Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells. IMPORTANCE: As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Comparison of three DNA extraction methods for recovery of microbial DNA from Arctic permafrost.

Permafrost soils, which contain one of Earth's largest terrestrial carbon stocks, are vulnerable to thaw and microbial decomposition, exacerbating climate change. Advancements in sequencing technologies have facilitated the identification and functional profiling of microbial communities in permafrost, but DNA extraction from these soils is challenging due to their high microbial diversity and low biomass. This study assessed the effectiveness of the DNeasy PowerSoil Pro kit in extracting DNA from permafrost samples and found that it produced significantly different results than the discontinued DNeasy PowerSoil kit. The study highlights the importance of consistent DNA extraction methods in permafrost studies.

Modelling of perceived sweetness in biscuits based on sensory analysis as a new tool to evaluate reformulation performance in sugar reduction studies.

Sugar reduction in foods is of global interest in food science and industry to limit excessive calorie intake for healthier nutrition. Therefore, a modified Weibull model-based approach is presented here to relate sweetness perception with sugar concentration for the first time. The model was tested by using sweetness perception data obtained from sensory analysis of biscuits (wholewheat flour, whey or hydrolysed pea protein, different sucrose forms, ethylvanillin, furaneol, phenylacetaldehyde) using a line scale and untrained panellists. Sweetness scores increased 56%, 59%, 41% by the addition of wholewheat flour, proteins, or aroma compounds at 17% sucrose containing biscuits, respectively. Wholewheat flour and proteins boosted Maillard reaction products imparting baked/caramel-like flavour. The Weibull model well fitted to the sweetness perception data with a sigmoidal curve and high predicting power. This approach allows to explain how much sugar reduction can be achieved to reach a targeted sweetness perception without performing further sensory analysis.

Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.

Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

Metagenomes and Metagenome-Assembled Genome Sequences from Nitrogen-Fixing Alder Nodules.

Bacterial nitrogen (N) fixation in alder nodules is a key process providing nitrogen to nutrient-limited arctic biomes. Here, 45 prokaryotic metagenome-assembled genome (MAG) sequences from root nodules of arctic alder are reported.

Effect of salts on the formation of acrylamide, 5-hydroxymethylfurfural and flavour compounds in a crust-like glucose/wheat flour dough system during heating.

Among many strategies known to mitigate acrylamide formation, addition of cations, particularly calcium, is effective and can be used in bakery products. In this study, the effects of NaCl, KCl, CaCl2, MgCl2, sodium lactate, calcium lactate, and magnesium lactate on aroma and acrylamide formation were investigated in glucose/wheat flour dough systems during heating. Addition of salts inhibited Maillard reaction in favour of caramelisation, with divalent cations found to be most effective. The impact of salts on acrylamide reduction became less effective with increasing temperature. Most Strecker aldehydes and pyrazines decreased in the presence of salts, however CaCl2 and calcium lactate increased the concentration of furans, furfurals, and diketones. Calcium lactate also increased some ethyl-substituted pyrazines at high temperatures. Reduction of acrylamide with salts is associated with higher amounts of furan derivatives and decreased amounts of Strecker aldehydes and pyrazines. The mechanisms behind these changes are discussed.

Effectiveness of asparaginase on reducing acrylamide formation in bakery products according to their dough type and properties.

Effect of asparaginase was tested in different biscuit and cracker doughs, and wafer batter by changing processing conditions such as enzyme dosage, dough resting time and temperature, mixing speed and time, and mixing procedure of the recipe components. Acrylamide reductions achieved were 96, 80, 54% in rotary cut biscuits, crackers and wire cut cookies, respectively due to high water activity of their dough. Asparaginase did not affect surface color or spread ratio. There was a positive correlation between asparagine content and acrylamide formation except for rotary molded biscuit doughs. No significant decrease was found in rotary molded biscuits because of low water (water activity of 0.70) and high fat content. This indicated that water activity of dough is an important factor for the effectiveness of asparaginase treatment. The results suggested that water activity value exceeding 0.75 is needed in the dough to effectively reduce asparagine, so acrylamide in bakery products.

Metagenomes from Arctic Soil Microbial Communities from the Barrow Environmental Observatory, Utqiagvik, AK, USA.

Here, we report 36 active-layer and 17 permafrost metagenomes from Utqiagvik, AK, USA. Samples were collected from different topographical features and depths to study Arctic tundra microbiomes.

Microbiome assembly in thawing permafrost and its feedbacks to climate.

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential.

Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal (>25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.

Acrylamide in Corn-Based Thermally Processed Foods: A Review.

Widely consumed thermally processed corn-based foods can have a great contribution to acrylamide dietary intake, thus bearing a high public health risk and requiring attention and application of strategies for its reduction. This paper reviews the literature on the acrylamide content of corn-based food products present in the market around the world. The potential of corn for acrylamide formation due to its content of free asparagine and reducing sugars is described. Human exposure to acrylamide from corn-based foods is also discussed. The content of acrylamide in corn/tortilla chips, popcorn, and corn flakes, as widely consumed products all over the world, is reported in the literature to be between 5 and 6360 µg/kg, between

Unravelling biogeochemical drivers of methylmercury production in an Arctic fen soil and a bog soil.

Arctic tundra soils store a globally significant amount of mercury (Hg), which could be transformed to the neurotoxic methylmercury (MeHg) upon warming and thus poses serious threats to the Arctic ecosystem. However, our knowledge of the biogeochemical drivers of MeHg production is limited in these soils. Using substrate addition (acetate and sulfate) and selective microbial inhibition approaches, we investigated the geochemical drivers and dominant microbial methylators in 60-day microcosm incubations with two tundra soils: a circumneutral fen soil and an acidic bog soil, collected near Nome, Alaska, United States. Results showed that increasing acetate concentration had negligible influences on MeHg production in both soils. However, inhibition of sulfate-reducing bacteria (SRB) completely stalled MeHg production in the fen soil in the first 15 days, whereas addition of sulfate in the low-sulfate bog soil increased MeHg production by 5-fold, suggesting prominent roles of SRB in Hg(II) methylation. Without the addition of sulfate in the bog soil or when sulfate was depleted in the fen soil (after 15 days), both SRB and methanogens contributed to MeHg production. Analysis of microbial community composition confirmed the presence of several phyla known to harbor microorganisms associated with Hg(II) methylation in the soils. The observations suggest that SRB and methanogens were mainly responsible for Hg(II) methylation in these tundra soils, although their relative contributions depended on the availability of sulfate and possibly syntrophic metabolisms between SRB and methanogens.

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile.

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

Metagenomic tools in microbial ecology research.

Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.

Anaerobic respiration pathways and response to increased substrate availability of Arctic wetland soils.

The availability of labile carbon (C) compounds in Arctic wetland soils is expected to increase due to thawing permafrost and increased fermentation as a result of decomposition of organic matter with warming. How microbial communities respond to this change will affect the balance of CO2 and CH4 emitted during anaerobic organic matter decomposition, and ultimately the net radiative forcing of greenhouse gas emissions from these soils. While soil water content limits aerobic respiration, the factors controlling methanogenesis and anaerobic respiration are poorly defined in suboxic Arctic soils. We conducted incubation experiments on two tundra soils from field sites on the Seward Peninsula, Alaska, with contrasting pH and geochemistry to determine the pathways of anaerobic microbial respiration and changes with increasing substrate availability upon warming. In incubation of soils from the circumneutral Teller site, the ratio of CO2 to CH4 dropped from 10 to <2 after 60 days, indicating rapid depletion of alternative terminal electron acceptors (TEAs). Addition of acetate stimulated production of CO2 and CH4 in a nearly 1 : 1 ratio, consistent with methanogenesis, and the composition of the microbial community shifted to favor clades capable of utilizing the added acetate such as the Fe(iii)-reducing Geobacter and the methanogenic archaea Methanosarcina. In contrast, both CO2 and CH4 production declined with acetate addition during incubation of soils from the more acidic Council site, and fermentative microorganisms increased in abundance despite the high availability of fermentation products. These results demonstrate that the degree to which increasing substrate availability stimulates greenhouse gas production in tundra wetlands will vary widely depending on soil pH and geochemistry.

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost.

Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.

Microbial community responses reduce soil carbon loss in Tibetan alpine grasslands under short-term warming.

Changes in labile carbon (LC) pools and microbial communities are the primary factors controlling soil heterotrophic respiration (Rh ) in warming experiments. Warming is expected to initially increase Rh but studies show this increase may not be continuous or sustained. Specifically, LC and soil microbiome have been shown to contribute to the effect of extended warming on Rh . However, their relative contribution is unclear and this gap in knowledge causes considerable uncertainty in the prediction of carbon cycle feedbacks to climate change. In this study, we used a two-step incubation approach to reveal the relative contribution of LC limitation and soil microbial community responses in attenuating the effect that extended warming has on Rh . Soil samples from three Tibetan ecosystems-an alpine meadow (AM), alpine steppe (AS), and desert steppe (DS)-were exposed to a temperature gradient of 5-25°C. After an initial incubation period, soils were processed in one of two methods: (a) soils were sterilized then inoculated with parent soil microbes to assess the LC limitation effects, while controlling for microbial community responses; or (b) soil microbes from the incubations were used to inoculate sterilized parent soils to assess the microbial community effects, while controlling for LC limitation. We found both LC limitation and microbial community responses led to significant declines in Rh by 37% and 30%, respectively, but their relative contributions were ecosystem specific. LC limitation alone caused a greater Rh decrease for DS soils than AMs or ASs. Our study demonstrates that soil carbon loss due to Rh in Tibetan alpine soils-especially in copiotrophic soils-will be weakened by microbial community responses under short-term warming.

Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost.

Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. These MAGs will provide information on metabolic pathways that could mediate biogeochemical cycles in Svalbard permafrost.

Investigation of serotonin, free and protein-bound tryptophan in Turkish hazelnut varieties and effect of roasting on serotonin content.

Hazelnuts and their skins are important sources of health-promoting compounds. In this study, serotonin, a neuroactive compound, and its precursor tryptophan in 14 hazelnuts, almost all hazelnut varieties in Turkey, in two consecutive harvest years were investigated. Serotonin content of hazelnut skins and the effect of roasting on the serotonin content of hazelnuts were also revealed for the first time. Serotonin and free tryptophan concentrations were determined after water extraction while an alkaline hydrolysis was performed for bound tryptophan before UPLC-MS/MS analysis. Free tryptophan ranged from 42 to 127 µg/g and bound tryptophan was between 3670 and 8904 µg/g in hazelnut varieties. Serotonin content of hazelnut varieties was ranged from 0.1 µg/g (Kalinkara) to 2.0 µg/g (Palaz). Significant differences (p < 0.05) were found in free, bound tryptophan, and serotonin contents of most of the hazelnut varieties depending on the harvest year. Mean serotonin content of hazelnut skins was 4 times higher than hazelnuts. Moreover, it was found that roasted hazelnuts were as valuable as raw hazelnuts in terms of their serotonin content as no significant differences (p > 0.05) were observed after roasting at 150 °C for 30 min.