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Eastern boundary upwelling systems (EBUS) contribute a disproportionate fraction of the global fish catch relative to their size and are especially susceptible to global environmental change. Here we present the evolution of communities over 50 d in an in situ mesocosm 6 km offshore of Callao, Peru, and in the nearby unenclosed coastal Pacific Ocean. The communities were monitored using multi-marker environmental DNA (eDNA) metabarcoding and flow cytometry. DNA extracted from weekly water samples were subjected to amplicon sequencing for four genetic loci: (1) the V1–V2 region of the 16S rRNA gene for photosynthetic eukaryotes (via their chloroplasts) and bacteria; (2) the V9 region of the 18S rRNA gene for exploration of eukaryotes but targeting phytoplankton; (3) cytochrome oxidase I (COI) for exploration of eukaryotic taxa but targeting invertebrates; and (4) the 12S rRNA gene, targeting vertebrates. The multi-marker approach showed a divergence of communities (from microbes to fish) between the mesocosm and the unenclosed ocean. Together with the environmental information, the genetic data furthered our mechanistic understanding of the processes that are shaping EBUS communities in a changing ocean. The unenclosed ocean experienced significant variability over the course of the 50 d experiment, with temporal shifts in community composition, but remained dominated by organisms that are characteristic of high-nutrient upwelling conditions (e.g., diatoms, copepods, anchovies). A large directional change was found in the mesocosm community. The mesocosm community that developed was characteristic of upwelling regions when upwelling relaxes and waters stratify (e.g., dinoflagellates, nanoflagellates). The selection of dinoflagellates under the salinity-driven experimentally stratified conditions in the mesocosm, as well as the warm conditions brought about by the coastal El Niño, may be an indication of how EBUS will respond under the global environmental changes (i.e., increases in surface temperature and freshwater input, leading to increased stratification) forecast by the IPCC.

Total dissolved inorganic carbon (CT) is one of the most frequently measured parameters used to calculate the partial pressure of carbon dioxide in seawater. Its determination has become increasingly important because of the rising interest in the biological effects of ocean acidification. Coulometric and infrared detection methods are currently favored in order to precisely quantify CT. These methods however are not sufficiently validated for CT measurements of biological experiments manipulating seawater carbonate chemistry with an extended CT measurement range (~1250–2400 μmol kg–1) compared to natural open ocean seawater (~1950–2200 μmol kg−1). The requirement of total sample amounts between 0.1–1 L seawater in the coulometric- and infrared detection methods potentially exclude their use for experiments working with much smaller volumes. Additionally, precise CT analytics become difficult with high amounts of biomass (e.g., phytoplankton cultures) or even impossible in the presence of planktonic calcifiers without sample pre-filtration. Filtration however, can alter CT concentration through gas exchange induced by high pressure. Addressing these problems, we present precise quantification of CT using a small, basic and inexpensive gas chromatograph as a CT analyzer. Our technique is able to provide a repeatability of ±3.1 μmol kg−1, given by the pooled standard deviation over a CT range typically applied in acidification experiments. 200 μL of sample is required to perform the actual CT measurement. The total sample amount needed is 12 mL. Moreover, we show that sample filtration is applicable with only minor alteration of the CT. The method is simple, reliable and with low cumulative material costs. Hence, it is potentially attractive for all researchers experimentally manipulating the seawater carbonate system.