Roadmap for naming uncultivated Archaea and Bacteria

Abstract

A s new environments are explored and technological innovations improve tools for the characterization of microbial biodiversity, insights into bacterial and archaeal diversity are continually emerging 1,2 , including improved understanding of physiological capacity, ecology and evolution of organisms across the tree of life. These advances are based on both cultivation strategies 3,4 and cultivation-independent methods that directly access diversity using single-cell 5,6 or metagenomic sequencing 7-9 (Box 1). Though our ability to culture fastidious microorganisms is improving, success seems to vary depending on the environment. For example, the microbial diversity of host-associated systems such as the human microbiome 11,12 may be more amenable to cultivation compared to some environments such as soil. At present, it seems clear that most archaeal and bacterial diversity remains yet to be cultured 10,13. The reasons are many, but as demonstrated recently by the cultivation of a member of the Asgard archaea 14 , syntrophic interactions, slow growth and media optimization can present formidable challenges. Rules of prokaryotic nomenclature and current challenges Describing biodiversity and identifying organisms are the scientific goals of taxonomy. Taxonomy integrates classification and nomenclature to describe biological diversity. Classification circumscribes and ranks taxa, and nomenclature is the process of assigning names. The commonly used Linnaean nomenclatural system focuses on the recognition of species as the basic unit, which are included in taxa of successively higher ranks (genus, family, order, class and phylum). There is some flexibility on how to circumscribe microbial species using phylogenetic, genotypic and phenotypic data. Once a species is delineated, rules of nomenclature given in the International Code of Nomenclature of Prokaryotes (ICNP or 'the Code' 14 ; see Box 2) guide the creation and assignment of names. This is true of all codes of nomenclature that currently exist-prokaryotes, viruses, animals, algae, fungi and plants-in addition to separate codes for cultivated plants and plant associations. Roadmap for naming uncultivated Archaea and Bacteria The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we b...

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