Revealing archaeal contributions to nitrogen cycling in large-scale swine wastewater treatment across China
6 affiliations
- 1Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; School of Biological Engineering, Henan University of Technology, Zhengzhou, China
- 2Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Zhaoqing Academy of Agricultural and Forestry Sciences, Zhaoqing, China
- 3State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou, China
- 4State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong, China; Corresponding author
- 5Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China; Corresponding author
- 6Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Corresponding author
Abstract
Archaea are important yet often neglected microorganisms, and their role in the wastewater nitrogen cycle remains unclear. Here, we analyze the distribution and nitrogen-cycling activity of archaea in swine wastewater using metagenomic and metatranscriptomic approaches based on samples collected from 34 large-scale swine wastewater treatment plants (WWTPs) across China. We find that archaea harbor diverse nitrogen-cycling genes, including several archaea-specific genes with high expression levels. Additionally, they carry relatively few antibiotic resistance genes and virulence factors. We also observe gene exchange involving nitrogen-related genes both among archaea and between archaea and bacteria. Archaea alone explain 2.0% of the variation in nitrogen-cycling genes, whereas their co-contribution with bacteria reaches 34.3%, suggesting that archaea not only directly participate in the nitrogen transformation but also interact synergistically with bacteria. These findings identify archaea as key functional microorganisms with low biosafety risk potential, underscoring their unique value for sustainable wastewater treatment. Science for society: Swine farming produces large amounts of wastewater rich in nitrogen, which poses a serious environmental threat if not properly treated. In China, the world’s largest pork producer, swine wastewater treatment plants (WWTPs) rely heavily on microorganisms to remove pollutants. While bacteria have long been recognized as key players in wastewater nitrogen removal, another group of microorganisms, Archaea, has been largely overlooked. Archaea represent one of the three domains of life, alongside Bacteria and Eukaryotes. Although often associated with extreme environments such as hot springs and deep-sea vents, archaea are also present in wastewater, soil, and the animal gut. However, their role in the nitrogen cycle of wastewater treatment systems remains unclear. In this study, we investigate archaea in 34 large-scale swine WWTPs across China using advanced genomic and transcriptomic tools. We find that archaea carry diverse nitrogen-cycling genes that are highly active, particularly those involved in breaking down nitrogen-containing compounds. Importantly, unlike many bacteria, the archaea we identify carry very few antibiotic resistance genes or virulence factors, suggesting a low risk of spreading antibiotic resistance or causing disease. We also discover that archaea and bacteria work together in the nitrogen cycle. Archaea not only directly transform nitrogen compounds but also exchange nitrogen-related genes with bacteria, contributing jointly to nitrogen removal. These findings highlight archaea as safe and effective microbial partners for sustainable wastewater treatment. Looking ahead, archaea hold great promise for biotechnological applications, including wastewater nitrogen removal, soil nitrogen fixation, and reducing harmful emissions. However, challenges remain, such as difficulties in cultivating archaea and their low natural abundance. Overcoming these challenges could unlock new, environmentally friendly solutions for managing nitrogen pollution and protecting water resources.
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BibTeX
@article{yang2026revealing,
title = {{Revealing archaeal contributions to nitrogen cycling in large-scale swine wastewater treatment across China}},
author = {Yiwen Yang and Feng Huang and Chunhao Mo and Jiandui Mi and Sheng Chen and Zhiguo Wen and Xindi Liao},
journal = {Cell Reports Sustainability},
year = {2026},
month = oct,
doi = {10.1016/j.crsus.2026.100787},
url = {https://doi.org/10.1016/j.crsus.2026.100787},
note = {CC BY},
}
RIS
TY - JOUR
TI - Revealing archaeal contributions to nitrogen cycling in large-scale swine wastewater treatment across China
AU - Yiwen Yang
AU - Feng Huang
AU - Chunhao Mo
AU - Jiandui Mi
AU - Sheng Chen
AU - Zhiguo Wen
AU - Xindi Liao
PY - 2026
DA - 2026/10/25
JO - Cell Reports Sustainability
DO - 10.1016/j.crsus.2026.100787
UR - https://doi.org/10.1016/j.crsus.2026.100787
AB - Archaea are important yet often neglected microorganisms, and their role in the wastewater nitrogen cycle remains unclear. Here, we analyze the distribution and nitrogen-cycling activity of archaea in swine wastewater using metagenomic and metatranscriptomic approaches based on samples collected from 34 large-scale swine wastewater treatment plants (WWTPs) across China. We find that archaea harbor diverse nitrogen-cycling genes, including several archaea-specific genes with high expression levels. Additionally, they carry relatively few antibiotic resistance genes and virulence factors. We also observe gene exchange involving nitrogen-related genes both among archaea and between archaea and bacteria. Archaea alone explain 2.0% of the variation in nitrogen-cycling genes, whereas their co-contribution with bacteria reaches 34.3%, suggesting that archaea not only directly participate in the nitrogen transformation but also interact synergistically with bacteria. These findings identify archaea as key functional microorganisms with low biosafety risk potential, underscoring their unique value for sustainable wastewater treatment. Science for society: Swine farming produces large amounts of wastewater rich in nitrogen, which poses a serious environmental threat if not properly treated. In China, the world’s largest pork producer, swine wastewater treatment plants (WWTPs) rely heavily on microorganisms to remove pollutants. While bacteria have long been recognized as key players in wastewater nitrogen removal, another group of microorganisms, Archaea, has been largely overlooked. Archaea represent one of the three domains of life, alongside Bacteria and Eukaryotes. Although often associated with extreme environments such as hot springs and deep-sea vents, archaea are also present in wastewater, soil, and the animal gut. However, their role in the nitrogen cycle of wastewater treatment systems remains unclear. In this study, we investigate archaea in 34 large-scale swine WWTPs across China using advanced genomic and transcriptomic tools. We find that archaea carry diverse nitrogen-cycling genes that are highly active, particularly those involved in breaking down nitrogen-containing compounds. Importantly, unlike many bacteria, the archaea we identify carry very few antibiotic resistance genes or virulence factors, suggesting a low risk of spreading antibiotic resistance or causing disease. We also discover that archaea and bacteria work together in the nitrogen cycle. Archaea not only directly transform nitrogen compounds but also exchange nitrogen-related genes with bacteria, contributing jointly to nitrogen removal. These findings highlight archaea as safe and effective microbial partners for sustainable wastewater treatment. Looking ahead, archaea hold great promise for biotechnological applications, including wastewater nitrogen removal, soil nitrogen fixation, and reducing harmful emissions. However, challenges remain, such as difficulties in cultivating archaea and their low natural abundance. Overcoming these challenges could unlock new, environmentally friendly solutions for managing nitrogen pollution and protecting water resources.
SN - 2949-7906
ER -