海洋微生物覆盖了细菌、古菌和真核三个生物域，在海洋生态系统中扮演着重要角色。探究海洋微生物群落多样性、空间分布格局及其主要控制因子，有助于加深对海洋微生物参与的生态系统过程的了解。本研究利用以16S rRNA和18S rRNA基因为分子标记的高通量测序技术，对我国近海（渤海海峡、南黄海）以及从近海到开阔大洋（渤海中部-南黄海-西太平洋）梯度上的三域微生物（细菌、古菌、真核微生物）群落分布格局及驱动因素进行分析，主要结果如下：

（1）渤海海峡表层水体细菌群落表现出显著的季节差异和空间差异。聚球藻属（Synechococcus）、Family I不可鉴定类群等在夏季具有明显优势，而远洋杆菌属（Pelagibacter）、OM43 clade等在冬季更具优势，群落结构的季节差异主要是由水温和营养盐（亚硝酸盐、磷酸盐）浓度的剧烈变化引起的。渤海海峡表层水体中细菌群落的空间异质性与已测定的局部环境因子（温度、盐度、无机营养盐浓度）及空间因子（地理距离）的相关性较弱，但与浮游植物群落结构有较好的耦联关系。弧菌科、Family I、Sva0996 marine group、Surface 2中的不可鉴定类群与具槽帕拉藻（Paralia sulcata）、夜光藻（Noctiluca scintillans）、圆筛藻（Coscinodiscus spp.）等浮游植物优势类群的分布有紧密联系。呈现出斑块分布特征的细菌类群，如SAR11 clade、弧菌科（Vibrionaceae）不可鉴定类群、Sva0996 marine group不可鉴定类群等，在对有机质利用的生态位上有着明显差异。总体上，渤海海峡表层水体的细菌群落空间差异性与局部环境的异质性更为相关，而水动力影响了细菌群落的α多样性。

（2）南黄海的冷水团区和非冷水团区（苏北沿岸区）中下层水体中的三域微生物群落组成和α多样性都有显著差异。冷水团区中下层水体由于水交换较弱，微生物α多样性（除真核微生物的Shannon、Shannoneven指数以外）显著低于非冷水团区，然而真核微生物Shannon和Shannoneven指数在冷水团区中下层水体显著高于非冷水团区中下层水体，反映出真核微生物在冷水团内部受到扰动较少。冷水团区中下层三域微生物群落组成的特殊性与该区域水深较深，溶解氧（DO）、盐度、磷酸盐（PO₄-P）浓度较高，以及水温、溶解无机氮（DIN）浓度较低有关，水深对微生物群落影响最显著，其次是水温。Clade Ia（SAR11）与DO浓度，Candidatus Nitrosopumilus、海金藻纲（Pelagophyceae）与水深、盐度，以及共甲藻（Syndiniales）、硅藻（Bacillariophyta）、放射虫RAD-B与DIN、硅酸盐（SiO₃-Si）浓度之间都有密切的联系。微生物共现网络显示，冷水团区的微生物网络较非冷水团区的网络更为简单，但互斥关系所占比例较非冷水团区高，反映出冷水团环境中的微生物对有限资源的竞争加剧。

（3）通过对渤海中部、南黄海（冷水团区和苏北沿岸区）、西太平洋（西部海域）三域微生物群落的对比分析发现，细菌和真核微生物在渤海中部、南黄海的物种丰富度（物种数、Chao、ACE）和多样性（Faith’s PD、Shannon、Shannoneven）都高于西太平洋，古菌物种丰富度也呈同样趋势，但多样性呈相反趋势。黄杆菌科（Flavobacteriaceae）、Clade I（SAR11）、Cyanobiaceae科、Nitrosopumilaceae科、共甲藻纲（Syndiniales）、甲藻纲（Dinophyceae）等在渤海中部、南黄海更占优势，而交替单胞菌科（Alteromonadaceae）、假单胞菌科（Pseudomonadaceae）、Marine group II（MGII）、Marine group III（MGIII）等在西太平洋更占优势。寡营养类群SAR11、SAR86、SAR116在渤海中部和南黄海的相对丰度较西太平洋高一个数量级；黄杆菌科（Flavobacteriaceae）、Candidatus Nitrosopumilus不同的子类群分别在近海和开阔大洋占优势；交替单胞菌科（Alteromonadaceae）（29.4%）在西太平洋1000~4000 m水深处较丰富；子囊菌纲（Ascomycota）（24.1%）、担子菌纲（Basidiomycota）（6.5%）在西太平洋3000~4000 m水深处较丰富；此外，还观测到MGII在西太平洋表层古菌群落中相对丰度高达58.2%。地理距离、局部理化环境因子（水温、盐度、DIN、PO₄-P、SiO₃-Si）、水深对三个海区微生物群落组成都有显著影响（P < 0.001），地理距离对细菌群落组成影响最显著，而局部环境因子对古菌和真核微生物群落组成影响最显著，但各因子对细菌群落的影响都较古菌和真核微生物弱。

综上，从中等尺度上，渤海海峡细菌群落和南黄海三域微生物群落空间分布受局部因素的影响更显著；从大尺度上，局部环境因素和空间因素都是驱动微生物群落从近海（渤海中部、南黄海）到开阔大洋（西太平洋）空间分布的重要因素。三域微生物分布格局的驱动因素有所不同，古菌、真核微生物对局部环境因素的响应强于细菌。

Marine microorganisms cover the three domains of life, i.e. Bacteria, Archaea and Eukarya, and play an important role in marine ecosystem. Exploring the spatial pattern of marine microbial diversity and its main controlling factors will deepen our understanding of the ecosystem processes in which marine plankton participate. In this study, using 16S rRNA and 18S rRNA gene high-throughput sequencing technology, we studied the distribution patterns and driving factors of microbial (bacterial, archaeal and microbial eukaryotic) communities in China coastal waters (the Bohai Strait, the southern Yellow Sea) and along the coastal-to-open ocean gradient (the central Bohai Sea-the southern Yellow Sea-the western Pacific). The main results are as follows:
(1) The bacterial community in the surface waters of the Bohai Strait showed remarkable seasonal and spatial differences. In response to the dramatic changes of temperature and nutrient (NO2-N and PO4-P) levels between seasons, Synechococcus and unclassified taxa in Family I predominated in summer, while some oligotrophic taxa (e.g., Pelagibacter, OM43 clade) are more abundant in winter. The spatial heterogeneity and patchiness of bacterial assemblages in the Bohai Strait had a weak correlation with the measured environmental factors (temperature, salinity and concentrations of inorganic nutrients) as well as the spatial factor (geographic distance), however, they showed a significant correlation with the phytoplankton community structure. Unclassified taxa within Vibrionaceae, Family I, Sva0996 marine group and Surface 2, were closely linked to the abundant phytoplankton taxa Paralia sulcata, Noctiluca scintillans, and Coscinodiscus spp. The bacterial taxa that were distributed in patchiness, e.g., SAR11 clade, unclassified taxa within Vibrionaceae and Sva0996 marine group, possess differentiated niches for utilization of organic matters. Besides, the distribution of OM43 clade was almost consistent with the area affected by the coastal current. In general, the spatial heterogeneity of bacterial communities were closely related to the heterogeneity of local environmental factors in the surface waters of the Bohai Strait, and the α-diversity of bacterial communities were influenced by the hydrodynamics.
(2) The microbial community composition across three domains and their α-diversity were significantly different in the deep waters between the cold water mass region (CWMR) and the outer region (OR, the region of the Northern Jiangsu coast) of the southern Yellow Sea. The microbial α-diversity in the deep waters of the CWMR was significantly lower than that of the OR, which was mainly due to the weak water exchange between the inner cold water mass and the external water column, while the Shannon and Shannoneven diversity indices of microbial eukaryotic community were significantly higher in the deep waters of the CWMR than of the OR, suggesting the less disturbance on the microbial eukaryotic communities in the cold water mass. The greater depth, the higher levels of DO, salinity and PO4-P concentration, and the lower water temperature and DIN concentration were responsible for the distinct microbial community composition in the cold water mass. Among these factors, water depth had the most significant effect on the microbial community structure, followed by water temperature. Close relationships were found between SAR11 Clade Ia and DO concentration, between Candidatus Nitrosopumilus, Pelagophyceae and water depth, salinity, and between Syndiniales, Bacillariophyta, RAD-B and DIN, SiO3-Si concentrations. According to the microbial co-occurrence networks, the network structure in the deep waters of the CWMR was less complex than that in the deep waters of the OR, but the proportion of mutual exclusion relationship was higher than that in the OR, which could be attributed to the intensified competition for limited resources among microorganisms in the environment of the cold water mass.
(3) By comparing the microbial communities across three domains in the central Bohai Sea, the southern Yellow Sea (the CWMR and the the region of the Northern Jiangsu coast) and the western Pacific (western area), we found that for bacterial and microbial eukaryotic communities, species richness (observed species, Chao, and ACE) and diversity (Faith’s PD, Shannon, and Shannoneven) in the central Bohai Sea and the southern Yellow Sea were higher than in the western Pacific; for archaeal communities, species richness displayed a similar trend, but diversity displayed a reverse trend. Flavobacteriaceae, SAR11 Clade I, Cyanobiaceae, Nitrosopumilaceae, Syndiniales, Dinophyceae, etc., had significantly higher relative abundances in the central Bohai Sea and the southern Yellow Sea. In contrast, Alteromonadaceae, Pseudomonadaceae, Marine group II (MGII) and Marine group III (MGIII) were more abundant in the western Pacific. The relative abundances of the oligotrophic taxa SAR11, SAR86 and SAR116 in the central Bohai Sea and the southern Yellow Sea were an order of magnitude higher than those in the western Pacific. Different sub-taxa within Flavobacteriaceae and Candidatus Nitrosopumilus were abundant in coastal areas and open ocean. Alteromonadaceae (29.4%) were relatively abundant at the depth of 1000~4000 m in the western Pacific, while Ascomycota (24.1%) and Basidiomycota (6.5%) were relatively abundant at the depth of 3000~4000 m in the western Pacific. In addition, the relative abundance of MGII in the surface waters of the western Pacific was up to 58.2%. Geographical distance, local physicochemical factors (temperature, salinity, DIN, PO4-P, SiO3-Si), and water depth all had significant effects (P < 0.001) on the microbial community compositions in the three areas. Geographical distance had the greatest effect on bacterial community composition, while local environmental factors had the greatest effect on archaeal and eukaryotic community compositions; the effects of these factors on bacterial community composition were weaker than those on archaeal and microbial eukaryotic community composition. 
To sum up, at the meso scale, the spatial patterns of the bacterial community in the Bohai Strait and the microbial community across three domains in the southern Yellow Sea were more influenced by local environmental factors. At the large scale, both local and spatial factors were important in driving the spatial pattern of the microbial community. The relative importances of these factors were different to the three domains of microorganisms, and archaea and microbial eukaryotes had a stronger response to local environmental factors than bacteria.