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Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone”

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What this work says

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

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Biogeochemical and metagenomic analysis of nitrite accumulation in the G ulf of M exico hypoxic zone
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Understanding marine dissolved organic matter production: Compositional insights from axenic cultures of Thalassiosira pseudonana
inferredcites →https://doi.org/10.1007/978-94-017-2464-7_4openalex-snapshot
Nutrient-enhanced productivity in the northern Gulf of Mexico: past, present and future
inferredcites →https://doi.org/10.1007/bf02841332openalex-snapshot
Hypoxia in the northern Gulf of Mexico: Does the science support the Plan to Reduce, Mitigate, and Control Hypoxia?
inferredcites →https://doi.org/10.1007/s00203-007-0255-4openalex-snapshot
Role of nitrite reductase in the ammonia-oxidizing pathway of Nitrosomonas europaea
inferredcites →https://doi.org/10.1007/s00248-013-0328-7openalex-snapshot
The Diversity and Functions of Choline Sulphatases in Microorganisms
inferredcites →https://doi.org/10.1007/s12237-015-9965-zopenalex-snapshot
Spatial and Temporal Patterns of Benthic Respiration and Net Nutrient Fluxes in the Atchafalaya River Delta Estuary
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Analysis of bacterial diversity in sponges collected off Chujado, an Island in Korea, using barcoded 454 pyrosequencing: Analysis of a distinctive sponge group containing Chloroflexi
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The bacterial cytochrome cbb3 oxidases
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Oxygen consumption in the water column and sediments of the northern Gulf of Mexico hypoxic zone
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Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead
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Compartmentalization and regulation of arylsulfatase activities in Streptomyces sp., Microbacterium sp. and Rhodococcus sp. soil isolates in response to inorganic sulfate limitation
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An analysis of diffuse light attenuation in the northern Gulf of Mexico hypoxic zone using the SeaWiFS satellite data record
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Co-regulation of redox processes in freshwater wetlands as a function of organic matter availability?
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Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum “Nitrospinae”
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Phylogeny of Actinobacteria Small Subunit (SSU) rRNA Gene Clones Recovered From Marine Bacterioplankton
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Seasonal and interannual variability within the Louisiana coastal current: stratification and hypoxia
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Nutrient-enhanced productivity in the northern Gulf of Mexico: past, present and future
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Seasonality and vertical structure of microbial communities in an ocean gyre
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Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean
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Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
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Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle
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Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians
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Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer
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Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
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Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system
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Impacts of chemical gradients on microbial community structure
inferredcites →https://doi.org/10.1038/ismej.2016.20openalex-snapshot
Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean
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A conspicuous nickel protein in microbial mats that oxidize methane anaerobically
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Insights into the phylogeny and coding potential of microbial dark matter
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Unusual biology across a group comprising more than 15% of domain Bacteria
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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
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Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone
inferredcites →https://doi.org/10.1038/ncomms7372openalex-snapshot
Diverse uncultivated ultra-small bacterial cells in groundwater
inferredcites →https://doi.org/10.1038/ncomms9933openalex-snapshot
Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea
inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot
Mapping and quantifying mammalian transcriptomes by RNA-Seq
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A new view of the tree of life
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Microbial ecology of expanding oxygen minimum zones
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Master recyclers: features and functions of bacteria associated with phytoplankton blooms
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Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
inferredcites →https://doi.org/10.1038/srep43247openalex-snapshot
Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila
inferredcites →https://doi.org/10.1042/bj20101185openalex-snapshot
A hierarchical classification of polysaccharide lyases for glycogenomics
inferredcites →https://doi.org/10.1073/pnas.0913533107openalex-snapshot
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
inferredcites →https://doi.org/10.1073/pnas.1013435107openalex-snapshot
Aerobic growth at nanomolar oxygen concentrations
inferredcites →https://doi.org/10.1073/pnas.1205009109openalex-snapshot
Microbial oceanography of anoxic oxygen minimum zones
inferredcites →https://doi.org/10.1073/pnas.1514645113openalex-snapshot
Deciphering ocean carbon in a changing world
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btq243openalex-snapshot
The Newick utilities: high-throughput phylogenetic tree processing in the U nix shell
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btw474openalex-snapshot
MSAViewer: interactive JavaScript visualization of multiple sequence alignments
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkn663openalex-snapshot
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
inferredcites →https://doi.org/10.1093/nar/gkn923openalex-snapshot
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
inferredcites →https://doi.org/10.1093/nar/gkt1178openalex-snapshot
The carbohydrate-active enzymes database (CAZy) in 2013
inferredcites →https://doi.org/10.1093/nar/gkt963openalex-snapshot
IMG 4 version of the integrated microbial genomes comparative analysis system
inferredcites →https://doi.org/10.1093/nar/gkv1103openalex-snapshot
The Transporter Classification Database (TCDB): recent advances
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1101/gr.142315.112openalex-snapshot
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
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/10.1111/1462-2920.12690openalex-snapshot
Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary
inferredcites →https://doi.org/10.1111/1462-2920.12853openalex-snapshot
Archaeal enrichment in the hypoxic zone in the northern G ulf of M exico
inferredcites →https://doi.org/10.1111/1462-2920.13023openalex-snapshot
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
inferredcites →https://doi.org/10.1111/j.1365-2958.2004.04248.xopenalex-snapshot
Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite‐sensitive transcription repressor
inferredcites →https://doi.org/10.1111/j.1462-2920.2004.00614.xopenalex-snapshot
Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae
inferredcites →https://doi.org/10.1111/j.1462-2920.2008.01627.xopenalex-snapshot
Abundance and activity of Chloroflexi ‐type SAR202 bacterioplankton in the meso‐ and bathypelagic waters of the (sub)tropical Atlantic
inferredcites →https://doi.org/10.1111/j.1462-2920.2009.01929.xopenalex-snapshot
Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02400.xopenalex-snapshot
Microbial metatranscriptomics in a permanent marine oxygen minimum zone
inferredcites →https://doi.org/10.1126/science.1120250openalex-snapshot
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
inferredcites →https://doi.org/10.1126/science.1147112openalex-snapshot
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
inferredcites →https://doi.org/10.1126/science.1156401openalex-snapshot
Spreading Dead Zones and Consequences for Marine Ecosystems
inferredcites →https://doi.org/10.1126/science.1196889openalex-snapshot
A Cryptic Sulfur Cycle in Oxygen-Minimum–Zone Waters off the Chilean Coast
inferredcites →https://doi.org/10.1126/science.1208239openalex-snapshot
Isotopic Signature of N 2 O Produced by Marine Ammonia-Oxidizing Archaea
inferredcites →https://doi.org/10.1126/science.1212665openalex-snapshot
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
inferredcites →https://doi.org/10.1126/science.1224041openalex-snapshot
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
inferredcites →https://doi.org/10.1128/aem.00521-17openalex-snapshot
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
inferredcites →https://doi.org/10.1128/aem.00888-09openalex-snapshot
Anaerobic Respiration of Elemental Sulfur and Thiosulfate by Shewanella oneidensis MR-1 Requires psrA , a Homolog of the phsA Gene of Salmonella enterica Serovar Typhimurium LT2
inferredcites →https://doi.org/10.1128/aem.01186-08openalex-snapshot
Epsilonproteobacteria Represent the Major Portion of Chemoautotrophic Bacteria in Sulfidic Waters of Pelagic Redoxclines of the Baltic and Black Seas
inferredcites →https://doi.org/10.1128/aem.01272-10openalex-snapshot
Characterization of Cyanate Metabolism in Marine Synechococcus and Prochlorococcus spp
inferredcites →https://doi.org/10.1128/aem.02411-13openalex-snapshot
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
inferredcites →https://doi.org/10.1128/aem.03443-13openalex-snapshot
Refined NrfA Phylogeny Improves PCR-Based nrfA Gene Detection
inferredcites →https://doi.org/10.1128/aem.03777-12openalex-snapshot
SUP05 Dominates the Gammaproteobacterial Sulfur Oxidizer Assemblages in Pelagic Redoxclines of the Central Baltic and Black Seas
inferredcites →https://doi.org/10.1128/aem.59.5.1294-1302.1993openalex-snapshot
Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans
inferredcites →https://doi.org/10.1128/aem.62.4.1171-1177.1996openalex-snapshot
Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans
inferredcites →https://doi.org/10.1128/aem.66.11.4829-4833.2000openalex-snapshot
Marine Planktonic Archaea Take Up Amino Acids
inferredcites →https://doi.org/10.1128/aem.68.9.4431-4440.2002openalex-snapshot
Molecular Evidence for a Uniform Microbial Community in Sponges from Different Oceans
inferredcites →https://doi.org/10.1128/aem.70.5.2836-2842.2004openalex-snapshot
Prevalence of the Chloroflexi -Related SAR202 Bacterioplankton Cluster throughout the Mesopelagic Zone and Deep Ocean
inferredcites →https://doi.org/10.1128/jb.00208-10openalex-snapshot
Genome Sequence of Lentisphaera araneosa HTCC2155 T , the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae
inferredcites →https://doi.org/10.1128/jb.01962-12openalex-snapshot
Gliding Motility and Por Secretion System Genes Are Widespread among Members of the Phylum Bacteroidetes
inferredcites →https://doi.org/10.1128/jb.187.18.6258-6264.2005openalex-snapshot
Towards a Genome-Based Taxonomy for Prokaryotes
inferredcites →https://doi.org/10.1128/mbio.00312-17openalex-snapshot
Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis
inferredcites →https://doi.org/10.1128/mbio.00413-17openalex-snapshot
SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
inferredcites →https://doi.org/10.1128/mbio.01669-15openalex-snapshot
Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs
inferredcites →https://doi.org/10.1128/mbio.01966-14openalex-snapshot
Oxygen at Nanomolar Levels Reversibly Suppresses Process Rates and Gene Expression in Anammox and Denitrification in the Oxygen Minimum Zone off Northern Chile
inferredcites →https://doi.org/10.1128/mbio.02083-14openalex-snapshot
Genomes of PlanktonicAcidimicrobiales: Widening Horizons for MarineActinobacteriaby Metagenomics
inferredcites →https://doi.org/10.1128/mbio.02164-15openalex-snapshot
The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions
inferredcites →https://doi.org/10.1128/msphere.00028-16openalex-snapshot
Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico
inferredcites →https://doi.org/10.1146/annurev-marine-120308-081003openalex-snapshot
The Impact of Microbial Metabolism on Marine Dissolved Organic Matter
inferredcites →https://doi.org/10.1146/annurev-marine-120709-142814openalex-snapshot
Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones
inferredcites →https://doi.org/10.1146/annurev.ecolsys.29.1.503openalex-snapshot
BACTERIAL GROWTH EFFICIENCY IN NATURAL AQUATIC SYSTEMS
inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150513openalex-snapshot
Gulf of Mexico Hypoxia, A.K.A. “The Dead Zone”
inferredcites →https://doi.org/10.1146/annurev.micro.61.080706.093329openalex-snapshot
Ins and Outs of Major Facilitator Superfamily Antiporters
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-13-264openalex-snapshot
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
inferredcites →https://doi.org/10.1186/1471-2148-10-210openalex-snapshot
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
inferredcites →https://doi.org/10.1186/gb-2009-10-8-r85openalex-snapshot
Community-wide analysis of microbial genome sequence signatures
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0063422openalex-snapshot
Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin
inferredcites →https://doi.org/10.1371/journal.pone.0119465openalex-snapshot
Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
inferredcites →https://doi.org/10.1371/journal.pone.0127499openalex-snapshot
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)
inferredcites →https://doi.org/10.2134/jeq2001.302320xopenalex-snapshot
Hypoxia in the Gulf of Mexico
inferredcites →https://doi.org/10.3354/ame039145openalex-snapshot
Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea
inferredcites →https://doi.org/10.3354/meps11062openalex-snapshot
Respiration quotient variability: bacterial evidence
inferredcites →https://doi.org/10.3389/fmicb.2012.00438openalex-snapshot
Analysis of Composition and Structure of Coastal to Mesopelagic Bacterioplankton Communities in the Northern Gulf of Mexico
inferredcites →https://doi.org/10.3389/fmicb.2013.00027openalex-snapshot
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer
inferredcites →https://doi.org/10.3389/fmicb.2013.00072openalex-snapshot
An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico
inferredcites →https://doi.org/10.3389/fmicb.2014.00581openalex-snapshot
Two distinct microbial communities revealed in the sponge Cinachyrella
inferredcites →https://doi.org/10.3389/fmicb.2015.01108openalex-snapshot
Marine Group II Archaea, potentially important players in the global ocean carbon cycle
inferredcites →https://doi.org/10.4319/lo.2012.57.3.0711openalex-snapshot
Quantification of ammonia oxidation rates and ammonia‐oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean
inferredcites →https://doi.org/10.5194/bg-11-1215-2014openalex-snapshot
Investigating hypoxia in aquatic environments: diverse approaches to addressing a complex phenomenon
inferredcites →https://doi.org/10.5194/bg-9-2419-2012openalex-snapshot
Production of oceanic nitrous oxide by ammonia-oxidizing archaea
inferredcites →https://doi.org/10.7717/peerj.243openalex-snapshot
PhyloSift: phylogenetic analysis of genomes and metagenomes

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s00248-020-01510-zopenalex-snapshot
Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient
inferred← citeshttps://doi.org/10.1016/j.crmicr.2025.100433openalex-snapshot
Microbial dark matter spearheading the biogeochemical cycle in the Solar Lake of Taba, Egypt
inferred← citeshttps://doi.org/10.1017/s0025315418000188openalex-snapshot
Comparison of bacterial communities associated withXestospongia testudinaria, sediment and seawater in a Singaporean coral reef ecosystem
inferred← citeshttps://doi.org/10.1038/s41467-023-40726-8openalex-snapshot
Cultivation of marine bacteria of the SAR202 clade
inferred← citeshttps://doi.org/10.1038/s41597-022-01392-5openalex-snapshot
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments
inferred← citeshttps://doi.org/10.1038/s42003-018-0086-7openalex-snapshot
Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria
inferred← citeshttps://doi.org/10.1038/s43705-021-00002-6openalex-snapshot
Transcriptional activity differentiates families of Marine Group II Euryarchaeota in the coastal ocean
inferred← citeshttps://doi.org/10.1093/gbe/evz201openalex-snapshot
Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia
inferred← citeshttps://doi.org/10.1101/349548openalex-snapshot
Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Offers Insight into Ecological Patterns
inferred← citeshttps://doi.org/10.1111/1462-2920.14109openalex-snapshot
Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones
inferred← citeshttps://doi.org/10.1128/mbio.00413-17openalex-snapshot
SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
inferred← citeshttps://doi.org/10.1128/msystems.00276-21openalex-snapshot
Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ( Gammaproteobacteria )
inferred← citeshttps://doi.org/10.1186/s40168-020-00910-0openalex-snapshot
Microbial dark matter filling the niche in hypersaline microbial mats
inferred← citeshttps://doi.org/10.1371/journal.pone.0209055openalex-snapshot
Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.4796openalex-snapshot
High-Throughput Cultivation of Bacterioplankton from the Gulf of Mexico and Genomics of the First Cultured LD12 Representative
inferred← citeshttps://doi.org/10.33540/117openalex-snapshot
The role of microorganisms in the cycling of organic matter in anoxic marine environments
inferred← citeshttps://doi.org/10.3389/fmicb.2019.02558openalex-snapshot
Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments
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