isabelle domaizon | National Institute of Agricultural Research (INRA) (original) (raw)

Papers by isabelle domaizon

Molecular Ecology Resources, 2021

Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered ... more Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments faster. In freshwater ecosystems, aquatic biofilms were used to catch eDNA from macroinvertebrates. Here, we test the capacity of aquatic biofilms to entrap fish eDNA in a large lake and, therefore, the possibility to perform fish eDNA metabarcoding from this matrix compared to the traditional fish eDNA approach from filtered water samples. Methodological aspects of the use of aquatic biofilms for fish eDNA metabarcoding (e.g. PCR replicates, biological replicates, bioinformatics pipeline, reference database and taxonomic assignment) were validated against a mock community. When using biofilms from habitats sheltered from wind and waves, ...

Scientific Reports

Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and b... more Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate ...

Journal of Aquaculture Research & Development, 2016

Environmental Microbiology Reports, 2015

second lake where deeper water layers exhibited only short periods of complete anoxia and constan... more second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.

The ISME Journal, 2012

It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges wide... more It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/ fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (Pp0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH 4 þ-availability that exist in the field.

Metabarcoding and Metagenomics, 2021

Methods for biomonitoring of freshwater phytoplankton are evolving rapidly with eDNA-based method... more Methods for biomonitoring of freshwater phytoplankton are evolving rapidly with eDNA-based methods, offering great complementarity with microscopy. Metabarcoding approaches have been more commonly used over the last years, with a continuous increase in the amount of data generated. Depending on the researchers and the way they assigned barcodes to species (bioinformatic pipelines and molecular reference databases), the taxonomic assignment obtained for HTS DNA reads might vary. This is also true for traditional taxonomic studies by microscopy with regular adjustments of the classification and taxonomy. For those reasons (leading to non-homogeneous taxonomies), gap-analyses and comparisons between studies become even more challenging and the curation processes to find potential consensus names are time-consuming. Here, we present a web-based application (Phytool), developed with ShinyApp (Rstudio), that aims to make the harmonisation of taxonomy easier and in a more efficient way, us...

Microorganisms

On the annual and interannual scales, lake microbial communities are known to be heavily influenc... more On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes—where the oldest DNA samples are dated to only a few hundred years...

This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP56... more This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, Activity A.T1.3, Deliverable D.T1.3.2 – 1, https://www.alpine-space.eu/projects/eco-alpswater/en/home

This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP56... more This protocol has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, Activity A.T1.3, Deliverable D.T1.3.2 – 2, https://www.alpine-space.eu/projects/eco-alpswater/en/home

These data supplement the article "Avoiding quantification bias in metabarcoding: applicatio... more These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal The directory contains the following files: 15 fastq files raw reads (5 mock communities, 3 replicates).rar - contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments). 15 fastq files information.xlsx : - contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq fil...

Marine and Freshwater Research

Planktonic communities from Juan de Nova lagoon were submitted to a single exposure of diuron or ... more Planktonic communities from Juan de Nova lagoon were submitted to a single exposure of diuron or naphthalene in triplicate outdoor 40-L mesocosms for 5 days. The study followed the temporal changes of the assemblages by determining abundances and taxonomic level of microbial (heterotrophic prokaryotes, picocyanobacteria, heterotrophic protists and phytoplankton) and metazooplankton communities. Exposure to both contaminants did not result in significant changes in phytoplankton abundances. Microscopic identification demonstrated the dominance of Bacillariophyta (mostly Chaetoceros tenuissimus) accounting for more than 95% of the microalgae detected in all mesocosms. Using 18S rRNA metabarcoding, temporal changes in the proportion of eukaryotic operational taxonomic units (OTUs) were highlighted for most taxonomic groups. Diuron had no significant effect on the abundance of eukaryotic picoheterotrophs, ciliates, whereas naphthalene had a significant positive effect on heterotrophic prokaryotes. Metazooplankton was not significantly modified under contaminant exposure, except for copepods nauplii in presence of diuron. Multivariate analysis indicated significant responses of communities linked to the experimental time and conditions. The analysis also revealed a modification of the trophic relationships among communities over time, from a dominant multivorous food web after 48 h towards a reduced microbial loop after 120 h of experiment time.

En guise d'introduction Ce qu'il faut retenir pour l'année 2011 Stratégie d'échantillonnage et Ta... more En guise d'introduction Ce qu'il faut retenir pour l'année 2011 Stratégie d'échantillonnage et Tableau de bord M é t é o r o l o g i e 2 E t u d e d e s a p p o r t s p a r l e s r i v i è r e s 2 Etudes portant sur la physico-chimie Etude relative à la chlorophylle a et la production primaire Etude relative au phytoplancton Etude portant sur les données fournies par la sonde bbe et P. rubescens Etudes portant sur les picocyanobactéries Etude relative au zooplancton 110 Etude pootant sur la ressource piscicole 118 Etude portant sur la qualité sanitaire 151 Indices 157 Conclusion 161 Bibliographie 165 Dossiers divers 173 L'année 2011 a été marquée par une forte hausse des concentrations en Ptot dans la Leysse et le Sierroz (+71 et +92%). Entre 2008 et 2011, les concentrations en Ptot ont été multipliées par 4 dans la Leysse et par 2 dans le Sierroz. Elles restent encore inférieures à 2004 pour la Leysse mais ont été quasiment atteintes sur le Sierroz. Avec une légère hausse des concentrations en PO 4 sur la Leysse (+16%). Cette hausse met fin à 6 années de baisse. Les concentrations mesurées dans le Sierroz sont égales à celles de 2010 et conforment aux résultats obtenus depuis 2008. L'évolution des éléments azotés a été plus contrastée. Ainsi NO 3 a présenté des concentrations plus élevées dans le Sierroz que dans la Leysse. Entre 2004 et 2008, celles-ci étaient en diminution sur les deux cours d'eau (40 % sur le Sierroz et 36% sur la Leysse). Les années 2009 et 2010 ont été marquées par une augmentation des concentrations en NO 3 : 22% sur la Leysse et 35% sur le Sierroz, des valeurs comparables aux années 2005-2006. En 2011, le Sierroz présente des concentrations en matières azotées plus élevées que dans la Leysse. L'année 2011 présente des concentrations moyennes pondérées en nitrates à nouveau en baisse par rapport aux deux dernières années. Les concentrations en NKT et NH 4 sont en forte hausse en 2011 (multipliée par 2 dans la Leysse).

L'etude a pour objectif de decrire les differentes techniques relevant de la microbiologie mo... more L'etude a pour objectif de decrire les differentes techniques relevant de la microbiologie moleculaire en termes d'etat d'avancement, de limites techniques et de sensibilite pour etudier l'abondance, la diversite, l'activite et les potentialites fonctionnelles des communautes microbiennes indigenes de diverses matrices environnementales (eau, sol, air, substrats dechets). On trouve dans l'etude neuf fiches de presentation des methodes, puis vingt-neuf fiches d'application sur les milieux/substrats eau, sol, air et dechets. Des indicateurs de microbiologie moleculaire permettant un diagnostic environnemental ont ete recherches. Une trentaine d'entreprise qui les propose en routine sont donnees dans le rapport. Ces indicateurs microbiens sont operationnels pour des prestations de diagnostic de la qualite de differentes matrices environnementales par differents types d'operateurs (agriculteurs, industriels, gestionnaires de dechets, amenageurs du ter...

Microscopiques, les parasites sont la plupart du temps invisibles, mais presents partout. Ils inf... more Microscopiques, les parasites sont la plupart du temps invisibles, mais presents partout. Ils infectent tous les organismes du monde vivant. La derniere decennie a revele une incroyable diversite chez les parasites viraux, bacteriens et eucaryotes. Ceux infectant le phytoplancton pourraient avoir une importance capitale dans la dynamique des populations algales et dans le fonctionnement des ecosystemes aquatiques, mais leur role est encore tres largement meconnu a ce jour (Brussaard, 2004). Sur ces questions, la recherche ne fait que commencer.