Open AccessBotanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi
Author(s) -
JohnstonMonje David,
Lopez Mejia Jessica
Publication year - 2020
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.1002/aps3.11334
Subject(s) - biology , ribosomal intergenic spacer analysis , terminal restriction fragment length polymorphism , microbiome , microbial ecology , amplicon , restriction fragment length polymorphism , temperature gradient gel electrophoresis , intergenic region , ribosomal rna , genetics , ribosomal dna , dna profiling , computational biology , microbial population biology , dna sequencing , 16s ribosomal rna , internal transcribed spacer , polymerase chain reaction , bacteria , dna , gene , genome , phylogenetics
High‐throughput sequencing technologies have revolutionized the study of plant‐associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant‐associated microbiomes using molecular fingerprinting methodologies, including single‐strand conformation polymorphism ( SSCP ), denaturing gradient gel electrophoresis ( DGGE ), amplicon length heterogeneity PCR ( LH ‐ PCR ), ribosomal intergenic spacer analysis ( RISA ) and automated ribosomal intergenic spacer analysis ( ARISA ), and terminal restriction fragment length polymorphism ( TRFLP ). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP ) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.