Biology subjects

Chaffron, S.

Publications and source records attributed to Chaffron, S..

28 records · Page 2Linked to original sources

bioRxiv2022

MAGNETO: an automated workflow for genome-resolved metagenomics

Metagenome-Assembled Genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyse uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAGs reconstruction but also emphasized several limitations, such as the non-binning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used, however, it still remains unclear which assembly strategy in combination with which binning approach, offers the best performance for MAGs recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to co-assemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAGs reconstruction, which includes a fully-automated co-assembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAGs recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCEGenome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic datasets. We propose a novel approach to automate co-assembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous co-assembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing co-assembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.

bioinformatics↗

bioRxiv2021

Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters

Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes determining marine species and community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts and ribosomal DNA metabarcoding from plankton samples collected biweekly over 8 years (2009-2016) at the SOMLIT-Astan station (Roscoff, Western English Channel). Considering the temporal structure of community dynamics (creating temporal correlation), we elucidated the recurrent seasonal pattern of the dominant species and OTUs (rDNA-derived taxa) that drive annual plankton successions. The use of morphological and molecular analyses in combination allowed us to assess absolute species abundance while improving taxonomic resolution, and revealed a greater diversity. Overall, our results underpinned a protist community characterised by a seasonal structure, which is supported by the dominant OTUs. We detected that some were partly benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. While the occurrence of these microorganisms is driven by the physical and biogeochemical conditions of the environment, internal community processes, such as the complex network of biotic interactions, also play a key role in shaping protist communities.

ecology↗

bioRxiv2021

Disentangling temporal associations in marine microbial networks

BackgroundMicrobial interactions are fundamental for Earths ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. ResultsA single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. ConclusionsOur results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems.

microbiology↗

bioRxiv2021

Disentangling marine microbial networks across space

Microbial interactions underpin ocean ecosystem function, but they remain barely known. Multiple studies have analyzed microbial interactions using static association networks based on omics data, yet microbial interactions are dynamic and can change across spatiotemporal scales. Understanding the dynamics of microbial interactions is needed for a better comprehension of ocean ecosystems. Here, we explored associations between archaea, bacteria, and picoeukaryotes along the water column, from the surface to the deep ocean, across the northern subtropical to the southern temperate ocean and the Mediterranean Sea by defining sample-specific subnetworks, which allowed us to examine changes in microbial associations across space. We found that associations tend to change with depth as well as with geographical scale, with a few associations being global (i.e., present across regions within the same depth layer) and 11-36% being regional within specific water layers. The lowest fraction of global associations was found in the bathypelagic zone, while associations restricted to certain regions increased with depth. The majority of associations observed in surface waters disappeared with depth, suggesting that surface ocean associations are not transferred to the deep sea, despite microbial sinking. Altogether, our results suggest that microbial associations have highly heterogeneous distributions in the horizontal and vertical dimensions of the ocean and that such distributions do not mirror taxonomic distributions. Our work contributes to better understand the dynamics of microbial interactions in the global ocean, which is urgently needed in a context of global change.

microbiology↗

bioRxiv2021

Insights into biotic and abiotic modulation of ocean mesopelagic communities

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO - and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.

ecology↗

bioRxiv2020

Environmental vulnerability of the global ocean plankton community interactome

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though global surveys are starting to reveal ecological drivers underlying planktonic community structure, and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network - the community interactome - and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar), and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change, and forecasted most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios, while identifying plausible plankton bioindicators for ocean monitoring of climate change.

ecology↗

bioRxiv2020

Ecogenomics of key prokaryotes in the Arctic Ocean

The Arctic Ocean is a key player in the regulation of climate and at the same time is under increasing pressure as a result of climate change. Predicting the future of this ecosystem requires understanding of the responses of Arctic microorganisms to environmental change, as they are the main drivers of global biogeochemical cycles. However, little is known about the ecology and metabolic potential of active Arctic microbes. Here, we reconstructed a total of 3,550 metagenomic bins from 41 seawater metagenomes collected as part of the Tara Oceans expedition, covering five different Arctic Ocean regions as well as the sub-Arctic North Atlantic Ocean and including various depths and different seasons (spring to autumn). Of these bins, 530 could be classified as Metagenome Assembled Genomes (MAGs) and over 75% of them represented novel species. We describe their habitat range and environmental preferences, as well as their metabolic capabilities, building the most comprehensive dataset of uncultured bacterial and archaeal genomes from the Arctic Ocean to date. We found a prevalence of mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic Arctic Ocean during spring and autumn. Finally, the catalogue of Arctic MAGs was complemented with metagenomes and metatranscriptomes from the global ocean to identify the most active MAGs present exclusively in polar metagenomes. These polar MAGs, which display a range of metabolic strategies, might represent Arctic sentinels of climate change and should be considered in prospective studies of the future state of the Arctic Ocean.

ecology↗

bioRxiv2020

MiBiOmics: An interactive web application for multi-omics data exploration and integration

BackgroundMulti-omics experimental approaches are becoming common practice in biological and medical sciences underlying the need to design new integrative techniques and applications to enable the holistic characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows us to acquire additional insights and generate novel hypotheses about a given biological system. However, it can often become challenging given the large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills. ResultsHere, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements advanced ordination techniques and the inference of omics-based (multi-layer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states. ConclusionsThrough an intuitive and interactive interface, MiBiOmics provides easy-access to ordination techniques and to a network-based approach for integrative multi-omics analyses. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics.

bioinformatics↗

bioRxiv2020

Polar opposites; bacterioplankton susceptibility and mycoplankton resistance to ocean acidification

Microorganisms form the basis of ocean ecosystems yet the effects of perturbations such as decreasing pH on microbial community structure, interactions and functionality remain compared to multicellular organisms. Using an experimental manipulation of Southern Ocean seawater, we subjected bacterioplankton and mycoplankton to artificial pH decreases, which are predicted to occur in the future. We show that acidification led to substantial increases of bacterioplankton diversity, while in contrast it had no effect on mycoplankton diversity. Our analyses revealed a loss of putative keystone taxa and a decrease in predicted community interactions as a response to lower pH levels. Bacterioplankton shifted from generalist to specialist community members, suggesting a specific stress response to unfavourable conditions. In addition, enzyme activities involved in nitrogen acquisition were lower at reduced pH levels, suggesting altered organic matter cycling in a more acidic ocean. Our findings suggest that bacterioplankton and mycoplankton may respond differentially to future ocean acidification, with potentially negative impacts on community structure and biogeochemical cycling in the Southern Ocean. IMPORTANCEOceans absorb the majority of anthropogenically produced CO2, the consequence of which is ocean acidification, a phenomenon already negatively impacting key marine organisms. Marine microbial communities form the basis of ocean food webs by generating nutrients for higher trophic levels, yet the response of these key microbial drivers to acidification remains unclear. This knowledge deficit is particularly true for understudied marine ecosystems such as the Southern Ocean. Using a mesocosm approach, we found that acidification severely impacts microbial community stability, by altering bacterioplankton community structure, reducing network complexity, and augmenting enzyme activities associated with nitrogen acquisition. This study adds to our understanding of the effects of ocean acidification on microbial communities, particularly within an environment expected to be largely effected by future anthropogenically driven climate change.

microbiology↗

bioRxiv2019

Viruses of the eukaryotic plankton are predicted to increase carbon export efficiency in the global sunlit ocean

The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earths carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral "shunt" and "shuttle"). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

ecology↗