Microbial drivers of high aquaculture productivity: decoupling of taxonomic and functional profiles enables efficient nitrogen cycling in greenhouse shrimp farming
- 1National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
Abstract
As a global cornerstone of animal protein, farmed shrimp production in China has been revolutionized by the Greenhouse Shrimp Farming Model (GSFM). However, the microbial mechanisms underpinning the productivity and biosafety of this intensive paradigm remain poorly understood. Through a large-scale metagenomic survey of 90 standardized aquaculture units in the core GSFM production regions of China, spanning a 15-degree latitudinal gradient, we deciphered the functional architecture of the GSFM microbiome. Our results reveal a striking functional convergence despite geographic taxonomic variation: while microbial compositions shifted across regions, the core metabolic pathways—particularly those governing nutrient cycling—remained conserved. High-productivity systems, notably in southern provinces (Guangxi and Guangdong), were characterized by a specialized microbial repertoire that optimized water chemistry through efficient nitrogen processing. We identified a sophisticated spatial division of labor, where the gut microbiota acts as a specialized nitrite detoxification unit, while the water column microbiota serves as the primary engine for ammonia assimilation. Furthermore, we characterized a diverse antibiotic resistome and utilized host-tracking to evaluate the ecological costs of intensification. These findings shift the focus from microbial identity to functional niche partitioning, providing a mechanistic blueprint for the sustainable intensification of aquaculture through targeted microbiome management.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s42523-026-00607-z.
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BibTeX
@article{shen2026microbial,
title = {{Microbial drivers of high aquaculture productivity: decoupling of taxonomic and functional profiles enables efficient nitrogen cycling in greenhouse shrimp farming}},
author = {Hongye Shen and Liangxiao Ma and Jinshan Li and Yongmei Hu and Nan Peng and Shumiao Zhao},
journal = {Animal Microbiome},
year = {2026},
month = aug,
doi = {10.1186/s42523-026-00607-z},
url = {https://doi.org/10.1186/s42523-026-00607-z},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Microbial drivers of high aquaculture productivity: decoupling of taxonomic and functional profiles enables efficient nitrogen cycling in greenhouse shrimp farming
AU - Hongye Shen
AU - Liangxiao Ma
AU - Jinshan Li
AU - Yongmei Hu
AU - Nan Peng
AU - Shumiao Zhao
PY - 2026
DA - 2026/08/08
JO - Animal Microbiome
DO - 10.1186/s42523-026-00607-z
UR - https://doi.org/10.1186/s42523-026-00607-z
AB - As a global cornerstone of animal protein, farmed shrimp production in China has been revolutionized by the Greenhouse Shrimp Farming Model (GSFM). However, the microbial mechanisms underpinning the productivity and biosafety of this intensive paradigm remain poorly understood. Through a large-scale metagenomic survey of 90 standardized aquaculture units in the core GSFM production regions of China, spanning a 15-degree latitudinal gradient, we deciphered the functional architecture of the GSFM microbiome. Our results reveal a striking functional convergence despite geographic taxonomic variation: while microbial compositions shifted across regions, the core metabolic pathways—particularly those governing nutrient cycling—remained conserved. High-productivity systems, notably in southern provinces (Guangxi and Guangdong), were characterized by a specialized microbial repertoire that optimized water chemistry through efficient nitrogen processing. We identified a sophisticated spatial division of labor, where the gut microbiota acts as a specialized nitrite detoxification unit, while the water column microbiota serves as the primary engine for ammonia assimilation. Furthermore, we characterized a diverse antibiotic resistome and utilized host-tracking to evaluate the ecological costs of intensification. These findings shift the focus from microbial identity to functional niche partitioning, providing a mechanistic blueprint for the sustainable intensification of aquaculture through targeted microbiome management. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s42523-026-00607-z.
SN - 2524-4671
ER -