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Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode

The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield f...

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Autores principales: Wang, Yi, Wang, Chen, Chen, Yonglun, Zhang, Dongdong, Zhao, Mingming, Li, Hailan, Guo, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219076/
https://www.ncbi.nlm.nih.gov/pubmed/34168630
http://dx.doi.org/10.3389/fmicb.2021.669570
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author Wang, Yi
Wang, Chen
Chen, Yonglun
Zhang, Dongdong
Zhao, Mingming
Li, Hailan
Guo, Peng
author_facet Wang, Yi
Wang, Chen
Chen, Yonglun
Zhang, Dongdong
Zhao, Mingming
Li, Hailan
Guo, Peng
author_sort Wang, Yi
collection PubMed
description The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.
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spelling pubmed-82190762021-06-23 Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode Wang, Yi Wang, Chen Chen, Yonglun Zhang, Dongdong Zhao, Mingming Li, Hailan Guo, Peng Front Microbiol Microbiology The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems. Frontiers Media S.A. 2021-06-08 /pmc/articles/PMC8219076/ /pubmed/34168630 http://dx.doi.org/10.3389/fmicb.2021.669570 Text en Copyright © 2021 Wang, Wang, Chen, Zhang, Zhao, Li and Guo. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Wang, Yi
Wang, Chen
Chen, Yonglun
Zhang, Dongdong
Zhao, Mingming
Li, Hailan
Guo, Peng
Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode
title Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode
title_full Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode
title_fullStr Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode
title_full_unstemmed Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode
title_short Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode
title_sort microbiome analysis reveals microecological balance in the emerging rice–crayfish integrated breeding mode
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219076/
https://www.ncbi.nlm.nih.gov/pubmed/34168630
http://dx.doi.org/10.3389/fmicb.2021.669570
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