eDNA metabarcoding reveals spatial structuring of bacterial communities in the volcanic crater Lake Holon, Philippines

Аннотация

Crater lakes of volcanic origin represent special cases of freshwater ecosystems where the morphology of the basin, hydrological isolation, and spatial gradients of physicochemical parameters might influence the microbial community structuring. To date, Lake Holon is an understudied volcanic crater lake in Southern Philippines at the microbial level. Here we report the first assessment of bacteria using environmental DNA (eDNA) metabarcoding of Lake Holon with respect to spatial differences of the central and peripheral regions of the lake. Samples of near-surface waters from six sites of the lake were taken in situ for physicochemical characterization and eDNA isolation. Total genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA genes were sequenced using high-throughput Illumina MiSeqi100 Plus platform. Sequence reads (total=944,206 ASVs) were processed by the EasyAmplicon, and DADA2 pipelines; community diversity was analyzed in R software. Functional profiles were predicted using PICRUSt in Parallel Meta-suite (PMS). Bacteria showed significant spatial differences in the studied crater lake. Central sites harbored distinct and very diverse communities including unclassified bacterial lineages potentially associated with acidic conditions including pelagic cyanobacterium Synechococcus rubescens, suggestive of possible selective pressure by localized physicochemical conditions and water column processes. In contrast, less acidic and better-oxygenated peripheral locations contained copiotrophic heterotrophs such as Pseudomonas aeruginosa, potentially due to greater connectivity with the littoral zone and terrestrial environment or possibly anthropogenic effects. Alpha and beta diversity analysis also showed heterogeneous community structure at central locations and relatively homogeneous community structure at peripheral locations of the lake, in agreement with environmental filtering at different locations. This research gives the first insight into the bacterial diversity in Lake Holon and previously unknown fine-scale biogeography of microbes in a volcanic crater lake basin. The research demonstrates eDNA metabarcoding and serves as a basis for future studies and limnological monitoring of tropical crater lakes.