Substrate‐driven enrichment and eDNA metabarcoding reveal indigenous microbiomes in mangrove sediments with potential for ammonia and nitrite transformation

Abstract

Effective management of ammonia and nitrite remains a major challenge in intensive shrimp aquaculture, where excessive nitrogen loading compromises water quality and animal health. Indigenous microbial communities inhabiting mangrove sediments are widely considered potential sources of ammonia‐ and nitrite‐transforming microorganisms; however, their presence and functional potential remain poorly characterized. This study aimed to explore potential ammonia‐ and nitrite‐transforming microbiomes in mangrove sediments using a molecular approach that combines substrate‐driven enrichment, environmental DNA (eDNA) metabarcoding, and PICRUSt2‐based functional inference. Ammonium chloride enrichment resulted in rapid ammonium/ammonia depletion, transient nitrite accumulation, and sustained nitrate production, consistent with nitrification‐related processes. Sodium nitrite enrichment was characterized by progressive nitrite depletion and associated shifts in nitrogen transformation pathways. Both enrichment conditions led to reduced microbial diversity and substantial restructuring of community composition. ASV‐level functional attribution indicated that genes involved in ammonia and nitrite transformation were primarily associated with low‐abundance, functionally specialized taxa, including Nitrosomonas ‐ and Nitrospira ‐like groups. Nitrite enrichment further suggested involvement of denitrification‐associated taxa, including Pseudomonas . Functional profiles inferred using PICRUSt2 indicate potential shifts in nitrogen‐cycling pathways, although these should be interpreted as predictive rather than direct measurements of microbial activity. These findings provide molecular evidence for the presence of indigenous microbiomes with potential roles in ammonia and nitrite transformation in mangrove sediments and establish a foundation for future isolation and functional validation of candidate microorganisms for shrimp aquaculture applications.