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Applied Microbiology and Biotechnology

, Volume 103, Issue 2, pp 995–1005 | Cite as

Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene

  • Han Meng
  • Zhichao Zhou
  • Ruonan Wu
  • Yongfeng Wang
  • Ji-Dong GuEmail author
Environmental biotechnology
  • 176 Downloads

Abstract

Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.

Keywords

nifH gene High-throughput sequencing Nitrogen cycle Community Diversity Forest soil Southern China 

Notes

Funding

This study was funded by the National Natural Science Foundation of China (grant no. 31470562 to YFW), a Hong Kong PhD Fellowship (HM), and RGC GRF grant no. 701913 (J-DG).

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

253_2018_9466_MOESM1_ESM.pdf (1.2 mb)
ESM 1 (PDF 1199 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of EnvironmentNanjing Normal UniversityNanjingChina
  2. 2.Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of ScienceThe University of Hong KongHong KongPeople’s Republic of China
  3. 3.Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouPeople’s Republic of China

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