Biology subjects

Waite, D. W.

Publications and source records attributed to Waite, D. W..

3 recordsLinked to original sources

bioRxiv2020

A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications

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).

microbiology↗

bioRxiv2020

Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem

Ecological theory suggests that habitat disturbance differentially influences distributions of generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and other conditions. Microbial community composition and function was profiled in intertidal and subtidal sediments using 16S amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Microbial abundance and composition significantly differed with sediment depth and, to a lesser extent, sampling date. Several generalist taxa were highly abundant and prevalent in all samples, including within orders Woeseiales and Flavobacteriales; genome reconstructions indicate these facultatively anaerobic taxa are highly metabolically flexible and adapt to fluctuations in resource availability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers (Desulfobacterales, Desulfobulbales) and proposed candidate phylum MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the generalist-associated processes of sulfide oxidation and hydrogenogenic fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. In addition, a manipulative experiment confirmed generalists outcompete specialist taxa during simulated habitat disturbance. Altogether, these findings suggest that metabolically flexible taxa become dominant in these highly dynamic environments, whereas metabolic specialism restricts bacteria to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.

microbiology↗

bioRxiv2018

A proposal for a standardized bacterial taxonomy based on genome phylogeny

Taxonomy is a fundamental organizing principle of biology, which ideally should be based on evolutionary relationships. Microbial taxonomy has been greatly restricted by the inability to obtain most microorganisms in pure culture and, to a lesser degree, the historical use of phenotypic properties as the basis for classification. However, we are now at the point of obtaining genome sequences broadly representative of microbial diversity by using culture-independent techniques, which provide the opportunity to develop a comprehensive genome-based taxonomy. Here we propose a standardized bacterial taxonomy based on a concatenated protein phylogeny that conservatively removes polyphyletic groups and normalizes ranks based on relative evolutionary divergence. From 94,759 bacterial genomes, 99 phyla are described including six major normalized monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into the single phylum Patescibacteria. In total, 73% of taxa had one or more changes to their existing taxonomy.

microbiology↗