# Integrated Analysis of Histophysiological Responses and Transcriptome–Metabolome Mechanisms in Coelomactra antiquata Under Ammonia Nitrogen Stress

## TL;DR

This study explores how a marine shellfish, Coelomactra antiquata, responds to ammonia nitrogen pollution, revealing its tolerance levels and the biological mechanisms involved.

## Contribution

The first systematic multi-omics study of ammonia nitrogen stress in Coelomactra antiquata, revealing molecular and physiological responses.

## Key findings

- Ammonia nitrogen exposure disrupts antioxidant defense and nitrogen metabolism in Coelomactra antiquata.
- Omics analysis identified thousands of genes and hundreds of metabolites involved in immune and metabolic pathways.
- Histopathological damage in gill and hepatopancreas tissues confirms irreversible effects of ammonia stress.

## Abstract

Coelomactra antiquata is a type of marine shellfish that is nutritious and economically valuable. However, little is known about how it responds to ammonia nitrogen, a common pollutant in aquatic environments, and how it adapts to this stress. This study aimed to determine C. antiquata’s ability to tolerate ammonia nitrogen and the internal processes that help it cope. We first determined C. antiquata’s ammonia tolerance, finding LC50-48 h (99.06 mg/L) and SC (9.91 mg/L). When exposed to a 99.06 mg/L concentration for 48 h, C. antiquata’s gill and hepatopancreas (a key metabolic organ) showed changes in important enzymes and substances, which disrupted its ability to fight cell damage and balance nitrogen in the body. The tissues also suffered permanent damage, and further analysis revealed changes in thousands of genes and hundreds of small molecules related to metabolism, immunity, and detoxification. These findings explain how C. antiquata deals with ammonia nitrogen stress and provide useful information for protecting its survival in aquaculture, supporting the sustainable development of the industry.

Coelomactra antiquata, a marine bivalve of high nutritional and economic value, lacks comprehensive data on its toxic responses and adaptive mechanisms to ammonia nitrogen. This study integrated histophysiology, transcriptomics, and metabolomics to investigate its ammonia tolerance and molecular mechanisms, determining a 48 h LC50 of 99.06 mg/L and a sublethal concentration of 9.91 mg/L. After 48 h of sublethal ammonia stress, SOD, CAT, GLDH, and GS activities in gill and hepatopancreas significantly increased, with notable changes in MDA, Gln, and urea contents, confirming disruption of antioxidant defense and nitrogen metabolism homeostasis. Tissue sections revealed irreversible histopathological damage to key tissues. Omics analyses identified 7823 differentially expressed genes (DEGs) and 737 differentially expressed metabolites (DEMs) in hepatopancreas. DEGs were enriched in metabolic pathways and multiple immune-related signaling pathways (e.g., NF-kappa B, RIG-I-like receptor), while DEMs were primarily involved in processes such as protein digestion/absorption, aminoacyl-tRNA biosynthesis, and amino acid metabolism. Research data indicate that ammonia nitrogen stress primarily regulates the antioxidant function and nitrogen metabolism homeostasis of C. antiquata by activating multiple immune- and metabolism-related pathways. This first systematic multi-omics study elucidates C. antiquata’s tolerance to ammonia nitrogen and its molecular responses, filling a gap in environmental toxicology research for sustainable aquaculture and genomic studies.