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Peptides are identified using a de novo‐discovery approach in suspended and sinking particles from the eastern tropical North Pacific oxygen‐deficient zone (ODZ) and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. The benchmarking experiment with Prochlorococcus shows de novo peptides to be taxonomically specific, and thus of value in augmenting database‐driven approaches. Analysis of the suspended and sinking particles using the de novo‐discovery approach reveals the presence of fungal proteins in deep sinking particles that were not in our original search database, contributing to growing recognition that fungi may play important roles in marine organic matter cycling. Cyanobacterial peptides that have been post‐translationally modified were tracked to depth, where they contribute ~ 1% of the phylum‐level identifiable peptide pool in the sediment trap sample. The majority of peptides found at depth in the detrital pool are associated with membranes, indicating that cellular location is associated with early preservation within the detrital pool. Modified amino acids in sinking and suspended particles include high levels of deamidation, suggesting that partial extracellular degradation of protein could fuel observed anammox and contribute to pools of refractory organic nitrogen. [ABSTRACT FROM AUTHOR]

Models and observations suggest that particle flux attenuation is lower across the mesopelagic zone of anoxic environments compared to oxic environments. Flux attenuation is controlled by microbial metabolism as well as aggregation and disaggregation by zooplankton, all of which shape the relative abundance of differently sized particles. Observing and modeling particle spectra can provide information about the contributions of these processes. We measured particle size spectrum profiles at one station in the oligotrophic Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) using an underwater vision profiler (UVP), a high‐resolution camera that counts and sizes particles. Measurements were taken at different times of day, over the course of a week. Comparing these data to particle flux measurements from sediment traps collected over the same time‐period allowed us to constrain the particle size to flux relationship, and to generate highly resolved depth and time estimates of particle flux rates. We found that particle flux attenuated very little throughout the anoxic water column, and at some time points appeared to increase. Comparing our observations to model predictions suggested that particles of all sizes remineralize more slowly in the ODZ than in oxic waters, and that large particles disaggregate into smaller particles, primarily between the base of the photic zone and 500 m. Acoustic measurements of multiple size classes of organisms suggested that many organisms migrated, during the day, to the region with high particle disaggregation. Our data suggest that diel‐migrating organisms both actively transport biomass and disaggregate particles in the ODZ core. Plain Language Summary: Marine snow are microscopic particles that form in the surface of the ocean and sink into the deep ocean. Most of these particles are the remains of dead algae and feces of tiny animals (zooplankton). The deeper the particles sink into the ocean before microbes or animals consume them, the longer it takes before the carbon in those particles can return to the atmosphere. In parts of the ocean where there is no oxygen, more particles sink to greater depths, for reasons that are not well‐understood. We used an underwater camera to observe marine snow particles in the ocean just west of Mexico where there is little to no oxygen at depth. We compared the observations to predictions from several computer simulations representing hypothesized mechanisms to explain why particles are consumed less in water without oxygen. Our measurements suggest that one reason that particles sink to deeper depths here is because microbes consume the particles slowly when there is no oxygen. Meanwhile, zooplankton still break large particles into smaller ones and produce fecal pellets in these low oxygen waters. Key Points: The upper mesopelagic of the oligotrophic Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) has low flux attenuationComparison of particle size observations to models suggests that the breakdown of particles of all sizes is slow throughout the ODZZooplankton appear to transport organic matter into, and disaggregate particles within, the ODZ above 500 m [ABSTRACT FROM AUTHOR]

Abstract: We describe a new, autonomous, incubation‐based instrument that is deployed in situ to determine rates of gross community respiration and net community production in marine and aquatic ecosystems. During deployments at a coastal pier and in the open ocean, the PHORCYS (PHOtosynthesis and Respiration Comparison‐Yielding System) captured dissolved oxygen fluxes over hourly timescales that were missed by traditional methods. The instrument uses fluorescence‐quenching optodes fitted into separate light and dark chambers; these are opened and closed with piston‐like actuators, allowing the instrument to make multiple, independent rate estimates in the course of each deployment. Consistent with other studies in which methods purporting to measure the same metabolic processes have yielded divergent results, respiration rate estimates from the PHORCYS were systematically higher than those calculated for the same waters using a traditional two‐point Winkler titration technique. However, PHORCYS estimates of gross respiration agreed generally with separate incubations in bottles fitted with optode sensor spots. An Appendix describes a new method for estimating uncertainties in metabolic rates calculated from continuous dissolved oxygen data. Multiple successful, unattended deployments of the PHORCYS represent a small step toward fully autonomous observations of community metabolism. Yet the persistence of unexplained disagreements among aquatic metabolic rate estimates—such as those we observed between rates calculated with the PHORCYS and two existing, widely accepted bottle‐based methods—suggests that a new community intercalibration effort is warranted to address lingering sources of error in these critical measurements. [ABSTRACT FROM AUTHOR]

Most measurements of respiration rates in large tropical rivers do not account for the influence of river flow conditions on microbial activity. We developed a ship‐board spinning incubation system for measuring O2 drawdown under different rotation velocities and deployed the system along the lower Amazon River during four hydrologic periods. Average respiration rates in incubation chambers rotated at 0.22 m s−1 and 0.66 m s−1 were 1.4 and 2.4 times higher than stationary chambers, respectively. On average, depth‐integrated respiration rates in chambers spun at 0.22 m s−1 and 0.66 m s−1 accounted for 64% ± 22% and 104% ± 36% of CO2 outgassing rates, respectively, in mainstem sites. Continuous measurements of in situ pCO2 were also made along with cross‐channel profiles of river velocity. A positive correlation between river velocity and pCO2 was observed along the lower river (r2 = 0.67–0.96) and throughout a tidal cycle. [ABSTRACT FROM AUTHOR]

Surface sediment samples from three interconnected fjords of Clayoquot Sound, British Columbia, were density fractionated (1.6 g cm-3) to isolate discrete organic debris (OD) from mineral-associated organic matter (MOM). Total organic carbon (OC) values varied greatly, ranging from <0.1% to 8.8% by weight, with a general decreasing trend from fjord head to the continental shelf. Within the sediment, terrestrial OM was present either as vascular plant debris or soil MOM. Down-fjord, the woody vascular plant material in the OD fraction acquires nitrogen, which is hypothesized to be due to the bacterial incorporation of nitrogen from the water. Terrestrial OC in the MOM is incompletely replaced by marine OC within the fjords, resulting in a 65% net loss of MOM. Sediments deposited under oxic and intermittently anoxic water column conditions have organic carbon to surface area ratios (OC:SA) ranging from 0.4 to 1.2 mg C m-2, similar to that of typical continental margin sediments. Given that temperate fjords contain an estimated 12% of the continental margin sediment deposited during the last 100,000 yr, and that they bury at least a margin-equivalent amount of OC (either weight or surface area normalized), we hypothesize that temperate fjords may contain 12% or more of the sedimentary OC buried during this time. [ABSTRACT FROM AUTHOR]

The preformed nitrate distribution throughout the subtropical North Pacific is characterized by a negative anomaly between 100 m and the 25.4 σθ surface. Its presence indicates that nitrogen remineralization in the upper thermocline deviates significantly from Redfield stoichiometry. It has been previously suggested that this feature is created during the degradation of nitrogen-poor dissolved organic matter (DOM) (Emerson and Hayward, 1995). Here we present evidence from two transects in the eastern subtropical North Pacific that degradation of DOM with a high C:N ratio is quantitatively responsible for negative preformed nitrate. We develop a simple isopycnal mass balance to determine preformed nitrate using apparent oxygen utilization (AOU), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) data. These results agree well with the traditional preformed nitrate calculation and indicate that the intensity of the anomaly is proportional to the magnitude of DOM remineralization and its C:N remineralization ratio. An analysis of preformed nitrate distributions in the eastern subtropical North Pacific between 1980 and 1997 reveals a significant increase in the negative anomaly. While a portion of this change may be attributable to a reduction in ventilation of the gyre, the majority of the signal is due to an increase in the magnitude and/or C:N ratio of DOM remineralization. This conclusion supports recent hypotheses that DOM production and cycling may have increased in this region in the past 2 decades as a result of changes in the phytoplankton community structure. [ABSTRACT FROM AUTHOR]

The rate of [3H-methyl] thymidine (3H-TdR) incorporation into DNA has been applied extensively to measure cell production by bacterial communities in aquatic environments. Here we describe a method to quantify 3H-TdR incorporation by specific, phylogenetically defined members of the bacterial community. The method involves selectively capturing DNA from targeted groups of bacteria and then quantifying its 3H radioactivity. The method was applied to measure 3H-TdR incorporation by the members of the phylum Bacteriodetes whose members, which include the Cytophaga- Flavobacter cluster, are ubiquitous in coastal waters. 3H-labelled DNA from Bacteriodetes was selectively biotinylated in PCR-like reactions that contained a Bacteriodetes-specific 16S rRNA gene primer, thermostable DNA polymerase and biotinylated dUTP. The biotinylated DNA was then captured on streptavidin-coated beads and its 3H radioactivity determined by scintillation counting. We have termed this method ‘selective nucleic acid polymerase-biotinylation and capture’ or ‘SNAP-BAC’. Internal 33P-labelled DNA standards were used to quantify the recovery of 3H-labelled DNA from the SNAP-BAC reactions. The method was verified by successfully targeting Bacteriodetes in simple laboratory mixtures of 3H-labelled DNA extracted from pure cultures of Bacteriodetes and γ-proteobacteria. Field application of this method in Puget Sound and off the Washington coast determined that Bacteriodetes were responsible for 56 ± 17% and 32 ± 5% of community 3H-TdR incorporation (1.3 ± 0.3 and 9.9 ± 1.7 pmol l−1 h−1) at these two locations. [ABSTRACT FROM AUTHOR]

Biogeochemical controls on the community structure of heterotrophic marine bacteria are not well understood, and these organisms play a critical role in the global carbon cycle. Through terminal restriction fragment length polymorphism (T-RFLP) analyses of bacterial 16S rRNA genes along a zonal transect in the eastern subarctic North Pacific, variations in community structure were compared to commonly obtained chemical and biological oceanographic measurements. It was found that heterotrophic bacterial community structure was strongly, but independently, related to both phytoplanktonic production and light. Based on computer-simulated T-RFLP analyses of database 16S rRNA gene sequences, it appeared that the relationship between bacterial community structure and light observed along the transect was driven by the distribution of α-proteobacteria with phototrophic capabilities. In addition, experiments were conducted at sea to measure the growth of heterotrophic bacteria in response to amendments of amino acids, protein, N-acetyl glucosamine, and chitin. Variation in the response of heterotrophic bacteria in the experiments did not correlate significantly with variation in community structure along the transect, which suggests that the ability of the heterotrophic bacterial community to use specific components of the dissolved organic carbon reservoir was not related to its phylogenetic structure as detected by T-RFLE However, a possible relationship between community structure and the cycling of chitin is discussed. Overall, the results stress the importance of both heterotrophic and phototrophic metabolisms when considering environmental controls on the structure of bacterial communities in the sea. [ABSTRACT FROM AUTHOR]

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