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TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

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What this work says

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

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Basic Local Alignment Search Tool

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Coherent dynamics and association networks among lake bacterioplankton taxa

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Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

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Catchment-scale biogeography of riverine bacterioplankton

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Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

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Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

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DADA2: High-resolution sample inference from Illumina amplicon data

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QIIME allows analysis of high-throughput community sequencing data

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

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MiDAS: the field guide to the microbes of activated sludge

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Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

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ARB: a software environment for sequence data

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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

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Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

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Ribosomal Database Project: data and tools for high throughput rRNA analysis

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Limits to robustness and reproducibility in the demarcation of operational taxonomic units

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Bacterial diversity along a 2600 km river continuum

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Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

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Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

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Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

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Lineage-Specific Responses of Microbial Communities to Environmental Change

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

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A Guide to the Natural History of Freshwater Lake Bacteria

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Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

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Erratum for Linz et al., “Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes”

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Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI

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The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier

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Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

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Variability of Prokaryotic Community Structure in a Drinking Water Reservoir (Marathonas, Greece)

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Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

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CREST – Classification Resources for Environmental Sequence Tags

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Biogeography of globally distributed bacteria in temperate and boreal Québec lakes as revealed by tag pyrosequencing of 16S rRNA genes

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A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan

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Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River

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Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

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VSEARCH: a versatile open source tool for metagenomics

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Ananke: temporal clustering reveals ecological dynamics of microbial communities

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RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

What points at this work

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

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Sedimentary DNA records long‐term changes in a lake bacterial community in response to varying nutrient availability

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Spatiotemporal dynamics of cyanobacterium Dolichospermum lemmermannii populations in a bloom-prone region of Lake Superior

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Environmental changes associated with drying climate are expected to affect functional groups of pro- and microeukaryotes differently in temporary saline waters

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Species invasions shift microbial phenology in a two-decade freshwater time series

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz136openalex-snapshot

metagenomeFeatures : an R package for working with 16S rRNA reference databases and marker-gene survey feature data

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Stratification in Microbial Communities with Depth and Redox Status in a Eutrophic Lake Across Two Years

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Nitrogen dynamics and fixation control cyanobacterial abundance, diversity, and toxicity in Lake of the Woods (USA, Canada)

inferred← citeshttps://doi.org/10.1101/231688openalex-snapshot

Microhabitats shape diversity-productivity relationships in freshwater bacterial communities

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Randomized lasso associates freshwater lake-system specific bacterial taxa with heterotrophic production through flow cytometry

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The evolution of realized niches within freshwater Synechococcus

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Microbial stowaways: Waterbirds as dispersal vectors of aquatic pro‐ and microeukaryotic communities

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Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans

inferred← citeshttps://doi.org/10.1128/aem.00188-19openalex-snapshot

Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

inferred← citeshttps://doi.org/10.3389/fmicb.2018.00438openalex-snapshot

Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria

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Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

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