Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient

Abstract

Biological diversities of multiple kingdoms potentially respond in similar ways to environmental changes. However, studies either compare details of microbial diversity across general vegetation or land use classes or relate details of plant community diversity with the extent of microbially governed soil processes, via physiological profiling. Here, we test the hypothesis of shared responses of plant and rhizosphere bacterial, fungal and metazoan biodiversities (especially across-habitat β-diversity patterns) along a disturbance gradient encompassing grazed to abandoned Alpine pasture, on acid soil in the European Central Alps. Rhizosphere biological diversity was inferred from eDNA fractions specific to bacteria, fungi and metazoans from contrasting plant habitats indicative of different disturbance levels. We found that soil β-diversity patterns were weakly correlated with plant diversity measures and similarly ordinated along an evident edaphic (pH, C:N, assimilable P) and disturbance gradient but, contrary to our hypothesis, did not demonstrate the same diversity patterns. While plant communities were well separated along the disturbance gradient, correlating with fungal diversity, the majority of bacterial taxa were shared between disturbance levels (75% of bacteria were ubiquitous, cf. 29% plant species). Metazoa exhibited an intermediate response, with communities at the lowest levels of disturbance partially overlapping. Thus, plant and soil biological diversities were only loosely dependent and did not exhibit strictly linked environmental responses. This probably reflects the different spatial scales of organisms (and their habitats) and capacity to invest resources in persistent multicellular tissues, suggesting that vegetation responses to environmental change are unreliable indicators of below-ground biodiversity responses.

Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

“…Raw sequencing data were treated with MOTHUR v1.33 [ 27 ] following the pipeline previously used by Montagna et al [ 28 ]. After making contigs using the make.contigs command with default settings, bacterial 16S rRNA raw sequences were filtered based on the following specifications: Phred score > 30, minimum fragment length of 250 bp, absence of ambiguous nucleotides (which are sometimes generated during contig formation when the delta between quality scores of a mismatched base is lower than 6), maximum 10 bp-long homopolymers, and maximum primer mismatch of 1 bp.…”

Methods and approaches to advance soil macroecology

“…In a Brazilian agricultural system, for example, geographical distance explained nearly 18 times more variance in soil fungal community composition than environmental factors such as soil and climate characteristics (Gumiere, Durrer, Bohannan, & Andreote, 2016). Biogeography of soil bacteria has been investigated at a range of scales from continental and global scales (e.g., Bahram et al, 2018;Barberán, Bates, Casamayor, & Fierer, 2012;Fierer & Jackson, 2006) to the landscape scale (Bru et al, 2011;Pasternak et al, 2013), and even at the cen- The scale at which similar processes act varies between taxonomic groups due to variation in body size and life history, and is an important consideration when studying spatial patterns of soil communities (Montagna et al, 2018). When studying landscape scale processes, Jackson and Fahrig (2012) highlight the concept of the 'scale of effect' (the scale at which an ecological response is best predicted by the habitat structure) and recommend sampling areas far enough apart to ensure sample points are independent (i.e., taxa in one sample point do not directly interact with those in others).…”

“…The scale at which similar processes act varies between taxonomic groups due to variation in body size and life history, and is an important consideration when studying spatial patterns of soil communities (Montagna et al., 2018). When studying landscape scale processes, Jackson and Fahrig (2012) highlight the concept of the ‘scale of effect’ (the scale at which an ecological response is best predicted by the habitat structure) and recommend sampling areas far enough apart to ensure sample points are independent (i.e., taxa in one sample point do not directly interact with those in others).…”

Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family

“…The DNA-based identification methods represented by DNA taxonomy, applicable also in DNA metabarcoding (Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, 2012), stand out as widely used approaches for biodiversity surveys (e.g., Telfer et al, 2015;Pavan-Kumar, Gireesh-Babu, & Lakra, 2015;deWaard et al, 2019). These methods, using standardized gene regions, allow the speeding up of organism identification and help overcoming issues in morphological taxonomy, for example by making it possible to detect the presence of organisms merely from their DNA, released in the environment (e.g., Ficetola, Miaud, Pompanon, & Taberlet, 2008;Montagna et al, 2018;Ruppert, Kline, & Rahman, 2019).…”