Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes

Abstract

The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

“…However, seda DNA studies have predominantly focused on microorganisms as proxies for ecosystems’ health (e.g. cyanobacteria 30 ; ciliates 16 ; parasitic taxa 31 ), with other taxonomic groups less well represented. Our study addresses some of the challenges of direct observations as it is not reliant on fossil remains.…”

Long‐term cyanobacterial dynamics from lake sediment DNA in relation to experimental eutrophication, acidification and climate change

“…According to sediment pigment archives, cyanobacterial biomass has increased in many temperate lakes, likely in response to wastewater pollution and the increased use of chemical fertilisers in agriculture since the 1940s (Taranu et al, 2015). Climate change and other environmental stressors may have also contributed to these increases in cyanobacterial biomass (Hou et al, 2014; Paerl & Huisman, 2008; Paerl & Otten, 2013; Picard, Pochon, et al, 2022). However, the lack of historical surface‐water monitoring of cyanobacteria and associated toxins for most aquatic systems limits our understanding of the effects of environmental stressors on cyanobacterial dynamics and the role of climate change.…”

“…However, some cyanobacterial pigments (such as zeaxanthin) can be found in other phytoplankton (Schlüter et al, 2006) and there are caveats in using pigments for analysing historical cyanobacterial dynamics (Picard, Wood, et al, 2022). Over the past decade, the feasibility and usefulness of other methods, including molecular and bioinformatics techniques, have been explored (Domaizon et al, 2017; Hobbs et al, 2021; Mejbel et al, 2021; Pal et al, 2015; Picard, Pochon, et al, 2022; Pilon et al, 2019).…”

“…There has been an increase in the use of sediment DNA (sedDNA) and quantitative PCR (Hou et al, 2014; Nwosu et al, 2021; Pal et al, 2015; Pilon et al, 2019), droplet digital PCR (ddPCR) (Hobbs et al, 2021; Mejbel et al, 2021; Picard, Pochon, et al, 2022; Picard, Wood, et al, 2022) and/or amplicon sequencing (Hobbs et al, 2021; Mejbel et al, 2021; Monchamp et al, 2018; Nwosu et al, 2021) as alternative approaches for the analysis of complex microbial communities in aquatic systems over varying time frames (Capo et al, 2021). The use of sedDNA is a more targeted method that allows for the analysis of organisms that typically do not leave behind morphological microfossils.…”

“…HTS, too, is a highly sensitive approach that provides unparalleled resolution of community compositions. Although primer specificity, bioinformatics processing and PCR inhibitors can interfere with the quantitative performance of these approaches (Hong et al, 2009; Shelton et al, 2016), recent sedDNA studies have revealed overall coherence between the two techniques (Mejbel et al, 2021; Picard, Pochon, et al, 2022).…”