As part of the California Current Ecosystem Long Term Ecological Research (CCE-LTER) Program, samples for epifluorescence microscopy and flow cytometry (FCM) were collected at ten 'cardinal' stations on the California Cooperative Oceanic Fisheries Investigations (CalCOFI) grid during 25 quarterly cruises from 2004 to 2010 to investigate the biomass, composition and size-structure of microbial communities within the southern CCE. Based on our results, we divided the region into offshore, and inshore northern and southern zones. Mixed-layer phytoplankton communities in the offshore had lower biomass (16±2μgCL-1; all errors represent the 95% confidence interval), smaller size-class cells and biomass was more stable over seasonal cycles. Offshore phytoplankton biomass peaked during the winter months. Mixed-layer phytoplankton communities in the northern and southern inshore zones had higher biomass (78±22 and 32±9μgCL-1, respectively), larger size-class cells and stronger seasonal biomass patterns. Inshore communities were often dominated by micro-size (20-200μm) diatoms; however, autotrophic dinoflagellates dominated during late 2005 to early 2006, corresponding to a year of delayed upwelling in the northern CCE. Biomass trends in mid and deep euphotic zone samples were similar to those seen in the mixed-layer, but with declining biomass with depth, especially for larger size classes in the inshore regions. Mixed-layer ratios of autotrophic carbon to chlorophyll a (AC:Chl a) had a mean value of 51.5±5.3. Variability of nitracline depth, bin-averaged AC:Chl a in the mixed-layer ranged from 40 to 80 and from 22 to 35 for the deep euphotic zone, both with significant positive relationships to nitracline depth. Total living microbial carbon, including auto- and heterotrophs, consistently comprised about half of particulate organic carbon (POC).

© 2015. American Geophysical Union. All Rights Reserved. In the offshore waters of Southern California, submesoscale processes associated with fronts may stimulate phytoplankton blooms and lead to biomass shifts at multiple trophic levels. Here we report the results of a study on the cycling of biogenic silica (bSiO 2 ) with estimates of the contributions of diatoms to primary and new production in water masses adjacent to (i.e., coastal or oceanic) and within an offshore front in the Southern California Current Ecosystem (CCE). The coastal and oceanic water were sampled in cyclonic and anticyclonic e ddies, respectively, with the frontal water being an interaction region between the eddy types. Concentrations of bSiO 2 varied by 25-fold across the front, with concentrations in frontal waters 20-25% of those in coastal waters. Rates of biogenic silica production spanned an equally large range, with rates within the frontal region that were half those in the coastal regions. Contributions of diatoms to primary and new production were disproportionately higher than their contribution to autotrophic biomass in all areas, ranging from 5-8%, 19-30%, and 32-43% for both processes in the oceanic, frontal and coastal waters, respectively. Across the frontal area, diatoms could account for < 1.0%, 6-8%, and 44-72% of organic matter export in the oceanic, frontal and coastal waters, respectively. The results suggest that the regions of frontal interactions between eddies in the southern CCE can account for variability in diatom biomass, productivity and export over very short spatial scales that is comparable to the variability observed across the Pacific basin.