A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
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DOI：
10.1038/s41598-020-60130-2
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发表时间：
2020-02-24
影响因子：
4.6
通讯作者：
Mehta, Pankaj
中科院分区：
文献类型：
--
作者：
Marsland, Robert, III;Cui, Wenping;Mehta, Pankaj
对微生物生物多样性的调查，如地球微生物组计划(EMP)和人类微生物组计划(HMP)，揭示了不同环境中强大的生态模式。生态学的一个主要目标是利用这些模式来确定塑造微生物生态系统的生态过程。一种有希望的方法是使用最小模型，这些模型可以将微生物规模的机械性假设与社区水平的模式联系起来。在这里，我们通过展示微生物消费者资源模型(MiCRM)--具有资源竞争、代谢交叉喂养和随机定居的微生物群落的最小模型--可以定性地再现调查数据中的模式，包括组成梯度、不同/重叠相关性、丰富度/粗糙度相关性和群落组成的嵌套性。通过使用MiCRM生成不同环境和分类结构的合成数据，我们表明，通过考虑在恶劣环境中生存的能量成本，EMP中的大规模模式可以重现，而HMP模式可能反映了环境过滤在塑造竞争中的重要性。我们还表明，最近在HMP中发现的不同-重叠相关性可能来自共享相似环境的社区，而不是反映普遍的动态。我们确定了参数中具有生态意义的变化，这些变化改变或破坏了这些模式中的每一个，为进一步研究提出了新的机制假设。这些发现突显了微生物生态学最小模型的前景。
Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) - a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization - can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.