Zhu Xue, Ji Lei, Cheng Mingyue, Wei Huimin, Wang Zhi, Ning Kang
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China.
Environ Microbiome. 2022 May 22;17(1):27. doi: 10.1186/s40793-022-00422-4.
While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.
虽然稻虾共作养殖（RCFP）模式是亚洲一种重要的水产养殖模式，通常被认为是一种可持续模式，但其在微生物群落特征方面的可持续性尚未得到评估。在本研究中，使用来自稻虾共作养殖模式以及其他水产养殖模式（包括蟹虾混养、小龙虾养殖和螃蟹养殖模式）的环境（即水和沉积物）和动物肠道（即小龙虾和螃蟹肠道）微生物样本，对微生物群落特征进行了多领域分析（即细菌、古菌、病毒和真核生物），以系统评估稻虾共作养殖模式的可持续性。结果表明，与其他水产养殖模式相比，稻虾共作养殖模式的样本富含一组独特的微生物，包括希瓦氏菌属、嗜铁菌属、利什曼原虫属和长尾噬菌体科。此外，稻虾共作养殖模式样本中的大多数微生物，尤其是来自不同领域的微生物，紧密且正向连接，这表明它们对环境压力具有较强的抵抗力。虽然不同水产养殖模式中的微生物在不同领域间表现出中等水平的横向基因转移（HGT），但稻虾共作养殖模式显示出相对较低的HGT事件频率，尤其是那些涉及抗生素抗性基因的事件。最后，环境因素，包括pH值、氧化还原电位、温度和总氮，对这些水产养殖模式中微生物群落的形成有深远影响。有趣的是，与其他模式相比，稻虾共作养殖模式的微生物群落受这些环境因素影响较小，这表明后者中的微生物具有更强的抵抗环境压力的能力。这些发现共同反映了稻虾共作养殖模式独特的多领域微生物模式，并表明从微生物群落特征的角度来看，该模式是一种可持续模式。
