Analysis of DNA archived in lake sediments

Abstract

The goal of this lecture is to provide aquatic scientists and interested laymen with an overview of the potential, methods and exemplary analyses of DNA preserved in lake sediments. This area is an emerging field, as new techniques are opening up avenues for novel studies of the sediment record. Numerous papers in this field have recently been published in Science, PNAS and PLoS ONE. Like many new fields, there are challenges as well as exciting lines of future inquiry, which we dedicate part of the lecture towards.

This lecture starts by providing a brief introduction to paleolimnology, with an emphasis on how DNA studies can expand this field. We then provide information on the ways in which DNA can be archived in sediments & how analyses can differ, depending on the question and target. Examples of the common genetic markers used and how DNA may be sequenced are also highlighted in the methods section. In the second portion of the lecture, we focus on the applications of sedimentary DNA: 1) to the study of particular phytoplankton group dynamics; 2) to the analysis of zooplankton DNA preserved in resting eggs; and, 3) to uncover community-wide changes in plankton. Finally, we close the lecture with a discussion on challenges and future directions in the field. Advances in the development and calibration of different extraction techniques, as well as further enhancement of genetic libraries and bioinformatics pipelines, are all areas ripe for new research.

This lecture has been prepared with a diverse audience in mind. For example, undergraduate or graduate courses that could be interested in our material include Aquatic Ecology, Limnology, Oceanography, Microbial Ecology, Environmental Genomics and Paleoecology. This lecture could also serve as a useful introduction to non-specialist audiences that are interested in the potential of the DNA archive preserved in lake sediments (including funding agencies).