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

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. To address the challenges and best practices for SBC and SBI, a group of mycologists met after the annual meeting of the Mycological Society of America (see Kennedy & Stajich, 2014, in this issue of New Phytologist, pp. 23–26) for a 2-d workshop supported by the US National Science Foundation. The key aims were: (1) to identify the potential benefits and challenges of merging SBC and SBI; (2) to assess the current strengths and limitations of resources for SBC and SBI; and (3), to consider changes in nomenclatural practices that could promote the integration of traditional specimen-based identification and classification with sequence based methods. The workshop specifically focused on the use of both SBC and SBI for fungi and organisms traditionally studied by mycologists – oomycetes, slime molds, etc. – but an overarching theme could be translated to all microorganisms – including bacteria, archaea, and metazoans – and the desire to characterize microbial interactions with plants, additionally, the issues presented here apply equally to all environmental sequences (e.g. animal and human microbiomes, soil fungi, microbes of the built environment, etc.).