Pyrosequencing analysis of the protist communities in a High Arctic meromictic lake: DNA preservation and change

Abstract

High Arctic meromictic lakes are extreme environments characterized by cold temperatures, low nutrient inputs from their polar desert catchments and prolonged periods of low irradiance and darkness. These lakes are permanently stratified with an oxygenated freshwater layer (mixolimnion) overlying a saline, anoxic water column (monimolimnion). The physical and chemical properties of the deepest known lake of this type in the circumpolar Arctic, Lake A, on the far northern coast of Ellesmere Island, Canada, have been studied over the last 15 years, but little is known about the lake’s biological communities. We applied high-throughput sequencing of the V4 region of the 18S ribosomal RNA gene to investigate the protist communities down the water column at three sampling times: under the ice at the end of winter in 2008, during an unusual period of warming and ice-out the same year, and again under the ice in mid-summer 2009. Sequences of many protist taxa occurred throughout the water column at all sampling times, including in the deep anoxic layer where growth is highly unlikely. Furthermore, there were sequences for taxonomic groups including diatoms and marine taxa, which have never been observed in Lake A by microscopic analysis. However, the sequences of other taxa such as ciliates, chrysophytes, Cercozoa, and Telonema varied with depth, between years and during the transition to ice-free conditions. These seasonally active taxa in the surface waters of the lake are thus sensitive to depth and change with time. DNA from these taxa is superimposed upon background DNA from multiple internal and external sources that is preserved in the deep, cold, largely anoxic water column.

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

“…Pyrosequencing has proven to be an adequate tool to assess the composition of microbial communities (Charvet et al, 2012;Logares et al, 2012;Kilias et al, 2013). Our pyrosequencing results are well supported in terms of group relative abundance by miTags.…”

“…High-throughput sequencing now allows a much more exhaustive assessment of microbial diversity. The Roche 454-pyrosequencing technique (Margulies et al, 2005) has been used in studies targeting the 18S rRNA gene of microbial eukaryotes inhabiting marine epipelagic waters (Edgcomb et al, 2011b;Logares et al, 2012;Kilias et al, 2013;Massana et al, 2015) and freshwaters (Charvet et al, 2012). This approach includes a PCR step, known to be prone to biases like DNA polymerase errors or primer selectivity, that may affect final amplicon ratios (Acinas et al, 2005).…”

Ace Lake: three decades of research on a meromictic, Antarctic lake

“…(Charvet et al 2012) and active over-wintering copepod populations (Van Hove et al 2001). The Arctic lakes have two species of planktonic copepod as opposed to the single species in Ace Lake.…”

Seasonal and Interannual Changes in Ciliate and Dinoflagellate Species Assemblages in the Arctic Ocean (Amundsen Gulf, Beaufort Sea, Canada)

“…All OTU representative reads were aligned in PyNast (Caporaso et al, 2010a), manually curated in BioEdit v.7.2.5 (Hall, 1999) and used to construct a phylogenetic tree (FastTree; Price et al, 2010). Assignment of taxonomic identity was performed in mothur with a 0.8 confidence threshold against the Northern Reference Database v.1.0 , which follows the Silva taxonomy but includes high-quality longer environmental sequences from the Arctic and North Atlantic (Terrado et al, 2009(Terrado et al, , 2011Charvet et al, 2012;Monier et al, 2013;Dasilva et al, 2014). However, using this database, around 30-45% of the reads were still not classified beyond "Other Dinoflagellates" or "Other Ciliates.…”