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Abstract Bacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental preferences. This diversity makes it challenging to interpret ecological patterns in microbiomes and understand why individual taxa, or assemblages, may vary across space and time. While we can use information from the rapidly growing databases of bacterial genomes to infer traits, we still need an approach to organize what we know, or think we know, about bacterial taxa to match taxonomic and phylogenetic information to trait inferences. Inspired by the periodic table of the elements, we have constructed a ‘periodic table’ of bacterial taxa to organize and visualize monophyletic groups of bacteria based on the distributions of key traits predicted from genomic data. By analyzing 50,745 genomes across 31 bacterial phyla, we used the Haar-like wavelet transformation, a model-free transformation of trait data, to identify clades of bacteria which are nearly uniform with respect to six selected traits - oxygen tolerance, autotrophy, chlorophototrophy, maximum potential growth rate, GC content and genome size. The identified functionally uniform clades of bacteria are presented in a concise ‘periodic table’-like format to facilitate identification and exploration of bacterial lineages in trait space. While our approach could be improved and expanded in the future, we demonstrate its utility for integrating phylogenetic information with genome-derived trait values to improve our understanding of the bacterial diversity found in environmental and host-associated microbiomes. 

Abstract Not all bacteria are fast growers. In soil as in other environments, bacteria exist along a continuum—from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs that are adapted to life in the “slow lane.” However, the field of microbiology is built almost exclusively on the study of copiotrophs due, in part, to the ease of studying them in vitro. To begin understanding the attributes of soil oligotrophs, we analyzed three independent datasets that represent contrasts in organic carbon availability. These datasets included 185 samples collected from soil profiles across the USA, 950 paired bulk soil and rhizosphere samples collected across Europe, and soils from a microcosm experiment where carbon availability was manipulated directly. Using a combination of marker gene sequencing and targeted genomic analyses, we identified specific oligotrophic taxa that were consistently more abundant in carbon-limited environments (subsurface, bulk, unamended soils) compared to the corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members of the Dormibacterota and Chloroflexi phyla. In general, putative soil oligotrophs had smaller genomes, slower maximum potential growth rates, and were under-represented in culture collections. The genomes of oligotrophs were more likely to be enriched in pathways that allow oligotrophs to metabolize a range of energy sources and store carbon, while genes associated with energy-intensive functions like chemotaxis and motility were under-represented. However, few genomic attributes were shared, highlighting that oligotrophs likely use a range of different metabolic strategies and regulatory pathways to thrive in resource-limited soils. 

Abstract Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.