Lake plankton sample collection from the field for downstream molecular analysis

The objective of this protocol is to provide a reliable and replicable method for the sampling of lake micro-plankton to be used for downstream DNA analysis. This protocol is one of those proposed by the EcoAlpsWater consortium to promote the implementation of High Throughput Sequencing (HT S) of environmental DNA (eDNA) in the biomonitoring and ecological assessment of water bodies. The application proposed here, in the context of EcoAlpsWater, aims at comparing DNA inventories to traditional phytoplanktonic inventories and at characterizing more broadly the micro-planktonic diversity through eDNA analysis (including bacteria). The sampling strategy is similar to that used for classical phytoplankton survey focusing on the euphotic zone, however the procedure for filtration and preservation is adapted for DNA samples. This protocol is part of the deliverables provided by the WP1 of the Eco-AlpsWater project. All members of the EcoAlpsWater consortium (http://www.alpinespace. eu/projects/eco-alpswater/en/home) contributed to the optimization of this protocol.