Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems

Abstract

Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 AD were selected to perform denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st century samples was clearly different than those of mid-19th century. This compositional change was correlated with shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real-time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in palaeolimnological studies to include key microbial community characteristics of great scientific and social interest.

Specific Chemical and Genetic Markers Revealed a Thousands-Year Presence of Toxic Nodularia spumigena in the Baltic Sea

“…The application of genetic markers in the analysis of old sediments still faces serious methodological constrains. A limited number of studies in which these markers were used as marine cyanobacteria tracers have been published [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ]. In most of the studies, the presence of cyanobacteria was reconstructed based on 16S rRNA ( Supplementary Material Table S4 ).…”

Influence of UV-B radiation on the fitness and toxin expression of the cyanobacterium Cylindrospermopsis raciborskii

“…The concentration and purity of cDNA were determined spectrophotometrically at 260 and 280 nm (Nanodrop), and tenfold dilution series were then used as a template for quantitative real-time PCR (qPCR). In order to quantify the absolute copy number of sxtU gene, qPCR was performed according to Martínez de la Escalera et al (2014).…”

Benthic Archives Reveal Recurrence and Dominance of Toxigenic Cyanobacteria in a Eutrophic Lake over the Last 220 Years

“…Thus, the real assessment of long-term cyanobacteria dynamics remains difficult. The sediment compartment, by stocking resting cells and macro-rests, represents a means of reconstituting the lake’s history; benthic archives are already known to store evidence of past aquatic ecosystems, including microbial diversity [ 4 , 5 ]. Concerning nostocalean cyanobacteria, their resistant cells, termed akinetes, have the ability to resist a huge panel of abiotic constraints, both in the water and in sediment, such as anoxia, desiccation and lack of light [ 6 ].…”