Metagenomic insights into carbon and nitrogen cycling functions in an integrated rice-crayfish farming system with straw return
5 affiliations
- 1Key Laboratory of Aquaculture and Stock Enhancement for Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences
- 2Feixi Longguanhe Ecological Agriculture Co., Ltd.
- 3Anhui Jie & Xiang Aquaculture Co. Ltd
- 4Tongcheng Sushi Agricultural Development Co., Ltd.
- 5Hefei Animal Husbandry and Aquatic Products Technology Extension Center
Abstract
Straw return is an important strategy for agricultural residue utilization, and functional microbial communities are known to play a pivotal role in straw decomposition and nutrient cycling. Nevertheless, the decomposition dynamics and associated microbial functional outcomes in rice-aquaculture systems remain poorly documented. This study established a rice-crayfish integrated system with straw return and assessed the mechanisms of straw decomposition and the resulting improvement on soil fertility through soil physicochemical characterization, enzyme activity assays, and metagenomic sequencing. Soil samples were obtained in July (PF7, the rice transplanting stage following the crayfish farming period) and November (PF11, the post-harvest field drying period), with surrounding ditches as controls (CK7 and CK11). The results showed that straw was effectively decomposed, releasing potassium and nitrogen nutrients, while urease and cellulase activities were markedly increased in the paddy field. Metagenomic analysis revealed that Pseudomonadota was the dominant phylum, whereas Euryarchaeota and Nitrososphaerota exhibited the most pronounced changes, with their abundances in PF11 being 0.23-fold and 10.57-fold of those in CK11, respectively. In the C cycle, C degradation was the most abundant pathway, in which amino acid degradation (primarily derived from crayfish farming) dominated, followed by aromatic compound degradation (associated with straw decomposition). For the methane metabolic pathway, the greenhouse gas emission potential was reduced, as evidenced by lower mcrA abundances in PF than in CK. N cycling was primarily mediated through organic N metabolism (81.63–84.14%), with the remaining fraction dominated by nitrification and denitrification. Furthermore, the relevant analysis consistently indicated that C cycling genes occupy more central positions and TN showed a negative effect on these genes. Collectively, this integrated system was associated with straw decomposition, facilitated terminal organic C and N mineralization, while greenhouse gas-related functional potentials were reduced, supporting sustainable straw utilization in rice-crayfish agroecosystems.
Related
- New Insights Into Nighttime Marine Sulfur and Nitrogen Chemistry and Related New Particle Formation Using the CLEPS Model
- Metagenomic insights into the metabolic versatility in iron-rich mats of the lucky strike hydrothermal field
- Nitrogen enrichment and Ulva green tide dynamics on Jeju Island: insights from biomass, physiological traits, and stable isotopes signatures
- Effects of cultivation of herbaceous perennials on soil microbial community structure and nitrogen cycling functions
- Rotation system reshapes soil profile environmental gradients to reorganize bacterial communities and decouple potential nitrogen cycling functions
BibTeX
@article{wang2026metagenomic,
title = {{Metagenomic insights into carbon and nitrogen cycling functions in an integrated rice-crayfish farming system with straw return}},
author = {Fen Wang and Zhu Chen and Xiang Zhou and Xuezhen Liu and Yangyang Jiang and Guoxia Fang and Youfeng Su and Chaozhen Rong and Suofei Ji and Guanjun Hou},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1940285},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1940285/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Metagenomic insights into carbon and nitrogen cycling functions in an integrated rice-crayfish farming system with straw return
AU - Fen Wang
AU - Zhu Chen
AU - Xiang Zhou
AU - Xuezhen Liu
AU - Yangyang Jiang
AU - Guoxia Fang
AU - Youfeng Su
AU - Chaozhen Rong
AU - Suofei Ji
AU - Guanjun Hou
PY - 2026
DA - 2026/10/26
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1940285
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1940285/full
AB - Straw return is an important strategy for agricultural residue utilization, and functional microbial communities are known to play a pivotal role in straw decomposition and nutrient cycling. Nevertheless, the decomposition dynamics and associated microbial functional outcomes in rice-aquaculture systems remain poorly documented. This study established a rice-crayfish integrated system with straw return and assessed the mechanisms of straw decomposition and the resulting improvement on soil fertility through soil physicochemical characterization, enzyme activity assays, and metagenomic sequencing. Soil samples were obtained in July (PF7, the rice transplanting stage following the crayfish farming period) and November (PF11, the post-harvest field drying period), with surrounding ditches as controls (CK7 and CK11). The results showed that straw was effectively decomposed, releasing potassium and nitrogen nutrients, while urease and cellulase activities were markedly increased in the paddy field. Metagenomic analysis revealed that Pseudomonadota was the dominant phylum, whereas Euryarchaeota and Nitrososphaerota exhibited the most pronounced changes, with their abundances in PF11 being 0.23-fold and 10.57-fold of those in CK11, respectively. In the C cycle, C degradation was the most abundant pathway, in which amino acid degradation (primarily derived from crayfish farming) dominated, followed by aromatic compound degradation (associated with straw decomposition). For the methane metabolic pathway, the greenhouse gas emission potential was reduced, as evidenced by lower mcrA abundances in PF than in CK. N cycling was primarily mediated through organic N metabolism (81.63–84.14%), with the remaining fraction dominated by nitrification and denitrification. Furthermore, the relevant analysis consistently indicated that C cycling genes occupy more central positions and TN showed a negative effect on these genes. Collectively, this integrated system was associated with straw decomposition, facilitated terminal organic C and N mineralization, while greenhouse gas-related functional potentials were reduced, supporting sustainable straw utilization in rice-crayfish agroecosystems.
SN - 1664-302X
ER -