Unraveling mechanisms of microbial community assembly using naturally replicated microbiomes

微生物群落在人类健康、工业生物技术和全球气候调节方面发挥着重要作用。人们通常认为，微生物群落的种类和功能组成是由中性和确定性组装过程控制的。本研究旨在系统地了解这些过程与群落的分类多样性、单个分类群的功能专业化程度和生态组织规模之间的相对影响。具体来说，它将检验以下假设：(i)中性过程对于分类单元丰富的群落更重要，而确定性过程对于相同大小的分类单元贫乏的群落更重要。（ii）中性过程对基材通才更重要，而确定性过程对基材专才更重要。（iii）中性过程在官能团内部更为重要，而确定性过程在官能团之间更为重要。为了验证这些假设，拟议中的研究将利用一种独特的系统，即最近在位于特立尼达和多巴哥的沥青湖的微小水滴中发现的微生物群落。沥青湖是世界上最大的天然石油渗漏点。这些微生物组是研究群落聚集的理想选择，因为它们代表了在长期孤立和空间和时间同质环境中进化的自然复制群落。该项目将通过16S rRNA基因扩增子测序分离和确定100个水滴群落的分类组成。然后，个体分类群将根据其功能基因被分配到具有相似生态功能的群体中，这将通过使用单细胞技术对几个水滴微生物组的微型宏基因组进行测序来确定。最后，将随机模拟应用于生成具有中性分类群和功能群模式的合成群落。这样就可以对中性和观察到的数据进行统计比较，并在群落规模、基质专业化和生态组织水平方面对中性过程和确定性过程进行区分。获得的见解将进一步提高我们预测和管理复杂微生物群落的能力。

Microbial consortia fulfill important functions for human health, industrial biotechnology and global climate regulation. It is often believed that the species and functional composition of microbial communities is controlled by neutral as well as deterministic assembly processes. The proposed research aims at obtaining a systematic understanding of the relative impact of these processes depending on the taxonomic diversity of the community, the degree of functional specialization of individual taxa, and the scale of ecological organization. Specifically, it will test the hypotheses that(i) neutral processes are more important for more taxon-rich communities, whereas deterministic processes are more important for taxon-poor communities of the same size.(ii) neutral processes are more important for substrate generalists, whereas deterministic processes are more important for substrate specialists. (iii) neutral processes are more important within functional groups, whereas deterministic processes are more important between functional groups. To test these hypotheses the proposed research will make use of a unique system, microbial consortia that have recently been discovered within tiny water droplets at Pitch Lake, the largest natural oil seep of the world situated in Trinidad and Tobago. These microbiomes are ideal for the study of community assembly as they represent naturally replicated communities that have evolved for a long period in isolation and within a spatially and temporally homogeneous environment. The project will proceed by isolating and determining the taxonomic composition of 100 water droplet communities using amplicon sequencing of the 16S rRNA gene. Individual taxa will then be assigned to groups of similar ecological function based on their functional genes, which will be determined by sequencing the mini-metagenomes of several water droplets microbiomes using single-cell techniques. Finally, stochastic simulations will be applied to generate synthetic communities with neutral taxon and functional group patterns. This allows for a statistical comparison of neutral and observed data and for a discrimination between neutral and deterministic processes with respect to community size, substrate specialization and the level of ecological organization. The obtained insights will further advance our ability to predict and manage complex microbial communities.