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Dynamics of Bacterial Diversity in Fish Farming Lagoons: Implications for the Ecosystem Trophic Status
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Environmental Science & Health Research Group, Facultad de Medicina Humana, Universidad Nacional del Centro del Perú, Av. Mariscal Castilla N° 3909, Huancayo 12006, Peru
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Facultad de Zootecnia, Universidad Nacional del Centro del Perú, Av. Mariscal Castilla N° 3909, Huancayo 12006, Peru
*
Author to whom correspondence should be addressed.
Biology 2025, 14(11), 1563; https://doi.org/10.3390/biology14111563
Submission received: 17 September 2025
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Revised: 5 November 2025
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Accepted: 5 November 2025
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Published: 7 November 2025
(This article belongs to the Section Ecology)
Simple Summary
This study addressed the impact of fish farming on Peru's high Andean lakes, key ecosystems for environmental health and fishery productivity. The problem is that uneaten food and fish waste introduce large amounts of nutrients, altering water quality and the bacterial communities present in the sediments. The objective of this study was to evaluate bacterial diversity and structure in four lakes. The results showed that, although species richness was similar, bacterial composition varied significantly, with Lake Tipicocha being the most diverse. The presence of bacteria indicative of high organic matter content and low oxygen levels is clear evidence that the organic load from fish farming is altering the chemistry of the lagoon bottoms. The conclusion is that fish farming modifies the nutritional status and microbial diversity of these sensitive lagoons. This knowledge is essential for designing strategies that allow fish farming without compromising the conservation of these important Andean ecosystems.
Abstract
Bacterial communities in lake sediments are key to ecosystem health and fish productivity, yet little is known about their composition in the high-altitude Andean lagoons of central Peru. In aquaculture systems, these microbial assemblages regulate nutrient recycling, organic matter degradation and oxygen availability, forming a key component of the microbial loop. Intensive trout farming introduces a continuous nutrient load through uneaten feed and metabolic byproducts, which fuels eutrophication and reshapes benthic microbial structure. This study evaluated the bacterial diversity and community structure in sediments from four fish farming lagoons (Pomacocha, Habascocha, Tipicocha, and Trancagrande). Environmental variables, including dissolved oxygen (DO), inorganic nitrogen, inorganic phosphorus, and chlorophyll-a, were measured to determine trophic status. Sediment bacterial composition was analyzed using Illumina sequencing of 16S rRNA gene amplicons, and community structure differences were assessed with diversity indices and SIMPER analysis. Microbial patterns were assessed at phylum and class levels to capture changes across taxonomic scales. Pseudomonadota, Actinobacteria, Cyanobacteria and Bacteroidetes dominated across lagoons, with significant among-site variation. Richness was similar, but Tipicocha showed the highest evenness (Shannon H′ = 2.769; Simpson 1-D = 0.8969). SIMPER identified Deltaproteobacteria, Alphaproteobacteria, Actinobacteria and Gammaproteobacteria as major contributors to dissimilarity. The presence of Methanomicrobia and Bacilli in Tipicocha and Trancagrande indicated micro-oxic to anoxic conditions, characteristic of systems with high organic load and redox heterogeneity. These results show that aquaculture alters trophic status and reshapes sediment bacterial communities in high-Andean lagoons. Understanding these patterns is essential to design monitoring and management strategies that balance aquaculture productivity with the conservation of sensitive ecosystems.
