2017/11/30 by Victoria J. Coles, Michael R. Stukel, Maureen T. Brooks +8 · 4 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Environmental Science · #Biogeochemical cycle #Biogeochemistry #Biology #Computational biology #Computer science #Ecology #Ecosystem #Evolutionary biology #Gene #Genetics #Genome #Genomics #Genomics and Phylogenetic Studies #Geology #Marine and coastal ecosystems #Marine ecosystem #Metagenomics #Microbial Community Ecology and Physiology #Oceanography #Trait #Transcriptome
paper · pdf · doi:10.1126/science.aan5712
openalex publication_date 2017/11/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.