Abstract
(1) Background: Paleolimnological studies use sediment cores to explore long-term changes
in lake ecology, including occurrences of harmful cyanobacterial blooms. Most studies are based on
single cores, assuming this is representative of the whole lake, but data on small-scale spatial variability
of microbial communities in lake sediment are scarce. (2) Methods: Surface sediments (top 0.5 cm)
from 12 sites (n = 36) and two sediment cores were collected in Lake Rotorua (New Zealand). Bacterial
community (16S rRNA metabarcoding), Microcystis specific 16S rRNA, microcystin synthetase gene E
(mcyE) and microcystins (MCs) were assessed. Radionuclide measurements (210Pb, 137Cs) were used to
date sediments. (3) Results: Bacterial community, based on relative abundances, differed significantly
between surface sediment sites (p < 0.001) but the majority of bacterial amplicon sequence variants
(88.8%) were shared. Despite intense MC producing Microcystis blooms in the past, no Microcystis
specific 16S rRNA, mcyE and MCs were found in surface sediments but occurred deeper in sediment
cores (approximately 19500
s). 210Pb measurements showed a disturbed profile, similar to patterns
previously observed, as a result of earthquakes. (4) Conclusions: A single sediment core can capture
dominant microbial communities. Toxin producing Microcystis blooms are a recent phenomenon in
Lake Rotorua. We posit that the absence of Microcystis from the surface sediments is a consequence of
the Kaikoura earthquake two years prior to our sampling.
