SSS4.5

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.

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.

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.

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 (pH_H2O 7.5, Germany) and a Calcaric Solonchak (pH_H2O 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.

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.

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.

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.

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.

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.

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.