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Ecogenomics of key prokaryotes in the arctic ocean

https://doi.org/10.1101/2020.06.19.156794

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9781118778371openalex-snapshot

Sea Ice

inferredcites →https://doi.org/10.1002/9781444325508.ch12openalex-snapshot

A Global Census of Marine Microbes

inferredcites →https://doi.org/10.1002/lno.10784openalex-snapshot

Nitrogen uptake and nitrification in the subarctic North Atlantic Ocean

inferredcites →https://doi.org/10.1007/978-3-642-18912-8_5openalex-snapshot

Particulate Organic Carbon Flux to the Arctic Ocean Sea Floor

inferredcites →https://doi.org/10.1016/j.cell.2019.10.008openalex-snapshot

Global Trends in Marine Plankton Diversity across Kingdoms of Life

inferredcites →https://doi.org/10.1016/j.cell.2019.10.014openalex-snapshot

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

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Characterization of topological keystone species

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Winter–spring dynamics in sea-ice carbon cycling in the coastal Arctic Ocean

inferredcites →https://doi.org/10.1016/j.pocean.2015.07.009openalex-snapshot

Diversity of planktonic microorganisms in the Arctic Ocean

inferredcites →https://doi.org/10.1016/j.tim.2016.12.013openalex-snapshot

Marine Bacterioplankton Seasonal Succession Dynamics

inferredcites →https://doi.org/10.1016/s0924-7963(02)00177-xopenalex-snapshot

Seasonal variation in vertical flux of biogenic matter in the marginal ice zone and the central Barents Sea

inferredcites →https://doi.org/10.1029/2007jc004262openalex-snapshot

The annual cycle of particulate organic carbon export in Franklin Bay (Canadian Arctic): Environmental control and food web implications

inferredcites →https://doi.org/10.1029/2007jg000415openalex-snapshot

A dynamic model of oceanic sulfur (DMOS) applied to the Sargasso Sea: Simulating the dimethylsulfide (DMS) summer paradox

inferredcites →https://doi.org/10.1029/jc090ic03p04833openalex-snapshot

Thermohaline circulation in the Arctic Mediterranean Seas

inferredcites →https://doi.org/10.1038/ismej.2009.134openalex-snapshot

Hydrography shapes bacterial biogeography of the deep Arctic Ocean

inferredcites →https://doi.org/10.1038/ismej.2009.23openalex-snapshot

Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing

inferredcites →https://doi.org/10.1038/ismej.2010.69openalex-snapshot

High bicarbonate assimilation in the dark by Arctic bacteria

inferredcites →https://doi.org/10.1038/ismej.2012.168openalex-snapshot

Biogeography of bacterial communities exposed to progressive long-term environmental change

inferredcites →https://doi.org/10.1038/ismej.2012.80openalex-snapshot

Mechanisms determining the fate of dispersed bacterial communities in new environments

inferredcites →https://doi.org/10.1038/ismej.2014.198openalex-snapshot

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

inferredcites →https://doi.org/10.1038/ismej.2015.1openalex-snapshot

Winter diversity and expression of proteorhodopsin genes in a polar ocean

inferredcites →https://doi.org/10.1038/ismej.2016.64openalex-snapshot

Global genetic capacity for mixotrophy in marine picocyanobacteria

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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

inferredcites →https://doi.org/10.1038/nbt.3893openalex-snapshot

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

inferredcites →https://doi.org/10.1038/nbt.4229openalex-snapshot

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

inferredcites →https://doi.org/10.1038/ncomms14007openalex-snapshot

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

inferredcites →https://doi.org/10.1038/ngeo1921openalex-snapshot

Microbial control of the dark end of the biological pump

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nrmicro1595openalex-snapshot

Distribution, diversity and ecology of aerobic CO-oxidizing bacteria

inferredcites →https://doi.org/10.1038/nrmicro3522openalex-snapshot

Microbial ecology of the cryosphere: sea ice and glacial habitats

inferredcites →https://doi.org/10.1038/s41396-019-0479-8openalex-snapshot

Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival

inferredcites →https://doi.org/10.1038/s41396-019-0499-4openalex-snapshot

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean

inferredcites →https://doi.org/10.1038/s41467-018-02974-xopenalex-snapshot

No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird

inferredcites →https://doi.org/10.1038/s41467-018-07641-9openalex-snapshot

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

inferredcites →https://doi.org/10.1038/s41564-018-0176-9openalex-snapshot

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

inferredcites →https://doi.org/10.1038/s41589-018-0067-7openalex-snapshot

Functional assignment of multiple catabolic pathways for d-apiose

inferredcites →https://doi.org/10.1038/sdata.2015.23openalex-snapshot

Open science resources for the discovery and analysis of Tara Oceans data

inferredcites →https://doi.org/10.1038/sdata.2017.203openalex-snapshot

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

inferredcites →https://doi.org/10.1038/sdata.2017.93openalex-snapshot

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

inferredcites →https://doi.org/10.1073/pnas.0908284106openalex-snapshot

Ecology of the rare microbial biosphere of the Arctic Ocean

inferredcites →https://doi.org/10.1073/pnas.0912765107openalex-snapshot

Dormancy contributes to the maintenance of microbial diversity

inferredcites →https://doi.org/10.1073/pnas.1201914109openalex-snapshot

Role for urea in nitrification by polar marine Archaea

inferredcites →https://doi.org/10.1073/pnas.1208160109openalex-snapshot

Pole-to-pole biogeography of surface and deep marine bacterial communities

inferredcites →https://doi.org/10.1073/pnas.1212424110openalex-snapshot

Marine bacteria exhibit a bipolar distribution

inferredcites →https://doi.org/10.1073/pnas.1319284111openalex-snapshot

Relating the metatranscriptome and metagenome of the human gut

inferredcites →https://doi.org/10.1073/pnas.1802470115openalex-snapshot

Sinking particles promote vertical connectivity in the ocean microbiome

inferredcites →https://doi.org/10.1080/10409230490496577openalex-snapshot

Life with Carbon Monoxide

inferredcites →https://doi.org/10.1080/15405702.2017.1376064openalex-snapshot

Arctic sea ice and the communication of climate change

inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btt403openalex-snapshot

nhmmer: DNA homology search with profile HMMs

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

inferredcites →https://doi.org/10.1093/bioinformatics/btz848openalex-snapshot

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

inferredcites →https://doi.org/10.1093/femsec/fiw146openalex-snapshot

The gut microbiome of the sea urchin, Lytechinus variegatus , from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles

inferredcites →https://doi.org/10.1093/femsec/fiw174openalex-snapshot

The importance of neutral and niche processes for bacterial community assembly differs between habitat generalists and specialists

inferredcites →https://doi.org/10.1093/jxb/erm361openalex-snapshot

Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships

inferredcites →https://doi.org/10.1093/molbev/msy234openalex-snapshot

Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea

inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1099/ijsem.0.002809openalex-snapshot

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

inferredcites →https://doi.org/10.1101/2020.03.17.996280openalex-snapshot

Heterotrophic Thaumarchaeota with ultrasmall genomes are widespread in the ocean

inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

inferredcites →https://doi.org/10.1101/gr.9.9.868openalex-snapshot

CAP3: A DNA Sequence Assembly Program

inferredcites →https://doi.org/10.1111/j.1462-2920.2008.01674.xopenalex-snapshot

Winter‐to‐summer changes in the composition and single‐cell activity of near‐surface Arctic prokaryotes

inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02154.xopenalex-snapshot

The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes

inferredcites →https://doi.org/10.1111/mec.15026openalex-snapshot

Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

inferredcites →https://doi.org/10.1126/science.1135999openalex-snapshot

Archaeal Type III RuBisCOs Function in a Pathway for AMP Metabolism

inferredcites →https://doi.org/10.1126/science.1261359openalex-snapshot

Structure and function of the global ocean microbiome

inferredcites →https://doi.org/10.1128/aem.00117-09openalex-snapshot

Photoheterotrophic Microbes in the Arctic Ocean in Summer and Winter

inferredcites →https://doi.org/10.1128/aem.01283-09openalex-snapshot

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea

inferredcites →https://doi.org/10.1128/aem.01431-14openalex-snapshot

Urea Uptake and Carbon Fixation by Marine Pelagic Bacteria and Archaea during the Arctic Summer and Winter Seasons

inferredcites →https://doi.org/10.1128/aem.01907-10openalex-snapshot

Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter

inferredcites →https://doi.org/10.1128/aem.02737-14openalex-snapshot

Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean

inferredcites →https://doi.org/10.1128/msystems.00415-20openalex-snapshot

Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean

inferredcites →https://doi.org/10.1146/annurev-marine-120710-100926openalex-snapshot

Shifting Patterns of Life in the Pacific Arctic and Sub-Arctic Seas

inferredcites →https://doi.org/10.1146/annurev.micro.53.1.189openalex-snapshot

Poles Apart: Biodiversity and Biogeography of Sea Ice Bacteria

inferredcites →https://doi.org/10.1186/gb-2011-12-5-r44openalex-snapshot

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

inferredcites →https://doi.org/10.1186/s40168-019-0618-5openalex-snapshot

Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

inferredcites →https://doi.org/10.1186/s40168-020-00806-zopenalex-snapshot

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

inferredcites →https://doi.org/10.1186/s40168-020-00826-9openalex-snapshot

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

inferredcites →https://doi.org/10.1371/journal.pbio.1001177openalex-snapshot

A Holistic Approach to Marine Eco-Systems Biology

inferredcites →https://doi.org/10.1371/journal.pcbi.1003118openalex-snapshot

Software for Computing and Annotating Genomic Ranges

inferredcites →https://doi.org/10.1371/journal.pgen.1000255openalex-snapshot

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1515/9780691209418openalex-snapshot

Evolution in Changing Environments

inferredcites →https://doi.org/10.1890/08-0851.1openalex-snapshot

Contrasts between habitat generalists and specialists: an empirical extension to the basic metacommunity framework

inferredcites →https://doi.org/10.2307/1934144openalex-snapshot

On the Measurement of Niche Breadth and Overlap

inferredcites →https://doi.org/10.3354/ame01155openalex-snapshot

Grazing of large-sized bacteria by sea-ice heterotrophic protists on the Mackenzie Shelf during the winterspring transition

inferredcites →https://doi.org/10.3354/ame01276openalex-snapshot

Mixotrophy: a widespread and important ecological strategy for planktonic and sea-ice nanoflagellates in the Ross Sea, Antarctica

inferredcites →https://doi.org/10.3389/fmicb.2014.00425openalex-snapshot

Winter bloom of a rare betaproteobacterium in the Arctic Ocean

inferredcites →https://doi.org/10.3389/fmicb.2016.02078openalex-snapshot

Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea

inferredcites →https://doi.org/10.4319/lo.2008.53.2.0813openalex-snapshot

Microbial community diversity and heterotrophic production in a coastal Arctic ecosystem: A stamukhi lake and its source waters

inferredcites →https://doi.org/10.5670/oceanog.2011.71openalex-snapshot

The Ocean Carbon Cycle in the Western Arctic Ocean: Distributions and Air-Sea Fluxes of Carbon Dioxide

inferredcites →https://doi.org/10.5670/oceanog.2011.74openalex-snapshot

Future Arctic Ocean Seasonal Ice Zones and Implications for Pelagic-Benthic Coupling

inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s11356-022-20160-xopenalex-snapshot

Keystone taxa and functional analysis in arsenic and antimony co-contaminated rice terraces

inferred← citeshttps://doi.org/10.1101/2021.04.08.436999openalex-snapshot

The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean

inferred← citeshttps://doi.org/10.1101/2021.07.12.451729openalex-snapshot

Disentangling microbial networks across pelagic zones in the global ocean

inferred← citeshttps://doi.org/10.1101/2025.02.13.638167openalex-snapshot

Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts

inferred← citeshttps://doi.org/10.1126/sciadv.abg1921openalex-snapshot

Environmental vulnerability of the global ocean epipelagic plankton community interactome

inferred← citeshttps://doi.org/10.1128/aem.01706-21openalex-snapshot

Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation

inferred← citeshttps://doi.org/10.1128/mbio.01306-21openalex-snapshot

A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean

inferred← citeshttps://doi.org/10.1128/msystems.01274-24openalex-snapshot

Bioenergetic trade-offs can reveal the path to superior microbial CO 2 fixation pathways

inferred← citeshttps://doi.org/10.21203/rs.3.rs-4735744/v1openalex-snapshot

Bioenergetic trade-offs can reveal the path to superior microbial CO2 fixation pathways

inferred← citeshttps://doi.org/10.26508/lsa.202201833openalex-snapshot

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

inferred← citeshttps://doi.org/10.3389/978-2-8325-4131-9openalex-snapshot

Marine Microbiomes: Towards Standard Methods and Best Practices

inferred← citeshttps://doi.org/10.3389/fmicb.2021.637526openalex-snapshot

Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities

inferred← citeshttps://doi.org/10.5821/dissertation-2117-369389openalex-snapshot

Disentangling ecological networks in marine microbes

inferred← citeshttps://doi.org/10.7554/elife.111488openalex-snapshot

Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts

inferred← citeshttps://doi.org/10.7554/elife.111488.1openalex-snapshot

Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts

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