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Soil microbial responses to environmental stress and climate change

Anthropogenic greenhouse-gas emissions are drastically shaping global climate, increasing temperatures and contributing to more frequent extreme weather events. Terrestrial ecosystem responses to climate change can induce a large feedback via the control of biogeochemical cycles, for instance by regulating carbon fluxes that are 10 times larger than human emissions. A large portion of carbon and nutrient cycling is controlled by soil processes, in which microorganisms play a central role. Soil microbial communities and their physiological traits are, in turn, influenced by both gradual climate changes and more extreme short-term weather events. Thus, understanding the impacts of climate on soil microbial communities and microbe-mediated processes is critical for improving predictions of the resistance and resilience of terrestrial ecosystems in the future.

This session aims to elucidate the impacts of different climate scenarios on soil microbial communities and biogeochemical cycling, and their feedback to climate change. We will focus on different aspects of climate change, ranging from gradual changes such as increasing atmospheric CO2 or temperature, to the effects of more extreme weather events such as heatwaves, drying-rewetting cycles or floods. We invite studies on the resilience and associated recovery dynamics of soil biota to the mentioned environmental disturbances, as well as on their resistance or adaptation mechanisms. Studies with a focus on links between microbial community composition and function, as well as interactions between soil microorganisms, plants and fauna, are particularly welcomed. We aim to connect researchers from different disciplines and to create a discussion platform to review the current state-of-the-art, identify knowledge gaps, share ideas, and tackle new challenges in the field.

Co-organized by BG6
Convener: Lucia FuchsluegerECSECS | Co-conveners: Lettice HicksECSECS, Alberto CanariniECSECS, Ainara LeizeagaECSECS, Albert C. BrangaríECSECS
| Mon, 23 May, 15:10–18:30 (CEST)
Room 0.49/50

Mon, 23 May, 15:10–16:40

Chairpersons: Albert C. Brangarí, Lucia Fuchslueger

Bruce Hungate

Climate warming can alter microbial activity, potentially altering the composition of the atmosphere and feeding back to climate, as well as health of soils that support production of food and fiber. The vast variation in microbial metabolism, physiology, and traits means that different microorganisms are likely to respond differently to the same forcings. For example, some microorganisms appear to thrive with warming, some are unresponsive, and others decline. Such differences in responses likely result in different contributions by microorganisms to terrestrial feedbacks to climate change, like carbon storage and loss from soils, as well as the release and exchange of the potent greenhouse gases nitrous oxide and methane. Characterizing the magnitude and significance of differential biological responses and feedbacks to environmental forcing is a major focus of ecosystem science and functional ecology. Doing so for microorganisms is challenging, but vitally important given the size and uncertainty of microbial feedbacks to the changing climate. Addressing these issues requires quantitative measurements of microbial responses to warming, responses that can be translated into the material flows in nature that constitute the feedbacks of interest. Further, we need to aim toward quantifying microbial responses under field conditions, under conditions where we can simultaneously characterize the magnitude of the feedback and thus have common context for connecting the two. Examples of efforts to make these connections will be presented, from warming experiments across biomes. Quantitative field-based microbial ecology can push the field by revealing the biology and evolution of the key drivers of important feedbacks to the changing climate and atmosphere, and may help identify organisms that are especially effective in promoting the ecosystem processes that protect the climate.

How to cite: Hungate, B.: The ecology of wild microorganisms in a changing climate, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-9064, https://doi.org/10.5194/egusphere-egu22-9064, 2022.


Andrea Söllinger et al.

How soil microorganisms respond to global warming is a key question in microbial ecology and eminently relevant for soil ecosystems, the terrestrial carbon cycle, and the climate system. However, physiological responses of soil microorganisms – key to infer future soil-climate feedbacks – are poorly understood.

We here make use of the longest lasting in situ soil warming experiment worldwide, ForHot, in which an Icelandic subarctic grassland site has been exposed to natural geothermal soil warming for more than 50 years. Using a metatranscriptomics approach, allowing the comprehensive study of the entire active soil microbial community and their functions by analysing expressed genes, we revealed key physiological responses of soil Bacteria to medium- (8 years) and long-term (>50 years) soil warming of +6 °C.

Irrespective of the duration of warming, we observed a community-wide upregulation of central (carbohydrate) metabolisms and cell replication and a downregulation of the bacterial protein biosynthesis machinery in the warmed soils. This coincided with a decrease of microbial biomass, a decrease of total and biomass-specific RNA content, and lower soil substrate concentrations in the warmed soils. We conclude that higher biochemical reaction rates, caused by higher temperatures, allow soil Bacteria to reduce their cellular number of ribosomes, the macromolecular complexes carrying out protein biosynthesis. To further test this we revisited the site and conducted a short-term warming experiment (6 weeks, +6 °C), which supported our conclusion.

The downregulation of the protein biosynthesis machinery (i.e., the reduction of ribosomes) liberates energy and matter, leading to a resource re-allocation, and allows soil Bacteria to maintain high metabolic activities and cell division rates even after decades of warming.

How to cite: Söllinger, A., Séneca, J., Dahl, M. B., Motleleng, L. L., Prommer, J., Verbruggen, E., Sigurdsson, B. D., Janssens, I., Peñuelas, J., Urich, T., Richter, A., and Tveit, A. T.: Physiological responses of soil microorganisms to weeks, years, and decades of soil warming, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-2657, https://doi.org/10.5194/egusphere-egu22-2657, 2022.

Maria Scheel et al.

Permafrost soils usually remain frozen in summer, often even for millennia. Due to low temperatures, decomposition rates are low and alone Arctic permafrost is estimated to store 1850 Gt carbon (C). This currently corresponds to about twice the amount of atmospheric CO2. While microorganisms within their seasonally thawing surface (active) layer are adapted to enormous temperature fluctuations, the intact permafrost microbiome contains spore-formers and extremophiles at low metabolic states. With global warming, seasonal thaw depth increases, not only leading to loss of ancient communities, but also to a growing availability of soil carbon for decomposition. Much of permafrost microbial taxonomic and metabolic diversity is unknown still, but our most urgent gaps of knowledge exist in monitoring this vulnerable microbiome’s ecological and metabolic adaptation in situ during permafrost thaw and erosion. Insights about microbial carbon sequestration in thawing soils is crucial - yet understudied, as permafrost environments are usually remote and modern sequencing techniques require elaborate sample storage and transport.

Here, we present our results of total RNA sequencing of abruptly eroding as well as intact 26200-year-old permafrost soils, from the high Arctic Northeast Greenland. Gene expression of samples describes the community composition (rRNA) and active metabolic pathways (mRNA) in zones of intensely degrading permafrost. The impact of changing physicochemical soil parameters with depth, such as pH, age, soil moisture and organic matter content was compared to determine possible metabolic and community-level responses. We revealed taxonomic composition and diversity, as well as metabolic pathways of microbial organic carbon remineralization especially at the crucial freshly thawed permafrost depths.

How to cite: Scheel, M., Zervas, A., Jacobsen, C. S., and Christensen, T. R.: Should I grow or should I go? - Transcriptomic responses of permafrost soil microbiomes to sudden thaw and erosion, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-5516, https://doi.org/10.5194/egusphere-egu22-5516, 2022.

Pablo García-Palacios

Anthropogenic warming is expected to accelerate global soil organic carbon (SOC) losses via microbial decomposition, yet, there is still no consensus on the loss magnitude. Here we argue that, despite the mechanistic uncertainty underlying these losses, there is confidence that a strong, positive land carbon–climate feedback can be expected. Two major lines of evidence support net global SOC losses with warming via increases in soil microbial metabolic activity: the increase in soil respiration with temperature and the accumulation of SOC in low mean annual temperature regions. Warming- induced SOC losses are likely to be of a magnitude relevant for emission negotiations and necessitate more aggressive emission reduction targets to limit climate change to 1.5 °C by 2100. We suggest that microbial community–temperature interactions, and how they are influenced by substrate availability, are promising research areas to improve the accuracy and precision of the magnitude estimates of projected SOC losses.

How to cite: García-Palacios, P.: Evidence for large microbial-mediated losses of soil carbon under anthropogenic warming, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-3539, https://doi.org/10.5194/egusphere-egu22-3539, 2022.

Carla Cruz Paredes et al.
Marleen Pallandt et al.

Soil organic carbon (SOC) is the largest terrestrial carbon pool. However, it is still uncertain how it will respond to climate change in the 21st century. Especially SOC losses due to soil warming are a source of uncertainty. It is generally accepted that microbially driven SOC decomposition will increase with warming, provided that sufficient assimilable substrate is available. Sorption to mineral surfaces or the soil moisture-dependent diffusion of substrates to microbial cells can limit substrate availability. Substrate supply is therefore a potentially rate limiting step for the temperature response of SOC decomposition.

In SOC decomposition models, the combined effects of temperature and soil moisture on the decomposition rate can be represented by the Dual Arrhenius Michaelis-Menten (DAMM) model (Davidson et al. 2012). For any substrate (S), it describes the reaction velocity V = Vmax [S]/(kMS+ [S]), where [S] is the substrate concentration and kMS is the half-saturation constant. The maximum reaction velocity, Vmax, is temperature dependent and follows an Arrhenius function. Also, a positive correlation between temperature and kM-values of different enzymes has been empirically shown, with Q10 values ranging from 0.71-2.8 (Allison et al., 2018). As kMS appears in the denominator of the Michaelis-Menten equation, an increase in kMS leads to a lower reaction velocity (V) and V would become less temperature sensitive at low substrate concentrations.

Besides temperature, substrate concentration [S] depends on soil moisture content. In a dry soil, substrate diffusion to the microbial surface is limited, whereas in a very wet soil, reduced oxygen availability can lower the reaction velocity (V). Changes in substrate supply in drying/(re)wetting soils coincide with changes in temperature which directly interact with the temperature sensitivities of Vmax and kMS. These interactions can have consequences for decomposition rates in the topsoil versus the deeper soil, since substrate concentrations and temperature are generally higher in the topsoil, but moisture could be more important for substrate limitation. In contrast, in the deep soil, soil moisture might be more available but substrate concentrations (and potentially soil temperatures) might be lower.

This study focuses on this interaction between climate change and substrate availability by comparing two model experiments: 1) a modelling experiment where only Vmax is temperature sensitive and 2) one where both Vmax and kMS are temperature sensitive. We also investigate the consequences of the counteracting temperature sensitivities of Vmax and kMS among a substrate gradient, and at different soil temperatures and soil moisture ranges. Finally, we look at dynamic changes in substrate supply, temperature sensitivities and changes in soil moisture and their effects on SOC decomposition in a microbially explicit dynamic SOC decomposition model which also includes organo-mineral interactions.

How to cite: Pallandt, M., Ahrens, B., Schrumpf, M., Lange, H., Zaehle, S., and Reichstein, M.: Modelling climate-substrate interactions in microbial SOC decomposition, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-10050, https://doi.org/10.5194/egusphere-egu22-10050, 2022.

Swamini Khurana and Stefano Manzoni

Carbon emissions from soil are large contributors to the global carbon cycle, but depend on processes occurring at a small scale. Carbon cycling in the soils is mediated by plant roots, soil fauna, and microorganisms including fungi and bacteria. Sophisticated molecular analytical techniques have been developed to characterize soil microbial communities, resulting in discovery of new microbial species that are not yet culturable in the laboratory. The unculturable fraction of soil microbial communities make for a large data gap since we are not able to characterize their activity, and even less so their role in the microbial community. As a result, soil carbon models cannot be readily parameterized from the bottom up—essentially, we cannot quantify functions at low taxonomic level and then scale up to the community level. In this numerical study, we aim to explore how soil carbon model predictions are affected by microbial diversity as characterized in silico by distribution of traits.

The resilience of soil microbial communities is related to distance to the surface and diversity. Diverse microbial communities that are closer to the surface, experiencing regular temporal fluctuations in environmental conditions are more resilient to disturbances than microbial communities deeper down in the subsurface. However, forest management practices and extreme climate conditions impose conditions that may be hitherto unforeseen. This makes prediction of response of soil microbial communities to new disturbances and soil carbon respiration thereof to be uncertain. In this contribution, we developed a microbial process network incorporating diverse organic matter compounds, and bacterial and fungal species characterized by distributions of trait values (including co-variations and trade-offs). With this framework, we explore if soil microbial diversity is a good predictor for soil carbon stocks and study diversity effect on community-level responses to disturbance and variations in environmental conditions. These results will assist in the development of a rate expression to capture the contribution of soil microbial community composition to carbon dynamics in soil.

How to cite: Khurana, S. and Manzoni, S.: Linking soil microbial biodiversity to soil carbon dynamics, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-6862, https://doi.org/10.5194/egusphere-egu22-6862, 2022.

Claire Chenu et al.

Global warming is leading to increased temperatures, accentuated evaporation of terrestrial water and increased the atmosphere moisture content, resulting in frequent droughts and heavy precipitation events. It necessary to assess the sensitivity of soil organic carbon (SOC) under storing practices in response to increasing soil moisture, temperature and frequent dry-wet cycles in order to anticipate future soil carbon losses. We evaluated the impact of these climatic events through an incubation experiment on temperate luvisols from conservation agriculture, organic agriculture, organic waste products applications, i.e. biowaste, residual municipal solid waste and farmyard manure composts compared with conventionally managemed soils. The alternative management options all have led to increased SOC stocks. Soil samples were incubated in the lab under different temperatures (20, 28 and 35°C), different moisture conditions (pF1.5; 2.5 and 4.2) and under dry(pF4.2)-wet (pF1.5) cycles. Dry-wet cycles caused CO2 flushes but overall did not stimulate soil carbon mineralization relative to wet controls (pF1.5 and pF2.5). Overall the additional SOC stored under alternative management options was not more sensitive to climate change (temperature, moisture, dry-wet cycles) than the existing SOC.

How to cite: Chenu, C., Kpemoua, I., Leclerc, S., Barre, P., Houot, S., Pouteau, V., and Plessis, C.: Are carbon-storing soils more sensitive to climate change? A laboratory evaluation for agricultural temperate soils., EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-12273, https://doi.org/10.5194/egusphere-egu22-12273, 2022.

Yang Ding et al.

A diverse range of soil microorganisms accumulate energy to secure their future needs under resource fluctuation or deficiency. Microbial intracellular storage can substantially mediate the stress of resource variability across time, thereby supporting growth and reproduction. Microbial storage is well known in industrial applications and under pure culture conditions, yet few studies address its importance in the soil. To evaluate how widespread microbial energy storage is in soil, we quantified the contents of two intracellular storage compounds, polyhydroxybutyrate (PHB) and triacylglycerides (TAGs), from seven permanent grasslands in Germany differing in field management (grazing/mowing and fertilizing) and soil types. In winter 2021, soil was collected from two depths, 5-10 cm called topsoil, and >30 cm called subsoil, to capture different soil carbon inputs from grass roots. The storage compound contents were determined by gas chromatography–mass spectrometry (GC-MS). We hypothesized that the carbon input controls the storage compound levels. From topsoil to subsoil, as root carbon inputs (estimated from the fresh root weight) drop with depth, microbial storage levels follow suit. Dissolved organic carbon (DOC) was measured to qualify carbon availability to microorganisms, and microbial biomass carbon (MBC) was to assess microbial biomass. The root weight in the topsoil was 20-50 times higher than in the subsoil, while MBC and DOC contents were 3-4 and 1.5-2.5 times higher, respectively. Storage levels and MBC decreased with depth, and showed a positive correlation with DOC. This experiment allowed us to quantify intracellular storage occurrence in soils and to understand how its distribution related to root carbon input. These results point out that microbial intracellular carbon storage might accumulate according to the available carbon level (root carbon inputs) for microorganisms. Thus, this carbon plays a pivotal role for microbial ecology of soils as it prepares the microbial cells to survive throughout the winter when less carbon is provided by plants.

How to cite: Ding, Y., Komainda, M., Mason-Jones, K., Dippold, M., and Banfield, C. C.: Intracellular energy storage mediating soil microbial resource stress, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-7699, https://doi.org/10.5194/egusphere-egu22-7699, 2022.

Steffen Schweizer et al.

Exchangeable sodium can have pronounced influences on physicochemical soil properties whereas the combined impact on microbial turnover of organic carbon (OC) remains elusive. In this work, we aimed to differentiate the effects of exchangeable sodium and soil pH on microbially mediated aggregate formation and turnover of cattle slurry. We incubated the soils under controlled laboratory conditions using artificial soil model minerals containing quartz grains, montmorillonite and goethite. The montmorillonite was pre-treated with NaCl solutions of sodium adsorption ratios (SAR) 0, 1 and 5 which resulted in exchangeable sodium percentages (ESP) of 1, 7 and 19 on average. The soil pH was adjusted within two treatments to 7.5 and 8.5 for each ESP at the start of the incubation. We incubated these six treatments with and without cattle slurry ground to < 200 µm after addition of a combined microbial inoculum, extracted from a Cambisol (pHH2O 7.5, Germany) and a Calcaric Solonchak (pHH2O 9.3, Spain) added to all samples. The microcosms were incubated with three replicates over a period of 30 days at constant pF of 2.2. The CO2 emission measurements of the microcosms with exchangeable sodium indicated a delayed respiration. The respiration under ESP 19 increased rapidly within the first days of incubation, whereas it was more delayed under ESP 7 until 15 days of incubation. The delayed CO2 respiration might be related to inhibited structural formation in treatments with higher exchangeable sodium. To test this, we are investigating the data on water-stable aggregation by wet sieving. The delayed CO2 respiration was reflected in lower microbial biomass, extracted after the incubation. The microbial biomass under ESP 19 and pH 8.5 was highest whereas the amount of leached C after two rainfall events (at day 7 and 15) was lowest, which could be related to a higher microbially mediated OC sequestration. The composition of exchangeable cations was monitored before and after the whole incubation which might help explaining the processes of microbially mediated aggregate formation and microbial carbon turnover under different levels of exchangeable sodium.

How to cite: Schweizer, S., Fiedler, J., Boehm, A., Dannenmann, M., Garcia-Franco, N., Han, J., Poll, C., Wong, V., and Bucka, F.: How soil sodification and pH restrict microbially mediated organic carbon turnover and aggregate formation: An artificial soil microcosm study, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-12833, https://doi.org/10.5194/egusphere-egu22-12833, 2022.


Mon, 23 May, 17:00–18:30

Chairpersons: Albert C. Brangarí, Lucia Fuchslueger

Luciana Bachega and Laynara Lugli and the Carlos Quesada1

It is projected that the Amazon Forest could act as a carbon (C) sink in future climate change scenarios by efficiently storing extra biomass produced. Under atmospheric dioxide carbon (CO2) elevation, the forest would experience an effect of C fertilization that could enhance nutrient requirements resulting in increased rates of nutrient cycling, soil enzymes activity, and soil microbial biomass stocks. However, we can expect that the potential effects of elevated CO2 (eCO2) could be restricted by soil nutrient limitation, especially in the low phosphorus (P) conditions found in central Amazonia. We aimed to estimate the effect of eCO2 belowground, focusing on soil microbial biomass and enzymes activity on bulk soil and rhizosphere in central Amazonia, Brazil. In 2019 we set up the AmazonFACE program a CO2 fertilization in a central Amazon rainforest in a factorial design experiment with eight Open-Top Chambers (OTC): four controls with ambient CO2 concentration (aCO2), and four with eCO2 (200 ppm above the control chambers). We grew six pots with Inga edulis, a native N-fixing species, per OTC; additionally, we added 600 mg/kg of P in three pots per OTC in a total of four treatments: aCO2, eCO2, aCO2+P and, eCO2+P. In 2021 we harvested the plants and evaluated total soil microbial biomass carbon (MBC) and the potential activity of extracellular enzymes acid phosphatase (AP), β-glucosidase (BG), N-acetyl-β-glucosaminidase (NAG), enzymatic stoichiometry (BG/AP, and BG/NAG), and the microbial biomass specific enzyme rate (the ratio of each enzyme/MCB) in the bulk soil and in the soil attached to the roots, that we considered the rhizosphere. We hypothesized that the effect of eCO2 and P addition would increase MBC and enzyme activity; higher MBC and enzymes activity would be found in the rhizosphere instead of bulk soil. We found that the effects of eCO2 were only present with the interaction with P addition: higher MBC, but lower AP and BG/MBC in eCO2+P compared to controls. We also found an interaction effect of eCO2 regarding bulk soil and rhizosphere: higher NAG activity on bulk soil, and higher BG/NAG on rhizosphere. We found a difference between bulk soil and rhizosphere in almost all variables, except for MBC and BG/MBC. Enzyme activity and AP/MBC and NAG/MBC were higher for bulk; nevertheless, the enzymatic stoichiometry was greater in the rhizosphere. As we expected, eCO2+P increased MBC, although we found a higher microbial biomass specific enzyme rate in controls, which can suggest nutrient limitation, such as P. In contrast to our assumption, the bulk soil showed higher enzymes activity and microbial specific enzyme rates than the rhizosphere. However, the higher ratio of BG/AP on the rhizosphere can indicate lower P investment. We also found that the effect of eCO2 on soil enzymes can be different between bulk soil and rhizosphere (high rhizosphere BG/NAG), potentially decreasing nitrogen investment on soil near the roots. Our results suggest that under eCO2, the Amazon Forest could increase soil C stock due to MBC and this effect can change nutrients demand especially on the rhizosphere.

How to cite: Bachega, L. and Lugli, L. and the Carlos Quesada1: Soil microbial biomass and enzyme activity under elevated CO2 in Central Amazon: how global changes can affect tropical forests belowground, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-8845, https://doi.org/10.5194/egusphere-egu22-8845, 2022.

Teresa Gimeno et al.

In temperate forests, ectomycorrhizal fungi (EMF) form the dominant mycorrhizal symbiotic association. EMF increase root uptake of nutrients and water in exchange for carbohydrates. The composition, structure and abundance of EMF communities are shaped by abiotic factors such as soil water availability, chemical and physical properties. Biotic factors also play a strong role especially tree species identity and plant physiological activity. Water availability affects both biotic and abiotic factors and thus is a major driver of EMF community structure and function. Under current climate change scenarios, seasonal drought risk is predicted to expand into areas where ecosystems may not be adapted to limited water availability. This is the case of European beech (Fagus sylvatica) forests growing along their southern distribution limit, in the Iberian Peninsula. Here, we characterized the abundance and composition of the EMF community and the patterns of root water uptake, in forests along a precipitation gradient (2500, 1100 and 900 mm/year), in northern Spain. We sampled soil, wood and fine roots in three mature pure beech forests at two times during the growing season, with contrasting soil water availabilities. DNA was extracted from EMF tips for molecular analyses (DNA meta-barcoding) to estimate species richness and diversity for each site and sampling campaign. Root colonization by EMF decreased in the late part of the growing season, when soil water availability was lower and this decline was larger at the rainiest site. We found that EMF species richness and diversity were similar across sites and sampling campaigns, irrespective of soil water availability. Yet, across sites, EMF communities were distinctly separated in the multidimensional space and did not change over the season, suggesting that EMF communities would be adapted to the local climatic and abiotic conditions. Analyses of water isotopic composition showed that root water uptake relied on upper soil moisture at the rainiest site, whereas it relied on deeper water reservoirs at the sites with more limiting water availability. Taken together our results suggest that EMF communities of F. sylvatica forests along their southern distribution limit would be adapted to low seasonal water availability, provided that trees had access to deep soil water. Also, at sites where water availability was more limiting, roots would take up water from deeper soil horizons, whereas nutrients and EMF would still concentrate in the shallower soil layers, which could suggest a spatial decoupling between nutrient and water uptake. Meanwhile, at sites with abundant rainfall, both nutrient and water uptake would be strongly linked to water availability in the upper soil and thus these functions could be potentially more vulnerable to changes in precipitation patterns, mainly increased frequency and duration of rainless periods.

How to cite: Gimeno, T., Moreno-Mateos, D., Matesanz, S., Fanin, N., Wingate, L., Porras, J., and Rodríguez-Uña, A.: Changes in the composition of ectomycorrhizal fungal communities and the water uptake of European beech forests across a natural precipitation gradient , EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-6050, https://doi.org/10.5194/egusphere-egu22-6050, 2022.

María José Fernández Alonso et al.

Atlantic coastal dunes are priority conservation areas highly sensitive to climate change. In the Iberian Peninsula, a large part of the coastal dunes are drylands where the chronic shortage of water acts as a major driver of the ecosystem structure and functioning. The predicted increase in aridity by the end of this century may compromise key ecosystems aspects in drylands, such as biotic cover, vegetation productivity and soil fertility. We know little about how changes in aridity and biotic cover may affect the abundance and diversity of soil microbial communities in coastal dunes, and as such their assembly and ecological interaction networks.

We investigated whether the exposure to different aridity regimes can induce differences in microbial co-occurrence networks as well as alter their spatial heterogeneity. Specifically, we aim to (1) assess whether soil fungal and bacterial networks respond differently  and (2) test the role of the biotic cover driving the bacterial and fungal network relationships, the soil attributes and functions. To that end, we used a climosequence of dune systems with minimal variation in the soil type that covered a wide range of aridity conditions including humid, dry-subhumid and drylands in the coastline of Portugal and Spain (~1500 km).

Our results show that aridity decreased the biotic cover, favoured the formation of shrub vegetation patches and negatively affected microbial diversity, organic matter content and potential nitrogen mineralisation in soils. We also observed that the biotic cover exerts a strong control on soil attributes whose effects depend on the degree of aridity (e.g. formation of fertile islands in arid areas and different control of soil inorganic nitrogen forms in wetter areas). At an ecosystem level, increases in aridity resulted in a strong increase in the coupling of the soil microbial network until a specific threshold (values of aridity index (P/ETP)= 0.5-0.6) beyond which it remained constant. Soil bacterial networks showed lower stability against changes in aridity than fungal networks. Surface microsites strongly drove the interactions among soil bacterial groups, but much less so for fungal groups. Our results suggest that climate change, through increased aridity and associated loss of the biotic cover, will have important implications for microbial communities and soil functioning in these coastal dune systems.

How to cite: Fernández Alonso, M. J., Rodríguez, A., Ochoa-Hueso, R., Maestre, F. T., and Durán, J.: Soil microbial co-occurrence networks and functioning along an aridity gradient in Atlantic coastal dunes, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-8880, https://doi.org/10.5194/egusphere-egu22-8880, 2022.

Rossano Ciampalini et al.

Abiotic factors have long been recognised as important factors in structuring microbial diversity and species associations, among which topography and hydro-geomorphic flows have an impact from plot to large scale. These factors are deeply involved in the dynamics of climate change. However, the actual impact of topography on microbial communities in spatially defined habitats remains unclear and, needing further development, represents a promising branch to investigate microbiological assets in the environment. In this study, we analysed a parcel in continental France which revealed a combined action of hydro-geomorphic fluxes and topography in structuring microbial assemblages. Species-habitat occurrence seems to respond to the effective energy locally displayed by fluxes. Largest richness and microbial variety occurred where fluxes are small such as on limited slope or reduced runoff concentrations. Species dominance was higher in zones with higher fluxes suggesting: 1) an impoverishment of the more sensible species, or 2) a selective adaptation of the most resistant species. This differentiation was evidenced by analysing the potential impact of topography and cumulated fluxes for runoff and sediments (i.e., WTI, LS RUSLE indexes) on microbial richness, dominance, and abondance at Phylum and Class levels.

How to cite: Ciampalini, R., Spor, A., Quiquerez, A., Philippot, L., Bru, D., Mounier, A., and Follain, S.: Topography and hydro-geomorphic fluxes drive the assemblage of microbial communities, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-11048, https://doi.org/10.5194/egusphere-egu22-11048, 2022.

Katy Faulkner et al.

Climate change is expected to alter global precipitation patterns, with unknown impacts on biodiversity and ecosystem functioning. Temperate forests are one of the largest terrestrial carbon stocks, acting as sinks for greenhouse gases such as carbon dioxide and methane thus playing a major role in ameliorating global warming. Predicted changes to precipitation intensity, duration and timing under future climates are likely to result in the alteration of soil moisture dynamics in forest soils. This will impact soil microbial functions, with shifts from oxic to hypoxic or anoxic conditions which could affect microbial metabolism and microbially-mediated nutrient cycling. The impacts of these changes on the terrestrial carbon balance under current and future atmospheric carbon dioxide levels is currently not known. Here, we use a novel in situ approach to simulate high rainfall in soil mesocosms within a mature temperate oak-dominated (Quercus robur) forest in Staffordshire, UK (Birmingham Institute of Forest Research Free-Air Carbon Dioxide Enrichment facility) where atmospheric CO2 levels are elevated 150 ppm above ambient levels. We show that an 8-week period of elevated rainfall and volumetric soil moisture (~ 30% increase in amended mesocosms vs controls) had significant impacts on soil functioning. The forest soil methane sink was significantly reduced in the high rainfall treated soils by ~ 21-67%, resulting in greater methane accumulation in the atmosphere, with no recovery 4 weeks post-event. Using 16S rRNA amplicon sequencing and qPCR approaches, we show how bacterial and archaeal diversity respond to altered precipitation regimes and show significant changes in the abundance of methanotrophic and methanogenic communities. The activities of soil extracellular enzymes, involved in the breakdown of organic carbon, nitrogen, and phosphorus compounds, were reduced during the high rainfall treatment. Our results demonstrate that important climate feedbacks could occur during modest alterations in precipitation which should be considered in climate models and forestry management plans.

How to cite: Faulkner, K., Oakley, S., Hilton, S., Mason, K., Ullah, S., van der Gast, C., McNamara, N., and Bending, G.: High summer precipitation reduces soil methane sink capacity and alters decomposition processes in a mature temperate forest, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-11452, https://doi.org/10.5194/egusphere-egu22-11452, 2022.

Sara Winterfeldt et al.

Intensified land-use management and climate change constitute two major challenges for maintaining the soil functions regulated by microbial communities. It is well known that tillage disturbs the soil structure by changing physical properties such as aggregation and water retention capacity, which both have an impact on microbial carbon cycling. In addition, extreme drought and rainfall events result in a significant release of carbon dioxide, where the amount of carbon respired depends on the legacy of precipitation. Thus, understanding the combined effect of land use and precipitation on microbial processes is important in order to predict the future terrestrial carbon cycle.

In this project, we investigated how both the precipitation history and the disruption of soil structure affect microbial growth and respiration during drying-rewetting. We expected that microorganisms in sites with lower historical precipitation might be used to drier conditions, and then exhibit a faster recovery after rewetting and lower respiration rates than those in wetter sites. We also expected that the disruption of soil aggregates would increase the respiration rates after rewetting. In addition, fungal growth would be more affected than bacterial growth due to a damaged hyphal network.

We selected 11 grasslands sites across an east-west precipitation gradient in Sweden ranging from 380 to 1220 mm mean annual precipitation. Three different experiments were carried out to determine the differences in microbial responses along this gradient, by measuring bacterial growth, fungal growth and respiration at high time resolution during seven days after drying-rewetting. First, we investigated the short-term effect of disturbing aggregates by grinding soils in the laboratory. We compared the results from undisturbed soils with those found after dry or wet crushing. Second, we studied the effect of soil structure disturbance in the field and if results from laboratory experiments could be extended to agricultural practices. For this, we established plots across the precipitation gradient, applied a tillage treatment with a rotary cultivator at the start of the growing season and measured microbial responses at the end of the summer. Third, we explored how the microbial responses to soil structure disturbances developed over time in the field. To do so, we used soil sampled from one site in the gradient after one week, one month and three months after disturbance.

Preliminary results showed that crushing soils in the laboratory accelerated the bacterial recovery after rewetting, but fungal growth and respiration were unaffected compared to undisturbed soil. In the field, the microbial responses over time strengthened up to one month after the tilled treatment. The microbial responses along the precipitation gradient showed the importance of land-use management for carbon cycling under future scenarios of intensified weather events.

How to cite: Winterfeldt, S., Hicks, L., Brangarí, A., and Rousk, J.: Microbial responses to drying and rewetting: The interaction between soil structure and precipitation history, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-13369, https://doi.org/10.5194/egusphere-egu22-13369, 2022.

Ella Sieradzki et al.

After the dry season in a Mediterranean climate grassland, the initial soil rewetting event causes a short period of high microbial activity, growth, and mortality. This wet up leads to microbial succession and community reassembly. Climate change in these semiarid environments is projected to cause reduced precipitation, which may affect the structure and function of the microbial community. However, we know little about how microbial functional traits underlie the rewetting succession, and how previous precipitation regimes affect these traits.

Using 18O-water stable isotope probing (SIP), we conducted a replicated wet-up experiment in annual grassland soils that had been previously subjected to either average precipitation or 50% of the annual average. We traced microbial succession through 5 time points (0h, 24h, 48h, 72h and 168h) post wet-up. By combining SIP with metagenomics, we identified the actively growing organisms in both precipitation treatments and determined ecophysiological traits that were significantly more represented in growing organisms in each precipitation regime. 

We observed a legacy effect of average vs. reduced precipitation by comparing the differential abundance of genes observed at time 0h in the two soil treatments. However, this legacy effect was surprisingly short-lived, implying that microbial community function rapidly “restarts itself” before the next growing season, regardless of the precipitation conditions experienced in the previous year. While growing organisms were significantly more abundant than non-growing organisms during the wet-up, the most abundant taxa were slow growers. In contrast, fast growing taxa were less abundant throughout the experiment, suggesting mortality plays a large role in the reformation of the microbial community.

We highlight temporal patterns and significant differences based on past precipitation in the abundance of carbohydrate utilization pathways, such as a higher representation of organisms capable of degrading cellulose in the reduced precipitation treatment. There were no temporal patterns in nitrogen cycling pathways; nitrogen acquisition appeared to be based mostly on ammonium assimilation and transport as well as proteases. In conclusion, altering preceding precipitation patterns had a large legacy effect on microbial community assembly and function upon rewetting. However, the functional and compositional changes that resulted from altered precipitation had remarkably short-lived effects after the soils were rewetted.

How to cite: Sieradzki, E., Greenlon, A., Firestone, M., Pett-Ridge, J., Blazewicz, S., and Banfield, J.: Ecophysiological traits underlying microbial succession after rewetting of soil from different precipitation regimes, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-9015, https://doi.org/10.5194/egusphere-egu22-9015, 2022.

Johannes Rousk et al.
Lingjuan Li et al.

Climate change is leading to an increased frequency and severity of alternating wet and dry spells. These fluctuations affect soil water availability and other soil properties which are crucial drivers of soil microbial communities. While soil microbial communities have a reasonable capacity to recover once a drought seizes, the expected alternation of strongly opposing regimes can pose a particular challenge in terms of their capacity to adapt. Here, we set up experimental grassland mesocosms where precipitation frequency was adjusted along a gradient while holding total precipitation constant. The gradients varied the duration of wet and dry "spells" from 1 to 60 days during a total of 120 days, where we hypothesized that especially intermediate durations would lead to stochastic community assembly due to frequent alternation of opposing environmental regimes. We examined bacterial and fungal community composition, diversity, co-occurrence patterns and assembly mechanisms across these different precipitation frequencies. Our results show that 1) intermediate frequencies of wet and dry spells increased the stochasticity of microbial community assembly whereas microbial communities at low and high regime persistence were subject to more deterministic assembly, and 2) more persistent precipitation regimes (> 6 days duration) reduced the fungal diversity and network connectivity but had a less strong effect on bacterial communities. Collectively, these findings indicate that recurring wet and dry events lead to a less predictable and connected soil microbial community. This study provides new insight into the likely mechanisms through which precipitation frequencies alter soil microbial communities and their predictability.

How to cite: Li, L., Beemster, G., Reynaert, S., Nijs, I., Laukens, K., Asard, H., Vinduskova, O., and Verbruggen, E.: More frequent dry and wet spells increase stochastic microbial community assembly in grassland soils, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-11613, https://doi.org/10.5194/egusphere-egu22-11613, 2022.

Nicholas Bouskill et al.

The frequency and intensity of environmental fluctuations play an important role in shaping microbial community composition, trait-distribution, and adaptive capacity. We hypothesize here that a communities’ climate history dictates it’s metabolic response to future perturbation under a changing climate. Such a response is significant as changes in microbial metabolism can, in turn, feedback onto metabolite exudation, the chemical structure of necromass, and the formation and stability of soil organic matter. Here we use laboratory and field experiments to examine the metabolic pathways invoked under osmotic and matric stress within semi-arid and tropical soils. For example, using non-destructive, synchrotron-based Fourier-transform infrared spectromicroscopy we profiled the stress response of phylogenetically similar bacteria isolated from soils with contrasting climate histories subjected to both matric and osmotic stress. We note a strong carbohydrate-based, metabolic response of tropical microbes that is entirely absent in semi-arid organisms. At the field scale, we use metagenomic sequencing and metabolite analysis to demonstrate how four different sites established across a 1 m precipitation gradient from the Caribbean coast to the interior of Panama respond to a 50 % reduction in throughfall. The precipitation gradient permits the development of distinct communities at each site that show clearly divergent response to imposed hydrological perturbation. Our contribution here will discuss how communities adapted to different precipitation regimes respond metabolically to drought conditions, and how these change feedback onto the structure and stability of soil organic matter.    

How to cite: Bouskill, N., Karaoz, U., Chacon, S., Khurram, A., Dietrich, L., Holman, H.-Y., and Cusack, D.: Climate history dictates microbial metabolic response to drought stress: from semi-arid soils to tropical forest precipitation gradients , EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-1233, https://doi.org/10.5194/egusphere-egu22-1233, 2022.

Megan Foley et al.

Earth system models project altered precipitation regimes across much of the globe. Soil microorganisms in Mediterranean climates must withstand both direct physiological stress during prolonged periods of low soil moisture and be able to compete for resources when seasonal rains return and plant growth resumes5. However, we do not have a mechanistic understanding of how altered soil moisture regimes affect microbial population dynamics and in turn how this will affect soil carbon (C) persistence.

We used quantitative stable isotope probing (qSIP) to compare total and growing soil microbial communities across three California annual grassland ecosystems with Mediterranean climates that span a rainfall gradient and have developed from similar parent material. Sampling was conducted during the wet season, when environmental conditions were most similar across the sites. We assessed multiple edaphic variables, including the radiocarbon (14C) age of soil C. We hypothesized that the long-term legacy effect of soil water limitation would be reflected in lower community growth capacity at the driest site. We also predicted that actively growing communities would be more compositionally similar across the gradient than the total (active + inactive) microbiome.

Community and phylum mean bacterial growth rates increased from the driest site to the intermediate site, and rates were similar at the intermediate and wettest sites. These differences were persistent across major phyla, including the Actinobacteria, Bacteroidetes, and Proteobacteria. Additionally, soil C at the driest site was younger than the wet or intermediate sites. The microbial families that grew fastest at the driest site include taxa that have been described as having traits that are advantageous for surviving dry spells, such as spore formation, polyhydroxyalkanoate accumulation, carotenoid biosynthesis, extracellular polymeric substances production, and trehalose synthesis. Microbial communities at the driest site displayed phylogenetic clustering, suggesting environmental filtering for slow-growing microbial taxa that can withstand water stress at this site. Taxonomic identity was a strong predictor of growth, such that the growth rates of a taxon at one site predicted its growth rates at the others. We think this finding reflects the influence of genetic and physiological constraints on growth which appear to persist across rainfall gradients, edaphic properties, and biological communities. Lastly, we found that actively growing taxa represented (28-58%) of the taxa comprising total communities and that the composition of growing and total communities were similar. The finding that the growing communities were just a subset of the total microbiome, despite environmental conditions being favorable for growth, raises questions about the mechanisms maintaining soil microbial diversity in ecosystems with Mediterannean-type climates.

How to cite: Foley, M., Blazewicz, S., McFarlane, K., Greenlon, A., Hayer, M., Kimbrel, J., Koch, B., Monsaint-Queeney, V., Morrisson, K., Morrissey, E., Pett-Ridge, J., and Hungate, B.: Historical precipitation regimes structure the growth of soil microorganisms in three California annual grasslands, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-13318, https://doi.org/10.5194/egusphere-egu22-13318, 2022.