ArticleNature microbiology2024
Environmentally dependent interactions shape patterns in gene content across natural microbiomes.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Niche specialization and prevalence of comammox Nitrospira in the alkaline sediments of thermokarst lakes on the Tibetan Plateau.Nature communications · 2026Article
- The ecological context of enzymatic variation.bioRxiv : the preprint server for biology · 2026Article
- Niche Construction: A Rational Engineering Strategy for Regulating Microbial Assembly to Enhance Flavor and Bioactivity of Fermented Foods.Comprehensive reviews in food science and food safety · 2026Review
- Minimizing co-growth as a broad predictor of community robustness.bioRxiv : the preprint server for biology · 2026Article
- Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.bioRxiv : the preprint server for biology · 2026Article
- Article
- Learning functional groups in complex microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Cross-domain cooperation drives nutrient acquisition and metabolism in the bark beetle holobiont.The ISME journal · 2026Article
- Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.Nature communications · 2025Article
- Article
- Dynamic coexistence driven by physiological transitions in microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Microbial functional guilds respond cohesively to rapidly fluctuating environments.bioRxiv : the preprint server for biology · 2025Article
- Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation.Biotechnology for biofuels and bioproducts · 2025Article
- Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium.Nature communications · 2025Article
- Timescale of environmental change modulates metabolic guild cohesion in microbial communities.The ISME journal · 2025Article
- Metabolic labour division trade-offs in denitrifying microbiomes.The ISME journal · 2025Review
- Genetic and species rearrangements in microbial consortia impact biodegradation potential.The ISME journal · 2025Article
- Environmental modulators of algae-bacteria interactions at scale.Cell systems · 2024Article
- Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
8 authors.
Funding
Abstract
Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.