MARINE ECOLOGY PROGRESS SERIES Mar Ecol Prog Ser Vol. 461: 31–46, 2012 doi: 10.3354/meps09782 Published August 8 INTRODUCTION Many productive pelagic environments have multi- vorous food webs, in which both classic herbivorous food chains (large phytoplankton, suspension-feed- ing zooplankton and fish) and microbial trophic com- ponents (heterotrophic bacteria, cyanobacteria, small eukaryotic algae and protozooplankton) contribute significantly to carbon fluxes. Thus, the fate of pri- mary production with regard to carbon cycling © Inter-Research 2012 · www.int-res.com *Email: lorenalinacre@gmail.com Temporal dynamics of carbon flow through the microbial plankton community in a coastal upwelling system off northern Baja California, Mexico Lorena Linacre 1, 2, * , Michael R. Landry 3 , Ramón Cajal-Medrano 4 , J. Rubén Lara-Lara 5 , J. Martín Hernández-Ayón 6 , Rosa R. Mouriño-Pérez 2 , Ernesto García-Mendoza 5 , Carmen Bazán-Guzmán 5 1 Programa de Doctorado en Oceanografía Costera, Facultad de Ciencias Marinas/Instituto de Investigaciones Oceanológicas, 4 Facultad de Ciencias Marinas, and 6 Instituto de Investigaciones Oceanológicas; Universidad Autónoma de Baja California (UABC), Ensenada, Baja California 22860, Mexico 2 Departamento de Microbiología, División de Biología Experimental y Aplicada, and 5 Departamento de Oceanografía Biológica, División de Oceanología; Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California 22860, Mexico 3 Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0227, USA ABSTRACT: We investigated the temporal dynamics of carbon flow through the microbial food web of a coastal upwelling system (ENSENADA station) off northern Baja California during 6 cruises (September 2007 to November 2008). Carbon biomass assessments for major autotrophic size groups (pico- to micro-sized cells) and their microzooplankton grazers were based on analyses using flow cytometry, HPLC pigments and epifluorescence microscopy. Taxon-specific phytoplankton growth and microzooplankton grazing rates were determined from 24 h in situ incubations in the euphotic zone using an abbreviated 3-treatment dilution technique. Carbon biomass and instantaneous growth and grazing rate determinations were used to estimate daily rates of taxon-specific production and losses due to microzooplankton grazing. Overall, microbial biomass showed a close balance between autotrophic and heterotrophic components, except during a period of very strong upwelling (April 2008), which favored large phytoplankters and high primary production. Through- out a wide range of environmental conditions, the community primary production (PP) attributed both to small (mostly picophytoplankton and prasinophytes) and large (mostly diatoms and au- totrophic dinoflagellates) autotrophs was significantly grazed (78 ± 9% of PP) by small (< 20 μm) and large (> 20 μm) ciliates and flagellates (including mixotrophic dinoflagellates), respectively, showing complementary temporal shifts in protistan grazer types that matched the dominant phytoplankton. While large diatoms were strongly consumed by large ciliates during the 2 most productive periods (September 2007 and April 2008), pico- and nano-sized phytoplankton were grazed most by nanofla- gellates and small ciliates from November 2007 to January 2008. Consequently, biogenic carbon pro- duction in this ecosystem is transferred through a multivorous food web. KEY WORDS: Biogenic carbon flow · Multivorous food web · Phytoplankton growth rate · Phytoplankton grazing rate · Primary production Resale or republication not permitted without written consent of the publisher