Trophic interactions and the relevance of the “classical” (CFW) versus the “microbial” (MFW) food webs were studied in the upwelling system of Antofagasta (23°S), northern Humboldt Current System (HCS) off Chile. Biological and ecological data gathered from the study area during 1996 and 1999–2002 and complementary data from the literature were analysed using the Ecopath with Ecosim software version 5.0 (EwE). The model includes the following functional groups: Detritus, dissolved organic matter (DOM), bacteria, phytoplankton, appendicularians, salps, calanoid copepods, cyclopoid copepods, chaetognaths, ctenophores, clupeiform fishes. The Antofagasta's model indicate that only 18% of the total trophic relationships up to clupeiforms include only organisms of the CFW, while it is increased up to 82% when trophic relationships with organisms of the MFW are included. Removing the MFW from a complex, multi-level, trophic pathways, the energy transfer efficiency that characterise the study area either decreased or increased their value from detritus (from 14.4% to 13.6%) and primary production (from 11.0% to 15.1%), respectively. The total net primary production (PP) of the system with and without the MFW is similar (2.3 grC m −2 d −1 and 2.2 grC m −2 d −1), however, the total energy throughput increased in a system with MFW from ∼4.7 grC m −2 d −1 to ∼9.8 grC m −2 d −1. Thus, although the energy transfer efficiency is higher in a system without the MFW, the total system throughput is two times higher when it is considered. This might be due to (1) the inclusion of large new compartments in different trophic levels (such as DOM, bacteria), (2) the inclusion of the MFW would enhance the recycling of materials and energy and (3) the inclusion of new pathways such as bacteria – appendicularians/salps – anchovy (clupeiforms), that might produce a close link between the base of the microbial loop and clupeiforms, bypassing most of the MFW. The exclusion of the microbial loop from trophic models should strongly affect different planktonic groups such as salps, small cyclopoid copepods and appendicularians because they feed mainly (or partially, such as euphausiids) on small-size particles such as bacteria, microflagellates and ciliates. Thus, both CFW and MFW constitute highly complementary and interconnected trophic pathways from microbes up to fishes, and where more resolution at lower trophic level would be required to derive sensible model results that satisfactorily represent the system behaviour (i.e. ecosystem approach).
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