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Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond
Deng, Min1; Hou, Jie1,2,3; Song, Kang4; Chen, Jieyu1; Gou, Jingwei1; Li, Dapeng1,2,3; He, Xugang1,2,3
Corresponding AuthorHe, Xugang(xgh@mail.hzau.edu.cn)
2020-04-15
Source PublicationAQUACULTURE
ISSN0044-8486
Volume520Pages:10
AbstractThe identities and functional capacities of the microbial populations within surface water (SW), bottom water (BW), surface sediment (SS) and deep sediment (DS) samples from a typical grass carp (Ctenopharyngodon idellus) culturing pond in central China were explored using metagenomics. In total, the community structure and microbial processes of the water columns was distinct from that of the SS and DS layers. Alphaproteobacteria, Actinobacteria, Cyanobacteria and Planctomycetes were abundant in the water, while Deltaproteobacteria, Gammaproteobacteria, Euryarchaeota (Archaea) and Nitrospirae were more abundant in the sediment (P < .05). The functional potential and microorganisms responsible for the N nutrient cycles were also reconstructed in silico. The high functional potential for N assimilation, protein synthesis and cell proliferation in pond water should be responsible for low ammonia concentration detected. Ammonia oxidation functional genes were present in very low abundances, and were mostly detected in the water columns and related to Nitrosomonas (100%). Denitrification were observed mostly in SS and the main taxon involved was Rhodocyclales. The potential for N fixation (nif genes) and dissimilatory nitrate reduction to ammonium was also observed mostly in sediment, which is a disadvantage for ammonia reduction in the pond ecosystem. Overall, these results offer a more detailed perspective on the microbial functional ecology of the aquaculture pond.
KeywordAquaculture pond Community structure Functional potential Metagenomics Nitrogen cycling
DOI10.1016/j.aquaculture.2019.734911
Funding OrganizationEarmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences
Indexed BySCI ; SCI
Language英语
Funding ProjectEarmarked Fund for China Agriculture Research System[CARS-45] ; Fundamental Research Funds for Innovation Center of Hubei Province[2016ZXPY02] ; Fundamental Research Funds for the Central Universities[2662015PY119] ; Fundamental Research Funds for the Central Universities[2662015BQ012] ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences[2017FB13]
WOS Research AreaFisheries ; Marine & Freshwater Biology
WOS SubjectFisheries ; Marine & Freshwater Biology
WOS IDWOS:000515498200034
WOS KeywordAMMONIA-OXIDIZING BACTERIA ; DIVERSITY ; TECHNOLOGY ; SEDIMENT ; ARCHAEA ; SHRIMP ; SLUDGE ; RATIO
PublisherELSEVIER
Funding OrganizationEarmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for Innovation Center of Hubei Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences ; Open Subject of the State Key Laboratory of Freshwater Ecology and Biotechnology of the Institute of Hydrobiology of the Chinese Academy of Sciences
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/35882
Collection水环境工程研究中心_期刊论文
Corresponding AuthorHe, Xugang
Affiliation1.Huazhong Agr Univ, Coll Fisheries, Wuhan, Peoples R China
2.Hubei Prov Engn Lab Pond Aquaculture, Wuhan, Peoples R China
3.Freshwater Aquaculture Collaborat Innovat Ctr Hub, Wuhan, Peoples R China
4.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China
Recommended Citation
GB/T 7714
Deng, Min,Hou, Jie,Song, Kang,et al. Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond[J]. AQUACULTURE,2020,520:10.
APA Deng, Min.,Hou, Jie.,Song, Kang.,Chen, Jieyu.,Gou, Jingwei.,...&He, Xugang.(2020).Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond.AQUACULTURE,520,10.
MLA Deng, Min,et al."Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond".AQUACULTURE 520(2020):10.
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