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    Authors: Mengqi Wang; Qichao Tu; Qichao Tu; Qichao Tu; +1 Authors

    Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.

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    Frontiers in Microbiology
    Article . 2022
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    Frontiers in Microbiology
    Article . 2022 . Peer-reviewed
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      Frontiers in Microbiology
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    Authors: Cózar, Andrés; Martí, Elisa; Duarte, Carlos M; García-de-Lomas, Juan; +10 Authors

    Tara Oceans particularly acknowledges the commitment of the following sponsors: the CNRS (in particular Groupement de Recherche GDR3280), the European Molecular Biology Laboratory, Genoscope/CEA, French Government “Investissements d’Avenir” programs OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, and European Union FP7 (Micro B3 no. 287589). We appreciate the support and commitment of agnès b. and E. Bourgois, Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, Eléctricité de France Foundation, Fondation pour la recherche sur la biodiversité, Prince Albert II de Monaco Foundation, Tara Foundation, its schooner, and its teams. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org/en/m/science/les-labos-impliques/). This article is contribution number 52 of Tara Oceans. This study is funded by Tara Oceans and the Malaspina 2010 Expedition project (Spanish Ministry of Economy and Competitiveness, CSD2008-00077) and has received additional support from the King Abdullah University of Science and Technology through baseline funding to X.I. and C.M.D., Campus de Excelencia Internacional del Mar (CEIMAR), and PLASTREND (BBVA Foundation) and MIDaS (CTM2016-77106-R, AEI/FEDER/UE) projects. The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris. Peer reviewed

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    Science Advances
    Article . 2017
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    Authors: Christopher R. Schvarcz; Samuel T. Wilson; Mathieu Caffin; Rosalina Stancheva; +6 Authors

    AbstractPersistent nitrogen depletion in sunlit open ocean waters provides a favorable ecological niche for nitrogen-fixing (diazotrophic) cyanobacteria, some of which associate symbiotically with eukaryotic algae. All known marine examples of these symbioses have involved either centric diatom or haptophyte hosts. We report here the discovery and characterization of two distinct marine pennate diatom-diazotroph symbioses, which until now had only been observed in freshwater environments. Rhopalodiaceae diatomsEpithemia pelagicasp. nov. andEpithemia catenatasp. nov. were isolated repeatedly from the subtropical North Pacific Ocean, and analysis of sequence libraries reveals a global distribution. These symbioses likely escaped attention because the endosymbionts lack fluorescent photopigments, havenifHgene sequences similar to those of free-living unicellular cyanobacteria, and are lost in nitrogen-replete medium. Marine Rhopalodiaceae-diazotroph symbioses are a previously overlooked but widespread source of bioavailable nitrogen in marine habitats and provide new, easily cultured model organisms for the study of organelle evolution.

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    Authors: M. Tangherlini; M. Miralto; C. Colantuono; M. Sangiovanni; +4 Authors

    Table summarizing the resulting contigs obtained from the Tara miTAGs assembly. (DOCX 33 kb)

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    Authors: Moore, Ryan M.; Harrison, Amelia O.; McAllister, Sean M.; Polson, Shawn W.; +1 Authors

    ABSTRACTPhylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

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      Article . Preprint . 2020 . Peer-reviewed
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      Article . 2020
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      Article . 2020
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    Authors: Mark V. Brown; Martin Ostrowski; Joseph J. Grzymski; Federico M. Lauro;

    Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa.

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    Marine Genomics
    Article . 2014 . Peer-reviewed
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      Marine Genomics
      Article . 2014 . Peer-reviewed
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    Authors: López-Escardó, David; Grau-Bové, Xavier; Guillaumet-Adkins, Amy; Gut, Marta; +2 Authors

    Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data has unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need broader taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangements processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal essential protein domains to maintain animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions.This article is part of the discussion meeting issue ‘Single cell ecology’.

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    Other literature type . 2019
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    Other literature type . 2019
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      Other literature type . 2019
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      Other literature type . 2019
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    Authors: Yawouvi Dodji Soviadan; Lars Stemmann; Fabio Benedetti; Manoela C. Brandão; +8 Authors

    AbstractVertical variations in physical and chemical conditions drive changes in marine zooplankton community diversity and composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (< 5µmol O2.kg−1) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the community structure of surface phytoplankton and the quantity and the quality of the produced particulate organic matter. We provide a consistent baseline of plankton community structure together with estimates of vertical flux and a contribution to our understanding of global zooplankton dynamics in the upper kilometer of the global ocean. Our results further suggest that future changes in surface phytoplankton composition and mesopelagic oxygen loss might lead to profound changes in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump

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    https://www.biorxiv.org/conten...
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    OpenAIRE
    Preprint . 2021
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      Preprint . 2021
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    Authors: Arianna I. Krinos; Natalie R. Cohen; Michael J. Follows; Harriet Alexander;

    Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

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    BMC Bioinformatics
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    BMC Bioinformatics
    Article . 2023
    Data sources: DOAJ
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      Article . 2023 . Peer-reviewed
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      Article . 2023
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    Authors: Roy El Hourany; Juan Pierella Karlusich; Lucie Zinger; Hubert Loisel; +2 Authors

    Ocean color remote sensing has been used for more than 2 decades to estimate primary productivity. Approaches have also been developed to disentangle phytoplankton community structure based on spectral data from space, in particular when combined with in situ measurements of photosynthetic pigments. Here, we propose a new ocean color algorithm to derive the relative cell abundance of seven phytoplankton groups, as well as their contribution to total chlorophyll a (Chl a) at the global scale. Our algorithm is based on machine learning and has been trained using remotely sensed parameters (reflectance, backscattering, and attenuation coefficients at different wavelengths, plus temperature and Chl a) combined with an omics-based biomarker developed using Tara Oceans data representing a single-copy gene encoding a component of the photosynthetic machinery that is present across all phytoplankton, including both prokaryotes and eukaryotes. It differs from previous methods which rely on diagnostic pigments to derive phytoplankton groups. Our methodology provides robust estimates of the phytoplankton community structure in terms of relative cell abundance and contribution to total Chl a concentration. The newly generated datasets yield complementary information about different aspects of phytoplankton that are valuable for assessing the contributions of different phytoplankton groups to primary productivity and inferring community assembly processes. This makes remote sensing observations excellent tools to collect essential biodiversity variables (EBVs) and provide a foundation for developing marine biodiversity forecasts.

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    https://doi.org/10.5194/egusph...
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      https://doi.org/10.5194/egusph...
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    Authors: Mengqi Wang; Qichao Tu; Qichao Tu; Qichao Tu; +1 Authors

    Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.

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    Frontiers in Microbiology
    Article . 2022
    Data sources: DOAJ
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    Frontiers in Microbiology
    Article . 2022 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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      Frontiers in Microbiology
      Article . 2022
      Data sources: DOAJ
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      Frontiers in Microbiology
      Article . 2022 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
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    Authors: Cózar, Andrés; Martí, Elisa; Duarte, Carlos M; García-de-Lomas, Juan; +10 Authors

    Tara Oceans particularly acknowledges the commitment of the following sponsors: the CNRS (in particular Groupement de Recherche GDR3280), the European Molecular Biology Laboratory, Genoscope/CEA, French Government “Investissements d’Avenir” programs OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, and European Union FP7 (Micro B3 no. 287589). We appreciate the support and commitment of agnès b. and E. Bourgois, Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, Eléctricité de France Foundation, Fondation pour la recherche sur la biodiversité, Prince Albert II de Monaco Foundation, Tara Foundation, its schooner, and its teams. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org/en/m/science/les-labos-impliques/). This article is contribution number 52 of Tara Oceans. This study is funded by Tara Oceans and the Malaspina 2010 Expedition project (Spanish Ministry of Economy and Competitiveness, CSD2008-00077) and has received additional support from the King Abdullah University of Science and Technology through baseline funding to X.I. and C.M.D., Campus de Excelencia Internacional del Mar (CEIMAR), and PLASTREND (BBVA Foundation) and MIDaS (CTM2016-77106-R, AEI/FEDER/UE) projects. The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris. Peer reviewed

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    Science Advances
    Article . 2017
    Data sources: NARCIS
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    Science Advances
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