Summary: The major sites of water column denitrification in the ocean are oxygen minimum zones (OMZ), such as one in the eastern South Pacific (ESP). To understand the structure of denitrifying communities in the OMZ off Chile, denitrifier communities at two sites in the Chilean OMZ (Antofagasta and Iquique) and at different water depths were explored by terminal restriction fragment length polymorphism analysis and cloning of polymerase chain reaction (PCR)‐amplified nirS genes. NirS is a functional marker gene for denitrification encoding cytochrome cd ₁ ‐containing nitrite reductase, which catalyses the reduction of nitrite to nitric oxide, the key step in denitrification. Major differences were found between communities from the two geographic locations. Shifts in community structure occurred along a biogeochemical gradient at Antofagasta. Canonical correspondence analysis indicated that O ₂ , NO ₃ ^– , NO ₂ ^– and depth were important environmental factors governing these communities along the biogeochemical gradient in the water column. Phylogenetic analysis grouped the majority of clones from the ESP in distinct clusters of genes from presumably novel and yet uncultivated denitrifers. These nirS clusters were distantly related to those found in the water column of the Arabian Sea but the phylogenetic distance was even higher compared with environmental sequences from marine sediments or any other habitat. This finding suggests similar environmental conditions trigger the development of denitrifiers with related nirS genotypes despite large geographic distances.

El gen nosZ, el cual codifica para la reducción de N2O a N2, fue usado para estudiar la estructura de las comunidades desnitrificantes en la zona de mínimo oxígeno frente a las costas de Chile y Perú, a través del polimorfismo de los fragmentos largos de restricción terminal (PFLRT) y clonamiento de los genes nosZ. El análisis del PFLRT mostró poca diversidad de genes nosZ en las profundidades subóxicas (núcleo de la zona de mínimo oxígeno-ZMO) comparado con las profundidades donde el O2 varío ampliamente (límite superior de la zona de mínimo oxígeno o LSZMO). Las comunidades desnitrificantes-nosZ presentaron diferencias en su estructura entre localidades geográficas y tiempo de muestreo sugiriendo asociación con la variación en las condiciones ambientales. El análisis de correspondencia canónica indicó que los parámetros ambientales seleccionados como variables predictoras (N2O, O2, NH4+ y NO2-) explicaron bien las diferencias en la composición de la comunidad nosZ entre sitios de muestreo. El análisis filogenético mostró poca diversidad de secuencias nosZ y agrupó el 81% de los clones cerca al clúster de secuencias de sedimentos del Pacífico. Las secuencias no se relacionaron con ninguna secuencia nosZ reportada en agua de mar, o de bacterias desnitrificantes conocidas, demostrando la novedad de los filotipos encontrados en esta área.

Nitrifying bacteria are essential in aquaponic systems because they transform nitrogenous waste into useful plant nutrients, preventing ammonium toxicity in fish. This study aimed to quantify and characterize cultivable nitrifying bacteria in an aquaponic system over time, using two replicated systems with watercress (Nasturtium officinale), and the fishes Nile tilapia (Oreochromis niloticus), red tilapia (Oreochromis sp.), and white pacu (Piaractus orinoquensis). Samples were collected at three moments (0, 3, and 6 months) from the fish tank, hydrocyclone, and biofilter. The highest bacterial abundance was detected in the fish tanks, likely due to higher oxygen levels and nutrient availability, with a consistent increase over time. Correlation analysis indicated that certain nutrients, such as potassium, phosphate, manganese, and nitrate, could favor the proliferation of nitrifying bacteria. Nine bacterial morphotypes were isolated and phenotypically characterized, with most displaying Gram-positive staining and negative urea hydrolysis. This study provides insight into the spatiotemporal dynamics of nitrifying bacteria in aquaponic systems, highlighting their role in nutrient cycling. The high bacterial abundance observed underscores the system’s potential for efficient nutrient reuse. Molecular techniques such as 16S rRNA gene sequencing and metagenomics are recommended to confirm bacterial identity and better understand community structure. These findings reinforce the ecological importance of nitrifying bacteria in system performance and advancing sustainable agricultural practices.