Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Post Office Box 775, Cambridge, MD 21613, USA.
Department of Earth, Ocean, and Atmospheric Science, Florida State University, 117 North Woodward Avenue, Tallahassee, FL 32306-4520, USA.
Science. 2017 Dec 1;358(6367):1149-1154. doi: 10.1126/science.aan5712.
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.
海洋生态系统模型已经发展到可以纳入基因组测序发现的代谢途径，但模型和“组学”数据之间直接比较的情况很少。我们开发了一种可以直接模拟宏基因组和宏转录组的模型，以便与观测结果进行比较。模型微生物被随机分配用于专门功能的基因，并且在大西洋中模拟了 68 个物种的群落。不适应的生物被替换，模型自我组织以开发群落基因组和转录组。从不同随机生成微生物队列初始化的模拟中出现的新兴群落都产生了现实的海洋垂直和水平营养、基因组和转录组梯度。因此，群落可用的基因功能库，而不是特定生物体之间功能的分布，驱动了模型海洋中的群落组装和生物地球化学梯度。
