从单基因到基因组研究河湾流域稀有和优势微生物演替规律与机制

Recent advances in high-throughput sequencing technologies revealed that microbial communities are characterized by a few number of dominant taxa in high abundance and a long tail of rare taxa in low abundance. Some rare taxa may conditionally bloom under favorable environmental conditions and conduct important eco-processes. Yet, more studies are needed to explore how dominant and rare taxa change among communities, so as to understand the succession of microbial community structures and further explore their ecological functions. Coastal urban areas are land-sea transitional zones with complex natural and anthropogenic disturbances. The microbial community structure in coastal waters and sediments changes spatially and temporally under such environmental stress. Thus, they present unique ecosystems allowing us to study ecological succession of rare and dominant prokaryotes. In this study, we will investigate the microbial community structure in the waters and sediments of Shenzhen River-Bay Watershed in order to reveal the roles and contribution of rare and dominant prokaryotes by 16S rRNA/rDNA gene, metagenome and metatranscriptome sequencing. First, microbial community structures will be studied through 16S rRNA/rDNA gene sequencing to examine whether rare and dominant taxa show similar or different spatiotemporal succession patterns along a river-bay continuum. Next, we also attempt to explore how dominant and rare taxa change among communities, and reconstruct the genomes of key species with abundance varying from rare to dominant from the metagenomic and metatranscriptomic data, and their ecological functions and stress-adaptation mechanisms will be analyzed. This study will allow us to have a better understanding of the succession patterns, metabolic potentials and ecological roles of rare and dominant microbes in Shenzhen River-Bay Watershed.

随着高通量测序技术快速发展，人们认识到微生物群落由少量高丰度的优势类群和大量低丰度的稀有类群组成。在适宜的环境条件下，稀有类群可转换为优势类群，主导重要生态过程。然而，稀有和优势微生物转换过程、演替规律和生态功能有待进一步研究。滨海城市河流-海湾区域作为陆海交互区，受人类活动干扰程度高，其中微生物群落时空演替活跃，为研究群落演替规律提供了理想环境。本研究以深圳河湾流域为研究区域，将扩增子、宏基因组及宏转录组三种组学手段结合，试图揭示稀有和优势微生物群落在河湾流域生态系统中的作用与贡献：1）采用16S rRNA和rDNA高通量测序考察稀有微生物群落沿河流-海湾连续体是否存在与优势微生物群落一样的时空演替规律；2）研究发生优势和稀有转换微生物的时空演替特征，在基因组和转录组水平明确参与转换的典型微生物功能及适应机制。本研究将有助于更加深入认知河湾流域稀有微生物群落演替规律、代谢潜能及生态作用。

浮游生物是水生态系统的重要组成部分，包括浮游植物、浮游动物、浮游细菌等类群，在维持水生态系统功能和过程中发挥重要作用。在全球变化背景下，河湾生态系统正经历着物种多样性和生态系统完整性的快速丧失阶段。然而，我们对河湾浮游生物的地理分布格局和影响其多样性的生态因子了解还十分有限。本研究综合采用分子生物学方法研究典型亚热带河湾浮游生物群落组成特征，并对导致微生物群落变化的地理和环境因子进行解析，揭示浮游生物时空分布规律和可能的生态学驱动机制。主要研究内容和结果如下：.自由生和颗粒附着态微生物在水生态系统的营养物质循环中扮演着重要的角色。然而，对它们的构建过程、功能及相互作用知之甚少。基于Illumina高通量测序方法分析干季和湿季分粒径浮游生物样本，本研究调查深圳河湾系统浮游细菌和古菌群落构建过程及共现性。结果发现细菌和古菌群落具有明显的分布格局，群落组成随粒径（自由生vs.颗粒附着态），生境（河流vs.河口）和季节（干季vs.湿季）不同而存在明显差异。尽管决定性因素和随机性因素都显著影响细菌和古菌群落构建过程，中性模型揭示细菌群落比古菌群落具有更强的随机性。零和模型显示，同质选择对自由生浮游细菌构建的贡献较高，而其对颗粒吸附态古菌的贡献较高。细菌和古菌群落组成变化及构建过程与盐度和水温关系最为密切。包含非性线关系的网络分析结果显示，相比自由生微生物群落，颗粒吸附态微生物群落内部物种之间具有更强的连接性。这些发现扩展了当前对海湾生态系统分粒径浮游生物动态和其驱动机制以及细古菌相互作用的认知。

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