The role of root community attributes in predicting soil fungal and bacterial community patterns

Roots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading of plant canopies and root systems. Thus, soil microbe–plant links are not completely understood. Using a combination of DNA metabarcoding and spatially explicit sampling at the plant neighbourhood scale, we assessed the influence of the plant root community on soil bacterial and fungal diversity (species richness, composition and b-diversity) in a dry Mediterranean scrubland. We found that root composition and biomass, but not richness, predict unique fractions of variation in microbial richness and composition. Moreover, bacterial b-diversity was related to root b-diversity, while fungal b-diversity was related to aboveground plant b-diversity, suggesting that plants differently influence both microbial groups. Our study highlights the role of plant distribution both belowground and aboveground, soil properties and other spatially structured factors in explaining the heterogeneity in soil microbial diversity. These results also show that incorporating data on both plant community compartments will further our understanding of the relationships between soil microbial and plant communities

Larger aboveground neighbourhood scales maximise similarity but do not eliminate discrepancies with belowground plant diversity in a Mediterranean shrubland

Aims: An unresolved question in plant ecology is whether diversity of the aboveground and belowground compartments of a plant community is similar at different neighbourhood scales. We investigated how the similarity between both compartments varies with the aboveground sampling grain and if significant discrepancies exist between aboveground and belowground plant diversity at the maximum similarity scale. Methods We fully mapped the aboveground perennial plant community of a 64 m2 plot in a Mediterranean shrubland and analysed this compartment by assessing diversity in 5 to 50 cm radii circles centred in soil cores. We sampled 2.5 cm radius root cores at two different depths and identified plant species by using DNA metabarcoding to characterise the belowground compartment. We quantified differences in species richness, composition and species’ spatial distribution above- and belowground. Results: The differences between aboveground and belowground communities were affected by the size of the aboveground sampling grain and were minimised when considering a circle of 20 cm radius in the aboveground. We found a significant dissimilarity in richness and composition between the two compartments, with larger differences when considering the deeper soil layer only. Conclusions: Our results showed that the spatial grain selected to sample a plant community aboveground and belowground is critical to characterise them in a comparable manner. Although their composition is related, species distribution patterns strongly differ, suggesting the simultaneous action of different assembly mechanisms. Our results call for caution when studying community assembly considering only the standing vegetation, since total plant diversity can be underappreciated

Estimating belowground plant abundance with DNA metabarcoding

Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species’ abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi‐arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field‐collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2 = .44–.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over‐ and under‐estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post‐sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species’ presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes