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Metabolic Network Analysis and Metatranscriptomics Reveals Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage aci
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups
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Nearly Identical 16S rRNA Sequences Recovered from Lakes in North America and Europe Indicate the Existence of Clades of Globally Distributed Freshwater Bacteria
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The large-scale organization of metabolic networks
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High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
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In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake
inferredcites →https://doi.org/10.1038/ismej.2012.86openalex-snapshot
Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
inferredcites →https://doi.org/10.1038/ismej.2014.135openalex-snapshot
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
inferredcites →https://doi.org/10.1038/ismej.2015.241openalex-snapshot
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
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High-throughput generation, optimization and analysis of genome-scale metabolic models
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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
inferredcites →https://doi.org/10.1038/ncomms15416openalex-snapshot
Metabolic network analysis reveals microbial community interactions in anammox granules
inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot
Mapping and quantifying mammalian transcriptomes by RNA-Seq
inferredcites →https://doi.org/10.1038/srep08365openalex-snapshot
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
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Genomic insights that advance the species definition for prokaryotes
inferredcites →https://doi.org/10.1073/pnas.0806162105openalex-snapshot
Large-scale reconstruction and phylogenetic analysis of metabolic environments
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.270openalex-snapshot
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nar/gkt1097openalex-snapshot
The Transporter Classification Database
inferredcites →https://doi.org/10.1093/nar/gkt1226openalex-snapshot
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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/10.1111/1462-2920.12083openalex-snapshot
Grazing resistant freshwater bacteria profit from chitin and cell‐wall‐derived organic carbon
inferredcites →https://doi.org/10.1111/1758-2229.12180openalex-snapshot
Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities
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Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes
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Actinorhodopsins: proteorhodopsin‐like gene sequences found predominantly in non‐marine environments
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Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake
inferredcites →https://doi.org/10.1111/j.1462-2920.2009.01960.xopenalex-snapshot
Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems
inferredcites →https://doi.org/10.1111/j.1462-2920.2009.02043.xopenalex-snapshot
Contrasting ability to take up leucine and thymidine among freshwater bacterial groups: implications for bacterial production measurements
inferredcites →https://doi.org/10.1111/j.1462-2920.2011.02639.xopenalex-snapshot
Rapid successions affect microbial N ‐acetyl‐glucosamine uptake patterns during a lacustrine spring phytoplankton bloom
inferredcites →https://doi.org/10.1111/j.1574-6941.2007.00326.xopenalex-snapshot
Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences
inferredcites →https://doi.org/10.1111/j.1758-2229.2011.00274.xopenalex-snapshot
Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC
inferredcites →https://doi.org/10.1111/mec.12985openalex-snapshot
Key roles for freshwater A ctinobacteria revealed by deep metagenomic sequencing
inferredcites →https://doi.org/10.1111/mec.13319openalex-snapshot
Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community
inferredcites →https://doi.org/10.1126/science.1153213openalex-snapshot
The Microbial Engines That Drive Earth's Biogeochemical Cycles
inferredcites →https://doi.org/10.1128/aem.00767-06openalex-snapshot
Bacterioplankton Community Composition along a Salinity Gradient of Sixteen High-Mountain Lakes Located on the Tibetan Plateau, China
inferredcites →https://doi.org/10.1128/aem.00794-07openalex-snapshot
Phylogenetic Ecology of the Freshwater Actinobacteria acI Lineage
inferredcites →https://doi.org/10.1128/aem.66.11.5053-5065.2000openalex-snapshot
Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria
inferredcites →https://doi.org/10.1128/mbio.00714-16openalex-snapshot
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges
inferredcites →https://doi.org/10.1128/mmbr.00028-10openalex-snapshot
A Guide to the Natural History of Freshwater Lake Bacteria
inferredcites →https://doi.org/10.1128/mmbr.05011-11openalex-snapshot
Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria
inferredcites →https://doi.org/10.1128/msphere.00202-18openalex-snapshot
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria
inferredcites →https://doi.org/10.1186/s40168-016-0154-5openalex-snapshot
Recovering complete and draft population genomes from metagenome datasets
inferredcites →https://doi.org/10.3354/ame01157openalex-snapshot
Clone library analysis reveals an unusual composition and strong habitat partitioning of pelagic bacterial communities in Lake Tanganyika
inferredcites →https://doi.org/10.3354/ame01789openalex-snapshot
Mixed cultures as model communities: hunting for ubiquitous microorganisms, their partners, and interactions
inferredcites →https://doi.org/10.3354/ame028141openalex-snapshot
Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers
inferredcites →https://doi.org/10.4319/lo.2010.55.2.0846openalex-snapshot
Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake
inferredcites →https://doi.org/10.4319/lo.2011.56.4.1179openalex-snapshot
Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton
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/10.1101/150078openalex-snapshot
Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes
inferred← citeshttps://doi.org/10.1128/msphere.00189-17openalex-snapshot
Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder
inferred← citeshttps://doi.org/10.1128/msphere.00277-17openalex-snapshot
Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
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