Co‐occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co‐occurrence data from the rocky intertidal zone in central Chile to a well‐resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co‐occurrence data to better detect known trophic or non‐trophic, positive or negative interactions. We found a poor correspondence between the co‐occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non‐interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non‐trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co‐occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co‐occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche‐expanding positive non‐trophic interactions. Detection of links (sensitivity or specificity) was not higher for well‐known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co‐occurrence networks must be interpreted with caution, especially when extending interaction‐based ecological theory to interpret network variability and stability. Co‐occurrence networks may be particularly valuable for analysis of community dynamics that blends interactions and environment, rather than pairwise interactions alone.

Large and usually unpredictable variation in species interaction strength has been a major roadblock to applying local experimental results to large-scale management and conservation issues. Recent studies explicitly considering benthic-pelagic coupling are starting to shed light on, and find regularities in, the causes of such large-scale variation in coastal ecosystems. Here, we evaluate the effects of variation in wind-driven upwelling on community regulation along 900 km of coastline of the southeastern Pacific, between 29°S and 35°S during 72 months. Variability in the intensity of upwelling occurring over tens of km produced predictable variation in recruitment of intertidal mussels, but not barnacles, and did not affect patterns of community structure. In contrast, sharp discontinuities in upwelling regimes produced abrupt and persistent breaks in the dynamics of benthic and pelagic communities over hundreds of km (regional) scales. Rates of mussel and barnacle recruitment changed sharply at ≈32°-33°S, determining a geographic break in adult abundance of these competitively dominant species. Analysis of satellite images demonstrates that regional-scale discontinuities in oceanographic regimes can couple benthic and pelagic systems, as evidenced by coincident breaks in dynamics and concentration of offshore surface chlorophyll- a . Field experiments showed that the paradigm of top-down control of intertidal benthic communities holds only south of the discontinuity. To the north, populations seem recruitment-limited, and predators have negligible effects, despite attaining similarly high abundances and potential predation effects across the region. Thus, geographically discontinuous oceanographic regimes set bounds to the strength of species interactions and define distinct regions for the design and implementation of sustainable management and conservation policies.