title: "Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.
abstract: The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as "everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Italy Computational Biology Group, University of Florence, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, Finland.
authors.forename: Antti
authors.initials: A
authors.lastname: Karkman
authors.affiliation: Department of Environmental Systems Science, ETH Zürich, Switzerland Department of Aquatic Ecology, Eawag, Switzerland.
authors.forename: Manu V
authors.initials: MV
authors.lastname: Tamminen
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Italy Computational Biology Group, University of Florence, Italy.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Bosi
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, Finland.
authors.forename: Marko
authors.initials: M
authors.lastname: Virta
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Italy Computational Biology Group, University of Florence, Italy.
authors.forename: Renato
authors.initials: R
authors.lastname: Fani
authors.affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology.
authors.forename: Eric
authors.initials: E
authors.lastname: Alm
authors.affiliation: Department of Biology, National University of Ireland Maynooth, County Kildare, Ireland Computational Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, United Kingdom james.mcinerney@manchester.ac.uk.
authors.forename: James O
authors.initials: JO
authors.lastname: McInerney
mesh_terms: D044822:Biodiversity; D004463:Ecology; D004777:Environment; D051456:Gene Flow; D053263:Gene Regulatory Networks; D033141:Genetic Determinism; D049810:Genetic Speciation; D005843:Geography; D006801:Humans; D008827:Microbiological Phenomena
keywords: antibiotic resistance; biogeography; horizontal gene transfer