A standardized archaeal taxonomy for the Genome Taxonomy Database

Abstract

An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence (RED). The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios, and expansion of the genome database. Rank normalization was shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. In total, 16 archaeal phyla are described, including reclassification of three major monophyletic units from the former Euryarchaeota and one phylum resulting from uniting the TACK superphylum into a single phylum. The taxonomy is publicly available at the GTDB website (https://gtdb.ecogenomic.org). MainCarl Woese's discovery of the Archaea in 1977, originally termed Archaebacteria (Woese and Fox, 1977) gave rise to the recognition of a new domain of life and fundamentally changed our view of cellular evolution .

Distribution of Denitrification among Haloarchaea: A Comprehensive Study

“…Annotation of the phylogenetic tree was accomplished with the online tool "Interactive Tree Of Life (iTol) v4" (https://itol.embl.de; accessed on 15 January 2021) [34]. Taxonomic classifications are according to the Genome Taxonomy Database (GTDB) (https://gtdb.ecogenomic.org; accessed on 15 January 2021) and to NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/ taxonomy; accessed on 15 January 2021) [31,[35][36][37].…”

“…From the analysis of this classification, it can be assumed that the number of available genomes from Halobacteria class is suitable and significant for this research. There are representatives from all described families in literature, and from the great part of the genera [35][36][37]. Nevertheless, due to the low number of species classified in each genus, it was concluded that genera classification is not suitable for a deeper study.…”

Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane

“…The numbers of ANME varies in different ecosystems, but usually ranges from 10 5 to 10 7 cell/g and accounts for 1-20% of the total microbial population [10,23]. These microorganisms, so far unavailable in pure culture, belong to the phylum Euryarchaeota (or to the phylum "Halobacteriota" according to GTDB [25] and are represented by three phylogenetic groups: ANME-1 with subgroups a and b (Candidatus Methanophagales), ANME-2 with subgroups a, b, c, d, and ANME-3. They are not monophyletic: ANME-2 and ANME-3 belong to Methanosarcinales while ANME-1 has a separate deep phylogenetic lineage [26,27].…”

The Archaeal Transcription Termination Factor aCPSF1 is a Robust Phylogenetic Marker for Archaeal Taxonomy

“…Metagenome information not only opens an avenue to explore the diversity and metabolic potentials, but also lays a foundation for phylogenomic studies of the largely uncultured archaeal species, which has resulted in a rapid growth of the archaeal phylogenetic tree with a number of new phyla, classes and orders ( 22 – 24 ). Very recently, Parks et al ( 25 , 26 ) have developed a Genome Taxonomy Database (GTDB), the first comprehensive prokaryote taxonomy based on phylogenomic analysis, which inferred phylogenetic trees from the concatenation of single-copy vertically inherited genes, and provided higher resolution than those based on single gene. The GTDB has also recorded amazingly diverse archaea, and more than 40 phyla are proposed, however, with the majority encompassing only a few or even no cultured species ( 26 ).…”

“…Very recently, Parks et al ( 25 , 26 ) have developed a Genome Taxonomy Database (GTDB), the first comprehensive prokaryote taxonomy based on phylogenomic analysis, which inferred phylogenetic trees from the concatenation of single-copy vertically inherited genes, and provided higher resolution than those based on single gene. The GTDB has also recorded amazingly diverse archaea, and more than 40 phyla are proposed, however, with the majority encompassing only a few or even no cultured species ( 26 ).…”