Locality or habitat? Exploring predictors of biodiversity in Amazonia

Abstract

Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large‐scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro‐organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced.

Peer Review #3 of "Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve (v0.1)"

“…On the contrary, we observed that the relative abundance of Ascomycota, over Basidiomycota, Zygomycota, and Rozellomycota, was predominant group in the JM, which was in agreement with previous research (Curlevski et al, 2010). Findings from other tropical regions indicated that in the broadleaf forests, Ascomycota was the most predominant phylum (Kerfahi et al, 2014;Ritter et al, 2018). In our study, the higher abundance of Ascomycota in JM suggested the enrichment of saprotrophic species, proving that Ascomycota tend to use the easily degradable residues (Lundell et al, 2010), which might be related to organic matter input (Lundell et al, 2010).…”

A practical guide to DNA metabarcoding for entomological ecologists

“…For example, during eDNA sampling, a trowel or soil corer is often decontaminated and reused repeatedly (e.g. Ritter et al ., ).…”

“…Many eDNA studies have adopted quantitative procedures for field sampling, such as soil sampling with corers (Ritter et al ., ; Zinger et al ., ), filtering fixed volumes of water (Lacoursiere‐Roussel et al ., ; Macher et al ., ), and using artificial substrate units for macroinvertebrate sampling (Cahill et al ., ). Standardised and robust protocols that provide quantitative and reproducible results will increase the uptake of eDNA metabarcoding (Dickie et al ., ).…”

Traits or habitat? Disentangling predictors of leaf‐litter decomposition in Amazonian soils and streams

“…), energy and nutrients fluxes, but also the factors regulating them (e.g., communities), may vary at (micro)habitat, and local and regional scales (e.g., Ritter et al. ). While terrestrial and aquatic systems are functionally linked in terms of energy transfers and nutrient cycle, the driver of OM decomposition has rarely been investigated simultaneously in these two environments (see review in Appendix ).…”

“…Moreover, the inter-and intraspecific phenological variability of plants results in differences in both the quantity and quality of resources returned to soils (e.g., H€ attenschwiler et al 2008H€ attenschwiler et al , Kattge et al 2011H€ attenschwiler et al , C ardenas et al 2014. Since individual plant species may have major effects on the components of the belowground biota, and, consequently, on the processes and functions they regulate (Wardle 2004, C ardenas et al 2015, Garc ıa-Palacios et al 2015, energy and nutrients fluxes, but also the factors regulating them (e.g., communities), may vary at (micro)habitat, and local and regional scales (e.g., Ritter et al 2019). While terrestrial and aquatic systems are functionally linked in terms of energy transfers and nutrient cycle, the driver of OM decomposition has rarely been investigated simultaneously in these two environments (see review in Appendix S1).…”