Biology

Towards the unification of sequence-based classification and sequence-based identification of host-associated microorganisms

Document Type

Article

Abstract

Plants interact with a wide assortment of microbial organisms – taking the role of pathogens, mutualists, and commensals. Our knowledge of plant-associated microorganisms has traditionally been based on macroscopic and microscopic structures. In recent decades, the use of both DNA and RNA sequence data derived directly from the environment has been used to study both the taxonomic and functional diversity of host-associated microorganisms. More recently, an explosion of data derived from a shift in nucleotide sequencing technologies has revealed an astonishing diversity of microorganisms (Hibbett & Taylor, 2013). To elucidate taxonomic and functional microbial diversity, researchers employ distinct but not mutually exclusive techniques when using molecular data – Sequence-based Classification (SBC) and Sequence-based Identification (SBI). Those who utilize SBC are predominantly concerned with the discovery and categorization of microbial organisms on the basis of phylogenetic relationships. Researchers who engage in SBI utilize databases as references, often using similarity-based (as opposed to phylogeny-based) approaches, to taxonomically and/or functionally identify the composition of microbial communities. Together, SBC and SBI encompass a range of activities using sequence data – predominantly from nucleic acids – to identify, describe, and functionally characterize microorganisms from the plant-based environment. Marker-based and metagenomic studies, in particular, have sequenced nucleotides from thousands to millions of unidentified species and underscore the need for resources developed for taxonomic and functional characterization of microbial diversity (Hibbett et al., 2011). Perhaps most importantly, new analysis techniques and resources need to integrate with existing taxonomic and systematic knowledge that is based traditionally on cultures and type-material (Lindahl et al., 2013). There is a dire need to develop unified community-based resources and analysis standards for the integration of SBC and SBI of fungi and other microorganisms.

Publication Title

New Phytologist

Publication Date

1-2015

Volume

205

Issue

1

First Page

27

Last Page

31

ISSN

0028-646X

DOI

10.1111/nph.13180

Keywords

database, fungi, genomics, metadata, Mycological Society of America, Mycorrhiza, sequenced-based classification, sequenced-based identification

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