Seasonal variation in near-surface seasonally thawed active layer and permafrost soil microbial communities

Abstract

Understanding how soil microbes respond to permafrost thaw is critical to predicting the implications of climate change for soil processes. However, our knowledge of microbial responses to warming is mainly based on laboratory thaw experiments, and field sampling in warmer months when sites are more accessible. In this study, we sample a depth profile through seasonally thawed active layer and permafrost in the Imnavait Creek Watershed, Alaska, USA over the growing season from summer to late fall. Amplicon sequencing showed that bacterial and fungal communities differed in composition across both sampling depths and sampling months. Surface communities were most variable, while those from the deepest samples, which remained frozen throughout our sampling period, showed little to no variation over time. However, community variation was not explained by trace metal concentrations, soil nutrient content, pH, or soil condition (frozen/thawed), except insofar as those measurements were correlated with depth. Our results highlight the importance of collecting samples at multiple times throughout the year to capture temporal variation, and suggest that data from across the annual freeze-thaw cycle might help predict microbial responses to permafrost thaw.

Iron Oxidation–Reduction Processes in Warming Permafrost Soils and Surface Waters Expose a Seasonally Rusting Arctic Watershed

“…Patzner et al (2020) found an abundance of Fe(III)-reducing bacteria that mobilized Fe during permafrost thaw in an actively thawing permafrost wetland in Sweden with water-logged and decreased O 2 conditions. Specific microbes known to reduce or oxidize Fe were not found in these soils at Imnavait Creek, 31 permafrost peatlands was correlated with redox conditions and that seasonality was a driving factor, which was a similar finding in the surface water samples at Imnavait Creek. Additionally, while this study did not investigate different Fe filtered fractions like others have done for boreal catchments, 16 investigating the Fe oxidation state as a function of filtered and unfiltered fractions may be an important next step in linking Fe redox cycling with seasonality in Arctic surface waters as mobilization of geochemical constituents found in hillslope soils could increase as a result of permafrost warming.…”

“…The cycling and mobility of redox-sensitive metals is often affected by the presence of microbes in the environment that can facilitate oxidation or reduction and use different oxidation states as an energy source. Our parallel investigation into the microbial community for the soil pits investigated in this study did not isolate any specific Fe/Mn-oxidizing or Fe/Mn-reducing bacteria, however further investigation using shotgun metagenomics to look for cycling genes or extracting RNA (transcriptomics) to look for active genes would be useful additions as microbial Fe/Mn cycling in the arctic remains poorly understood …”

“…Patzner et al (2020) found an abundance of Fe(III)-reducing bacteria that mobilized Fe during permafrost thaw in an actively thawing permafrost wetland in Sweden with water-logged and decreased O 2 conditions. Specific microbes known to reduce or oxidize Fe were not found in these soils at Imnavait Creek, so attributes to Fe(III)-reducing bacteria and the findings of Patzner et al (2020) remains minimal. However, in a later study, the authors found that Fe cycling in thawing permafrost peatlands was correlated with redox conditions and that seasonality was a driving factor, which was a similar finding in the surface water samples at Imnavait Creek.…”

“…The probe was calibrated with 4.01, 7.00, and 10.01 pH buffer solutions at 25 °C with a calibration curve R 2 ≥ 0.97. 31 For determination of solid-phase Fe oxidation state, subsets of the frozen soils were allowed to thaw just until they started to become malleable (approximately after 10 min) and then they were smeared in an even layer using a metal spatula in one-layer and two-layer samples using double-sided tape ("tape samples") and then immediately frozen. The tape samples remained frozen until placement on sample holder for analysis.…”

“…Porewater concentrations as a function of soil profile depth (Baker et al (2023) generally saw enrichments of Fe, Mn, Mn, Ba, and Zn in the permafrost for SP1 and SP2. Porewater concentration profiles for SP3 displayed opposite behavior for all metals except Mn.…”