Microbial communities and assembly processes in the sediments of marine and lacustrine environments

Microbial communities inhabiting marine and lacustrine sediments play important roles in biogeochemical cycles and ecosystem functioning. However, the processes that shape the assembly of these communities remain poorly understood. To address this knowledge gap, this thesis employed a range of molecular approaches, ecological models, and statistical analyses to investigate the drivers of microbial community assembly in sediments from four distinct locations in China. Specifically, this research focused on sediment microbial communities and assembly processes in (i) two bays situated in the Bohai Sea, a marginal sea; (ii) the Pearl River Estuary, a large river-dominated estuary, and its adjacent shelf; (iii) Lake Ranwu, a glacier-fed lake; and (iv) Lake Taihu, a shallow eutrophic lake. 
High-throughput sequencing of 16S rRNA was used to identify the phylogenetic and taxonomic diversity of microbial communities. Multiple methods including multivariate analysis, the neutral community model, and the null model were employed to test hypotheses regarding the relative importance of deterministic and stochastic processes in shaping microbial community assembly. The correlation-based network was employed to investigate the role of biotic forcing in regulating microbial communities. Furthermore, special attention was paid to the response of habitat specialists and generalists to environmental changes in lacustrine sediments and how these changes affected the diversity of microbial communities.
The results showed that both deterministic and stochastic processes played important roles in shaping microbial communities in marine and lacustrine sediments, but the relative importance of these processes varied depending on the main features of the ecosystems. In surface sediments of the studied marine environments, stochastic processes dominated community assembly. The environmental heterogeneity resulting from river inflows and coastal circulation was identified as the primary factor in community assembly. The difference in pollutant loads also contributed to the microbial co-occurrence relationship patterns and the assembly of communities.
In the near-surface sediments of the studied lacustrine environments, a significant change was observed in the community assembly processes along the sediment depth. While deterministic processes played a more significant role in Lake Ranwu, stochastic processes were dominant in Lake Taihu. The relative importance of homogenizing dispersal and homogeneous selection was critical in governing community assembly in both lakes. Furthermore, bioturbation was observed to have a significant impact on homogenizing dispersal in Lake Taihu, and habitat specialists were found to be crucial in regulating community assembly in both lakes.
Overall, this thesis contributes to a more comprehensive understanding of the drivers that shape microbial community assembly in distinct marine and lacustrine sediment environments, highlighting the varying degrees of influence of deterministic and stochastic processes, and emphasizing the role of habitat specialists and generalists in regulating microbial community assembly within lacustrine ecosystems.

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