Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions

Elizaveta Rivkina,Tatiana Vishnivetskaya,Maria Tutukina,Lyubov Shmakova,Arthur Meyers,Kirill Krivushin,Lada Petrovskaya,Fyodor Kondrashov

doi:10.5194/bg-13-2207-2016

Abstract

Abstract. A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments.

Highlights

Permafrost, including constantly frozen sediments of the Arctic, is a unique subsurface complex environment where microorganisms retain viability over a long period of time, from thousands to millions of years (Gilichinsky and Rivkina, 2011)
Studies conducted on Kurungnakh Island, which is situated in the southern part of the Lena River delta, showed the presence of biogenic methane in Holocene sediments, while methane concentrations in the majority of samples from late Pleistocene Ice Complex were at a detection level and only some samples from Ice Complex sediments approximately 28 000 years old showed the presence of methane in a concentration of 1.0 mmol kg−1
The theoretical levels of the prokaryotic cell populations for studied samples were calculated from the total genomic DNA (gDNA) recovered, an average genome length of 4.7 Mb for the soil bacterial/archaeal population estimated from the metagenomics data (Angly et al, 2009; Raes et al, 2007), and a weight of 4.05 fg (Ellenbroek and Cappenberg, 1991) for a genome of this size

Summary

Introduction

Permafrost, including constantly frozen sediments of the Arctic, is a unique subsurface complex environment where microorganisms retain viability over a long period of time, from thousands to millions of years (Gilichinsky and Rivkina, 2011). The permafrost deposits of northeastern Siberia, which did not thaw during the Holocene climatic optimum, have attracted particular interest, especially the late Pleistocene Ice Complex deposits (Yedoma Suite) that are widespread on the eastern Siberian coastal plains (Lena– Anabar, Yana–Indigirka, and Kolyma lowlands) (Schirrmeister et al, 2011). Studies conducted on Kurungnakh Island, which is situated in the southern part of the Lena River delta, showed the presence of biogenic methane in Holocene sediments (up to 3.5 mmol kg−1), while methane concentrations in the majority of samples from late Pleistocene Ice Complex were at a detection level and only some samples from Ice Complex sediments approximately 28 000 years old showed the presence of methane in a concentration of 1.0 mmol kg−1

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