The vertical distribution and abundance of microbial assemblages and the grazing of nanoheterotrophs upon prokaryotes in oxic and suboxic waters were examined in two coastal upwelling areas off northern Chile where a shallow Oxygen Minimum Zone (OMZ) is characteristic. Prokaryotic prey included bacterioplankton and cyanobacteria (Synechococcus); both displayed a bimodal distribution, with abundance maxima above and within the upper OMZ. Flagellates numerically dominated the nanoplankton and were mostly concentrated in the oxic layer. Mean ingestion rates of cyanobacteria by nanoflagellates (vacuole content method) ranged from 0.2 to 1.1 cells flagellate⁻¹ h⁻¹ and mean consumption rates (34–160 cells mL⁻¹ h⁻¹) were four times higher in the oxic layer. With the selective inhibitors technique, specific grazing rates on bacteria were low (100% of bacterial production). With the same method, the specific grazing rate on cyanobacteria ranged between zero and 0.23 h⁻¹ with no clear differences between oxygen conditions; prey growth and production were always higher than the grazing pressure (accounting for <17% of cyanobacterial production). The impact of grazing by nanoheterotrophs in regulating the production of prokaryotes in oxic and suboxic waters in this region is discussed.

The vertical variability in the oxygen minimum zone (OMZ) in the eastern South Pacific (ESP; 0–40°S) is characterized by the influence of anticyclonic intrathermocline eddies (ITEs), which are subsurface‐intensified mesoscale features that are frequently generated in the coastal upwelling zone off Peru and Chile. The unique lens‐shaped signatures that ITEs leave on temperature, salinity, and dissolved oxygen vertical distributions are used as proxies to assess their influences on vertical OMZ boundaries and thickness. Data from in situ profiles in the region (World Ocean Database and Argo databases) are used in correlation analyses between anomalous depths (and vertical displacements) of oxyclines and isopycnals/isotherms, together with an objective eddy detection method based on satellite altimetry to identify the location of such profiles (i.e., outside or inside cyclonic and anticyclonic eddies). The results indicate that most of the vertical fluctuations in the climatological OMZ have a lens‐shaped signature and that those at the mesoscale are largely due to ITEs. ITEs are a main driver of the upper oxycline variability in the coastal band, the coastal transition zone (CTZ, 3–10° from the coast) and beyond at mid‐latitudes (12–26°S). The influence of ITEs on the upper and lower oxycline variability is mostly observed within the horizontal (offshore) climatological boundary of the OMZ, suggesting that ITEs play a role in the OMZ offshore extension in the ESP. ITEs may produce mesoscale variations in the thickness of the surface‐oxygenated layer, resulting in potential changes in prey‐predator interactions and in food web functioning.

The annual cycle and phenology of phytoplankton (satellite‐derived chlorophyll‐a, Chl‐a) in the coastal upwelling region off central‐southern Chile, their time‐space variation, the extent of their coupling with those of wind‐driven upwelling (as Zonal Ekman Transport, ZET), Sea Surface Temperature (SST), and Photosynthetically Active Radiation (PAR) were analyzed using a ∼10 year satellite time series (2002–2012). Wavelet analysis (WA) was applied to extract the dominant frequencies of variability and their recurrence, to derive the phenological indexes, and to assess the extent of the coupling between Chl‐a and environmental forcing in the annual frequency. Index estimates were obtained from minimum and maximum accumulated values in two different frequency bands, annual (WA‐ANF) and all except the synoptic (WA‐ALF). The annual frequency was dominant in all the variables; however, the annual cycle and phenology of Chl‐a displayed higher submeso and mesoscale variability. The mean onset date of Chl‐a was similar to those of PAR and ZET with WA‐ALF and cross WA indicated that, for the most part, their annual cycles were coupled or coherent. Few interannual changes in Chl‐a phenology were detected, including a ∼1 month longer duration (WA‐ALF) during La Niña 2010–2011. The mean anomalies in the magnitudes of Chl‐a and ZET during the upwelling season showed a slight but significant trend, negative for Chl‐a and positive for ZET, while SST remained relatively constant. This pattern was unexpected since three La Niña‐related conditions were identified during the 2007–2012 period.

The impact of grazing by natural assemblages of microzooplankton was estimated in an upwelling area (Concepción, Chile) during the non-upwelling season in 2003 and 2004. Seawater dilution experiments using chlorophyll a (Chl a) as a tracer were used to estimate daily rates of phytoplankton growth and microzooplankton grazing. Initial Chl a concentrations ranged from 0.4 to 1.4 mg Chl a m⁻³ and phytoplankton prey biomass and abundance were numerically dominated by components 100%) during the non-upwelling period.

Understanding the influence of mesoscale and submesoscale features on the structure of phytoplankton is a key aspect in the assessment of their influence on marine biogeochemical cycling and cross-shore exchanges of plankton in Eastern Boundary Current Systems (EBCS). In this study, the spatio-temporal evolution of phytoplankton size classes (PSC) in surface waters associated with mesoscale eddies in the EBCS off central-southern Chile was analyzed. Chlorophyll-a (Chl-a) size-fractionated filtration (SFF) data from in situ samplings in coastal and coastal transition waters were used to tune a three-component (micro-, nano-, and pico-phytoplankton) model, which was then applied to total Chl-a satellite data (ESA OC-CCI product) in order to retrieve the Chl-a concentration of each PSC. A sea surface, height-based eddy-tracking algorithm was used to identify and track one cyclonic (sC) and three anticyclonic (ssAC1, ssAC2, sAC) mesoscale eddies between January 2014 and October 2015. Satellite estimates of PSC and in situ SFF Chl-a data were highly correlated (0.64 < r < 0.87), although uncertainty values for the microplankton fraction were moderate to high (50 to 100% depending on the metric used). The largest changes in size structure took place during the early life of eddies (~2 months), and no major differences in PSC between eddy center and periphery were found. The contribution of the microplankton fraction was ~50% (~30%) in sC and ssAC1 (ssAC2 and sAC) eddies when they were located close to the coast, while nanoplankton was dominant (~60–70%) and picoplankton almost constant (<20%) throughout the lifetime of eddies. These results suggest that the three-component model, which has been mostly applied in oceanic waters, is also applicable to highly productive coastal upwelling systems. Additionally, the PSC changes within mesoscale eddies obtained by this satellite approach are in agreement with results on phytoplankton size distribution in mesoscale and submesoscale features in this region, and are most likely triggered by variations in nutrient concentrations and/or ratios during the eddies’ lifetimes.

Time-space fluctuations of chlorophyll-a (Chl-a) within the region off central-southern Chile (33–42°S), and their association with meteorological-oceanographic conditions, were analyzed using satellite time series data (2002–2012). The mean distribution of moderate values of Chl-a (~0.5 mg∙m⁻³) in the northern section (33–38°S) extended out to ~200 km of the coast whereas they were restricted to a narrower band in the southern section (38–42°S). Mean wind stress and wind stress curl were upwelling favorable for most part of the year in the northern section whereas upwelling-downwelling periods were distinct in the southern section. The dominant frequency of Chl-a variability in the coastal zone and the coastal transition zone was annual, as it was for the rest of the variables, except in a transitional band between these zones and where a semi-permanent jet is located. At the annual frequency, the alongshore distribution of coastal Chl-a presented strong discontinuities, with minimum values around upwelling centers (~37 and 40°S) and higher values (> 2 mg∙m⁻³) in between. Also at the annual frequency, correlation analyses suggest that Ekman transport and Ekman pumping might act synchronously to extend the offshore distribution of the highest Chl-a values during the spring-summer period whereas mesoscale activity appears to contribute to Chl-a increases in the coastal transition zone. Sea surface temperature does not appear to be associated with the annual cycle of Chl-a in the coastal zone and in the coastal transition zone it might be linked to Chl-a variability through the effects of internal waves.