural soils. These soils are often fertilized with mineral nutrients, but it remains unclear how this fertilization may alter the capacity of soil multifunctionality (SMF) to be maintained under drought, and how plant-soil interactions shape these effects. In this study, we used a mountain grassland soil to test the interactive effect of mineral nutrient (Nitrogen and Phosphorous) addition and drought on SMF with and without plants (Lolium perenne) in a mesocosm experiment. We calculated SMF based on 8 microbial properties associated with the capacity of soil microbes to store carbon (C), nitrogen (N) and phosphorous (P) in their biomass, and to process these elements through organic matter depolymerization, mineralization, nitrification and denitrification processes. To investigate mechanisms underlying the SMF response we characterized the associated changes in soil stoichiometry and microbial community composition using 16S and 18S rRNA amplicon sequencing. Our results showed that fertilization decreased the SMF drought resistance when plants were present, but the opposite was observed in the unplanted mountain grassland soil. Our analysis suggested this was due to the interaction of plants, fertilization and drought in influencing four coupled properties related to high SMF: high soil moisture, low microbial C limitation, high bacterial diversity and low bacteria gram positive:gram negative ratio. Altogether, our results suggested that reducing the use of mineral fertilizer for plant production in mountain grassland could improve the ability of their soils to maintain their multifunctionality during drought period. Finally, our study clearly further demonstrated the importance of plant in the complex responses of SMF to global changes and showed that combining stoichiometric and microbial diversity assessment represents a powerful approach to disentangle the underlying mechanisms.

ecology↗

bioRxiv2023

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of their biodiversity. DNA metabarcoding is increasingly used to assess nematode biodiversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In-silico analyses have a great potential to assess key parameters of primers, including their taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in-silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, as amplified most of sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in-silico analyses provide new insights for the identification of most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

zoology↗

bioRxiv2020

Promising potential of high-throughput molecular phenotyping of freshwater fishes for environmental assessment

The recent democratization of high-throughput molecular phenotyping allows the rapid expansion of promising untargeted multi-dimensional approaches (e.g. epigenomics, transcriptomics, proteomics, metabolomics, ...). Indeed, these emerging omics tools, processed for ecologically relevant species, may present innovative perspectives for environmental assessments, that could provide early warning of eco(toxico)logical impairs. In a previous pilot study (Sotton et al., Chemosphere 2019), we explore by 1H NMR the bio-indicative potential of metabolomics analyses on the liver of 2 sentinel fish species (Perca fluviatilis and Lepomis gibbosus) collected in 8 water bodies of the peri-urban Paris area (France). In the present study, we further investigate on the same samples the great potential of high-throughput UHPLC-HRMS/MS analyses. We show that the LC-MS metabolome remarkably allows clear separation of individuals according to the species, but also according to their respective sampling lakes. Interestingly, similar variations of Perca and Lepomis metabolomes occur locally indicating that site-specific environmental constraints drive the metabolome variations beyond the obvious genetic differences between the two species, and seem to be influenced by the production of noxious metabolites by cyanobacterial blooms in certain lakes. Thus, the development of such reliable environmental metabolomics approaches is constituting an innovative bio-indicative tool for ecological stress assessment, such as toxigenic cyanobacterial blooms, and aim at being further follow up.

ecology↗

bioRxiv2018

Double-digest RAD-sequencing: do wet and dry protocol parameters impact biological results?

O_LINext-generation sequencing technologies have opened a new era of research in genomics. Among these, restriction enzyme-based techniques such as restriction-site associated DNA sequencing (RADseq) or double-digest RAD-sequencing (ddRADseq) are now widely used in many population genomics fields. From DNA sampling to SNP calling, both wet and dry protocols have been discussed in the literature to identify key parameters for an optimal loci reconstruction.\nC_LIO_LIThe impact of these parameters on downstream analyses and biological results drawn from RADseq or ddRADseq data has however not been fully explored yet. In this study, we tackled this issue by investigating the effects of ddRADseq laboratory (i.e. wet protocol) and bioinformatics (i.e. dry protocol) settings on loci reconstruction and inferred biological signal at two evolutionary scale using two systems: a complex of butterfly species (Coenonympha sp.) and populations of Common beech (Fagus sylvatica).\nC_LIO_LIResults suggest an impact of wet protocol parameters (DNA quantity, number of PCR cycles during library preparation) on the number of recovered reads and SNPs, the number of unique alleles and individual heterozygosity. We also found that bioinformatic settings (i.e. clustering and minimum coverage thresholds) impact loci reconstruction (e.g. number of loci, mean coverage) and SNP calling (e.g. number of SNPs, heterozygosity). We however do not detect an impact of parameter settings on three types of analysis performed with ddRADseq data: measure of genetic differentiation, estimation of individual admixture, and demographic inferences. In addition, our work demonstrates the high reproducibility and low rate of genotyping inconsistencies of the ddRADseq protocol.\nC_LIO_LIThus, our study highlights the impact of wet parameters on ddRADseq protocol with strong consequences on experimental success and biological conclusions. Dry parameters affects loci reconstruction and descriptive statistics but not biological conclusion for the two studied systems. Overall, this study illustrates, with others, the relevance of ddRADseq for population and evolutionary genomics at the inter- or intraspecific scales.\nC_LI

molecular biology↗

bioRxiv2017

Soil community assembly varies across body sizes in a tropical forest

The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.

ecology↗