原生动物在水体生态系统中通过捕食链和腐生链参与碳、氮、磷等关键生源要素循环和能量流动，从而对水体初级生产、环境自净和水产养殖等具有重要的意义。然而，原生动物分类和生态研究一直都受形态鉴定制约，使得大规模、系统性研究其时空演替规律及相关生态功能受到了一定限制。伴随着针对细菌、真菌等微生物群落宏基因组研究的推广，我们探讨了对不同环境原生动物群落进行高通量测序分析，结果证明是切实可行的。本课题以淡水养殖水体这一受人类生产活动直接影响的生态系统为对象，围绕不同养殖水体原生动物群落系统发育多样性的形成和维持机制、原生动物与养殖鱼类的相互关联和影响机制、以及原生动物对水产养殖的贡献和环境预警作用开展研究，重点阐述原生动物群落构建和演替规律及其对水产养殖的生态学意义。这不仅能增强我们对淡水养殖水体原生动物生态功能的认识，而且也可为养殖水环境的健康和可持续发展提供科学依据，具有重要理论研究和实际应用价值。

Protozoa in the aquatic ecosystem link different trophic levels together through saprophytic and/or predatory chains, they play important roles in the biogeochemical cycling of carbon (C), nitrogen (N) and phosphorus (P), and are also of great importance to energy flow. Therefore, the protozoa community as a whole makes significant contribution to the primary production and natural purification in aquatic ecosystem, which further provides ecosystem service for aquaculture. However, most studies of protozoa taxonomy and ecology have been restricted to morphological identification, which has historically been a difficult task (even for seasoned taxonomists) due to the lack of distinguishing features for many of these small eukaryotes. Therefore, the methods available have greatly restricted large scale and systematic study to understand the spatiotemporal turnover and some other related ecological functions of protozoa community. Accompanying the extend of metagenomic analysis to the natural communities of bacteria and fungi from various types of environments; we explored the possibility of applying high-throughput sequencing analysis for studying the eukaryotic protozoa communities collected from different environments. Targeting the fresh water bodies for aquaculture, which directly affected by the human activities, this proposal will focus on the following three tasks: i) uncover the mechanisms that govern the phylogenetic diversity of protozoa communities in different water bodies that used for aquaculture; ii) elucidate the relationships between protozoa and fishes in particular water bodies, and reveal their mutual responses to each other; iii) how the protozoa community contribute to aquaculture and how it reflect the water environments. The goal of this study is to reveal the assembly and turnover of freshwater protozoa communities and its ecological significances for aquaculture. All of these works will not only strength our understanding of ecological functions of protozoa community in the fresh water bodies for aquaculture, but will also provide us necessary biological evidences for healthy and sustainable development of water environments that used for aquaculture. In a word, this study is of great importance for both academic study and practical application.