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Metabolic ecology, microbial community structure, and gene-centric metagenomics

https://doi.org/10.1101/2025.08.05.668563

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

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Average genome size: a potential source of bias in comparative metagenomics

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Achieving temperature-size changes in a unicellular organism

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The effect of extrinsic mortality on genome size evolution in prokaryotes

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Challenges in microbial ecology: building predictive understanding of community function and dynamics

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Metagenomic covariation along densely sampled environmental gradients in the Red Sea

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The evolution of bacterial cell size: the internal diffusion-constraint hypothesis

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

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Computational meta'omics for microbial community studies

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Scaling metabolism from organisms to ecosystems

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Environmental drivers of a microbial genomic transition zone in the ocean’s interior

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Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

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Bromeliaceae subfamilies show divergent trends of genome size evolution

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Integrated metagenomics and network analysis of soil microbial community of the forest timberline

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Kinetic effects of temperature on rates of genetic divergence and speciation

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Global patterns in bacterial diversity

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Temperature dependence, spatial scale, and tree species diversity in eastern Asia and North America

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Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life

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Systematic variation in the temperature dependence of physiological and ecological traits

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Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

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Gene-centric approach to integrating environmental genomics and biogeochemical models

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Scaling laws predict global microbial diversity

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Microbial communities in the tropical air ecosystem follow a precise diel cycle

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Cell size as a link between noncoding DNA and metabolic rate scaling

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Food-web constraints on biodiversity–ecosystem functioning relationships

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Island Biogeography of Genes and Species

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Effects of Body Size and Temperature on Population Growth

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Integrating the Effects of Area, Isolation, and Habitat Heterogeneity on Species Diversity: A Unification of Island Biogeography and Niche Theory

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Metabolic Theory and the Temperature-Size Rule Explain the Temperature Dependence of Population Carrying Capacity

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Economy, Speed and Size Matter: Evolutionary Forces Driving Nuclear Genome Miniaturization and Expansion

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Correlation between genome reduction and bacterial growth

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The Infinitely Many Genes Model for the Distributed Genome of Bacteria

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Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation

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The Considerable Genome Size Variation of Hordeum Species (Poaceae) Is Linked to Phylogeny, Life Form, Ecology, and Speciation Rates

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KEGG: Kyoto Encyclopedia of Genes and Genomes

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Joint scaling laws in functional and evolutionary categories in prokaryotic genomes

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Linking species abundance distributions in numerical abundance and biomass through simple assumptions about community structure

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Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom

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Comparative Metagenomics of Microbial Communities

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Genome Streamlining in a Cosmopolitan Oceanic Bacterium

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The Microbial Engines That Drive Earth's Biogeochemical Cycles

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Bacterial Community Variation in Human Body Habitats Across Space and Time

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Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

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Structure and function of the global ocean microbiome

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Patterns and Processes of Microbial Community Assembly

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Population density and size of bacteria in the course of cultivation of their small forms

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Metagenomics - a guide from sampling to data analysis

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Temperature responses of mutation rate and mutational spectrum in an Escherichia coli strain and the correlation with metabolic rate

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MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

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

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Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

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Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

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Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

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Variation in cell volume and community composition of bacteria in response to temperature

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Microbial population dynamics and diversity during a bloom of the marine coccolithophorid Emiliania huxleyi (Haptophyta)

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The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

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Experimental Warming Decreases the Average Size and Nucleic Acid Content of Marine Bacterial Communities

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Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

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Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs

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Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

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Constancy of bacterial abundance in surficial marine sediments

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Effect of temperature on diatom volume, growth rate, and carbon and nitrogen content: Reconsidering some paradigms

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