海岸带是海洋与陆地交界的区域，是地球上生产力和生物多样性最高的生态系统之一，也是海洋环境中受人类活动影响最大、生物地球化学循环最为活跃的区域之一。海岸带包括海洋植物着生区（如海草床，红树林和盐沼）及人工构建的海洋牧场等多种生境，受到不同程度的人类活动的影响。海岸带沉积物是有机质埋藏、营养盐再生和温室气体排放的重要场所，其中微生物在底栖物质循环中扮演重要角色。沉积物的理化性质受上覆水氧含量、植物定植和季节变化等多种因素影响。在海草床生态系统中，海草生长状态、光合作用受季节变化影响，进而可能对沉积物中的微生物多样性及其生态功能产生影响；海洋牧场由于人类活动干扰强烈（经济动植物养殖等），水体通常富营养化，且海底富集大量养殖动物粪便，在微生物的作用下分解耗氧，夏季高温期水层间氧气交换受限，很可能引起底层海水低氧事件。然而，目前有关海草床在季节变化过程中及海洋牧场季节性低氧事件发生过程中的沉积物微生物多样性与群落结构动态和相关驱动因素尚不清楚。

本工作对山东荣成天鹅湖自然保护区内的大叶藻（鳗草，Zostera marina）海草床季节变化过程中和烟台牟平海洋牧场季节性低氧事件发生过程中的沉积物微生物动态开展了分子生态学研究。通过16S rDNA高通量测序与荧光定量PCR技术，分析了沉积物中古菌和细菌的多样性、群落结构、丰度和代谢潜力的时空分布格局，剖析了群落结构的变化规律；结合沉积物及其上覆水的理化性质进行了关联分析，探究相关的驱动因素；并对微生物的代谢潜力进行了预测，比较了其变化趋势。主要研究结果如下：

1、海草床表层沉积物中，古菌主要由乌斯菌门（平均相对丰度48.94%）、奇古菌门（23.48%）、深古菌门（14.83%）和广古菌门（3.14%）组成。乌斯菌门的优势子类群为Woese-5b（32.79%），Woese-5a（1.75%），Woese-25（1.32%）和Woese-Other（5.38%）；深古菌门的优势子类群为Bathy-6（6.88%），Bathy-8（2.84%）和Bathy-17（2.5%）。

季节变化是古菌群落结构和丰度动态变化的主要驱动力：季节变化对古菌的α和β多样性均有显著影响（P<0.05）；春、冬季节古菌的α多样指数和16S rRNA基因拷贝数显著高于夏、秋季节；同时，古菌的代谢潜力也呈现明显的季节变化模式，冬季的物质代谢潜力明显强于夏、秋两季。RDA分析显示，古菌群落结构与盐度、温度、pH和总氮显著关联（P<0.05）。海草定植也会影响古菌的丰度和多样性：古菌的16S rRNA基因拷贝数在海草定植区显著高于非草区（P<0.05，t-test）；α多样性在草区较非草区降低，但不显著（P>0.05）。

2、海草床表层沉积物中，细菌群落比例最高的是变形杆菌（64.63 %），其次是放线菌（8.44 %）、拟杆菌门（8.15 %）、绿弯菌门（5%）、酸杆菌门（2.27 %）、浮霉菌门（2.16 %）和厚壁菌门（1.97 %）。

季节变化是细菌群落结构和丰度动态变化的主要驱动力：季节变化对细菌的β多样性有显著影响（P<0.05，ADONIS）；α多样指数随季节变化趋势为春季>夏季>秋季>冬季（P<0.001，ANOVA）；春、冬季节细菌的16S rRNA基因拷贝数显著高于夏、秋季节（P<0.05，ANOVA）；代谢潜力呈现春、冬季节强于夏、秋季节的趋势。RDA分析显示，细菌群落与盐度、pH、温度和金属铁显著相关（P<0.05）。海草定植对细菌16S rRNA基因拷贝数的促进作用不显著，但显著地降低了α多样性（P<0.05，t-test），并对细菌β多样性有显著影响（P<0.05，ADONIS）。

3、在海草床柱状沉积物中，古菌和细菌的群落结构和丰度均呈现出明显的垂直分布特征：古菌中奇古菌门相对丰度随深度增加而显著增加（P<0.05，ANOVA），而细菌中δ-变形菌的相对丰度随深度增加而显著降低（P<0.05）；深度对古菌和细菌的α和β多样性均无显著影响（P>0.05）；细菌和古菌16S rRNA基因拷贝数随深度的增加而降低，在沉积物5 cm深处，细菌的16S rRNA基因拷贝数显著高于20 cm和30 cm层（ANOVA，P<0.05）。

4、在海洋牧场表层沉积物中，奇古菌门（58.55%）是古菌的最优势类群，其次是深古菌门（19.34%）、乌斯古菌门（16.76%）、广古菌门（1.54%）和洛基古菌门（1.30%）。底层海水低氧发生过程中，古菌的α多样性在高氧组（H组，DO>5 mg L^-1）低于中氧组（M组，3≤5 mg L^-1）和低氧组（L组，DO≤3 mg L^-1）；古菌的16S rRNA基因拷贝数在M组高于H和L组。RDA结果显示，古菌群落结构与DO、DIN和TOC显著相关（P<0.05）。

5、在海洋牧场表层沉积物中，细菌优势类群为变形杆菌（62.28 %），其次是放线菌门（12.77 %）、酸杆菌门（5.69 %）、拟杆菌（4.7 %）、绿弯菌门（4.4 %），芽单胞菌门（2.52 %）、厚壁菌门（1.48 %）、黏胶球形菌门（1.21%）和硝化螺旋菌门（1.19 %）。低氧发生过程中，细菌的α多样性指数随DO的下降而显著上升，L组最高（P<0.05，ANOVA）；细菌的16S rRNA基因拷贝数受低氧影响不显著（P>0.05，ANOVA）。RDA结果显示，细菌的群落结构与DO、温度和TOC显著相关（P<0.05）。

综上，在海草床沉积物中，季节是古菌和细菌群落结构和丰度动态变化的主要驱动力；低氧事件发生过程中，海洋牧场底层水氧含量、温度和沉积物有机质含量（TOC和DIN）是沉积物中古菌和细菌群落结构动态变化的主要驱动力。

The coastal zone is one of the ecosystems with the highest productivity and biodiversity on earth, and it is also one of the regions strongly affected by human activities. The coastal habitats are complex, including seagrass meadows, mangroves, and marine farms. Coastal sediments are important sites for organic matter burial, nutrient regeneration and greenhouse gas emission, where microorganisms play an important role in benthic ecology and chemical cycle. The sediment physical and chemical properties are affected by plant colonization and seasonal changes. In seagrass meadows, seagrass growth and photosynthesis are affected by seasonality, which may affect benthic microbial diversity and biogeochemical functions. In addition, due to the strong interference of human activities (economic animal and plant breeding, etc.), the seawater in marine farms is usually eutrophic, and a large amount of cultivated animal feces is enriched on the seabed. Microbes degrade organic matters consuming oxygen and leading to hypoxia in summer with high temperature. However, the seasonal dynamics of microbial community structure, diversity and abundance in seagrass meadow sediments, and the response of microbes during hypoxia in marine farm sediments remained poorly understood.

In this work, sediment archaea and bacteria community structure, diversity and abundance in the seagrass (Zostera marina) meadow of the Swan Lake Nature Reserve in Shandong Rongcheng and Muping marine farm were investigated through 16S rDNA high-throughput sequencing and real-time qPCR. Meanwhile, the physical-chemical properties and hydrological factors were determined to find the key factors regulating the dynamics of microbial commnities.

The main findings were as follows:

1. The archaeal community in the surface sediments of the seagrass meadow was mainly composed of Woesearchaeota (48.94%), Thaumarchaeota (23.48%), Bathyarchaeota (14.83%), and Euryarchaeota (3.14%). The dominant subgroups of Woesearchaeota included Woese-5b (32.79%), Woese-5a (1.75%), Woese-25. (1.32%) and Woese-Other (5.38%), and the dominant subgroups of Bathyarchaeota were Bathy-6 (6.88%), Bathy-8 (2.84%) and Bathy-17 (2.5%).

Seasonality was the main driving force for the dynamic change of archaeal community structure and abundance: seasonality had significant impacts on archaeal α and β diversities (P<0.05); in spring and winter, archaeal α diversity index and 16S rRNA gene copies were significantly higher than that in summer and autumn; meanwhile, the archaeal metabolic potential in winter was stronger than that in summer and autumn. RDA analysis showed that archaeal community structure was significantly correlated with salinity, temperature, pH and total nitrogen (P<0.05). Seagrass colonization promoted archaeal 16S rRNA gene copies (P<0.05, t-test), and reduced the α diversity.

2. The bacterial community of seagrass meadow sediments was dominated by Proteobacteria (64.63%), and followed by Actinobacteria (8.44%), Bacteroidetes (8.15 %), Chloroflexi (5 %), Acidobacteria (2.27%), Planctomycetes (2.16%) and Firmicutes (1.97 %).

Seasonality was also the main driving force for the dynamics of bacterial community structure and abundance: it had a significant influence on bacterial β diversity (P<0.05, ADONIS); the seasonal trend of bacterial α diversity was spring > summer > autumn > winter (P < 0.05, ANOVA); the bacterial 16S rRNA gene copies in spring and winter were significantly higher than those in summer and autumn; the bacterial metabolic potential was much stronger in spring and winter than that in summer and autumn. RDA analysis showed that the bacterial community was significantly correlated with salinity, pH, temperature and iron (P < 0.05). Seagrass colonization had no significant effect on bacterial 16S rRNA gene copies, but significantly reduced α diversity (P < 0.05) and dramaticly influenced the β diversity (P < 0.05, ADONIS).

3. In the sediment columns of the seagrass meadow, bacterial and archaeal communities and abundances presented obvious vertical patterns: the relative abundance of Thaumarchaeota significantly increased with increasing sediment depth, while that of Deltaproteobacteria significantly decreased with increasing sediment depth (P < 0.05, ANOVA); depth had no significant effect on archaeal and bacterial α and β diversities (P > 0.05); the 16S rRNA gene copy numbers of bacteria and archaea decreased with the increasing sediment depth, and the bacterial copy numbers in the 5-cm layer was significantly higher than those in the 20-cm and 30-cm layers (ANOVA test, P<0.05).

4. In the Muping marine farm sediments, the archaeal community was dominated by Thaumarchaeota (58.55%), and followed by Bathyarchaeota (19.34%), Woesearchaeota (16.76%), Euryarchaeota (1.54%) and Lokiarchaeota (1.30%). During the hypoxia, archaeal α diversity was lower in the high oxygen (H, DO>5 mg L^-1) group than that in the middle (M, 3≤5 mg L^-1) and low (L, DO≤3 mg L^-1) oxygen groups; archaeal 16S rRNA gene copy numbers were highest in M group than in H and L groups. The RDA results showed that the archaeal community structure was significantly related to DO, DIN and TOC (P <0.05).

5. Among the benthic bacterial community of Muping marine farm, the dominant phylum was Proteobacteria (62.28%), and followed by Actinobacteria (12.77 %), Acidobacteria (5.69 %), Bacteroidetes (4.7 %), Chloroflexi (4.4 %), Gemmatimonadetes (2.52 %), Firmicutes (1.48 %), Lacecibacteria (1.21%) and Nitrospirae (1.19 %). During the hypoxia, bacterial α diversity significantly increased with decreaseing DO level, and the highest value was in L group (P<0.05, ANOVA); the impact of hypoxia on bacterial 16S rRNA gene copy numbers was not significant (P>0.05, ANOVA), and were least in M group. RDA results showed that the bacterial community structure was significantly related to DO, temperature, and TOC (P <0.05).

In general, in seagrass meadow sediments, seasonalinty was the main driving force for regulating archaeal and bacterial community structure. During the process of hypoxic event, the bottom water oxygen content, temperature, and sediment organic matter content (TOC and DIN) were the main driving forces for regulating benthic archaeal and bacterial community structures.