Cargando…

Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

BACKGROUND: Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction. METH...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Mengzhi, Chen, Zhongjian, Qian, Jun, Wei, Fugang, Zhang, Guozhuang, Wang, Yong, Wei, Guangfei, Hu, Zhigang, Dong, Linlin, Chen, Shilin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418314/
https://www.ncbi.nlm.nih.gov/pubmed/32793300
http://dx.doi.org/10.1186/s13020-020-00364-4
_version_ 1783569669210243072
author Li, Mengzhi
Chen, Zhongjian
Qian, Jun
Wei, Fugang
Zhang, Guozhuang
Wang, Yong
Wei, Guangfei
Hu, Zhigang
Dong, Linlin
Chen, Shilin
author_facet Li, Mengzhi
Chen, Zhongjian
Qian, Jun
Wei, Fugang
Zhang, Guozhuang
Wang, Yong
Wei, Guangfei
Hu, Zhigang
Dong, Linlin
Chen, Shilin
author_sort Li, Mengzhi
collection PubMed
description BACKGROUND: Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction. METHODS: This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields. RESULTS: At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields. CONCLUSIONS: This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.
format Online
Article
Text
id pubmed-7418314
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-74183142020-08-12 Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields Li, Mengzhi Chen, Zhongjian Qian, Jun Wei, Fugang Zhang, Guozhuang Wang, Yong Wei, Guangfei Hu, Zhigang Dong, Linlin Chen, Shilin Chin Med Research BACKGROUND: Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction. METHODS: This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields. RESULTS: At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields. CONCLUSIONS: This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system. BioMed Central 2020-08-10 /pmc/articles/PMC7418314/ /pubmed/32793300 http://dx.doi.org/10.1186/s13020-020-00364-4 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Li, Mengzhi
Chen, Zhongjian
Qian, Jun
Wei, Fugang
Zhang, Guozhuang
Wang, Yong
Wei, Guangfei
Hu, Zhigang
Dong, Linlin
Chen, Shilin
Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
title Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
title_full Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
title_fullStr Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
title_full_unstemmed Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
title_short Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
title_sort composition and function of rhizosphere microbiome of panax notoginseng with discrepant yields
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418314/
https://www.ncbi.nlm.nih.gov/pubmed/32793300
http://dx.doi.org/10.1186/s13020-020-00364-4
work_keys_str_mv AT limengzhi compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT chenzhongjian compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT qianjun compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT weifugang compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT zhangguozhuang compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT wangyong compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT weiguangfei compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT huzhigang compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT donglinlin compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields
AT chenshilin compositionandfunctionofrhizospheremicrobiomeofpanaxnotoginsengwithdiscrepantyields