Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site

PLoS One. 2014 Oct 31;9(10):e111744. doi: 10.1371/journal.pone.0111744. eCollection 2014.

Abstract

We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant) and a new planting site (NewPlant) in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil) and from the new planting site (NewSoil) was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant). More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria). The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics*
  • Bacteria / growth & development*
  • Biodiversity
  • Biomass
  • Malus / microbiology*
  • Phylogeny
  • Plant Diseases / genetics
  • Plant Diseases / microbiology*
  • Principal Component Analysis
  • RNA, Ribosomal, 16S / genetics*
  • Rhizosphere*
  • Seedlings / growth & development
  • Sequence Analysis, RNA / methods*
  • Soil
  • Species Specificity

Substances

  • RNA, Ribosomal, 16S
  • Soil

Grants and funding

This work was supported by China Agriculture Research System, CARS-28, Minister of Agriculture (PRC), (http://english.agri.gov.cn/) (QPW), and Beijing Technology Foundation for Selected Overseas Chinese Scholar, Human Resource and Social Security Bureau of Beijing (http://www.bjld.gov.cn/) (JS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.