Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils

Impacts of snow-farming on alpine soil and vegetation: A case study from the Swiss Alps

Snow-farming is one of the adaptive strategies used to face the snow deficit in ski resorts. We studied the impact of a shifting snow-farming technique on a pasture slope in Adelboden, Switzerland. Specifically, we compared plots covered by a compressed snow pile for 1.5, 2.5 or 3.5 years, which then recovered from the snow cover for three, two or one vegetation seasons, respectively, with control plots situated around the snow pile. In plots with >1.5 years of compressed snow pile, plant mortality was high, recovery of vegetation was very slow, and few plant species recolonized the bare surface. Soil biological activity decreased persistently under prolonged snow cover, as indicated by reduced soil respiration. The prolonged absence of fresh plant litter and root exudates led to carbon (C) limitation for soil microbial respiration, which resulted in a significant decrease in the ratio of total organic carbon to total nitrogen (TOC/TN) under the snow pile. Microbial C, nitrogen (N) and phosphorus (P) immobilization decreased, while dissolved N concentration increased with compressed snow cover. Longer snow cover and a subsequent shorter recovery period led to higher microbial C/P and N/P but lower microbial C/N. Nitrate and ammonium were released massively once the biological activity resumed after snow clearance and soil aeration. The soil microbial community composition persistently shifted towards oxygen-limited microbes with prolonged compressed snow cover. This shift reflected declines in the abundance of sensitive microorganisms, such as plant-associated symbionts, due to plant mortality or root die-off. In parallel, resistant taxa that benefit from environmental changes increased, including facultative anaerobic bacteria (Bacteroidota, Chloroflexota), obligate anaerobes (Euryarchaeota), and saprophytic plant degraders. We recommend keeping snow piles in the same spot year after year to minimize the area of the impacted soil surface and plan from the beginning soil and ecosystem restoration measures.

Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes

Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.

Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics

Methane (CH₄) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH₄ uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH₄ uptake by forest soils, subjected to compaction by heavy machinery 7 years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH₄ microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10 cm depth interval and in summer in the 10-20 cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH₄ fluxes and the potential effect of physical disturbances.

Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance

Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.

Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH₄) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH₄ cycle. To better predict the responses of soil CH₄-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH₄ fluxes were observed for forest and pasture, indicating that these soils can act as both CH₄ sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH₄ emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH₄ emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH₄ cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

Characteristics of Soil Structure and Greenhouse Gas Fluxes on Ten-Year Old Skid Trails with and without Black Alders (Alnus glutinosa (L.) Gaertn.)

Forest soil compaction caused by heavy machines can cause ecosystem degradation, reduced site productivity and increased greenhouse gas (GHG) emissions. Recent studies investigating the plant-mediated alleviation of soil compaction with black alder showed promising results (Alnus glutinosa). This study aimed to measure soil recovery and GHG fluxes on machine tracks with and without black alders in North-East Switzerland. In 2008, two machine tracks were created under controlled conditions in a European beech (Fagus sylvatica) stand with a sandy loam texture. Directly after compaction, soil physical parameters were measured on one track while the other track was planted with alders. Initial topsoil bulk density and porosity on the track without alders were 1.52 g cm−3 and 43%, respectively. Ten years later, a decrease in bulk density to 1.23 g cm−3 and an increase in porosity to 57% indicated partial structure recovery. Compared with the untreated machine track, alder had no beneficial impact on soil physical parameters. Elevated cumulative N2O emission (+30%) under alder compared with the untreated track could result from symbiotic nitrogen fixation by alder. Overall, CH4 fluxes were sensitive to the effects of soil trafficking. We conclude that black alder did not promote the recovery of a compacted sandy loam while it had the potential to deteriorate the GHG balance of the investigated forest stand.

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.

Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities

Soil microorganisms such as bacteria and fungi play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.

Effects of Soil Moisture and Temperature on Microbial Regulation of Methane Fluxes in a Poplar Plantation

Improved mechanistic understanding of soil methane (CH4) exchange responses to shifts in soil moisture and temperature in forest ecosystems is pivotal to reducing uncertainty in estimates of the soil-atmospheric CH4 budget under climate change. We investigated the mechanism behind the effects of soil moisture and temperature shifts on soil CH4 fluxes under laboratory conditions. Soils from the Huai River Basin in China, an area that experiences frequent hydrological shifts, were sampled from two consecutive depths (0–20 and 20–50 cm) and incubated for 2 weeks under different combinations of soil moisture and temperature. Soils from both depths showed an increase in soil moisture and temperature-dependent cumulative CH4 fluxes. CH4 production rates incubated in different moisture and temperature in surface soil ranged from 1.27 to 2.18 ng g−1 d−1, and that of subsurface soil ranged from 1.18 to 2.34 ng g−1 d−1. The Q10 range for soil CH4 efflux rates was 1.04–1.37. For surface soils, the relative abundance and diversity of methanotrophs decreased with moisture increase when incubated at 5 °C, while it increased with moisture increase when incubated at 15 and 30 °C. For subsurface soils, the relative abundance and diversity of methanotrophs in all samples decreased with moisture increase. However, there was no significant difference in the diversity of methanogens between the two soil depths, while the relative abundance of methanogens in both depths soils increased with temperature increase when incubated at 150% water-filled pore space (WFPS). Microbial community composition exhibited large variations in post incubation samples except for one treatment based on the surface soils incubated at 15 °C, which showed a decrease in the total and unique species number of methanotrophs with moisture increase. In contrast, the unique species number of methanogens in surface soils increased with moisture increase. The analysis of distance-based redundancy analysis (db-RDA) showed that soil pH, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), microbial biomass carbon (MBC), NO3−-N, and NH4+-N mainly performed a significant effect on methanotrophs community composition when incubated at 60% WFPS, while they performed a significant effect on methanogens community composition when incubated at 150% WFPS. Overall, our findings emphasized the vital function of soil hydrology in triggering CH4 efflux from subtropical plantation forest soils under future climate change.

Divergent drivers of the microbial methane sink in temperate forest and grassland soils

Aerated topsoils are important sinks for atmospheric methane (CH₄ ) via oxidation by CH₄ -oxidizing bacteria (MOB). However, intensified management of grasslands and forests may reduce the CH₄ sink capacity of soils. We investigated the influence of grassland land-use intensity (150 sites) and forest management type (149 sites) on potential atmospheric CH₄ oxidation rates (PMORs) and the abundance and diversity of MOB (with qPCR) in topsoils of three temperate regions in Germany. PMORs measurements in microcosms under defined conditions yielded approximately twice as much CH₄ oxidation in forest than in grassland soils. High land-use intensity of grasslands had a negative effect on PMORs (-40%) in almost all regions and fertilization was the predominant factor of grassland land-use intensity leading to PMOR reduction by 20%. In contrast, forest management did not affect PMORs in forest soils. Upland soil cluster (USC)-α was the dominant group of MOBs in the forests. In contrast, USC-γ was absent in more than half of the forest soils but present in almost all grassland soils. USC-α abundance had a direct positive effect on PMOR in forest, while in grasslands USC-α and USC-γ abundance affected PMOR positively with a more pronounced contribution of USC-γ than USC-α. Soil bulk density negatively influenced PMOR in both forests and grasslands. We further found that the response of the PMORs to pH, soil texture, soil water holding capacity and organic carbon and nitrogen content differ between temperate forest and grassland soils. pH had no direct effects on PMOR, but indirect ones via the MOB abundances, showing a negative effect on USC-α, and a positive on USC-γ abundance. We conclude that reduction in grassland land-use intensity and afforestation has the potential to increase the CH₄ sink function of soils and that different parameters determine the microbial methane sink in forest and grassland soils.

Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils

Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.

Soil net nitrogen mineralisation across global grasslands

Soil nitrogen mineralisation (Nmin), the conversion of organic into inorganic N, is important for productivity and nutrient cycling. The balance between mineralisation and immobilisation (net Nmin) varies with soil properties and climate. However, because most global-scale assessments of net Nmin are laboratory-based, its regulation under field-conditions and implications for real-world soil functioning remain uncertain. Here, we explore the drivers of realised (field) and potential (laboratory) soil net Nmin across 30 grasslands worldwide. We find that realised Nmin is largely explained by temperature of the wettest quarter, microbial biomass, clay content and bulk density. Potential Nmin only weakly correlates with realised Nmin, but contributes to explain realised net Nmin when combined with soil and climatic variables. We provide novel insights of global realised soil net Nmin and show that potential soil net Nmin data available in the literature could be parameterised with soil and climate data to better predict realised Nmin.

Sustainability Assessment of Alternative Strip Clear Cutting Operations for Wood Chip Production in Renaturalization Management of Pine Stands

In Mediterranean regions, afforested areas were planted to ensure the permanence of land cover, and to protect against erosion and to initiate the vegetation processes. For those purposes, pine species were mainly used; however, many of these stands, without silvicultural treatments for over fifty-sixty years, were in a poor state from physical and biological perspective, and therefore, clear-cutting on strips was conducted as silvicultural operation with the aim to eliminate 50% of the pine trees and to favor the affirmation of indigenous broadleaves seedlings. At the same time, the high and increasing demand of the forest based sector for wood biomass related to energy production, needs to be supplied. In a modern and multifunctional forestry, in which society is asking for sustainable forestry and naturalistic forest management, forestry operations should ideally be carried out in a sustainable manner, thus support the concept of sustainable forest management. All these aspects are also related to the innovation in forestry sector for an effective energetic sustainability. Three different forest wood chains were applied in pine plantations, all differing in the extraction system (animal, forestry-fitted farm tractor with winch, and double drum cable yarder). The method of the sustainability impact assessment was used in order to assess potential impacts of these alternative management options, and a set of 12 indicators covering economic, environmental, and social dimensions was analyzed. Further, to support decision makers in taking informed decisions, multi-criteria decision analysis was conducted. Decision makers gave weight towards the indicators natural tree regeneration and soil biological quality to support the achievement of the forest management goal. Results showed that first ranked alternative was case 2, in which extraction was conducted by a tractor with a winch. The main reason for that lies in the fact that this alternative had best performance for 80% of the analyzed criteria.

Black Alder (Alnus glutinosa (L.) Gaertn.) on Compacted Skid Trails: A Trade-off between Greenhouse Gas Fluxes and Soil Structure Recovery?

The compaction of forest soils can deteriorate soil aeration, leading to decreased CH4 uptake and increased N2O efflux. Black alder (Alnus glutinosa) may accelerate soil structure regeneration as it can grow roots under anaerobic soil conditions. However, symbiotic nitrogen fixation by alder can have undesirable side-effects on greenhouse gas (GHG) fluxes. In this study, we evaluated the possible trade-off between alder-mediated structure recovery and GHG emissions. We compared two directly adjacent 15-year old beech (Fagus sylvatica) and alder stands (loamy texture, pH 5–6), including old planted skid trails. The last soil trafficking on the skid trails took place in 1999. GHG fluxes were measured over one year. Undisturbed plots with beech had a moderately higher total porosity and were lower in soil moisture and soil organic carbon than undisturbed alder plots. No differences in mineral nitrogen were found. N2O emissions in the undisturbed beech stand were 0.4 kg ha−1 y−1 and 3.1 kg ha−1 y−1 in the undisturbed alder stand. CH4 uptake was 4.0 kg ha−1 y−1 and 1.5 kg ha−1 y−1 under beech and alder, respectively. On the beech planted skid trail, topsoil compaction was still evident by reduced macro porosity and soil aeration; on the alder planted skid trail, soil structure of the uppermost soil layer was completely recovered. Skid trail N2O fluxes under beech were five times higher and CH4 oxidation was 0.6 times lower compared to the adjacent undisturbed beech stand. Under alder, no skid-trail-effects on GHG fluxes were evident. Multiple regression modelling revealed that N2O and CH4 emissions were mainly governed by soil aeration and soil temperature. Compared to beech, alder considerably increased net fluxes of GHG on undisturbed plots. However, for skid trails we suggest that black alder improves soil structure without deterioration of the stand’s greenhouse gas balance, when planted only on the compacted areas.

Microbial succession on decomposing root litter in a drought-prone Scots pine forest

Decomposition is a major flux of the carbon cycle in forest soils and understanding the involved processes is a key for budgeting carbon turnover. Decomposition is constrained by the presence of biological agents such as microorganisms and the underlying environmental conditions such as water availability. A metabarcoding approach of ribosomal markers was chosen to study the succession of bacterial and fungal decomposers on root litter. Litterbags containing pine roots were buried in a pine forest for two years and sequentially sampled. Decomposition and the associated communities were surveyed under ambient dry and long-term irrigation conditions. Early decomposition stages were characterized by the presence of fast-cycling microorganisms such as Bacteroidetes and Helotiales, which were then replaced by more specialized bacteria and litter-associated or parasitic groups such as Acidobacteria, white rots, and Pleosporales. This succession was likely driven by a decrease of easily degradable carbohydrates and a relative increase in persistent compounds such as lignin. We hypothesize that functional redundancy among the resident microbial taxa caused similar root decomposition rates in control and irrigated forest soils. These findings have important implications for drought-prone Alpine forests as frequent drought events reduce litter fall, but not litter decomposition, potentially resulting in lower carbon stocks.

Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones

Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the effects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in five ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profile variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment effects on gene profiles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these effects varied among ecozones. Our results suggest that ecozone-specific nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub- and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N.

Changes of soil prokaryotic communities after clear-cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes

To understand the temporal responses of soil prokaryotic communities to clear-cutting disturbance, we examined the changes in soil bacterial and archaeal community composition, structure and diversity along a chronosequence of forest successional restoration using high-throughput 16S rRNA gene sequencing. Our results demonstrated that clear-cutting significantly altered soil bacterial community structure, while no significant shifts of soil archaeal communities were observed. The hypothesis that soil bacterial communities would become similar to those of surrounding intact primary forest with natural regeneration was supported by the shifts in the bacterial community composition and structure. Bacterial community diversity patterns induced by clear-cutting were consistent with the intermediate disturbance hypothesis. Dynamics of bacterial communities was mostly driven by soil properties, which collectively explained more than 70% of the variation in bacterial community composition. Community assembly data revealed that clear-cutting promoted the importance of the deterministic processes in shaping bacterial communities, coinciding with the resultant low resource environments. But assembly processes in the secondary forest returned a similar level compared to the intact primary forest. These findings suggest that bacterial community dynamics may be predictable during the natural recovery process.

Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils

Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO₃, N₂O, CO₂, and CH₄. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N₂O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our mechanistic understanding of biogeochemical cycles.

Methanogenesis affected by the co-occurrence of iron(III) oxides and humic substances

Iron oxides and humic substances (humics) have substantial effects on biochemical processes, such as methanogenesis, due to their redox reactivity and ubiquitous presence. This study aimed to investigate how methanogenesis is affected by the common occurrence of these compounds, which has not been considered to date. The experiment was conducted with anoxic paddy soil microcosms receiving a humics surrogate compound (anthraquinone-2,6-disulfonate, AQDS) and three iron(III) oxides (ferrihydrite, hematite, and magnetite) differing in crystallinity and conductivity. Ferrihydrite suppressed methanogenesis, whereas AQDS, hematite, and magnetite facilitated methanogenesis. CH4 production in co-occurring ferrihydrite + AQDS, hematite + AQDS, and magnetite + AQDS cultures was 4.1, 1.3, and 0.9 times greater than the corresponding cultures without AQDS, respectively. Syntrophic cooperation between Geobacter and Methanosarcina occurred in the methanogenesis-facilitated cultures. Experimental results suggested that the conductive characteristics of iron(III) oxides was an important factor determining the methanogenic response to the co-occurrence of iron(III) oxides and humics in anaerobic paddy soil. This work indicated that the type of iron(III) oxides may significantly affect carbon cycling under anoxic conditions in natural wetlands.

Extracellular quinones affecting methane production and methanogenic community in paddy soil

This study investigated the change of CH4 production and methanogenic community in response to the presence of humic substances (humics) analogue, anthraquinone-2,6-disulfonate (AQDS). Anaerobic experiments used a Chinese paddy soil, and three concentration levels of 0.5, 5, and 20 mM AQDS were conducted. Results suggested that the effect of AQDS on methanogenesis was time-dependent and concentration-dependent. Twenty millimolars of AQDS was toxic for methanogenic activity almost for the entire experimental period. Slight inhibition of methanogenesis by AQDS respiration in the 0.5- and 5-mM AQDS-supplemented treatments occurred within the early period, while CH4 accumulated throughout the later period was approximately five and ten times greater than that of the controls without AQDS, respectively. AQDS reduction coupling to acetate oxidization enriched Geobacter species, and the mcrA-targeted T-RFLP profiles revealed significant increase of Methanosarcina at the expense of Methanobacterium in the 0.5- and 5-mM AQDS treatments. The enriched syntrophic association between Geobacter and Methanosarcina was deduced to be an effective methanogenic pathway for converting acetate to CH4 via direct interspecies electron transfer. This study implied the ecological importance of syntrophic interaction between methanogens and microorganisms enriched by anaerobic respiration of non-methanogenic terminal electron acceptors in paddy soils.

Resistance and resilience of the forest soil microbiome to logging-associated compaction

Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.

Identification of biomass utilizing bacteria in a carbon-depleted glacier forefield soil by the use of 13C DNA stable isotope probing

As Alpine glaciers are retreating rapidly, bare soils with low organic C and N contents are becoming exposed. Carbon availability is a key factor regulating microbial diversity and ecosystem functioning in these soils. The aim of this study was to investigate how bacterial activity, community structure and composition are influenced by organic carbon availability. Bare soils were supplied with (13)C-labelled fungal (Penicillium sp.) and green algal (Chlorella sp.) biomass and the CO2 evolution and its δ(13)C signature were monitored up to 60 days. These organisms have previously been isolated near the glacier terminus. DNA stable isotope probing followed by T-RFLP profiling and sequencing of 16S rRNA genes was employed to identify consumers able to assimilate carbon from these biomass amendments. Higher respiration and higher bacterial activity indicated a more efficient utilization of algal cells than fungal cells. Flavobacterium sp. predominantly incorporated fungal-derived C, whereas the algal-derived C was mainly incorporated by Acidobacteria and Proteobacteria. This study emphasizes the important role of both fungal and algal biomass in increasing the carbon pool in recently deglaciated bare soils, as only 20% of the added C was respired as CO2, and the rest, we presume, remained in the soil.

Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales

Understanding the dynamics of methane (CH4 ) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2 ) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr(-1) , which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry models.

Methylation of mercury in earthworms and the effect of mercury on the associated bacterial communities

Methylmercury compounds are very toxic for most organisms. Here, we investigated the potential of earthworms to methylate inorganic-Hg. We hypothesized that the anaerobic and nutrient-rich conditions in the digestive tracts of earthworm's promote the methylation of Hg through the action of their gut bacteria. Earthworms were either grown in sterile soils treated with an inorganic (HgCl₂) or organic (CH₃HgCl) Hg source, or were left untreated. After 30 days of incubation, the total-Hg and methyl-Hg concentrations in the soils, earthworms, and their casts were analyzed. The impact of Hg on the bacterial community compositions in earthworms was also studied. Tissue concentrations of methyl-Hg in earthworms grown in soils treated with inorganic-Hg were about six times higher than in earthworms grown in soils without Hg. Concentrations of methyl-Hg in the soils and earthworm casts remained at significantly lower levels suggesting that Hg was mainly methylated in the earthworms. Bacterial communities in earthworms were mostly affected by methyl-Hg treatment. Terminal-restriction fragments (T-RFs) affiliated to Firmicutes were sensitive to inorganic and methyl-Hg, whereas T-RFs related to Betaproteobacteria were tolerant to the Hg treatments. Sulphate-reducing bacteria were detected in earthworms but not in soils.

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.