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A targeted method for the quantification of bioavailable amide N found in marine DON (bDON) is presented. The method utilizes mild acid hydrolysis to convert amide N found in proteins andN‐acetyl amino polysaccharides to primary amine containing products that are measured using a highly sensitive (nanomolar range and precision) fluorometric technique with addition ofO‐phthaldialdehyde. We find amidic bDON concentrations ranging from 0.08 to 1.82 μM N within waters from the upper 300 m in the southern California Current, Southern California Bight, and subtropical North Pacific representing 15–33% of bulk DON concentrations. Bioassay experiments from the North Pacific revealed consumption of ~20% of the in situ bDON within 5 days. The method represents a simple and rapid tool for the quantification of bioavailable DON concentrations in seawater with improved analytical precision over traditional estimates of bulk DON concentrations.

The 2014–2015 warm anomaly (aka “the Blob”), the largest of periodic and intensifying marine heat wave (MHW) perturbations in the northeast Pacific, may provide some insight about the future warmer ocean. Here, we use mixed‐layer carbon estimates for total phytoplankton, major size classes and functional groups from 45 CalCOFI cruises to: (1) compare 2014–2015 MHW impacts in the southern California Current System to baseline estimates from 2004 to 2013 and (2) to test a space‐for‐time exchange hypothesis that links biomass structure to variability of nitracline depth (NCD). Seasonal and inshore‐offshore analyses from nine stations revealed almost uniform 2°C MHW warming extending 700 km seaward, fourfold to sixfold declines in nitrate concentration and 18‐m deeper NCDs. Phytoplankton C decreased 16–21% compared to 45–65% for Chla, with the threefold difference due to altered C : Chla. Among size classes, percent composition of nanoplankton decreased and picophytoplankton increased, driven by higherProchlorococcusbiomass, whileSynechococcusand picoeukaryotes generally declined. Diatom and dinoflagellate C decreased in both onshore and offshore waters. Seasonally, the MHW delayed the normal winter refresh of surface nitrate, resulting in depressed stocks of total phytoplankton and nanoplankton,Synechococcusand picoeukaryotes during winter. Consistent with the space‐for‐time hypothesis, biomass variations for baseline and MHW cruises followed similar (not significantly different) slope relationships to NCD. All biomass components, exceptProchlorococcus, were negatively related to NCD, and community biomass structure realigned according to regression slopes differences with NCD variability. Empirically derived biomass‐NCD relationships could be useful for calibrating models that explore future food‐web impacts in this coastal upwelling system.

Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.

Cryptophytes (class Cryptophyceae) are bi‐flagellated eukaryotic protists with mixed nutritional modes and cosmopolitan distribution in aquatic environments. Despite their ubiquitous presence, their molecular diversity is understudied in coastal waters. Weekly 18S rRNA gene amplicon sequencing at the Scripps Institution of Oceanography pier (La Jolla, California) in 2016 revealed 16 unique cryptophyte amplicon sequence variants (ASVs), with two dominant “clade 4” ASVs. The diversity of cryptophytes was lower than what is often seen in other phytoplankton taxa. One ASV represented a knownSynechococcusgrazer, while the other one appeared not to have cultured representatives and an unknown potential for mixotrophy. These two dominant ASVs were negatively correlated, suggesting possible niche differentiation. The cryptophyte population in nearby San Diego Bay was surveyed in 2019 and showed the increasing dominance of a different clade 4 ASV toward the back of the bay where conditions are warmer, saltier, and shallower relative to other areas in the bay. An ASV representing a potentially chromatically acclimating cryptophyte species also suggested that San Diego Bay exerts differing ecological selection pressures than nearby coastal waters. Cryptophyte andSynechococcuscell abundance at the SIO Pier from 2011 to 2017 showed that cryptophytes were consistently present and had a significant correlation withSynechococcusabundance, but no detectable seasonality. The demonstrated mixotrophy of some cryptophytes suggests that grazing on these and perhaps other bacteria is important for their ecological success. Using several assumptions, we calculated that cryptophytes could consume up to 44% (average 6%) of theSynechococcuspopulation per day. This implies that cryptophytes could significantly influenceSynechococcusabundance.

Photosynthesis in the surface ocean and subsequent export of a fraction of this fixed carbon leads to carbon dioxide sequestration in the deep ocean. Ecological relationships among plankton functional groups and theoretical relationships between particle size and sinking rate suggest that carbon export from the euphotic zone is more efficient when communities are dominated by large organisms. However, this hypothesis has never been tested against measured size spectra spanning the >5 orders of magnitude found in plankton communities. Using data from five ocean regions (California Current Ecosystem, North Pacific subtropical gyre, Costa Rica Dome, Gulf of Mexico, and Southern Ocean subtropical front), we quantified carbon‐based plankton size spectra from heterotrophic bacteria to metazoan zooplankton (size class cutoffs varied slightly between regions) and their relationship to net primary production and sinking particle flux. Slopes of the normalized biomass size spectra (NBSS) varied from −1.6 to −1.2 (median slope of −1.4 equates to large 1–10 mm organisms having a biomass equal to only 7.6% of the biomass in small 1–10 μm organisms). Net primary production was positively correlated with the NBSS slope, with a particularly strong relationship in the microbial portion of the size spectra. While organic carbon export co‐varied with NBSS slope, we found only weak evidence that export efficiency is related to plankton community size spectra. Multi‐variate statistical analysis suggested that properties of the NBSS added no explanatory power over chlorophyll, primary production, and temperature. Rather, the results suggest that both plankton size spectra and carbon export increase with increasing system productivity.

Multiple processes transport carbon into the deep ocean as part of the biological carbon pump, leading to long-term carbon sequestration. However, our ability to predict future changes in these processes is hampered by the absence of studies that have simultaneously quantified all carbon pump pathways. Here, we quantify carbon export and sequestration in the California Current Ecosystem resulting from (1) sinking particles, (2) active transport by diel vertical migration, and (3) the physical pump (subduction + vertical mixing of particles). We find that sinking particles are the most important and export 9.0 mmol C m⁻²d⁻¹across 100-m depth while sequestering 3.9 Pg C. The physical pump exports more carbon from the shallow ocean than active transport (3.8 vs. 2.9 mmol C m⁻²d⁻¹), although active transport sequesters more carbon (1.0 vs. 0.8 Pg C) because of deeper remineralization depths. We discuss the implications of these results for understanding biological carbon pump responses to climate change.

Locally enhanced biological production and increased carbon export are persistent features at oceanic density fronts. Studies often assume biological properties are uniform along fronts or hypothesize that along‐ and across‐front gradients reflect physical‐biological processes occurring in the front. However, the residence times of waters in fronts are often shorter than biological response times. Thus, an alternate—often untested—hypothesis is that observed biological patchiness originates upstream of a front. To test these two hypotheses, we explore an eddy‐associated front in the California Current System sampled during two surveys, separated by 3 weeks. Patches of high phytoplankton biomass were found at the northern ends of both surveys, and phytoplankton biomass decreased along the front. While these patches occurred in similar locations, it was unclear whether the same patch was sampled twice, or whether the two patches were different. Using an advection‐reaction framework combined with field and satellite data, we found that variations in along‐front gradients in dissolved oxygen, particle biovolume, and salinity support the conclusion that the two phytoplankton patches were different. They were only coincidentally sampled in similar locations. Backward‐ and forward‐in‐time tracking of water parcels showed that these phytoplankton patches had distinct origins, associated with specific, strong coastal upwelling pulses upstream of the front. Phytoplankton grew in these recently upwelled waters as they advected into and along the frontal system. By considering both local and upstream physical‐biological forcings, this approach enables better characterizations of critical physical and biogeochemical processes that occur at fronts across spatial and temporal scales.

The uptake of³H‐labeled leucine into proteins, a widely used method for estimating bacterial carbon production (BCP), is suggested to underestimate or overestimate bacterial growth in the open ocean by a factor of 40 uncertainty. Meanwhile, an alternative BCP approach, by the dilution method, has untested concerns about potential overestimation of bacterial growth from dissolved substrates released by filtration. We compared BCP_Diland BCP_Leuestimates from three cruises across a broad trophic gradient, from offshore oligotrophy to coastal upwelling, in the California Current Ecosystem. Our initial analyses based on midday microscopical estimates of bacterial size and a priori assumptions of conversions relationships revealed a mean two‐fold difference in BCP estimates (BCP_Dilhigher), but no systematic bias between low and high productivity stations. BCP_Diland BCP_Leuboth demonstrated strong relationships with bacteria cell abundance. Reanalysis of results, involving a different cell carbon‐biovolume relationship and informed by forward angle light scatter from flow cytometry as a relative cell size index, demonstrated that BCP_Diland BCP_Leuare fully compatible, with a 1 : 1 fit for bacteria of 5 fg C cell⁻¹. Based on these results and considering different strengths of the methods, the combined use of³H‐labeled leucine and dilution techniques provide strong mutually supportive constraints on bacterial biomass and production.