Biology subjects

de Vargas, C.

Publications and source records attributed to de Vargas, C..

29 records · Page 2Linked to original sources

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

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Biological nitrogen fixation plays a critical role in marine primary production, yet, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of molecular markers for mining >2,000,000 images and >1,300 metagenomes in surface, deep chlorophyll maximum and mesopelagic samples across 6 size fractions (<0.2-2000 m). Imaging and PCR-free molecular data were remarkably congruent. Sequences from diazotrophs were detected from the ultrasmall bacterioplankton (<0.2 m) to mesoplankton (180-2000 m), while images predicted symbiotic and colonial-forming diazotrophs (>20 {micro}m). Imaging and molecular data estimated that polyploidy can significantly impact gene abundances of symbiotic vs colonial-forming diazotrophs. In general our results support the canonical view that larger sized diazotrophs (>10 m) dominate the tropical belts, while sequences from unicellular cyanobacterial and non-cyanobacterial diazotrophs were globally distributed in surface and the mesopelagic. Co-occurring diazotrophic lineages of different lifestyles were frequently encountered, and several new high density regions of diazotrophs were identified in the global ocean. Overall, this work provides an update of marine diazotroph biogeographical diversity and contributes a new bio-imaging-informatic workflow.

microbiology↗

bioRxiv2020

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Marine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years. CoverNavigating on the map of plankton genomics with Tara Oceans and anvio: a comprehensive genome-resolved metagenomic survey dedicated to eukaryotic plankton. O_FIG O_LINKSMALLFIG WIDTH=153 HEIGHT=200 SRC="FIGDIR/small/341214v2_ufig1.gif" ALT="Figure 1"> View larger version (82K): org.highwire.dtl.DTLVardef@536fe5org.highwire.dtl.DTLVardef@1d72cc9org.highwire.dtl.DTLVardef@1bd5281org.highwire.dtl.DTLVardef@739512_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Plankton Planet: 'seatizen' oceanography to assess open ocean life at the planetary scale

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called plankton, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modelled at the planetary scale, but biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce Plankton Planet, an initiative whose goal is to merge the creativity of researchers, makers, and mariners to (i) develop frugal scientific instrumentation and protocols to assess the genetic and morphological diversity of plankton life, and (ii) organize their systematic deployment through fleets of volunteer sailors, fishermen, or cargo-ships to generate comparable and open-access plankton data across global and long-term spatio-temporal scales. As proof-of-concept, we show how 20 crews of sailors ("planktonauts") were abl to sample plankton biomass from the world surface ocean in a single year, generating the first citizen-based, planetary dataset of plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. This dataset has unveiled significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems across the dimensions of the Earth system.

ecology↗

bioRxiv2020

EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotic life

AO_SCPLOWBSTRACTC_SCPLOWEukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for gene-based research across the spectrum of eukaryotic life, such as phylogenomics and gene family evolution. Each species is placed within the UniEuk taxonomic framework in order to facilitate downstream analyses, and each data set is associated with a unique, persistent identifier to facilitate comparison and replication among analyses. The database is regularly updated, and all versions will be permanently stored and made available via FigShare. The current version has a number of updates, notably The Comparative Set (TCS), a reduced taxonomic set with high estimated completeness while maintaining a substantial phylogenetic breadth, which comprises 196 predicted proteomes. A BLAST web server and graphical displays of data set completeness are available at http://evocellbio.com/eukprot/. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, with the goal of building a collaborative resource that will promote research to understand eukaryotic diversity and diversification.

evolutionary biology↗

bioRxiv2019

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the seascape) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

ecology↗

bioRxiv2019

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

Protists - all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonomic and functional diversity of eukaryotic life on the planet and drive many ecosystem processes. However, knowledge of protist communities and their diversity lags behind that of most other groups of organisms, largely due to methodological constraints. While protist communities differ markedly between habitats and biomes, they can be studied in very similar ways. Here we provide a guide to current molecular approaches used for studying protist diversity, with a particular focus on amplicon-based high-throughput sequencing (metabarcoding). We highlight that the choice of suitable primers artificially alters community profiles observed in metabarcoding studies. While there are no true universal primers to target all protist taxa as a whole, we identify some primer combinations with a wide taxonomic coverage and provide detailed information on their properties. Although environmental protistan ecological research will probably shift towards PCR-free metagenomics or/and transcriptomic approaches in a near future, metabarcoding will remain the method of choice for in-depth community analyses and taxon inventories in biodiversity surveys and ecological studies, due its great cost-efficiency, sensitivity, and throughput. In this paper we provide a guide for scientists from a broad range of disciplines to implement protists in their ecological analyses.

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↗

bioRxiv2018

Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

The smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts that selection, dispersal and drift are main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.\n\nSIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmental selection, dispersal and random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

ecology↗

bioRxiv2018

EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

microbiology↗

bioRxiv2018

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified based on molecular data a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.

microbiology↗