A synthesis of bacterial and archaeal phenotypic trait data

Abstract

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.

Fig. 1

A visual representation of the microbe trait data integration workflow for four hypothetical datasets (red, blue, green and orange). Grey bands represent consistent taxonomy and trait detail that applies across the datasets. Each of the four steps—(a) prepare, (b) combine, (c) condense traits and (d) condense to NCBI species—are summarised in the Methods and explained in detail along with scripted steps in R at the GitHub repository.

Fig. 2

A graphical representation of data coverage and gaps for the 21 core traits mapped onto a phylogeny (black tree). The phylogeny was created by grafting star phylogenies (NCBI species to phylum) onto a recent molecular phylogeny (phylum and above) and was created here purely for illustrative purposes. To avoid clutter, only the six most speciose phyla are delineated at the outer rim (>100 species). Coloured bands represent the presence of traits in the dataset for 14,884 species. In order for the centre outwards, green are habitat traits (isolation source, optimum pH, optimum temperature, growth temperature), blue are organism trait (gram stain, metabolism, metabolic pathways, carbon substrate, sporulation, motility, doubling time, cell shape, any cell diameter), and red are genomic traits (genome size, GC content, coding genes, rRNA16S genes, tRNA genes).

Fig. 3

Graphical summaries of each of 23 traits in Online-only Table 2. Barplots are used for categorical traits and frequency histograms for continuous traits. Due to the high number of distinct metabolic pathways (>80) (d) and carbon substrates (>100) (e) included in this data, to simplify presentation each of these were grouped into major categories; pathways were grouped by the primary compound involved or distinct processes where no primary compound exists, and carbon substrates were grouped by chemical classification.