Diversity and ecological footprint of Global Ocean RNA viruses

Science, Journal Year: 2022, Volume and Issue: 376(6598), P. 1202 - 1208

Published: June 9, 2022

DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global RNA virus diversity, ecology, ecosystem roles. In this study, we uncover patterns predictors of community- “species”-level diversity contextualize their ecological impacts from pole to pole. Our analyses revealed four zones, latitudinal depth patterns, environmental correlates for viruses. findings only partially parallel those cosampled plankton show unexpectedly high polar interactions. The influence on ecosystems appears be large, predicted hosts ecologically important. Moreover, the occurrence auxiliary metabolic genes indicates that cause reprogramming diverse host metabolisms, including photosynthesis carbon cycling, abundances predict ocean export.

Language: Английский

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Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Science Advances, Journal Year: 2022, Volume and Issue: 8(5)

Published: Feb. 4, 2022

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) abyssal and lower bathyal surficial sediments euphotic aphotic ocean pelagic layers distinguish plankton diversity in material. Based 1685 samples collected throughout world ocean, show that DOS is at threefold realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These communities spatially structured basins particulate organic carbon (POC) flux upper ocean. Plankton reaching originates species, maximal deposition high latitudes. Its seafloor signature predicts variations POC export surface reveals previously overlooked taxa may drive biological pump.

Language: Английский

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The seas around China in a warming climate

Nature Reviews Earth & Environment, Journal Year: 2023, Volume and Issue: 4(8), P. 535 - 551

Published: July 18, 2023

Language: Английский

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Human‐induced salinity changes impact marine organisms and ecosystems

Global Change Biology, Journal Year: 2023, Volume and Issue: 29(17), P. 4731 - 4749

Published: July 12, 2023

Abstract Climate change is fundamentally altering marine and coastal ecosystems on a global scale. While the effects of ocean warming acidification ecology ecosystem functions services are being comprehensively researched, less attention directed toward understanding impacts human‐driven salinity changes. The water cycle operates through fluxes expressed as precipitation, evaporation, freshwater runoff from land. Changes to these in turn modulate shape environment by affecting currents, stratification, oxygen saturation, sea level rise. Besides direct impact physical processes, changes biological with ecophysiological consequences poorly understood. This surprising may diversity, habitat structure loss, community shifts including trophic cascades. model future projections (of end century changes) indicate magnitudes that lead modification open plankton suitability coral reef communities. Such also capable diversity metabolic capacity microorganisms impairing photosynthetic (coastal ocean) phytoplankton, macroalgae, seagrass, downstream ramifications biogeochemical cycling. scarcity comprehensive data dynamic regions warrants additional attention. datasets crucial quantify salinity‐based function relationships project such ultimately link into carbon sequestration well food availability human populations around globe. It critical integrate vigorous high‐quality interacting key environmental parameters (e.g., temperature, nutrients, oxygen) for anthropogenically induced its health economy.

Language: Английский

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Using artificial intelligence to document the hidden RNA virosphere

Cell, Journal Year: 2024, Volume and Issue: 187(24), P. 6929 - 6942.e16

Published: Oct. 9, 2024

Highlights•AI-based metagenomic mining greatly expands the diversity of global RNA virosphere•Developed a deep learning model that integrates sequence and structural information•161,979 putative virus species 180 supergroups were identified•RNA viruses are ubiquitous even found in most extreme environmentsSummaryCurrent tools can fail to identify highly divergent viruses. We developed algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences 10,487 metatranscriptomes generated from diverse ecosystems. LucaProt both predicted information, enabling accurate detection RdRP sequences. Using this approach, we identified 161,979 potential supergroups, including many previously poorly studied groups, as well genomes exceptional length (up 47,250 nucleotides) genomic complexity. A subset these novel was confirmed by RT-PCR RNA/DNA sequencing. Newly discovered present environments, air, hot springs, hydrothermal vents, with abundance varying substantially among This study advances discovery, highlights scale virosphere, provides computational better document virome.Graphical abstract

Language: Английский

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Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

The ISME Journal, Journal Year: 2020, Volume and Issue: 15(4), P. 981 - 998

Published: Nov. 16, 2020

Abstract Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved photosynthesis, central carbon metabolism, nutrient cycling. While previous studies have focused on AMG diversity sunlit dark ocean, less is known about shaping networks along redox gradients associated with oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether might impact nitrogen (N) cycling via AMGs. Identified genomes encoded six N-cycle AMGs denitrification, nitrification, assimilatory nitrate reduction, nitrite transport. The majority these (80%) were identified T4-like Myoviridae phages, predicted to infect Cyanobacteria Proteobacteria, or unclassified archaeal Thaumarchaeota. Four exclusive anoxic waters had distributions paralleled homologous genes. Together, findings suggest modulate N-cycling processes within ETSP may contribute loss throughout global oceans thus providing a baseline for their inclusion ecosystem geochemical models.

Language: Английский

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Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

Nature Ecology & Evolution, Journal Year: 2020, Volume and Issue: 4(12), P. 1639 - 1649

Published: Sept. 7, 2020

Language: Английский

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Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples

GigaScience, Journal Year: 2020, Volume and Issue: 9(5)

Published: May 1, 2020

The rise of antibiotic resistance (AR) in clinical settings is great concern. Therefore, the understanding AR mechanisms, evolution, and global distribution a priority for patient survival. Despite all efforts elucidation mechanisms strains, little known about its prevalence evolution environmental microorganisms. We used 293 metagenomic samples from TARA Oceans project to detect quantify genes (ARGs) using machine learning tools.

Language: Английский

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Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(12), P. 1561 - 1574

Published: Nov. 15, 2021

Language: Английский

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Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale

Environment International, Journal Year: 2021, Volume and Issue: 154, P. 106558 - 106558

Published: April 23, 2021

Dissolved organic matter (DOM) changes in quantity and quality over time space, especially highly dynamic coastal estuaries. Bacterioplankton usually display seasonal spatial variations abundance composition the regions, influence DOM pool via assimilation, transformation release of molecules. The change can also affect bacterial community. However, little is known on correspondence between molecules composition, particularly through a systematic field survey. In this study, spatiotemporal signatures microbial communities subtropical estuary Xiamen are investigated one half years. co-occurrence analysis bacteria suggested microorganisms likely transformed from relatively high (>400 Da) to low (<400 molecular weight, corresponding an apparent increase overall aromaticity. This might be reason why renders "dark" visible mass spectrometry due more efficient ionization metabolites, as well photodegradation processes. K- r-strategists exhibited different correlations with two-size categories owing their lifestyles responses environmental nutrient conditions. A comparison variables showed that environmental/DOM played important role shaping than vice versa. study sheds light interactions populations at scale, improving our understanding roles marine biogeochemical cycles.

Language: Английский

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