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

Authors

  • Jeroen Raes,

    1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    2. Molecular and Cellular Interactions Department, VIB – Vrije Universiteit Brussel, Brussels, Belgium
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  • Ivica Letunic,

    1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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  • Takuji Yamada,

    1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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  • Lars Juhl Jensen,

    1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    2. NNF Center for Protein Research, Copenhagen, Denmark
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  • Peer Bork

    Corresponding author
    1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    2. Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
    • Corresponding author. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany. Tel.: +49 6 221 387 8526; Fax: +49 6 221 387 8517; E-mail: bork@embl.de

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Abstract

Using metagenomic ‘parts lists’ to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20°N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology.

Synopsis

Metagenomics (shotgun sequencing of pooled DNA of complete microbial communities) is widely used to investigate ecosystem functioning of environmental and clinical samples. However, the nature of this data (usually a gigantic collection of gene fragments of 1000s of organisms) makes it very hard to infer global patterns on microbial ecology of the environment at hand. To address important ecological questions such as ‘How do microbial communities adapt to the environmental conditions?’, ‘What drives the functional variation across the globe and to what extent do genes disperse?’ and ‘What drives variation of CO2 uptake across different locations and communities?’, we integrated 25 ocean metagenomes from the Global Ocean Sampling project with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the functional and phylogenetic composition of an environment and the main limiting factor on whether functions dispersal across the planet. We find a distinct latitudinal gradient in the size and diversity of the functional repertoire of ocean microbial communities, peaking at 20°N, and which correlates with oceanic CO2 uptake. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes can be used as quantitative predictor for molecular trait-based biogeography and ecology.

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