Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared to clustering-based methods, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. We compared the respective influences of two widely used methods, namely DADA2 (a denoising method) vs. Mothur (a clustering method) on 16S rRNA gene amplicon datasets (hypervariable region v4), and compared such effects to the rarefaction of the community table and OTU identity threshold (97% vs. 99%) on the ecological signals detected. We used a dataset comprising freshwater invertebrate (three Unionidae species) gut and environmental (sediment, seston) communities sampled in six rivers in the southeastern USA. We ranked the respective effects of each methodological choice on alpha and beta diversity, and taxonomic composition. The choice of the pipeline significantly influenced alpha and beta diversities and changed the ecological signal detected, especially on presence/absence indices such as the richness index and unweighted Unifrac. Interestingly, the discrepancy between OTU and ASV-based diversity metrics could be attenuated by the use of rarefaction. The identification of major classes and genera also revealed significant discrepancies across pipelines. Compared to the pipeline’s effect, OTU threshold and rarefaction had a minimal impact on all measurements

Gut microbiomes of freshwater mussels (Unionidae) are taxonomically and phylogenetically variable across years but remain functionally stable

Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from the same river in 2016 and 2019. We examined the taxonomic, phylogenetic, and inferred functional (from 16S rRNA sequences) facets of their microbiome diversity. Significant differences between the two years were identified in five of the six species sampled. However, not all species that exhibited a temporally variable microbiome were functionally distinct across years, indicating functional redundancy within the mussel gut mi-crobiome. Inferred biosynthesis pathways showed temporal variation in pathways involved in deg-radation, while pathways involved in cellular metabolism were stable. There was no evidence for phylosymbiosis across any facet of microbiome biodiversity. These results indicate that temporal variation is an important factor in the assembly of the gut microbiomes of freshwater mussels and provides further support that the mussel gut microbiome is involved in host development and ac-tivity

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea)

The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is known of how intrinsic and extrinsic factors, including co-occurring native species, influence its microbiome. We investigated the gut bacterial microbiome across genetically differentiated populations of C. fluminea in the Tennessee and Mobile River Basins in the Southeastern United States and compared them to those of six co-occurring species of native freshwater mussels. The gut microbiome of C. fluminea was diverse, differed with environmental conditions and varied spatially among rivers, but was unrelated to host genetic variation. Microbial source tracking suggested that the gut microbiome of C. fluminea may be influenced by the presence of co-occurring native mussels. Inferred functions from 16S rRNA gene data using PICRUST2 predicted a high prevalence and diversity of degradation functions in the C. fluminea microbiome, especially the degradation of carbohydrates and aromatic compounds. Such modularity and functional diversity of the microbiome of C. fluminea may be an asset, allowing to acclimate to an extensive range of nutritional sources in invaded habitats, which could play a vital role in its invasive success

Skin microbiome of marine vertebrates : variability, drivers and role in the ecosystem

Les milliers d’espèces de microorganismes présentes dans les océans sont essentiellement connus pour être planctoniques ou benthiques. Moins décrits, de nombreux micro-organismes colonisent également la surface et le tube digestif des macro-organismes marins, formant des communautés appelées microbiomes. Ces microbiomes ont des conséquences cruciales sur la fitness de leur hôte. Les récents progrès en biologie moléculaire ont ouvert la voie à une caractérisation des différentes facettes de sa biodiversité, à la fois taxonomique, phylogénétique, et fonctionnelle. L’objectif de cette thèse est donc de caractériser la biodiversité des microbiomes cutanés des organismes marins, d’identifier ses échelles de variabilité, ses déterminants, et son importance à l’échelle de l’écosystème. Dans un premier temps j’ai mesuré l’efficacité d’indices de biodiversité à détecter des signaux écologiques dans le cas spécifique de communautés microbiennes. Puis, j’ai décrit le microbiome cutané des principaux grands clades d’animaux marins (poissons téléostéens, cétacés et invertébrés de plusieurs classes). J’ai démontré que le microbiome cutané était très différent des communautés présentes dans l’eau environnante. J’ai aussi montré qu’il était variable, à la fois entre individus et entre espèces, mais ne présentait pas de patron de phylosymbiose. Enfin, j’ai évalué la contribution de la diversité des microbiomes cutanés à la diversité de la communauté microbienne globale d’un écosystème corallien. J’ai ainsi démontré que les animaux marins hébergent collectivement une richesse microbienne presque vingt fois supérieure à celle de l’eau les environnant, et 75% de la richesse phylogénétique à l’échelle de l’écosystème. Dans un contexte d’érosion massive de la diversité des macro-organismes marins, ces résultats soulignent la nécessité d’évaluer plus exhaustivement la biodiversité microbienne marine et sa vulnérabilité face aux pressions anthropiques.Oceans contain thousands of microbial species playing crucial roles for the functioning of the marine ecosystem. These microorganisms are present everywhere in the water column. Some microorganisms also colonize the surface and the digestive tract of marine macro-organisms, forming communities called microbiomes. These microbiomes have positive effects for their host’s fitness. The diversity of these marine animal surface microbiome is still largely understudied, despite recent progress in molecular biology that now permits to fully assess its different facets of biodiversity, i.e. taxonomic, phylogenetic and functional. The goal of this thesis is therefore to describe the diversity of the surface microbiome of marine animals, to assess its variability at different levels, as well as its determinants, and the significance of such diversity at the ecosystem’s scale. Firstly, I have assessed the efficiency of various diversity indices to detect ecological signals in the specific case of microbial communities. Secondly, I have described the surface microbiome of major marine animal clades (teleostean fishes, cetaceans and several classes of invertebrates). I found that these microbiomes are highly distinct from the surrounding planktonic communities. I demonstrated that these microbiomes are variable both between individuals from the same species and between species, but do not show a phylosymbiosis pattern. Last, I assessed the contribution of surface microbiomes to the global microbial community at the scale of a coral reef ecosystem. I demonstrated that marine animal surfaces host almost twenty times more microbial species than the water column, and 75% of the phylogenetic richness present in the ecosystem. In a context of massive erosion of marine macroscopic organisms, it is therefore urgent to exhaustively assess marine microbial biodiversity and its vulnerability facing anthropic pressures

Biodiversité du microbiome cutané des organismes marins : variabilité, déterminants et importance dans l’écosystème

Oceans contain thousands of microbial species playing crucial roles for the functioning of the marine ecosystem. These microorganisms are present everywhere in the water column. Some microorganisms also colonize the surface and the digestive tract of marine macro-organisms, forming communities called microbiomes. These microbiomes have positive effects for their host’s fitness. The diversity of these marine animal surface microbiome is still largely understudied, despite recent progress in molecular biology that now permits to fully assess its different facets of biodiversity, i.e. taxonomic, phylogenetic and functional. The goal of this thesis is therefore to describe the diversity of the surface microbiome of marine animals, to assess its variability at different levels, as well as its determinants, and the significance of such diversity at the ecosystem’s scale. Firstly, I have assessed the efficiency of various diversity indices to detect ecological signals in the specific case of microbial communities. Secondly, I have described the surface microbiome of major marine animal clades (teleostean fishes, cetaceans and several classes of invertebrates). I found that these microbiomes are highly distinct from the surrounding planktonic communities. I demonstrated that these microbiomes are variable both between individuals from the same species and between species, but do not show a phylosymbiosis pattern. Last, I assessed the contribution of surface microbiomes to the global microbial community at the scale of a coral reef ecosystem. I demonstrated that marine animal surfaces host almost twenty times more microbial species than the water column, and 75% of the phylogenetic richness present in the ecosystem. In a context of massive erosion of marine macroscopic organisms, it is therefore urgent to exhaustively assess marine microbial biodiversity and its vulnerability facing anthropic pressures.Les milliers d’espèces de microorganismes présentes dans les océans sont essentiellement connus pour être planctoniques ou benthiques. Moins décrits, de nombreux micro-organismes colonisent également la surface et le tube digestif des macro-organismes marins, formant des communautés appelées microbiomes. Ces microbiomes ont des conséquences cruciales sur la fitness de leur hôte. Les récents progrès en biologie moléculaire ont ouvert la voie à une caractérisation des différentes facettes de sa biodiversité, à la fois taxonomique, phylogénétique, et fonctionnelle. L’objectif de cette thèse est donc de caractériser la biodiversité des microbiomes cutanés des organismes marins, d’identifier ses échelles de variabilité, ses déterminants, et son importance à l’échelle de l’écosystème. Dans un premier temps j’ai mesuré l’efficacité d’indices de biodiversité à détecter des signaux écologiques dans le cas spécifique de communautés microbiennes. Puis, j’ai décrit le microbiome cutané des principaux grands clades d’animaux marins (poissons téléostéens, cétacés et invertébrés de plusieurs classes). J’ai démontré que le microbiome cutané était très différent des communautés présentes dans l’eau environnante. J’ai aussi montré qu’il était variable, à la fois entre individus et entre espèces, mais ne présentait pas de patron de phylosymbiose. Enfin, j’ai évalué la contribution de la diversité des microbiomes cutanés à la diversité de la communauté microbienne globale d’un écosystème corallien. J’ai ainsi démontré que les animaux marins hébergent collectivement une richesse microbienne presque vingt fois supérieure à celle de l’eau les environnant, et 75% de la richesse phylogénétique à l’échelle de l’écosystème. Dans un contexte d’érosion massive de la diversité des macro-organismes marins, ces résultats soulignent la nécessité d’évaluer plus exhaustivement la biodiversité microbienne marine et sa vulnérabilité face aux pressions anthropiques

Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared to clustering-based methods, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. We compared the respective influences of two widely used methods, namely DADA2 (a denoising method) vs. Mothur (a clustering method) on 16S rRNA gene amplicon datasets (hypervariable region v4), and compared such effects to the rarefaction of the community table and OTU identity threshold (97% vs. 99%) on the ecological signals detected. We used a dataset comprising freshwater invertebrate (three Unionidae species) gut and environmental (sediment, seston) communities sampled in six rivers in the southeastern USA. We ranked the respective effects of each methodological choice on alpha and beta diversity, and taxonomic composition. The choice of the pipeline significantly influenced alpha and beta diversities and changed the ecological signal detected, especially on presence/absence indices such as the richness index and unweighted Unifrac. Interestingly, the discrepancy between OTU and ASV-based diversity metrics could be attenuated by the use of rarefaction. The identification of major classes and genera also revealed significant discrepancies across pipelines. Compared to the pipeline’s effect, OTU threshold and rarefaction had a minimal impact on all measurements

Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable

Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from the same river in 2016 and 2019. We examined the taxonomic, phylogenetic, and inferred functional (from 16S rRNA sequences) facets of their microbiome diversity. Significant differences between the two years were identified in five of the six species sampled. However, not all species that exhibited a temporally variable microbiome were functionally distinct across years, indicating functional redundancy within the mussel gut microbiome. Inferred biosynthesis pathways showed temporal variation in pathways involved in degradation, while pathways involved in cellular metabolism were stable. There was no evidence for phylosymbiosis across any facet of microbiome biodiversity. These results indicate that temporal variation is an important factor in the assembly of the gut microbiomes of freshwater mussels and provides further support that the mussel gut microbiome is involved in host development and activity

High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species

International audienceAnimal-associated microbiota of animals form complex communities, which are suspected to play crucial functions for their host fitness. However, the biodiversity of these communities, including their differences between host species and individuals, have been scarcely studied, especially in case of skin-associated communities. In addition, the intra-individual variability (i.e. between body parts) has never been assessed to date. The objective of this study was to characterize skin bacterial communities of two teleostean fish species, namely the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata), using a high-throughput DNA sequencing method. In order to focus on intrinsic factors of host-associated bacterial community variability, individuals of the two species were raised in controlled conditions. Bacterial diversity was assessed using a set of four complementary indices, describing the taxonomic and phylogenetic facets of biodiversity and their respective composition (based on presence/absence data) and structure (based on species relative abundances) components. Variability of bacterial diversity was quantified at the interspecific, inter- and intra-individual scales. We demonstrated that fish surfaces host highly diverse bacterial communities, whose composition was very different from that of surrounding bacterioplankton. This high total biodiversity of skin-associated communities was supported by the important variability, between host species, individuals and the different body parts (dorsal, anal, pectoral and caudal fins)

Patterns of genetic variation in native and non-native populations of European catfish Silurus glanis across Europe

peer reviewedBiological invasions are a major component of global change worldwide. But paradoxically, an invasive species might also have threatened populations within its native range. Designing efficient management policies is needed to prevent and mitigate range expansions of invasive alien species (IAS) in non-native areas, while protecting them within their native range. Characterizing genetic variation patterns for IAS populations and deciphering the links between their native and introduced populations is helpful to (i) assess the genetic state of both native and non-native populations, (ii) reveal potential invasion pathways, (iii) define IAS management strategies in invaded areas, and (iv) identify native populations requiring conservation measures. The European catfish (Silurus glanis) is the largest European predatory fish. Introduced since the seventies from Eastern to Western Europe, it has colonized many waterbodies. Yet, little is known about the genetic status of non-native populations and the invasion pathways used by the species. Besides, some native populations are threatened, requiring conservation actions. Here, we describe current patterns of genetic variability of native and non-native S. glanis populations across Europe. Using microsatellite markers, we first assessed genetic variation within and between native and non-native populations. Second, we performed genetic clustering analyses to determine the genetic structure of multiple catfish populations across Europe and highlight their potential links. We revealed that native populations are more genetically diverse than non-native populations, and highlight complex introduction pathways involving several independent sources of introduction, which likely explain the invasion success of this large predatory fish across western Europe.FRISK (PTDC/AAGMAA/0350/2014)MEGAPREDATOR project (PTDC/ASP-PES/4181/2021)14. Life below wate

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modeling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the “Impact of climate change on the distribution of plankton functional and phylogenetic diversity” (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: (1) What can we learn about plankton communities from the new wealth of high-throughput “omics” data? (2) What is the link between plankton diversity and ecosystem function? (3) How can species distribution models be adapted to represent plankton biogeography? (4) How will plankton biogeography be altered due to anthropogenic climate change? and (5) Can a new unifying theory of macroecology be developed based on plankton ecology studies? In this review, we discuss potential future avenues to address these questions, and challenges that need to be tackled along the way