The Punta Coles Natural Reserve (PCNR), located on the southern coast of the province of Ilo, Moquegua Region, Peru, houses an area rich in marine biodiversity which is composed of natural banks of benthic invertebrates, which constitute the potential and dynamic fishery of commercial interest for artisanal fishermen that impact the area. To mitigate this impact, all stakeholders need to know, understand, value, and balance the dependence of benthic biodiversity with the ecosystem for its preservation and the promotion of sustainable fishing. Along these lines, the components studied are bathymetry, lithology, and the tapestry of bioengineers that make up the reserve’s seabed. Mapping of the complexity of the benthic habitat of the seabed was developed on the basis of an integrated analysis of multibeam bathymetric data, geoscientific information associated with the antecedents of benthic biodiversity of the PCNR, sediment maps of the seabed, subtidal sedimentological texture, and photographic records. The characterization and granulometry of the sediments that make up the PCNR were determined according to the Udden–Wentworth classification criterion (Φ). The utility of the GPSMAP 178C multibeam echosounder for the interpretation of seabed sediments stands out. The kriging interpolation method was used to extrapolate the characteristics of the benthic habitat, which is suitable for large areas of the sea. As a result, three habitats were derived and mapped, and three structures (bioengineers), namely, “subtidal kelps” (Lessonia trabeculata), “mussels” (Aulacomya atra), and “red sea squirt” (Pyura chilensis), were associated mainly with sedimentary rock habitats and mixed substrates. In the sand substrate, these algae were found to a lesser extent. The results show that this study is a conceptual model that summarizes the understanding of ecology and prospects for the sustainability of profitable, ecoefficient fishing activities in the Moquegua Region, Peru.
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