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

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.https://www.frontiersin.org/journals/microbiologydm2022GeneticsMicrobiology and Plant Patholog

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield

Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition

Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate

Fast and persistent responses of alpine permafrost microbial communities to in situ warming

Global warming in mid-latitude alpine regions results in permafrost thawing, together with greater availability of carbon and nutrients in soils and frequent freeze–thaw cycles. Yet it is unclear how these multifactorial changes will shape the 1 m-deep permafrost microbiome in the future, and how this will in turn modulate microbially-mediated feedbacks between mountain soils and climate (e.g. soil CO2 emissions). To unravel the responses of the alpine permafrost microbiome to in situ warming, we established a three-year experiment in a permafrost monitoring summit in the Alps. Specifically, we simulated conditions of warming by transplanting permafrost soils from a depth of 160 cm either to the active-layer topsoils in the north-facing slope or in the warmer south-facing slope, near the summit. qPCR-based and amplicon sequencing analyses indicated an augmented microbial abundance in the transplanted permafrost, driven by the increase in copiotrophic prokaryotic taxa (e.g. Noviherbaspirillum and Massilia) and metabolically versatile psychrotrophs (e.g. Tundrisphaera and Granulicella); which acclimatized to the changing environment and potentially benefited from substrates released upon thawing. Metabolically restricted Patescibacteria lineages vastly decreased with warming, as reflected in the loss of α-diversity in the transplanted soils. Ascomycetous sapro-pathotrophs (e.g. Tetracladium) and a few lichenized fungi (e.g. Aspicilia) expanded in the transplanted permafrost, particularly in soils transplanted to the warmer south-facing slope, replacing basidiomycetous yeasts (e.g. Glaciozyma). The transplantation-induced loosening of microbial association networks in the permafrost could potentially indicate lesser cooperative interactions between neighboring microorganisms. Broader substrate-use microbial activities measured in the transplanted permafrost could relate to altered soil C dynamics. The three-year simulated warming did not, however, enhance heterotrophic respiration, which was limited by the carbon-depleted permafrost conditions. Collectively, our quantitative findings suggest the vulnerability of the alpine permafrost microbiome to warming, which might improve predictions on microbially-modulated transformations of mountain soil ecosystems under the future climate.ISSN:0048-9697ISSN:1879-102

A low-tech, low-cost passive sampler for the long-term monitoring of phosphate loads in rivers and streams

The concentration of dissolved reactive phosphorus (DRP) in rivers can change intermittently within minutes depending on the weather and water discharge (Q), or activities in the watershed. Accordingly, accurate estimation of the annual DRP load requires frequent sampling or even continuous monitoring, which is laborious and cost-intensive. We present the design and laboratory evaluation of a new, robust, low-cost, low-tech device based on passive samplers (P-traps). The traps use Fe-(oxy)hydroxide coated quartz sand as an adsorbent enclosed in a vertical grid of individual cells separated from the river water by filter membranes. They are inexpensive, easy to handle, resistant to repeated desiccation and immersion and exposable for several months. They permit estimation of discharge dependent time weighted average DRP concentrations (C-Q relationships) and annual P loads of rivers characterized by highly variable DRP concentrations with a relative accuracy of +/- 3%

Bacterial and fungal community responses to reciprocal soil transfer along a temperature and soil moisture gradient in a glacier forefield

The influence of soil physicochemical properties on microbial communities can be large, especially in developing soils of glacier forefield chronosequences. However, small-scale expositional differences in bare soils and their impacts on soil microbial communities have so far been largely neglected. Here we studied the changes of microbial communities in three deglaciated unvegetated sites along a soil moisture and temperature gradient near a glacier terminus. In order to elucidate the driving forces for these changes, fine granite sediment was reciprocally transferred and regularly sampled during 16 months to determine microbial activities and the bacterial and fungal community structures and compositions using T-RFLP profiling and sequence analysis. Microbial activities only responded to soil transfer from the warmer and drier site to the colder and moister site, whereas the bacterial and fungal community structures responded to transfer in both directions. Bacterial phylotypes found to react to soil transfer were mainly the Acidobacteria, Actinobacteria, alpha- and beta-Proteobacteria. The common fungal phylogenetic groups Pezizomycetes and mitosporic Ascomycetes also reacted to soil transfer. It seemed that the soil moisture was the limiting factor for the microbial activities. We concluded that for the microbial community structures transferring soil from a colder to a warmer site induced a higher rate of change due to a higher microbial activity and faster species turnover than the reverse transfer. (C) 2013 Elsevier Ltd. All rights reserved

Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes

Background: Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze–thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found. Results: We observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming. Conclusions: Our study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.ISSN:2524-637

Ability of fungi isolated from plastic debris floating in the shoreline of a lake to degrade plastics.

Plastic waste in the environment is a significant threat due to its resistance to biological processes. Here we report the ability of fungal strains found on floating plastic debris to degrade plastics. In particular, we wanted to know which fungi grow on plastic debris floating in the shoreline, whether these fungi have the ability to degrade plastics, whether the plastic-degrading fungi can degrade other complex C-polymers such as lignin, and whether lignin-degraders vice versa can also break down plastics. Overall, more than a hundred fungal strains were isolated from plastic debris of the shoreline of Lake Zurich, Switzerland, and grouped morphologically. Representative strains of these groups were then selected and genetically identified, altogether twelve different fungal species and one species of Oomycota. The list of fungi included commonly occurring saprotrophic fungi but also some plant pathogens. These fungal strains were then used to test the ability to degrade polyethylene and polyurethane. The tests showed that none of the strains were able to degrade polyethylene. However, four strains were able to degrade polyurethane, the three litter-saprotrophic fungi Cladosporium cladosporioides, Xepiculopsis graminea, and Penicillium griseofulvum and the plant pathogen Leptosphaeria sp. A series of additional fungi with an origin other than from plastic debris were tested as well. Here, only the two litter-saprotrophic fungi Agaricus bisporus and Marasmius oreades showed the capability to degrade polyurethane. In contrast, wood-saprotrophic fungi and ectomycorrhizal fungi were unable to degrade polyurethane. Overall, it seems that in majority only a few litter-saprotrophic fungi, which possess a wide variety of enzymes, have the ability to degrade polyurethane. None of the fungi tested was able to degrade polyethylene