Proteinaceous materials are major components of marine organic matter, and can account for up to 80% of the organic nitrogen in marine organisms. Although proteinaceous materials are generally considered to be labile, some of them are protected from heterotrophic attack and remineralization. In this study, we discussed the possible mechanisms how proteinaceous materials are preserved and transported in marine environments. First, the accumulation of refractory prokaryotic cell membranes has been suggested as one of the possible sources of the proteinaceous materials observed in the deep ocean. The refractory nature of these membranes presumably results from the highly diverse and complicated membrane structures, e.g., peptidoglycan and phospholipid bilayer. Surface layer protein (S-layer) is a specific membrane glycoprotein that is widely found in both Eubacteria and Archaea. This heavily glycosylated protein covers the outermost cell surface in a regularly ordered planar crystalline structure. With special attention to changes in S-layer protein and peptidoglycan, we studied the degradation of two species of marine cyanobacteria, Synechococcus CCMP2370 and CCMP1334, with and without S-layer structures, respectively. We also studied degradation of both these species after they had been treated with buffers that strip the S-layer from the cell surface. The changes in degradation biomarkers, elemental composition and cell morphology were followed during the incubation experiments, suggesting that S-layer protein functions as the skeleton to support the cell structures and removal of S-layer accelerates the degradation of cyanobacterial cells in marine environments. Second, we provide evidence using electron microscopy (EM) and energy dispersive X-ray spectroscopy (EDS) that Si is deposited on the extracellular polymeric substances (EPS) produced by cyanobacteria, particularly when they begin to decompose. We also found that Si associated with organic micro-blebs collected from the deep ocean. Both nano-particle imaging analysis and bulk organic geochemical analysis show a surprisingly similar appearance between EPS-associated Si in cyanobacteria and micro-blebs in the open ocean. Accordingly, EPS-associated Si might be a precursor of the Si-enriched organic micro-blebs observed in the ocean. The previously unexplored source of particulate silicate minerals may play an important role in the oceanic silicate cycling as well as organic matter export from the surface waters. Third, a new fluorescent analog, Lucifer Yellow Anhydride-alanine-valine-phenylalanine-alanine (LYA-AVFA), was developed to measure extracellular peptide hydrolysis. Peptide hydrolysis was compared to the uptake of various organic nitrogen species (urea, glutamic acid and dialanine) along transects of the James River estuary and lower Chesapeake Bay salinity gradient during the summer of 2008. Changes in the abundance and composition of dissolved amino acids were also examined. Results from the James River estuary suggest that peptide hydrolysis and organic nitrogen uptake are not always tightly coupled to each other along the salinity transects as a response to the changing environmental conditions in the studied area. This is because diverse input and removal processes can influence both peptide hydrolysis and uptake, but not necessarily simultaneously. A change of dissolved amino acid abundance and composition was observed from the fresh end of the estuary to the mouth of Chesapeake Bay, which are most likely resulting from the mixing of multiple sources and their impacts on hydrolysis and uptake, e.g. terrestrial input, sediment resuspension and local phytoplankton growth.