The Evolution of Ecological Diversity in Acidobacteria

Abstract

Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.

Soil health increases primary productivity across Europe

“…Structural equation models confirmed a positive direct effect of increased richness of Acidobacteria and Firmicutes on cropland productivity, while the opposite was observed for Chytridiomycota (i.e., increased OTU richness led to lower productivity). Acidobacteria are abundant soil-borne microorganisms known to be involved in nutrient mineralization and organic matter degradation (Banerjee et al, 2016; Kielak et al, 2016; Sikorski et al, 2022). Our results also align with a recent study where Acidobacteria positively correlated with cropland productivity in a four-decade fertilization experiment (Fan et al, 2021).…”

“…Predictor ranking based on relative importance following multi-model averaging indicated that the best predictor of primary productivity in croplands was the richness of Acidobacteria (Figure 4). Acidobacteria are abundant soil-borne microorganisms known to be involved in nutrient mineralization and organic matter degradation (Banerjee et al, 2016; Kielak et al, 2016; Sikorski et al, 2022). Here we demonstrate for the first time that the positive effect of Acidobacteria on primary productivity is comparatively higher in croplands than in woodlands or grasslands (Figure S8).…”

Plant G x Microbial E: Plant genotype interaction with soil bacterial community shapes rhizosphere composition during invasion

“…These were taxa that were more abundant in native soils, and also more abundant on native genotypes when grown in the invaded soils in which these same groups were more depauperate (again suggesting preferential accumulation). These groups have a variety of potential functions of interest, and include an uncultured Gaiellales family (a group that has been associated with plant colonizers, and may regulate organic and fatty acids in soils (Ye et al 2021; L. Sun et al 2022)); a family in Subgroup 1 of the Acidobacteriaceae (a diverse group of oligotrophs abundant in soils, some of which have adapted to specific dry soil conditions; (Kielak et al 2016; Sikorski et al 2022)), a family in the CPla-3 termite group (a more highly specialized group in the soil, often in acidic environments; (Fickling et al 2024)), and the family Polyangiaceae (a group of predatory social bacteria, among the most common predators of bacteria in the soil, with the potential to structure the diversity of the entire microbial community (Petters et al 2021; Z. Wu et al 2022; Thakur and Geisen 2019)).…”

Effect of severe wildfire on soil phosphorus fractions and adsorption in a cold temperate coniferous forest after 5 years

“…Soil texture was determined by the sieve‐pipette method, SOM was removed by oxidation with hydrogen peroxide, in which soil aggregates were dispersed. Afterwards, the sand (2–0.02 mm), silt (0.02–0.002 mm) and clay (<0.002 mm) fractions were determined by sieving and sedimentation (Sikorski et al, 2022).…”