A georeferenced rRNA amplicon database of aquatic microbiomes from South America.

The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.

Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria.

Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.

Comparison of two DNA extraction methods widely used in aquatic microbial ecology.

In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.