Methane cycling archives from warming Arctic lakes: Retrieving the genomic blueprints of Holocene microbes

Arctic landmasses and lakes release significant amounts of methane (CH4), a potent greenhouse gas that contributes to global climate change. Yet, the effect of rapid warming in the Arctic on the fate of CH4 emissions is poorly understood, particularly over decadal to millennial timescales. The recent advance of high-throughput sequencing to analyse ancient environmental DNA (eDNA), or paleogenomics, has tremendously heightened analytical sensitivity and thus unlocked a wealth of new information on past ecosystems. PolarCH4ives has used paleogenomics to uncover the environmental genomic information naturally archived year after year in sediment at the bottom of lakes to determine the impact of long-term climate change on CH4 cycling by microbes in the Arctic. PolarCH4ives has collected Holocene sediment cores and geochemical profiles along major environmental gradients in N-Norway (4 lakes); Sweden (3 lakes) and Svalbard (3 lakes). These have been clean sub-sampled and analysed for ancient eDNA. In total, we will have conducted these cutting-edge, metagenomic analyses on 344 ancient eDNA sediment samples from a unique lake sediment core collection of 21 Arctic lakes, including Greenland. We completed a 2-week field expedition to Svalbard in the summer of 2022 and obtained new sediment cores from lakes in northern Svalbard. This fieldwork was delayed for two years because of the COVID-19 pandemic, and with this we have finally completed all field data collection for the project. Recent game changing developments in our Danish collaborator’s bioinformatic pipeline for identifying ancient microbes and their metabolic functions enable us to conduct paired analyses on samples of both modern and ancient communities i.e., currently actively processing CH4 and inherited from the time of deposition in the sediments, respectively. This advance will strengthen our quantification of the impact of climate change on past CH4 microbial communities and their ecosystem through the Holocene. Our extensive sequencing and bioinformatic efforts on 260 modern soil samples significantly improved the representation of Arctic microbiomes by generating >5300 metagenomic assembled genomes (MAGs) of microbes, most of which are from microbial taxa that had never been described. Those novel MAGs contribute thousands of new species to some of the most ubiquitous groups of Archaea and Bacteria on Earth and significantly boost other groups that were much less well known with hundreds of new taxa. We also show that microbial diversity differs from north to south of the Arctic regions and is most sensitive to specific environmental and climatic conditions, such as pH, Nitrogen content, organic matter quality, and precipitation. We are currently evaluating how specific microbial metabolic functions involved in the cycling of the major greenhouse gases respond to Arctic greening with increased temperature. We also plan to explore the life of Arctic microbes from this dataset further in relation to plants and nutrient providers (fungi and birds). Finally, we have been quantifying the concentration, origin, and age of the CH4 gas being emitted from the sediments at these lakes at present to determine potential lags and historical legacies between climate change and microbial processing of organic matter into CH4. By combining geosciences and ancient eDNA analysis, PolarCH4ives has improved our understanding of microbial diversity in the Arctic and the role of past climate change on microbial ecology and biogeochemical cycling of greenhouse gases.

• PolarCH4ives has boosted the Norwegian contribution in interdisciplinary research by integrating geosciences and ancient eDNA on a national scale (Schomacker, Hodson and Alsos Labs). • PolarCH4ives has strengthened Norway's role in research into the Earth's microbiomes in the Arctic and globally. This project has significantly expanded the availability of archival materials and complete genomes from Arctic environments into global databases that may be used as reference and baseline for the future. • Postdoc Rouillard has consolidated her expert knowledge and high-quality technical expertise with world leaders in ancient eDNA analyses at UiT and CGG in emerging paleogenomics that opens up a whole new path of investigation into Arctic ecosystem processes as a future group leader to solve fundamental questions on climate issues. • The involvement of educators and actors from the tourism industry in the Arctic in our large-scale microbiome collection and our overall public outreach strategy has and will continue to promote a more sustainable view on Arctic landscapes and their sensitivity to climate change. • PolarCH4ives has provided a framework and complementary datasets for 4 chapters of a PhD thesis (M. Buli´nova´, UiT; expected graduation in 2025).

Arctic landmasses and lakes release significant amounts of methane (CH4), a potent greenhouse gas that contributes to global climate change. Yet, the effect of rapid warming in the Arctic on the fate of CH4 emissions is poorly understood, particularly over decadal to millennial timescales. The recent advance of high-throughput sequencing to analyse ancient environmental DNA (eDNA), or paleogenomics, from Arctic lake sediment has tremendously heightened analytical sensitivity and thus unlocked a wealth of new information on past ecosystems. We will combine paleogenomics to a robust paleoecological framework to determine the impact of climate change on microbial CH4 dynamics in high latitude lakes since the onset of the present interglacial, the Holocene, ~11,700 years ago. We will control for catchment processes underpinning microbial CH4 exchange, and isolate the influence of climate on their dynamics. This interdisciplinary research relies on a unique collection of Arctic lake sediment cores from Greenland, mainland Norway and Svalbard jointly assembled by the Schomacker, Håkansson, Alsos and Kjær Labs (The Arctic University of Norway/UiT, The University Centre in Svalbard/UNIS, Tromsø Museum/TromsøM (UiT), and Natural History Museum of Denmark/NHMD, respectively). PolarCH4ives will foster a new platform for interdisciplinary climate research in Norway by bringing together a high-functioning team of Quaternary scientists (Schomacker, Håkansson and Kjær) with world's leading ancient DNA facilities and expertise (TromsøM and NHMD). In addition to acquiring groundbreaking knowledge into Quaternary sciences, ancient eDNA and microbial ecology, we seek to bring new insights into the contribution of Artic ecosystems to the global carbon cycle and their sensitivity to climate change. By strengthening our understanding of long-term ecosystem processes that influence the release and degradation of CH4 in the Arctic, we will help constrain models of global climate change.