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Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?

Authors
  • Sare, Abdoul Razack1
  • Stouvenakers, Gilles1
  • Eck, Mathilde1
  • Lampens, Amber2, 3
  • Goormachtig, Sofie2, 3
  • Jijakli, M. Haïssam1
  • Massart, Sebastien1
  • 1 (S.M.)
  • 2 (S.G.)
  • 3 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
Type
Published Article
Journal
Microorganisms
Publisher
MDPI AG
Publication Date
Feb 28, 2020
Volume
8
Issue
3
Identifiers
DOI: 10.3390/microorganisms8030342
PMID: 32121205
PMCID: PMC7142977
Source
PubMed Central
Keywords
License
Green

Abstract

Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.

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