Biology subjects

Gaudriault, S.

Publications and source records attributed to Gaudriault, S..

4 recordsLinked to original sources

bioRxiv2025

Priority effects drive fungal and nematode emergence from insect larvae

Priority effects, in which species arrival history influences community assembly, are increasingly recognized to affect host-parasite systems. However, priority effects across disparate groups of parasitic organisms are poorly understood despite the wide range of taxonomic groups involved. In California oak woodland, we investigated how priority effects between two insect-parasitic fungi (Metarhizium and Beauveria) influenced emergence of nematodes from insect larvae. Field and laboratory results indicated that both fungi were common, but priority effects prevented them from co-emerging from the same larva. Metarhizium- and Beauveria-infected insects did not differ in the species composition of emerging nematodes, but larvae without fungal emergence had distinct nematode communities, with Oscheius almost always emerging without fungi. Experiments indicated that none of the commonly found nematodes (Acrobeloides, Mesorhabditis, Oscheius, and Rhabditis) were entomopathogenic, but that Oscheius could exclude Beauveria if arrived early. This time-dependent exclusion was likely caused by an Ochrobactrum bacterium that Oscheius nematodes carried. Together, these findings suggest that fungi enter insects as primary arrivers, while nematodes come as secondary arrivers to exploit fungus-killed insects, with priority effects influencing both groups. We suggest that this system is a promising natural microcosm for understanding priority effects across disparate groups in host-parasite systems.

ecology↗

bioRxiv2025

Nested PCR to optimize rpoB metabarcoding for low-concentration and host-associated bacterial DNA

BackgroundHousekeeping genes have proved effective taxonomic markers for characterizing bacterial microbiota in short-read amplicon metabarcoding studies. A region of the rpoB gene, in particular, has been shown to minimize OTU overestimation bias with a high degree of accuracy, providing better species-level taxonomic resolution (Ogier et al. BMC Microbiol. 19:171). However, the primers for rpoB are highly degenerate, leading to potential problems in the amplification of bacterial DNA present at low concentration in the sample or embedded within eukaryotic matrices, as for the host-associated microbiota. We addressed these limitations by using a two-step PCR approach to optimize the rpoB procedure. The first PCR amplifies a 906-nucleotide region of the rpoB gene with the classical primers, referred to here as outer primers, and the second PCR then uses primers incorporating Illumina adapters, referred to here as inner primers, to amplify a 435-nucleotide subregion, the taxonomic marker for metabarcoding. ResultsWe first used in silico approaches to evaluate the universality of the outer and inner rpoB primers. We then tested the nested rpoB PCR method on commercial mock samples of known composition. The nested PCR approach increased amplification efficiency for dilute samples without biasing the bacterial composition of the mock sample revealed by metabarcoding relative to single-step PCR. We also tested the nested rpoB PCR method on field-collected samples of the lepidopteran Spodoptera frugiperda. The nested PCR outperformed single-step PCR, increasing amplification efficiency for bacterial DNA present at low concentrations (oral secretions from S. frugiperda) or embedded in eukaryotic DNA matrices (S. frugiperda larvae). ConclusionsThis method provides a promising new strategy for characterizing insect-associated microbiota that can also be applied to other host microbiomes.

microbiology↗

bioRxiv2019

rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

BackgroundMicrobiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3V4 hypervariable region of the 16S rRNA gene.\n\nResultsWe first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3V4. We applied both primers to infective juveniles of the nematode Steinernema glaseri. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium Xenorhabdus poinarii.\n\nConclusionsOur results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene.

microbiology↗

bioRxiv2018

Changes in rearing conditions rapidly modify gut microbiota structure in Tenebrio molitor larvae

The gut microbiota of multicellular organisms has been shown to play a key role in their host biology. In mammals, it has an invariant component, responsible for establishing a mutualistic relationship with the host. It also contains a dynamic fraction which facilitates adaptation in response to changes in the environment. These features have been well described in mammals, but little is known about microbiota stability or plasticity in insects. We assessed changes in microbiota composition and structure in a reared insect after a change in rearing conditions. We reared Tenebrio molitor (Coleoptera, Tenebrioninae) larvae for five days in soil samples from two river banks and analyzed their gut microbial communities by a metabarcoding technique, using the V3-V4 region of the 16S rRNA gene and the housekeeping gene gyrB. We found that soil-reared insects had a significantly more diverse microbiota than the control insects and that insects reared in soil from different sites had significantly different microbiota. We confirmed this trend by absolute quantification of the two mains fluctuating taxonomic groups: the Enterobacteriaceae family and the Pseudomonas genus, dominant in the soil-reared insects and in the control insects, respectively. Our results suggest the existence of a resident microbiota in T. molitor gut, but indicate that rearing changes can induce rapid and profound changes in the relative abundance of some of the members of this resident microbiota.

microbiology↗