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A brief guide for the measurement and interpretation of microbial functional diversity

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What this work says

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

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Functional analysis and classification of phytoplankton based on data from an automated flow cytometer

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Genotypic Microbial Community Profiling: A Critical Technical Review

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Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms

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Microfluidic single cell analysis: from promise to practice

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Use of flow cytometric methods for single-cell analysis in environmental microbiology

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Single cell genomics: an individual look at microbes

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Past, present and future applications of flow cytometry in aquatic microbiology

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Emerging horizons in biodiversity and ecosystem functioning research

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A functional approach reveals community responses to disturbances

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Fitness of multidimensional phenotypes in dynamic adaptive landscapes

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The Application of Rarefaction Techniques to Molecular Inventories of Microbial Diversity

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Vive la différence: plant functional diversity matters to ecosystem processes

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Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

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Quantitative analysis of a deeply sequenced marine microbial metatranscriptome

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Single-cell mass spectrometry reveals the importance of genetic diversity and plasticity for phenotypic variation in nitrogen-limited Chlamydomonas

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Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness

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Toward molecular trait‐based ecology through integration of biogeochemical, geographical and metagenomic data

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Functional metagenomic profiling of nine biomes

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Biodiversity loss and its impact on humanity

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Consequences of biodiversity loss for litter decomposition across biomes

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The global spectrum of plant form and function

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

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Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

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The role of physiological heterogeneity in microbial population behavior

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Single-cell genomics

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Light limitation increases multidimensional trait evenness in phytoplankton populations

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Metatranscriptome of human faecal microbial communities in a cohort of adult men

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Functional diversity (FD), species richness and community composition

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Self-generated diversity produces “insurance effects” in biofilm communities

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The diversity and biogeography of soil bacterial communities

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Microbial community gene expression in ocean surface waters

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Spatial scaling of functional gene diversity across various microbial taxa

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Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

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Functional diversity within the simple gut microbiota of the honey bee

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Relating the metatranscriptome and metagenome of the human gut

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Plant functional traits and the multidimensional nature of species coexistence

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Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

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Phenotypic diversity and ecosystem functioning in changing environments: A theoretical framework

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Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

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Single-cell RNA-seq: advances and future challenges

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Clustering: how much bias do we need?

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Individual‐level trait diversity concepts and indices to comprehensively describe community change in multidimensional trait space

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The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

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Generality of associations between biological richness and the rates of metabolic processes across microbial communities

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The n ‐dimensional hypervolume

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Functional richness, functional evenness and functional divergence: the primary components of functional diversity

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Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules

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Scaling environmental change through the community‐level: a trait‐based response‐and‐effect framework for plants

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Beyond species: functional diversity and the maintenance of ecological processes and services

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Inferring community assembly mechanisms from functional diversity patterns: the importance of multiple assembly processes

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Species divergence and trait convergence in experimental plant community assembly

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Functional diversity: back to basics and looking forward

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Quantifying the evidence for biodiversity effects on ecosystem functioning and services

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Biodiversity in a complex world: consolidation and progress in functional biodiversity research

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A trait‐based approach for modelling microbial litter decomposition

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Targeted metagenomics: a high‐resolution metagenomics approach for specific gene clusters in complex microbial communities

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amoA ‐based consensus phylogeny of ammonia‐oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

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Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities

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Functional diversity predicts overyielding effect of species combination on primary productivity

inferredcites →https://doi.org/10.1126/science.1124234openalex-snapshot

Metagenomic Analysis of the Human Distal Gut Microbiome

inferredcites →https://doi.org/10.1126/science.1160662openalex-snapshot

Functional Traits and Niche-Based Tree Community Assembly in an Amazonian Forest

inferredcites →https://doi.org/10.1126/science.276.5313.734openalex-snapshot

A Molecular View of Microbial Diversity and the Biosphere

inferredcites →https://doi.org/10.1126/science.277.5330.1300openalex-snapshot

The Influence of Functional Diversity and Composition on Ecosystem Processes

inferredcites →https://doi.org/10.1126/science.aac9323openalex-snapshot

Microbiomes in light of traits: A phylogenetic perspective

inferredcites →https://doi.org/10.1128/aem.03286-14openalex-snapshot

Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities

inferredcites →https://doi.org/10.1146/annurev-ecolsys-120213-091917openalex-snapshot

Biodiversity and Ecosystem Functioning

inferredcites →https://doi.org/10.1146/annurev-marine-010814-015955openalex-snapshot

Cell Size as a Key Determinant of Phytoplankton Metabolism and Community Structure

inferredcites →https://doi.org/10.1146/annurev.ecolsys.39.110707.173549openalex-snapshot

Trait-Based Community Ecology of Phytoplankton

inferredcites →https://doi.org/10.1186/s13059-015-0611-7openalex-snapshot

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

inferredcites →https://doi.org/10.1371/journal.pcbi.1003531openalex-snapshot

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

inferredcites →https://doi.org/10.1371/journal.pcbi.1004573openalex-snapshot

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

inferredcites →https://doi.org/10.1371/journal.pgen.1004126openalex-snapshot

Single Cell Genomics: Advances and Future Perspectives

inferredcites →https://doi.org/10.1371/journal.pone.0015545openalex-snapshot

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

inferredcites →https://doi.org/10.1371/journal.pone.0049138openalex-snapshot

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

inferredcites →https://doi.org/10.1371/journal.pone.0071677openalex-snapshot

Individual Cell Based Traits Obtained by Scanning Flow-Cytometry Show Selection by Biotic and Abiotic Environmental Factors during a Phytoplankton Spring Bloom

inferredcites →https://doi.org/10.1890/0012-9658(2000)081[0099:atoteo]2.0.co;2openalex-snapshot

A TEST OF THE EFFECTS OF FUNCTIONAL GROUP RICHNESS AND COMPOSITION ON GRASSLAND INVASIBILITY

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A TRAIT-BASED TEST FOR HABITAT FILTERING: CONVEX HULL VOLUME

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THE INVASIBILITY OF MARINE ALGAL ASSEMBLAGES: ROLE OF FUNCTIONAL DIVERSITY AND IDENTITY

inferredcites →https://doi.org/10.1890/03-0799openalex-snapshot

PLANT FUNCTIONAL MARKERS CAPTURE ECOSYSTEM PROPERTIES DURING SECONDARY SUCCESSION

inferredcites →https://doi.org/10.1890/04-0922openalex-snapshot

EFFECTS OF BIODIVERSITY ON ECOSYSTEM FUNCTIONING: A CONSENSUS OF CURRENT KNOWLEDGE

inferredcites →https://doi.org/10.1890/07-1206.1openalex-snapshot

NEW MULTIDIMENSIONAL FUNCTIONAL DIVERSITY INDICES FOR A MULTIFACETED FRAMEWORK IN FUNCTIONAL ECOLOGY

inferredcites →https://doi.org/10.1890/08-2244.1openalex-snapshot

A distance‐based framework for measuring functional diversity from multiple traits

inferredcites →https://doi.org/10.1890/10-1245.1openalex-snapshot

Functional and phylogenetic diversity as predictors of biodiversity–ecosystem-function relationships

inferredcites →https://doi.org/10.1890/11-1204.1openalex-snapshot

Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone

inferredcites →https://doi.org/10.2307/1934352openalex-snapshot

Diversity and Evenness: A Unifying Notation and Its Consequences

inferredcites →https://doi.org/10.3389/fmicb.2014.00251openalex-snapshot

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

inferredcites →https://doi.org/10.3389/fmicb.2014.00324openalex-snapshot

Opportunities and challenges in deriving phytoplankton diversity measures from individual trait-based data obtained by scanning flow-cytometry

What points at this work

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

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A Diversity of Primary Producers in Lakes

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Ecological forces dictate microbial community assembly processes in bioreactor systems

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Taxonomical and functional composition of strawberry microbiome is genotype-dependent

inferred← citeshttps://doi.org/10.1093/femsec/fiab017openalex-snapshot

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

inferred← citeshttps://doi.org/10.1093/femsre/fuae031openalex-snapshot

Microbial functional diversity and redundancy: moving forward

inferred← citeshttps://doi.org/10.1101/2024.02.07.579265openalex-snapshot

Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities

inferred← citeshttps://doi.org/10.1111/1462-2920.15910openalex-snapshot

Incorporating genome‐based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes

inferred← citeshttps://doi.org/10.1111/sum.12997openalex-snapshot

Combined biochar and manure addition to an agricultural soil benefits fertility, microbial activity, and mitigates manure‐induced CO 2 emissions

inferred← citeshttps://doi.org/10.1128/spectrum.03886-23openalex-snapshot

Estimating taxonomic and functional structure along a tropical estuary: linking metabolic traits and aspects of ecosystem functioning

inferred← citeshttps://doi.org/10.1186/s40168-023-01723-7openalex-snapshot

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

inferred← citeshttps://doi.org/10.29086/10413/23011openalex-snapshot

Metagenomics assessment of Anthropogenic impact on coral reef-associated microorganisms on the Kenyan Indian Ocean

inferred← citeshttps://doi.org/10.3389/fmicb.2021.673128openalex-snapshot

Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean

inferred← citeshttps://doi.org/10.6084/m9.figshare.26654614openalex-snapshot

Additional file 1 of Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

inferred← citeshttps://doi.org/10.6084/m9.figshare.26654617openalex-snapshot

Additional file 2 of Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

inferred← citeshttps://doi.org/10.6084/m9.figshare.26654620openalex-snapshot

Additional file 3 of Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

inferred← citeshttps://doi.org/10.6084/m9.figshare.26654626openalex-snapshot

Additional file 4 of Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

inferred← citeshttps://doi.org/10.6084/m9.figshare.26654629openalex-snapshot

Additional file 5 of Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

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