Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics.

Magdalena K Stoeva,Holger Hintelmann,Stéphane Aris-Brosou,Alexandre J Poulain,John Chételat,Philip Pelletier,A. Mark Ibekwe

doi:10.1371/journal.pone.0089531

Magdalena K Stoeva, Holger Hintelmann + Show 5 more

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https://doi.org/10.1371/journal.pone.0089531

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Abstract

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake.

Highlights

In response to climate warming, northern aquatic ecosystems are rapidly changing
Little is known about the structure and identity of active members of bacterial and archaeal communities from aquatic ecosystems set in high Arctic polar deserts
These results suggest that methanogenesis and overall bacterial activity are confined to the uppermost layer of lake sediments, while occurring deeper in the wetland

Summary

Introduction

In response to climate warming, northern aquatic ecosystems are rapidly changing. This change begins as an alteration of the landscape (e.g., retrogressive thaw slumps), which in turn affects the hydrology as well as the cycling of organic carbon, contaminants and other nutrients [1,2,3]. Recent data underscore the diversity of potential mercury methylators including the well-known sulfate- (SRB) and iron- (FeRB) reducing bacteria, and methanogenic archaea, syntrophic, acetogenic, and fermentative Firmicutes [14] These recent findings highlight the necessity to carefully assess the presence and activity of these microbial communities when quantifying the flux of such contaminants through the environment [15,16,17]. The question of how microbial communities are vertically structured within sediments in these environments has received little attention This is a critical gap in our basic knowledge of microbial processes at high latitudes: polar deserts are sensitive to climate change [18,19], and aquatic ecosystems have already started to be irreversibly altered [20] and are increasingly subject to deposition of anthropogenic contaminants, such as Hg [3]

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