Is a Central Sediment Sample Sufficient? Exploring Spatial and Temporal Microbial Diversity in a Small Lake

(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),Microcystisspecific 16S rRNA, microcystin synthetase gene E (mcyE) and microcystins (MCs) were assessed. Radionuclide measurements (Pb-210,Cs-137) 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 producingMicrocystisblooms in the past, noMicrocystisspecific 16S rRNA,mcyEand MCs were found in surface sediments but occurred deeper in sediment cores (approximately 1950 ' s).Pb-210 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 producingMicrocystisblooms are a recent phenomenon in Lake Rotorua. We posit that the absence ofMicrocystisfrom the surface sediments is a consequence of the Kaikoura earthquake two years prior to our sampling.