Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. These data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as well as the rapid responses of indigenous microbial species in the degradation of marine particulate organic matter (POM) in situ in the ocean's interior.

Marine bacterial and archaeal communities control global biogeochemical cycles through nutrient acquisition processes that are ultimately dictated by the metabolic requirements of individual cells. Currently lacking, however, is a sensitive, quick, and quantitative measurement of activity in these single cells. We tested the applicability of copper (I)-catalyzed cycloaddition, or "click," chemistry to observe and estimate single-cell protein synthesis activity in natural assemblages and isolates of heterotrophic marine bacteria. Incorporation rates of the non-canonical methionine bioortholog L-homopropargylglycine (HPG) were quantified within individual cells by measuring fluorescence of alkyne-conjugated Alexa Fluor®488 using epifluorescence microscopy. The method's high sensitivity, along with a conversion factor derived from two Alteromonas spp. isolates, revealed a broad range of cell-specific protein synthesis within natural microbial populations. Comparison with 35 S-methionine microautoradiography showed that a large fraction of the natural marine bacterial assemblage (15-100%), previously considered inactive by autoradiography, were actively synthesizing protein. Data pooled from 21 samples showed that cell-specific activity scaled logarithmically with cell volume. Activity distributions of each sample were fit to power-law functions, providing an illustrative and quantitative comparison of assemblages that demonstrate individual protein synthesis rates were commonly partitioned between cells in low-and high-metabolic states in our samples. The HPG method offers a simple approach to link individual cell physiology to the ecology and biogeochemistry of bacterial (micro)environments in the ocean.

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