The predictive power of phylogeny on growth rates in soil bacterial communities

Abstract

Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.

The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management

“…In addition to fungi, the utilization of bacteria for possible biodegradation processes is beginning to gain recognition due to their extensive functional diversity and versatility [ 121 ]. That can be explained by the ability to exhibit rapid growth rates and a remarkable tolerance range in terms of temperature, pH, and salinity, enabling them to adapt to a diverse array of environmental conditions [ 122 , 123 , 124 , 125 ]. In addition, some bacteria have the ability to meet their nitrogen needs through the process of biological nitrogen fixation [ 126 ].…”

Unravelling the factors of evolutionary repeatability: insights and perspectives on predictability in evolutionary biology

“…These trees, constructed using statistical methods such as maximum likelihood (Steel and Rodrigo, 2008;Amiroch et al, 2018) or Bayesian interference (Makarenkov et al, 2006;Boussau et al, 2013), enable the estimation of ancestral states and the anticipation of future evolutionary trajectories. Phylogenetic analysis has been successfully used to predict growth rates of soil bacteria (Walkup et al, 2023), plant bioprospecting (Saslis-Lagoudakis et al, 2012) and identifying evolutionary drivers of mammalian brain development (Barton and Harvey, 2000).…”

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

“…A contemporary question regarding microbiome function relates to whether groups of microbes with shared functions are composed of phylogenetically close organisms or unrelated organisms that share similar metabolic capabilities. Traits such as photosynthesis, methanogenesis, maximum growth rates, and response to soil wet-up tend to be strongly correlated with phylogeny, while others, such as use of specific carbon sources, have weak or no phylogenetic signals (74)(75)(76). Here, we found some phylogenetic trends in corrinoid traits, but overall, the distribution of these traits is patchy across the phylogenetic tree, suggesting that gene loss has occurred at various evolutionary points, possibly due to the frequent emergence of corrinoid dependence and independence (9), or that horizontal gene transfer (HGT) is important in sustaining corrinoid biosynthesis and use.…”