In-depth characterization of denitrifier communities across different soil ecosystems in the tundra

Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. Results We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. Conclusions By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.Peer reviewe

Sources of nitrous oxide and fate of mineral nitrogen in sub-Arctic permafrost peat soils

Nitrous oxide (N2O) emissions from permafrost-affected terrestrial ecosystems have received little attention, largely because they have been thought to be negligible. Recent studies, however, have shown that there are habitats in the subarctic tundra emitting N2O at high rates, such as bare peat (BP) surfaces on permafrost peatlands. Nevertheless, the processes behind N2O production in these high-emission habitats are poorly understood. In this study, we established an in situ 15N-labeling experiment with two main objectives: (1) to partition the microbial sources of N2O emitted from BP surfaces on permafrost peatlands and (2) to study the fate of ammonium and nitrate in these soils and in adjacent vegetated peat (VP) surfaces showing low N2O emissions. Our results confirm the hypothesis that denitrification is mostly responsible for the high N2O emissions from BP. During the study period, denitrification contributed ∼ 79 % of the total N2O emissions from BP, whereas the contribution from ammonia oxidation was less (about 19 %). Both gross N mineralization and gross nitrification rates were higher in BP than in VP, with high C/N ratios and a low water content likely limiting N transformation processes and, consequently, N2O production in the latter soil type. Our results show that multiple factors contribute to high N2O production in BP surfaces on permafrost peatlands, with the most important factors being the absence of plants, an intermediate to high water content and a low C/N ratio, which all affect the mineral-N availability for soil microbes, including those producing N2O. The process understanding produced here is important for the development of process models that can be used to evaluate future permafrost–N feedbacks to the climate system.peerReviewe

NUMERICAL SIMULATION OF METHANE EMISSION FROM SUBARCTIC LAKE IN KOMI REPUBLIC (RUSSIA)

During last decades, a special attention has been paid to methane emission from lakes [Bastviken et al., 2004; Wik et al., 2016 and etc.] as one of the significant sources of this important greenhouse gas to the atmosphere. However, attempts to simulate methane production and efflux at the air-water interface are scarce [Stepanenko et al., 2011; Tan et al., 2015a; Tan et al., 2015b] and models proposed so far need further validation using observation datasets. In this study, we use the 1D + numerical model LAKE [Stepanenko et al., 2011; Stepanenko et al., 2016]. The LAKE model was applied to a small subarctic lake in the Seida study site (Komi Republic, Russia) for identification of the key factors influencing the surface CH4flux and its concentration in the lake. We carried out a calibration of biogeochemical constants involving qualitative considerations of the character of biogeochemical and physical processes occurring in the lake and aiming at a satisfactory agreement with observations, performed by the University of Eastern Finland (UEF) [Lind et al., 2009; Marushchak et al., 2016]. Comparing our model calibration results to earlier studies suggest that the crucial parameter of the model – methane production rate constant (Pnew, 0) – has similar values for lakes of different types in high latitudes

A review of the importance of mineral nitrogen cycling in the plant-soil-microbe system of permafrost-affected soils—changing the paradigm

The paradigm that permafrost-affected soils show restricted mineral nitrogen (N) cycling in favor of organic N compounds is based on the observation that net N mineralization rates in these cold climates are negligible. However, we find here that this perception is wrong. By synthesizing published data on N cycling in the plant-soil-microbe system of permafrost ecosystems we show that gross ammonification and nitrification rates in active layers were of similar magnitude and showed a similar dependence on soil organic carbon (C) and total N concentrations as observed in temperate and tropical systems. Moreover, high protein depolymerization rates and only marginal effects of C:N stoichiometry on gross N turnover provided little evidence for N limitation. Instead, the rather short period when soils are not frozen is the single main factor limiting N turnover. High gross rates of mineral N cycling are thus facilitated by released protection of organic matter in active layers with nitrification gaining particular importance in N-rich soils, such as organic soils without vegetation. Our finding that permafrost-affected soils show vigorous N cycling activity is confirmed by the rich functional microbial community which can be found both in active and permafrost layers. The high rates of N cycling and soil N availability are supported by biological N fixation, while atmospheric N deposition in the Arctic still is marginal except for fire-affected areas. In line with high soil mineral N production, recent plant physiological research indicates a higher importance of mineral plant N nutrition than previously thought. Our synthesis shows that mineral N production and turnover rates in active layers of permafrost-affected soils do not generally differ from those observed in temperate or tropical soils. We therefore suggest to adjust the permafrost N cycle paradigm, assigning a generally important role to mineral N cycling. This new paradigm suggests larger permafrost N climate feedbacks than assumed previously

A globally relevant stock of soil nitrogen in the Yedoma permafrost domain

Nitrogen regulates multiple aspects of the permafrost climate feedback, including plant growth, organic matter decomposition, and the production of the potent greenhouse gas nitrous oxide. Despite its importance, current estimates of permafrost nitrogen are highly uncertain. Here, we compiled a dataset of >2000 samples to quantify nitrogen stocks in the Yedoma domain, a region with organic-rich permafrost that contains ~25% of all permafrost carbon. We estimate that the Yedoma domain contains 41.2 gigatons of nitrogen down to ~20 metre for the deepest unit, which increases the previous estimate for the entire permafrost zone by ~46%. Approximately 90% of this nitrogen (37 gigatons) is stored in permafrost and therefore currently immobile and frozen. Here, we show that of this amount, ¾ is stored >3 metre depth, but if partially mobilised by thaw, this large nitrogen pool could have continental-scale consequences for soil and aquatic biogeochemistry and global-scale consequences for the permafrost feedback

Arctic soil methane sink increases with drier conditions and higher ecosystem respiration

Arctic wetlands are known methane (CH4) emitters but recent studies suggest that the Arctic CH4 sink strength may be underestimated. Here we explore the capacity of well-drained Arctic soils to consume atmospheric CH4 using >40,000 hourly flux observations and spatially distributed flux measurements from 4 sites and 14 surface types. While consumption of atmospheric CH4 occurred at all sites at rates of 0.092 ± 0.011 mgCH4 m−2 h−1 (mean ± s.e.), CH4 uptake displayed distinct diel and seasonal patterns reflecting ecosystem respiration. Combining in situ flux data with laboratory investigations and a machine learning approach, we find biotic drivers to be highly important. Soil moisture outweighed temperature as an abiotic control and higher CH4 uptake was linked to increased availability of labile carbon. Our findings imply that soil drying and enhanced nutrient supply will promote CH4 uptake by Arctic soils, providing a negative feedback to global climate change

Towards constraining the circumpolar nitrous oxide budget

Arctic soils and sediments are well known for their huge carbon stocks and the significant positive feedback carbon dioxide (CO2) and methane (CH4) emissions can have on climate change. However, the vast amounts of nitrogen (N) and possible emissions of the strong greenhouse gas nitrous oxide (N2O) from Arctic soils are much less considered in this context. Arctic soils have been neglected in global N2O accounting, since their N2O emissions were traditionally thought to be low due to the general N-limitation of biological processes. Recent results suggest, however, that this assumption is unwarranted and needs to be revised. Still, although we know about the risk for increasing N2O emissions from the Arctic with warming, data are available only from a handful of sites and we are lacking any estimate on the circumarctic N2O budget even under the present climate. This presentation will introduce our plan to produce the first circumarctic N2O budget, an important baseline scenario against which changes in circumarctic N2O emissions can be observed with ongoing warming and global change. In order to estimate the first circumarctic N2O budget, we synthesize existing data and organize large-scale surveys of N2O fluxes across the Circumarctic. In our synthesis effort, we collect published and unpublished data on N2O emissions and N2O soil gas concentrations and analyze the data for driving variables and mechanisms underlying the N2O fluxes from various sites with different soil and vegetation characteristics. In addition, we organize measurement campaigns (via the INTERACT remote access program) to quantify N2O fluxes across a wide variety of Arctic sites using a network of collaborator stations with simple, standardized methods, and combine this N2O screening with GIS approaches to scale up the N2O fluxes step-wise from plot to regional and circumarctic levels. Ultimately, these data will be combined with existing data-sets and archived in a database that will be made available for process modelers in order to develop and improve the performance N2O models for permafrost soils. N2O flux data were published in 21 articles from 16 Arctic sites. In the frame of this project, N2O flux measurements were conducted in 2018 at 18 study sites located in Russia, Scandinavia, Svalbard, Canada and Alaska. First analyses show that N2O is released from a range of environmentally distinct sites and at variable magnitudes with soil N content, soil C/N ratios, vegetation cover, water availability, and nutrient content likely playing significant roles. Ultimately, this project will not only provide a valuable input towards the first estimate of the circumarctic N2O budget but also towards understanding the controls of Arctic N2O fluxes which is necessary for future projections. There is urgent need for collaboration among partners in this effort and we would thus like to invite interested researchers to contribute with further published or unpublished data on N2O fluxes/concentrations from Arctic sites to support our synthesis effort. Scientists are also highly requested to sample additional N2O data from “their” Arctic sites with the simple methods introduced here, in order to help us filling large data gaps