||Larval settlement and metamorphosis affect both subsequent adult population establishment and distributions of other species in benthic habitats, hence play a significant role in maintaining the ecosystem function of the benthic environment. Yet the habitat selection and the molecular mechanisms behind metamorphosis remain to be described in many species of polychaetes. Pseudopolydora vexillosa (Polychaeta: Spionidae) is a recently-described tube dweller inhabiting estuarine and shallow subtidal sediment, but their biology and ecology are largely unknown. The main objective of this thesis is to study the settlement and metamorphosis of P. vexillosa. First, I investigated the larval growth and survival to competence when P. vexillosa larvae were fed with microalgae with different nutritional values. I also examined habitat selection of settling larvae when presented with sediment with different organic contents. I found that larvae reached metamorphic competence in 6 – 8 days when fed with Chaetoceros gracilis or Dunaliella tertiolecta, and 70% of these larvae metamorphosed successfully. Significantly more larvae settled with the highest organic content when tested using manipulated substrates, but the opposite occurred when tested with field sediment, showing that P. vexillosa larvae respond to sedimentary cues in a complex way during settlement. Second, I analyzed the total proteome expressions in the pre-competent larvae, competent larvae, and newly-metamorphosed juveniles using a 2-dimensional gel electrophoresis approach. The total proteomes of P. vexillosa competent larvae and newly-metamorphosed juveniles were highly similar. The total number of protein detected in P. vexillosa larvae doubled as the larvae developed from pre-competent to the competent. Eleven proteins that were up-regulated in the competent stage were identified, including calreticulin, tyrosin 3-monooxygenase activation protein, and matrix metallopeptidase. I took a further step by analyzing the protein phosphorylation dynamics before and after metamorphosis in P. vexillosa. Two times more phosphoproteins were detected in competent larvae than in the other two stages. Competent larvae also had the highest percent of protein phosphorylation. From 32 protein spots showing significant phosphorylation in the three developmental stages, all of them showed significant decreases in the phosphoprotein:protein ratio during metamorphosis, suggesting dephosphorylation occurred during metamorphosis. These proteins were selected and will be subjected to mass spectrometry analysis. As a side project, I used a mesocosm experiment to study the responses of the surface sediment bacterial community and their enzymatic activities in response to phytodetritus enrichment, under faunated and defaunated conditions. A decrease in the number of bacterial cells and bacterial species richness but an increase in proteolytic activities was observed in faunated sediments three days after phytodetritus addition. While in the defaunated condition, the bacterial community structures of surface sediments remained unchanged after the organic enrichment, but the glycolytic activities increased. The findings of this thesis showed that larvae of P. vexillosa are capable of responding to sedimentary cues upon settlement, contributed species-specific data towards the development of a proteome database for marine invertebrates during metamorphosis, elucidated protein expression dynamics underlying larval metamorphosis in a non-model polychaete, and enhanced the understanding of the responses of sediment bacteria upon organic enrichment.