Environmentally dependent interactions shape patterns in gene content across natural microbiomes

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 observe...

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Published inNature microbiology Vol. 9; no. 8; pp. 2022 - 2037
Main Authors Crocker, Kyle, Lee, Kiseok Keith, Chakraverti-Wuerthwein, Milena, Li, Zeqian, Tikhonov, Mikhail, Mani, Madhav, Gowda, Karna, Kuehn, Seppe
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.08.2024
Nature Publishing Group
Subjects
631/158/853
631/57
639/766/747
Acidic soils
Bacteria - classification
Bacteria - genetics
Bacteria - metabolism
Biomedical and Life Sciences
Community composition
Denitrification
Enrichment
Environmental conditions
Genes
Genotype
Genotypes
Hydrogen-Ion Concentration
Infectious Diseases
Life Sciences
Medical Microbiology
Metabolism
Metagenomics
Microbiology
Microbiomes
Microbiota - genetics
NAR gene
Nitrogen
Oceans
Parasitology
pH effects
Phenotypes
Physics
Soil - chemistry
Soil Microbiology
Soil microorganisms
Surveys
Taxonomy
Virology
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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. Global soil sequencing data and enrichment experiments show trade-offs in denitrification phenotypes driven by pH, underscoring how the environment shapes ecological interactions and gene content.
AbstractList 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.
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. Global soil sequencing data and enrichment experiments show trade-offs in denitrification phenotypes driven by pH, underscoring how the environment shapes ecological interactions and gene content.
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.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.
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.Global soil sequencing data and enrichment experiments show trade-offs in denitrification phenotypes driven by pH, underscoring how the environment shapes ecological interactions and gene content.
Author Li, Zeqian
Gowda, Karna
Lee, Kiseok Keith
Kuehn, Seppe
Crocker, Kyle
Chakraverti-Wuerthwein, Milena
Mani, Madhav
Tikhonov, Mikhail
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  givenname: Milena
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  surname: Chakraverti-Wuerthwein
  fullname: Chakraverti-Wuerthwein, Milena
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  givenname: Karna
  orcidid: 0000-0001-6812-4745
  surname: Gowda
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  email: karna.gowda@gmail.com
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Snippet Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental...
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SubjectTerms 631/158/853
631/57
639/766/747
Acidic soils
Bacteria - classification
Bacteria - genetics
Bacteria - metabolism
Biomedical and Life Sciences
Community composition
Denitrification
Enrichment
Environmental conditions
Genes
Genotype
Genotypes
Hydrogen-Ion Concentration
Infectious Diseases
Life Sciences
Medical Microbiology
Metabolism
Metagenomics
Microbiology
Microbiomes
Microbiota - genetics
NAR gene
Nitrogen
Oceans
Parasitology
pH effects
Phenotypes
Physics
Soil - chemistry
Soil Microbiology
Soil microorganisms
Surveys
Taxonomy
Virology
Title Environmentally dependent interactions shape patterns in gene content across natural microbiomes
URI https://link.springer.com/article/10.1038/s41564-024-01752-4
https://www.ncbi.nlm.nih.gov/pubmed/38977908
https://www.proquest.com/docview/3090081317
https://www.proquest.com/docview/3077176177
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