Permafrost organic matter quality and biolability in the Vault Lake thermokarst environment, Interior Alaska, USA

Thesis (Ph.D.) University of Alaska Fairbanks, 2017Warming and thawing of permafrost soils removes a major barrier to soil organic carbon (SOC) mineralization, leading to the mobilization and microbial degradation of previously frozen, inactive permafrost organic carbon (OC) into the greenhouse gases carbon dioxide (CO₂) and methane (CH₄). Many thermokarst (thaw) lakes formed in permafrost-dominated landscapes have high rates of CO₂ and CH₄ emission; however, the composition and biodegradability of the thawed permafrost OC as they relate to the relative magnitudes of anaerobic OC mineralization at different depths throughout the vertical profile of a thermokarst-lake talik system have, to my knowledge, never been measured. My research examined OC composition and mineralization potentials at the Vault Creek (VC) permafrost tunnel and Vault Lake, located 20 km north of Fairbanks, Alaska, USA, to better constrain these uncertainties. I found that, in a 590-cm long sediment core collected from the center of Vault Lake, whole-column CH₄ production is dominated by methanogenesis in the organic-rich mud facies, which occurred in the surface 0 to 152 cm. CH₄ production potential rates positively associated with substrate availability (carbon and nitrogen concentrations) and the relative abundances of terrestrially-derived organic matter compounds (alkanes, alkenes, lignin products, and phenols and phenolic precursors), measured using pyrolysis-gas chromatography-mass spectrometry. Temperature sensitivity analyses conducted on a subset of samples from the Vault Lake sediment core suggest century-scale time since permafrost thaw affects temperature sensitivities of CH₄ production. Freshly-thawed taberite sediments at the base of the talik (thaw bulb) were most sensitive to warming at lower incubation temperatures (0 °C to 3 °C), while the overlying taberite sediments thawed in situ longer periods of time (up to 400 years based on radiocarbon dating) did not experience statistically significant increases in CH₄ production until higher incubation temperatures (10 °C to 25 °C). Finally, using anaerobic incubations and ultrahigh-resolution mass spectrometry of water-extractable organic matter along a 12-m yedoma profile in the VC permafrost tunnel, I show that yedoma OC biolability increases with depth as indicated by increasing proportions of aliphatics and peptides (reduced, high H/C compounds). These compounds also positively correlated with anaerobic CO₂ and CH₄ production, and corresponded to high proportions (5.6% to 118 %) of OC mineralization rates in incubations. This suggests that as yedoma permafrost thaws beneath a thermokarst lake greenhouse gas production potentials may increase with thaw depth

Thermokarst-lake methanogenesis along a complete talik (thaw bulb) profile

Thermokarst (thaw) lakes emit methane (CH4) to the atmosphere, with the carbon (C) originating from terrestrial sources such as the Holocene soils of the lakes’ watersheds, thaw of Holocene- and Pleistoceneaged permafrost soil beneath and surrounding the lakes, and decomposition of contemporary organic matter (OM) in the lakes. However, the relative magnitude of CH4 production in surface lake sediments versus deeper thawed permafrost horizons is not well understood. We assessed anaerobic CH4 production potentials from 22 depths along a 590 cm long lake sediment core from the center of an interior Alaska thermokarst lake, Vault Lake, that captured the entire package of surface lake sediments, the talik (thaw bulb), and the top 40 cm of thawing permafrost beneath the talik. We also studied the adjacent Vault Creek permafrost tunnel that extends through icerich yedoma permafrost soils surrounding the lake and into underlying fluvial gravel. Our results show, in the center of a first generation thermokarst-lake, whole-column CH4 production is dominated by methanogenesis in the organic-rich surface lake sediments [151 cm thick; mean ± SD 5.95 ± 1.67 μg C-CH4 per g dry weight sediment per day (g dw−1 d−1); 125.9 ± 36.2 μg C-CH4 per g organic carbon per day (g Corg−1 d−1)]. The organic-rich surface sediments contribute the most (67%) to whole-column CH4 production despite occupying a lesser fraction (26%) of sediment column thickness. High CH4 production potentials were also observed in recently-thawed permafrost (1.18 ± 0.61 μg C-CH4 g dw−1 d−1; 59.60 ± 51.5 μg CCH4 g Corg−1 d−1) at the bottom of the talik, but the narrow thicknesses (43 cm) of this horizon limited its overall contribution to total sediment column CH4 production in the core. Lower rates of CH4 production were observed in sediment horizons representing permafrost that has been thawed in the talik for longer periods of time. The thickest sequence in the Vault Lake core, which consisted of combined Lacustrine silt and Taberite facies (60% of total core thickness), had low CH4 production potentials, contributing only 21% of whole sediment column CH4 production potential. No CH4 production was observed in samples obtained from the permafrost tunnel, whose sediments represent a non-lake environment. Our findings imply that CH4 production is highly variable in thermokarstlake systems and that both modern OM supplied to surface sediments and ancient OM supplied to both surface and deep lake sediments by in situ thaw, as well as shore erosion of yedoma permafrost, are important to lake CH4 production. Knowing where CH4 originates and what proportion of produced CH4 is emitted will aid in estimations of how C release and processing in a thermokarst-lake environment differs from other thawing permafrost and non-permafrost environments. References: Heslop, J.K.; Walter Anthony, K.M.; Sepulveda-Jauregui, A.; Martinez-Cruz, K.; Bondurant, A.; Grosse, G. and Jones, M.C. [2015]: Thermokarst lake methanogenesis along a complete talik profile. Biogeosciences, 12:4317–4331, doi:10.5194/bg-12-4317-2015

Mechanistic evaluation of primary human hepatocyte culture using global proteomic analysis reveals a selective dedifferentiation profile

© 2016 The Author(s)The application of primary human hepatocytes following isolation from human tissue is well accepted to be compromised by the process of dedifferentiation. This phenomenon reduces many unique hepatocyte functions, limiting their use in drug disposition and toxicity assessment. The aetiology of dedifferentiation has not been well defined, and further understanding of the process would allow the development of novel strategies for sustaining the hepatocyte phenotype in culture or for improving protocols for maturation of hepatocytes generated from stem cells. We have therefore carried out the first proteomic comparison of primary human hepatocyte differentiation. Cells were cultured for 0, 24, 72 and 168 h as a monolayer in order to permit unrestricted hepatocyte dedifferentiation, so as to reveal the causative signalling pathways and factors in this process, by pathway analysis. A total of 3430 proteins were identified with a false detection rate of <1 %, of which 1117 were quantified at every time point. Increasing numbers of significantly differentially expressed proteins compared with the freshly isolated cells were observed at 24 h (40 proteins), 72 h (118 proteins) and 168 h (272 proteins) (p < 0.05). In particular, cytochromes P450 and mitochondrial proteins underwent major changes, confirmed by functional studies and investigated by pathway analysis. We report the key factors and pathways which underlie the loss of hepatic phenotype in vitro, particularly those driving the large-scale and selective remodelling of the mitochondrial and metabolic proteomes. In summary, these findings expand the current understanding of dedifferentiation should facilitate further development of simple and complex hepatic culture systems

Century-scale time since permafrost thaw affects temperature sensitivity of net methane production in thermokarst-lake and talik sediments

Permafrost thaw subjects previously frozen soil organic carbon (SOC) to microbial degradation to the greenhouse gases carbon dioxide (CO2) and methane (CH4).Emission of these gases constitutes a positive feedback to climate warming. Among numerous uncertainties in estimating the strength of this permafrost carbon feedback (PCF), two are: (i) how mineralization of permafrost SOC thawed in saturated anaerobic conditions responds to changes in temperature and (ii) how microbial communities and temperature sensitivities change over time since thaw. To address these uncertainties,we utilized a thermokarst-lake sediment core as a natural chronosequence where SOC thawed and incubated in situ under saturated anaerobic conditions for up to 400 years following permafrost thaw. Initial microbial communities were characterized, and sediments were anaerobically incubated in the lab at four temperatures (0 °C, 3 °C, 10 °C, and 25 °C) bracketing those observed in the lake's talik. Net CH4 production in freshly-thawed sediments near the downward-expanding thaw boundary at the base of the talik were most sensitive to warming at the lower incubation temperatures (0 °C to 3 °C), while the overlying sediments which had been thawed for centuries had initial low abundant methanogenic communities (b 0.02%) and did not experience statistically significant increases in net CH4 production potentials until higher incubation temperatures (10 °C to 25 °C). We propose these observed differences in temperature sensitivities are due to differences in SOM quality and functional microbial community composition that evolve over time; however further research is necessary to better constrain the roles of these factors in determining temperature controls on anaerobic C mineralization

Temperature sensitivity of methanogenesis in a thermokarst lake sediment core

Little is known about temperature sensitivity of permafrost organic carbon (OC) mineralization over time scales of years to centuries following thaw. Due to their formation and thaw histories, taliks (thaw bulbs) beneath thermokarst lakes provide a unique natural laboratory from which to examine how permafrost thawed in saturated anaerobic conditions responds to changes in temperature following long periods of time since thaw. We anaerobically incubated samples from a 590 cm thermokarst lake sediment core near Fairbanks, Alaska at four temperatures (0, 3, 10, and 25 ºC) bracketing observed talik temperatures. We show that since initial thaw ~400 yr BP CH4 production shifts from being most sensitive to at lower (0-3 ºC; Q10-EC=1.15E7) temperatures to being most sensitive at higher (10-25 ºC; Q10-EC=67) temperatures. Frozen sediments collected from beneath the talik, thawed at the commencement of the incubation, had significant (p ≤ 0.05) increases in CH4 production rates at lower temperatures but did not show significant CH4 production rate increases at higher temperatures (10-25 ºC). We hypothesize the thawing of sediments removed a major barrier to C mineralization, leading to rapid initial permafrost C mineralization and preferential mineralization of the most biolabile OC compounds. In contrast, sediments which had been thawed beneath the lake for longer periods of time did not experience statistically significant increases in CH4 production at lower temperatures (0-10 ºC), but had high temperature sensitivities at higher temperatures (10-25 ºC). We believe these rate increases are due to warmer temperatures in the experimental incubations crossing activation energy thresholds, allowing previously recalcitrant fractions of OC to be utilized, and/or the presence of different microbial communities adapted to thawed sediments. Recently-deposited sediments at shallow depths in the lake core experienced increases in CH4 production across all incubation temperatures (Q10-ST=4.4)

A synthesis of methane dynamics in thermokarst lake environments

Greenhouse gas emissions from physical permafrost thaw disturbance and subsidence, including the formation and expansion of thermokarst (thaw) lakes, may double the magnitude of the permafrost carbon feedback this century. These processes are not accounted for in current global climate models. Thermokarst lakes, in particular, have been shown to be hotspots for emissions of methane (CH4), a potent greenhouse gas with 32 times more global warming potential than carbon dioxide (CO2) over a 100-year timescale. Here, we synthesize several studies examining CH4 dynamics in a representative first-generation thermokarst lake (Vault Lake, informal name) to show that CH4 production and oxidation potentials vary with depth in thawed sediments beneath the lake. This variation leads to depth-dependent differences in both in situ dissolved CO2:CH4 ratios and net CH4 production responses to additional warming. Comparing CH4 production, oxidation, and flux values from studies at Vault Lake suggests up to 99% of produced CH4 is oxidized and/or periodically entrapped before entering the atmosphere. We summarize these findings in the context of CH4 literature from thermokarst lakes and identify future research directions for incorporating thermokarst lake CH4 dynamics into estimates of the permafrost carbon feedback

Variable respiration rates of incubated permafrost soil extracts from the Kolyma River lowlands, north-east Siberia

Thawing permafrost supplies dissolved organic carbon (DOC) to aquatic systems; however, the magnitude, variability and fate of this DOC is not well constrained. Our objective was to examine DOC respiration from seasonally thawed and near-surface (&lt;1.5 m) permafrost soils collected from five locations in the Kolyma River Basin, north-east Russia. We measured soil organic carbon (OC) content, water-soluble macronutrients (DOC, NH4, PO4) and the heterotrophic respiration potentials of soil extract DOC in five-day laboratory incubations. DOC concentrations ranged from 2.8 to 27.9 mg L−1 (n = 14). Carbon respiration was 0.03–0.47 mg C (n = 16) and 8.7–31.4%, total DOC (n = 14). While DOC concentration was a function of soil OC concentration, we did not find a relationship between C respiration and soil OC or DOC concentrations. Respiration was highest in the top active layer, but varied widely among sites, and lowest at the bottom of the active layer. Respiration from yedoma varied across sites (0.04–0.47 mg C respired, 8.7–31.4% total DOC). Despite the small sample size, our study indicates near-surface soils and permafrost are spatially variable in terms of both soil OC content and C respiration rates, and also that OC contents do not predict C respiration rates. While a larger sample size would be useful to confirm these results at broader geographic scales, these initial results suggest that soil OC heterogeneity should be considered in efforts to determine the fate of soil OC released from permafrost-dominated terrestrial ecosystems to aquatic ecosystems following permafrost thaw