Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)

Yongbin Li; Rui Yang; Max M Häggblom; Mengyan Li; Lifang Guo; Baoqin Li; Max Kolton; Zhiguo Cao; Mohsen Soleimani; Zheng Chen; Zhimin Xu; Wenlong Gao; Bei Yan; Weimin Sun

doi:10.1186/s40168-022-01379-9

Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)

Microbiome. 2022 Nov 3;10(1):186. doi: 10.1186/s40168-022-01379-9.

Authors

Yongbin Li^#^{1

2}, Rui Yang^#¹, Max M Häggblom³, Mengyan Li⁴, Lifang Guo¹, Baoqin Li¹, Max Kolton^{1

2

5}, Zhiguo Cao⁶, Mohsen Soleimani⁷, Zheng Chen⁸, Zhimin Xu⁹, Wenlong Gao^{1

2}, Bei Yan^{1

2}, Weimin Sun^{10

11}

Affiliations

¹ Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China.
² Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
³ Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA.
⁴ Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
⁵ French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel.
⁶ School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China.
⁷ Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran.
⁸ Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China.
⁹ Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
¹⁰ Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, 510650, China. wmsun@soil.gd.cn.
¹¹ Joint Laboratory for Environmental Pollution and Control, Guangdong-Hong Kong-Macao, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China. wmsun@soil.gd.cn.

^# Contributed equally.

Abstract

Background: Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments.

Results: Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using ¹⁵N₂ identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth.

Conclusions: This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.

Keywords: Bacterial colonization; Diazotrophic endophytes; Metagenomic-binning; Stable isotope probing (SIP).

Publication types

Video-Audio Media
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Bacteria
China
DNA
Endophytes*
Nitrogen Fixation
Plant Roots / microbiology
Plants / genetics
Poaceae* / microbiology
Pseudomonas / genetics

Substances

DNA