渤海及比邻海域的核心微生物组及其探讨

	渤海及比邻海域的核心微生物组及其探讨
	王斌1,2
学位类型	博士
导师	胡晓珂
	2017-05-09
学位授予单位	中国科学院大学
学位授予地点	北京
关键词	近海微生物生态系统微生物生态网络核心微生物组
摘要	微生物是海洋生态系统中分解者、消费者、生产者三位一体的重要组成部分。因此研究近海微生物生态系统对维持近海生态系统的健康稳定具有重要意义。近海微生物生态系统的组织结构是研究近海微生物生态系统的基础问题。微生物构建稳定微生物生态系统的策略是这一研究方向的前沿科学问题。关于这一问题的研究目前处在从群落组成到网络及模型的阶段。渤海是位于中国北方的半封闭边缘海，是中国北方的重要渔业经济区。渤海生态系统的健康稳定是环渤海地区可持续发展先决条件。由于关注渤海微生物生态系统对修复保护渤海生态环境具有重要的意义，因此本研究以渤海及其比邻海域细菌群落为代表，探索“渤海及比邻海域细菌群落维持稳定生态系统的策略”这一重要的前沿科学问题。我们的研究结果表明：（1）通过搭载2013年10月至2016年2月共计7次渤海调查航次，获得了渤海及其比邻海域127个表层沉积物及116个水体样本。借助高通量测序技术并以16S rRNA V4+V5区为标记基因，我们获得了上述样本中的细菌群落组成数据。根据采样时间和样本类型，数据被分为6组表层沉积物及5组水体细菌群落数据。群落分析结果表明，渤海及其比邻海域表层沉积物中的广分布类群包括30个纲、50个科以及18个属，这一数据在水体中为27个纲、58个科、36个属。（2）通过构建细菌生态网络并分析其拓扑属性，在科水平上获得了13类核心微生物的代表性类群，包括Cryomorphaceae、Dehalococcoidaceae、Desulfobacteraceae、Desulfobulbaceae、Flavobacteriaceae、koll13、Pirellulaceae、Piscirickettsiaceae、Planctomycetaceae、Rhodobacteraceae、Rhodospirillaceae、Saprospiraceae、Thermodesulfovibrionaceae。通过分析这些代表性核心微生物的特征，我们提出了渤海及其比邻海域核心微生物组假说：渤海及其比邻海域的微生物通过彼此之间复杂的互作关系构成了应对环境变化的主体—微生物生态网络；渤海及比邻海域的微生物群落在响应环境变化的过程中会倾向于选择对环境具有广泛适应性且具有重要生态功能的微生物、以及可以应对特殊环境胁迫压力的微生物作为核心微生物。（3）作为对核心微生物组假说的验证性讨论，我们探索了基于核心微生物组的胁迫响应策略。我们分析了两次独立的渤海沉积物中微生物群落对石油烃胁迫的响应实验，结果表明两次独立实验的结论一致。微生物群落以形成在功能基因上存在互补的功能菌群的方式来共适应石油烃胁迫并重建稳态，核心微生物在其中具有重要作用；部分第一类具有广泛适应性的核心微生物（如黄杆菌及红杆菌）在重度胁迫的条件下仍然存在且表现出核心地位；同时一些具有石油烃降解功能的微生物如赤杆菌成为新的第二类核心微生物。此外，微生物群落对石油烃胁迫的响应因石油烃结构的不同而不同，第二类核心微生物也会因石油烃结构的不同而存在差异。（4）进一步地，我们探索了渤海及比邻海域的核心微生物组对环境中非生物因素与生物因素的响应。我们探索了渤海及比邻海域表层水体中的核心微生物与环境因子、浮游植物之间的关系，以及蓬莱19-3溢油事故海域表层沉积物中细菌群落、核心微生物组与环境因子之间的关系。结果表明渤海及比邻海域的核心微生物组受营养盐水平影响显著，包括但不限于硝态氮、铵态氮、硅氮比、氮磷比。渤海及比邻海域浮游细菌与浮游植物在相对丰度上明显相关，如具有溶藻潜能的CFB菌群丰度与浮游植物的丰度负相关，表明渤海及比邻海域核心微生物与浮游植物群落之间存在紧密联系。（5）海峡的特点、外海入侵以及人类活动造就了渤海海峡的特殊性，因此我们以2013年冬季及2014年夏季渤海表层沉积物中细菌群落为研究对象进一步探索了它们对外海输入及人类活动的响应。结果表明，渤海海峡海域的优势菌包括γ-变形杆菌、δ-变形杆菌以及芽孢杆菌，其中芽孢杆菌的优势来源于与渔业疾病有关的微生物Lactobacillus属与Lactococcus属；基于PICRUSt的预测结果，渤海海峡的反硝化细菌群落主要属于γ-变形杆菌纲、鱼类立克次体科；影响渤海海峡海域微生物群落结构的主要因素是硝态氮及总碳；渔业活动及黄海暖流的入侵可能加剧了人类活动对该海域的微生物群落及生态功能的影响。
其他摘要	Microorganisms, as the trinity of decomposer, consumer and producer, play key roles in marine ecosystem. Investigations on the coastal microbial ecosystem are crucial for the healthy and stable development of costal ecosystem. The assemblage of microbial ecosystem is a fundamental question. How to keep stable microbial ecosystem is a frontier scientific issue in this topic. Current researches on the question are on the transition from the community compositions to the network and models. The semi-closed marginal Bohai Sea, an important fishery located in the northern China, presents importance for the sustainable development of Circum-Bohai Sea Region. Laying emphasis on the microbial ecosystem is therefore critical for the ecology health of Bohai Sea. This study with the topic of microbial communities in Bohai Sea and its adjacent sea aimed to focus on the important scientific question “How to keep stable microbial ecosystem in Bohai Sea”? (1) During the seven scientific investigation voyages to Bohai Sea from Oct, 2013 to Feb, 2016, 127 surface sediments and 116 water samples were collected. With high throughput sequencing and the marker gene 16S rRNA V4+V5, the microbial communities in the mentioned samples above were investigated in this study. The samples were divided into 6 and 5 groups according to the sampling time and the samples' type. The compositions analysis revealed that the ubiquitous populations were comprised by 30 classes, 50 families and 18 genera in sediments and 27 classes, 58 families and 36 genera in the water. (2) Based on the topological attributes of the microbial network, 13 families were identified to compose the representatives of the core microbiome. They were Cryomorphaceae, Dehalococcoidaceae, Desulfobacteraceae, Desulfobulbaceae, Flavobacteriaceae, koll13, Pirellulaceae, Piscirickettsiaceae, Planctomycetaceae, Rhodobacteraceae, Rhodospirillaceae, Saprospiraceae and Thermodesulfovibrionaceae. The characteristics of the core microbiome suggested a first proposed hypothesis, that is, the response body of microbial communities to the changing environments in Bohai Sea is the microbial ecological network comprised by the microbes and the complex interactions among them; the microbial communities prefer to choose two types of microbes to be the core microbiome in the response process, the microbes are those with broad adaptability and important ecological functions (type I) and those with specific ability in response to special environmental conditions such as pollution and anaerobism (type II). (3) As the confirmatory discussion of the hypothesis, we studied the core microbiome under the serious stress. Two separate studies on the response of the microbial communities to the hydrocarbon pollutions were analyzed and indicated accordant conclusions. By forming the functional groups with complementary genes function, the microbial communities co-acclimated the stress from hydrocarbon pollutions and rebuilt the steady stable, in which process the core microbiome play crucial roles. Some type I key families, for instance, Flavobacteriaceae and Rhodobacteraceae, still occured and play key roles despite the serious stress by hydrocarbon. At the same time, some hydrocarbon degrading phylotypes such as Erythrobacter were enriched and worked as the newcome type II core microbiome. The responses of microbial communities to the stress were different, as well as the newcome type II core microbiome, resulting from the strcuturally different hydrocarbons. (4) With the purpose of further investigation on the core microbiome’s response to the changing environmental conditions, the relationships between the core microbiome in the surface water and the environmental variables and the phytoplankton communities were studied in Bohai Sea. The relationships between the surface sediments microbial communities including the core microbiome and the environmental variables in the region where the Penglai 19-3 oil spill accidents occurred in were explored. The results indicated that the structure of microbial communities in the surveyed regions were driven by the nutrients level including, but not limited to, the contents of nitrate and ammonium, Si/N and N/P. The significant correlations between the microbial communities in the surface water and the phytoplankton communities, for instance, the algicidal members from CFB groups (Cytophaga-Flavobacterium-Bacteroides) mainly negatively correlated with the phytoplankton indicated tight relationship between the core microbiome and the phytoplankton communities in Bohai Sea. (5) The characteristics of straits, oceanic inputs and anthropogenic influences lead to the particularity of Bohai Strait. Another related study was therefore carried out in Bohai Strait in the winter, 2013 and in the summer, 2014 to investigate the responses of microbial communities in Bohai Sea to the oceanic inputs and human activities. The microbial communities in the surface sediments in the surveyed region were investigated. The dominant groups in the samples were Gammaproteobacteria, Deltaproteobacteria and Bacilli at class level. The high relative abundance of Bacilli was contributed by the genera Lactobacillus and Lactococcus, both of the two genera maybe related to the fish disease. By applying the metagenome prediction software PICRUSt, the denitrifying bacteria in the samples were predicted, and the results indicated that the family Piscirickettsiaceae and the class Gammaproteobacteria pre-dominated the dentrifying bacteria. The contents of nitrate and total carbon were two major drivers of microbial communities in the surveyed region. The fishery and the inputs of Yellow Sea Warm Current may indirectly influence the structure and ecological functions of microbial communities. Key Words: Costal Microbial Ecosystem; Microbial Ecological Network; Core Microbiome
文献类型	学位论文
条目标识符	http://ir.yic.ac.cn/handle/133337/22461
专题	中国科学院烟台海岸带研究所知识产出_学位论文
作者单位	1.中国科学院烟台海岸带研究所 2.中国科学院大学
第一作者单位	中国科学院烟台海岸带研究所
推荐引用方式 GB/T 7714	王斌. 渤海及比邻海域的核心微生物组及其探讨[D]. 北京. 中国科学院大学,2017.

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