SSS4.1

Habitat structure is a key factor controlling the structure of ecological communities. For example, complex habitat structure may increase species number, minimise competition and facilitate the retention of nutrients. Alteration and disturbance of habitat structure may thus negatively affect biodiversity. Soil is an extremely complex and highly structured environmental matrix. Soil structure, defined as a distribution of aggregate/pore space of different sizes, can thus be a major control of soil biological communities, which are for example highly structured in their size distribution. Soil organisms, however, also affect and modify soil structure, and for many organisms the soil habitat structure is thus not just a condition to which they have to adapt but, rather, an environmental feature they also affect. In this talk, I discuss all these aspects from a community ecology point of view and with an emphasis on statistical and dynamical models that soil ecologists are trying to develop to describe and predict the mutual interactions between soil structure and biological communities. I will focus on the different rates at which soil structure affects soil organisms and vice versa, to emphasise that the temporal scales at which we have to measure the two parts of this mutual feedback (i.e. soil structure -> biota vs. biota -> soil structure) are very different, and also variable in space and time. 

How to cite: Caruso, T.: Modelling mutual interactions between soil structure and soil biological communities., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1177, https://doi.org/10.5194/egusphere-egu21-1177, 2021.

Accelerating climate change and biodiversity loss calls for agricultural practices that can sustain productivity with lower greenhouse gas emissions while maintaining biodiversity. Biodiversity-friendly agricultural practices have been shown to increase earthworm populations, but according to a recent meta-analyses, earthworms could increase soil CO₂ and N₂O emissions by 33 and 42%, respectively. However, to date, many studies reported idiosyncratic and inconsistent effects of earthworms on greenhouse gases, indicating that the underlying mechanisms are not fully understood. Here we report the effects of earthworms (anecic, endogeic and their combination) with or without plants on CO₂ and N₂O emissions in the presence of soil-moisture fluctuations from a mesocosms experiment. The experimental set-up was explicitly designed to account for the engineering effect of earthworms (i.e. burrowing) and investigate the consequences on soil macroporosity, soil water dynamic, and microbial activity. We found that plants reduced N₂O emissions by 19.80% and that relative to the no earthworm control, the cumulative N₂O emissions were 17.04, 34.59 and 44.81% lower in the anecic, both species and endogeic species, respectively. CO₂ emissions were not significantly affected by the plants or earthworms but depended on the interaction between earthworms and soil water content, an interaction that was also observed for the N₂O emissions. Soil porosity variables measured by X-ray tomography suggest that the earthworm effects on CO₂ and N₂O emissions were mediated by the burrowing patterns affecting the soil aeration and water status. N₂O emissions decreased with the volume occupied by macropores in the deeper soil layer, whereas CO₂ emissions decreased with the macropore volume in the top soil layer. This study suggests that experimental setups without plants and in containers where the earthworm soil engineering effects via burrowing and casting on soil water status are minimized may be responsible, at least in part, for the reported positive earthworm effects on greenhouse gases.

How to cite: Ganault, P., Nahmani, J., Capowiez, Y., Bertrand, I., Buatois, B., Shihan, A., Fromin, N., and Milcu, A.: No evidence that earthworms increase soil greenhouse gas emissions (CO2 and N2O) in the presence of plants and soil-moisture fluctuations, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8599, https://doi.org/10.5194/egusphere-egu21-8599, 2021.

An understanding of the drivers of hotspot/hot moments of N₂O production is required to better constrain the global N₂O budget and to plan the mitigation strategies. Hot spots are areas with very high N₂O emission rates relative to the surrounding area, while hot moments are short periods of time with very high emission rates. As the decomposition of fresh organic matter is transitory in nature, it may have a strong influence on hotspot and hot moment N₂O production. Roots are well known to be hotspots for microbial activity but roots direct contribution to N₂O production and emissions in soil remain poorly understood.

In this study, we evaluated the role of root decomposition on N₂O production and emissions, as a function of soil pore size and water content. We hypothesized that (i) the greatest N₂O emissions will be observed from root decomposition in the soil dominated by large (>30 µm Ø) pores due to their high connectivity and (ii) enhanced N₂O production by denitrification will be observed due to local anaerobic conditions, generated by O₂ consumption by decomposers.

To evaluate the role of root decomposition on N₂O production we used soil microcosms cultivated with switchgrass (Panicum virgatum L. variety Cave-in-rock). From the same composite soil samples we created two soil materials with contrasting pore architectures, namely soil with prevalence of large pores (≥ 35 μm Ø) and small pores (≤ 10 μm Ø). After four months of growing in a greenhouse, plants were cut and soil microcosms with roots were incubated in the dark at room T for 21 days, at two contrasting soil moisture conditions: 40% and 70% water filled pore space (WFPS). Gas headspace samples were collected at different time points during incubation for N₂O and CO₂ concentration analysis and isotopic characterization of N₂O (δ¹⁵N^bulk, site preference (S_P), and δ¹⁸O).

The daily emissions of N₂O and CO₂ from soil microcosms with grown roots showed the same trend during the incubation period and were significantly higher compared to soil microcosms without roots (control) (p < 0.05). Microcosm with large pores soil had significantly higher N₂O flux rates compared to the microcosms with small pore soil for both soil moisture treatments (p < 0.001). The relationship between S_P  and δ¹⁸O (isotope mapping) indicated that heterotrophic bacterial denitrification strongly dominated N₂O production between day 1 to 7 of the incubation (≥ 97%) and N₂O reduction was higher during this period (40 – 60%) in soil microcosms with both pore size and moisture treatment. Later on, N₂O reduction decreased (1 – 35%) while the share of nitrification/fungal sources increased for soil microcosms with large pores.

Our results indicated that decomposing roots acted as hotspots enhancing N₂O emissions and N₂O hotspots occurring during root decomposition are strongly influenced by soil pore architecture. While differences in soil pore architecture did not cause differences in N₂O production process at the initial phase of decomposition, it might influence the relative contribution of N₂O microbial production pathways in later stage of decomposition.

How to cite: Gil, J., Kim, K., Gandhi, H., Oerther, M., Ostrom, N., and Kravchenko, A.: The influence of root decomposition on N2O fluxes and N2O microbial production pathways in soil with contrasting pore characteristics, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13818, https://doi.org/10.5194/egusphere-egu21-13818, 2021.

Applying cover crop residues to increase soil organic matter (SOM) is a widely used strategy to sustainably intensify agricultural systems.  However, fresh residue inputs create “hot spots” of microbial activity during decomposition which could also “prime” the decomposition of native SOM, resulting in accelerated SOM depletion and greenhouse gas emissions. Microbes exert control over SOM decomposition and stabilisation as a consequence of their carbon use efficiency (CUE), the balance between microbial catabolism and anabolism. The CUE during residue decomposition and the extent to which native SOM decomposition is primed by residue addition may depend on residue biochemical quality.  Given that cover crops may be grown in monoculture, or in species mixes with the aim of providing multiple benefits to agricultural ecosystem services, it is important to understand whether applying cover crop residues as a mixture results in a different CUE and soil carbon stock, than would be expected by observations made on the application of individual residues. We used ¹³C labelled cover crop residues (buckwheat, clover, radish, and sunflower) to track the fate of cover crop residue-derived carbon and SOM derived carbon in treatments comprising a quaternary mixture of the residues and the average effect of the four individual residues (non-mixture) one day after residue incorporation in a laboratory microcosm experiment. The soil microbial community composition was measured by phospholipid-derived fatty acids (PLFA) fingerprint. Our results indicate that, despite all treatments receiving the same amount of plant-added carbon (1 mg C g^-1 soil), the total microbial biomass (¹²C + ¹³C) in the treatment receiving the residue mixture was significantly greater, by 3.69 µg C g^-1, than the average microbial biomass observed in the four treatments receiving individual components of the mixture. The microbial biomass in the quaternary mixture, compared to the average of the individual residue treatments, that can be attributed directly to the plant matter applied, was also significantly greater by 3.61 µg C g^-1. However, there was no evidence that the mixture resulted in any more priming of native SOM than average priming observed in the individual residue treatments. The soil microbial community structure measured by analysis of similarities (ANOSM) was significantly different in the soil receiving the residue mixture, compared to the average structure of the four communities in soils receiving individual residues. Differences in the biomass of fungi and Gram-positive bacteria were responsible for the observed synergistic effect of cover crop residue mixtures on total microbial biomass and plant-derived microbial biomass; especially biomarkers 16:0, 18:1ω9, 18:2ω6 and 18:3ω3. Our study demonstrates that applying a mixture of cover crop residues initially increases soil microbial biomass to a greater extent than would be expected from applying individual components of the mixture and that this increase may occur either due to faster decomposition of the cover crop residues or greater CUE, but not due to greater priming of native SOM decomposition. Therefore, applying cover crop residue mixtures could be an effective method to increase soil microbial biomass, and ultimately soil carbon stocks in arable soils.

How to cite: Shu, X., Zou, Y., Shaw, L., Todman, L., Tibbett, M., and Sizmur, T.: The mixture of cover crop residues induced a synergistic effect on microbial communities and an additive effect on soil organic matter priming, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2159, https://doi.org/10.5194/egusphere-egu21-2159, 2021.

Green manuring and crop rotation are important management practices with the potential to reduce the dependence on mineral fertilizers and to maintain soil health. Soil extracellular enzyme activities (EEAs) serve as a proxy for estimating the availability and cycling of soil nutrients and thus widely used as biological indicators of soil health. However, the effects of green manure application under different crop rotations on soil EEAs remain unclear. Here, a 5-year field experiment (2015-2020) was conducted and two crop rotations were established in the Loess Plateau of China. Specifically, forage rape (Brassica napus L.) (R) or common vetch (Vicia sativa L.) (V) was cultivated during the fallow period (F) of monoculture system, winter wheat (Triticum astivum L.) (W). Aboveground biomass of R and V were harvest in September 2020 and 50% of the biomass was chopped and returned to the soil surface. Soil EEAs activities [β-glucosidase (BG), cellobiohydrolase (CBH), β-xylosidase (Xylo) (XYL), and N-acetyl-glucosaminidase (NAG)] at 0-5 cm were determined in September and October. Observed EEAs activities were strongly affected by the pattern of crop rotation and sampling time, with greater EEAs activities in W-V-W-V than in W-R-W-R in September. Whereas, EEAs activities was higher in W-R-W-R than in W-V-W-V in October, expert for BG that had no difference between two crop rotations. Overall, our study demonstrated that green manuring shifted the effects of crop rotation on soil EEAs activities in the topsoil in the Loess Plateau of China.

Keywords: Annual forage, Residue retention, Soil health, The Loess Plateau

How to cite: Tao, H., Deng, J., and Li, Y.: Green manuring shifted the effects of crop rotation on soil EEAs activities in the Loess Plateau of China, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-10757, https://doi.org/10.5194/egusphere-egu21-10757, 2021.

Biological soil crusts (referred to as biocrusts hereafter) represent communities comprising a fraction of photoautotrophs (photoautotrophic bacteria, algae, lichens, and bryophytes) growing together with heterotrophic organisms like bacteria, archaea, and fungi. The organisms are all poikilohydric, which means they are only active if water is present. They occur frequently in dryland ecosystems, where vascular vegetation is sparse or even absent, or wherever dry microclimatic conditions occur. Biocrusts fulfill a wide range of important ecosystem services, as they are relevant in regional water cycling, soil stabilization, plant germination and growth, and also global carbon (C) and nitrogen (N) cycling. According to initial estimates, they are supposed to globally emit ~1.7 Tg of reactive nitrogen (N_r) per year, corresponding to ~20% of the global nitrogen oxide emissions from soils under natural vegetation. The underlying mechanisms of N_r emissions in biocrusts, however, are not well understood and are still a focus of ongoing research.

This study aimed to explore the functional roles of microbial organisms in N_r emissions along a full wetting and drying cycle. Therefore, N_r fluxes were analyzed at three key hydration stages, i.e., immediately after wetting (T1), prior to (T2), and after maximum N_r fluxes (T3). At all three stages, the transcriptome (microarray analysis) and proteome (metaproteomics) were profiled to highlight changes in biological processes linked to nitrogen transformation. Additionally, at T1 and T2, the bacterial, archaeal, and nitrite-oxidizing bacterial communities were quantified utilizing catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Soil nitrite and nitrate contents of both intact and sterilized biocrust samples were analyzed before and after a measurement cycle.

Our results showed a fast recovery of microbial activity minutes after wetting of the biocrusts (T1) by means of mRNA expression of nitrogen transformative genes. Transcripts of genes encoding all major N-cycling processes that are already known from soil were detected. The number of N-transforming species and processes detected by the microarray analysis significantly increased from T1 to T2 to T3. The most prominent nitrogen transforming microorganisms belonged to Alpha- and Gammaproteobacteria. The CARD-FISH data showed a significant increase in archaeal numbers from T1 to T2, which is in line with an observed increase in N_r emissions. The majority of identified proteins were related to ATP synthesis, photosynthesis, protein biosynthesis and stress response, whereas proteins assigned to N transformation could not be observed. Soil N-content analysis showed a significant increase of nitrite in living biocrusts after a wetting and drying cycle, which was likely promoted by nitrifying Archaea and Proteobacteria, but also by various denitrifying bacteria, as suggested by microarray analysis and CARD-FISH. This indicates that N_r fluxes largely originated from nitrite formed by various aerobic and anaerobic biotic processes, likely occurring simultaneously in different microhabitats within the biocrust.

How to cite: Weber, J., Maier, S., Kratz, A., Prass, M., Fobang, L., Clark, A. T., Abed, R. M. M., Thines, E., Pöhlker, C., Su, H., Cheng, Y., Eickhorst, T., Fiedler, S., Pöschl, U., and Weber, B.: Impact of water on microbial nitrogen transformation in soil causing atmospheric nitrous acid (HONO) and nitric oxide (NO) emissions, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13675, https://doi.org/10.5194/egusphere-egu21-13675, 2021.

Understanding of ongoing biogeochemical processes (natural attenuation) within contaminated soils is crucial for the development of plausible remediation strategies. We studied a tar oil contaminated soil with weak grass vegetation at a former manufactured gas plant site in Germany. Despite of the apparent toxicity (the soil contained up to 120 g kg^-1 petroleum hydrocarbons, 26 g kg^-1 toxic metals, and 100 mg kg^-1 polycyclic aromatic hydrocarbons), the contaminated layers have 3-5 times as much cell counts as an uncontaminated control soil nearby. To test, if the geometry of the pore space provides favourable living space for microorganisms, we applied scanning electron microscopy to the thin sections and calculated on sets of 15 images per layer three specific Minkowski functionals, connected to soil total porosity, interface, and hydraulic parameters.

Our investigation showed that the uncontaminated control soil has a relatively low porosity of 15-20 %, of which 50-70 % is comprised of small (< 15 µm) pores. These pores are poorly connected and show high distances between them (mean distance to the next pore 10 µm). The dominating habitats in the control soil are therefore created by small pores. They provide good protection from predators and desiccation, but input of dissolved organic C and removal of metabolic products are diffusion limited. Coarser pores (>15 µm) provide less space (< 50 % of total porosity) and solid surface area (< 20 %), are prone to desiccation and offer less protection from predators. However, they serve as preferential flow paths for the soil solution (input of nutrients) and are well aerated, therefore we expect the microbial activity in them to appear in “hot moments”, i.e. after rain events.

All layers of the contaminated profile have higher porosities (20-70 %) than the control. Coarse pores comprise 83-90 % of total pore area and create 34-52 % of total interface. Pores are also more connected and tortuous than in the control soil, which implies a better aeration and circulation of soil solution. The loops of pore channels may retain soil solution and be therefore preferably populated with microorganisms. The small (< 15 µm) pores comprise less than 17 % of total porosity but represent a substantial proportion of the interface (48-66 % vs 82-91 % in control). In the uppermost layer of the contaminated profile, such pores occur in plant residues, are close to the largest pores (mean distance to the next pore 4 µm) and therefore, along with good protection, are supplied with air, water, and non-tar C. In the middle of the profile, the small pores, presumably constantly filled with water, are located within dense tar pieces remote from the neighbouring pores (mean distance to the next pore 22 µm), and therefore, with hindered aeration and no supply of non-tar C, may create anaerobic domains of tar attenuation.

Our results show that the contaminated soil offers more favourable conditions for microorganisms than the control soil, probably because the hydrocarbons provide suitable energy and nutrition sources and a beneficial pore space geometry.

How to cite: Ivanov, P., Eusterhues, K., and Totsche, K. U.: Numerical analysis of soil microstructure reveals conditions for natural attenuation in aged tar oil contaminated soil, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4810, https://doi.org/10.5194/egusphere-egu21-4810, 2021.

The effect of habitat complexity on microbial processes

The way microbes behave in nature can vary widely depending on the spatial characteristics they are located in. This aspect of the microbial environment can determine whether processes such as organic matter degradation, nitrogen fixation, or microbial speciation, among others, occur and the extent to which they occur. Investigating how the different spatial characteristics of microhabitats influence microbes has been challenging mainly due to methodological limitations. In the case of soil sciences, attempts to describe the inner structure of the soil pore space, and to connect it to microbial processes, has been one of the main goals of the field in the last years. A major challenge in soil microbial ecology is to reveal the mechanisms that prevent nutrient limited soil microorganisms to access the soil organic matter pools. My project is directed towards answering the question of how spatial complexity affects microbial growth, and how this can lead to organic matter stabilization.

Using microfluidic devices that were designed to mimic the inner soil pore physical complexity, we followed the effect of an increasing complexity in the growth and substrate degradation of bacterial and fungal lab strains. The parameters we used to measure complexity were two: the turning angle and order of pore channels, and the fractal order of a pore maze. When we tested the effect of an increasing in turning angle sharpness on microbial growth, we found that that as angles became sharper, bacterial and fungal growth decreased, but fungi were more affected than bacteria. We also found that the substrate degradation was only affected when bacteria and fungi grew together, being lower as the angles were sharper. This confirms the hypothesis that an increasing angle sharpness in an elongated pore space would decrease organic matter degradation. Our next series of experiments, testing the effect of maze fractal complexity, however, showed a different picture. While the effect of complexity on fungi was negative, similar to the previous experiments, bacteria were positively affected by maze complexity, growing more as mazes increased fractal iterations. Substrate degradation was also higher as mazes were more complex. In this case, the results were contrary to our hypothesis, especially for bacteria. To see the relevance of our results in natural microbial communities, we repeated both experiments on a soil microbial extract (containing mainly bacteria) and followed the substrate degradation patterns over time. We found, in this case, that as complexity increased, both in terms of angle sharpness and fractal order, the substrate consumption also increased. Our results show that the spatial complexity provides microbes an environment for a wide variety of ecological interactions to occur that lead to a higher substrate degradation efficiency.

How to cite: Arellano-Caicedo, C., Ohlsson, P., and Hammer, E. C.: The effect of habitat complexity on microbial processes, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-12264, https://doi.org/10.5194/egusphere-egu21-12264, 2021.

Denitrification is an important microbial process and potential source for nitrous oxide (N₂O), an important greenhouse gas and destructor of stratospheric ozone. Quantitative predictions of denitrification in soils are difficult as denitrification, an anaerobic respiration process,  appears to occur even in well-areated soils. It is assumed that denitrification is active in dense aggregates over short time periods - so called hot spots and hot moments. While soil microbial metabolism occurs at the pore scale, the interest in denitrification is mostly at the field and landscape scale. Simulating both scales simultaneously is not feasible. Therefore, denitrification has to be upscaled from the pore to the aggregate scale without losing essential properties of the aggregates. An important key to effectively upscale is the anaerobic aggregate volume fraction.

In order to compare different upscaling techniques we conducted pure culture experiments with varying spatial structures. To avoid confounding effects associated with the transition of bacteria switching from oxic respiration to denitrification, we used bacteria only capable of the former. The investigated upscaling techniques include simplifying the microbial reaction as well as creating an effective one-dimensional diffusion model. We compare computation intensity and approximation quality of experimental results.

How to cite: Zawallich, J., Frohloff, D., Spanner, T., Horn, M. A., Dörsch, P., and Ippisch, O.: How to upscale reaction-diffusion models, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13208, https://doi.org/10.5194/egusphere-egu21-13208, 2021.

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly diverse as they are. Mathematically based modeling can facilitate the understanding of their development and function in soils, e.g. with respect to habitat and carbon cycling.

Our mechanistic model is based on [1,2] and allows studying the spatiotemporal dynamics of bacteria in unsaturated soil samples. In this presentation, different levels of saturation are investigated, for which the fluid (liquid and gas) distributions are calculated according to a morphological model. As in [3] various bacteria strains and organic matter are heterogeneously distributed in CT scans of various soil samples.

The bacteria strains grow based on Michaelis-Menten kinetics due to the uptake of oxygen and dissolved organic carbon (DOC) present in the liquid phase. The development of bacterial colonies is realized in a cellular automaton framework (CAM) as presented in [1,2]. DOC is either present as a carbonaceous solution or hydrolized by a first order kinetic from heterogeneously distributed particulate organic matter (POM) sources. The diffusion of both nutrients oxygen and DOC are described by means of reactive transport equations, which include a Henry conditions for the transfer from/into the gas phase. We apply the local discontinuous Galerkin (LDG) method as a discretization scheme.

Our simulations show that the impact heterogeneity in nutrient and bacteria distribution has on overall biodegradation kinetics strongly depends on the scale of interest. On the scale of soil microaggregates (<250 μm), only very specific cases can be distinguished globally, e.g. when nutrient sources are isolated from bacteria due to a disconnected liquid phase. Locally however, heterogeneities in nutrient distribution impact the development of bacteria populations, e.g. a lower geodesic distance of bacteria to nutrient promotes bacteria growth locally. Such local effects can have an important role for competing bacterial species.

On larger scales (millimeter scale), such heterogeneities can also have a large impact. We conclude that the heterogeneous spatial structure must be resolved scale-dependently.

[1] N. Ray, A. Rupp and A. Prechtel. Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media, Adv. Water Resour. 107, 393-404 (2017), doi:10.1016/j.advwatres.2017.04.001.

[2] A. Rupp, K. Totsche, A. Prechtel and N. Ray. Discrete-continuum multiphase model for structure formation in soils including electrostatic effects, Front. Environ. Sci. 6:96 (2018), doi:10.3389/fenvs.2018.00096.

[3] X. Portell, V. Pot, P. Garnier, W. Otten and P.C. Baveye. Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: insights from computer simulations., Front. Microbiol. 9:1583 (2018), doi:10.3389/fmicb.2018.01583.

How to cite: Zech, S., Ray, N., Ritschel, T., Totsche, K. U., and Prechtel, A.: Modeling the effect of microscale heterogeneities on soil bacterial dynamics and the impact on soil functions, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1265, https://doi.org/10.5194/egusphere-egu21-1265, 2021.

Soil ecosystems are composed of microhabitats that often differ in composition and ecological strategies at the microscale. Besides, the assumption that soil organism behaviour at the ecosystem level is similar to that at microscale may drive unexpected findings. Soil pH at microsites either can differ significantly from whole soil pH. Moreover, the large porosity measured in the whole soil can contrast with water, nutrient, air and waste flow limitations and dramatic constraints to microbial mobility and access to food, when analysed at the microscale, consequent to local pore geometry, connectivity and tortuosity. Incidentally, soil microorganisms, which are present in billions of individuals per gram of soil, have micrometre sizes and prevalently interact with the other soil components at the nano-to-microscale. They colonise soil microhabitat based on the local concentration and composition of air, nutrients and materials. Finally, different organic materials and minerals in the soil induce distinct interactions at microsites, generating diverse organo-mineral associations and different microbial populations. 

The study of soil microhabitats can enable comprehending how the microsites' dynamics can drive to ecosystems' macroscale behaviours. However, the study of soil microhabitats in real conditions, even when investigated in soil mesocosms and microcosms, can be challenging or require complicated and expensive instrumentations to achieve such outcomes. 

The rebuilding of soil microhabitats in model systems can help study the microhabitats' mutual interactions at the microscale. However, it is impossible to reproduce any possible combination of soil components to replicate the multitude of microhabitats existing in natural soil ecosystems. Then, approximations are necessary. 

The present study proposes to recreate an artificial model 3D soil-like microhabitat resulting from the aggregation of the major classes of soil components (mineral particles, organic polymeric components, and microorganisms) in nano- to macro-architectures to study organo-mineral-microbe interactions at the microscale, and enable reproducible works. Electrospinning/electrospraying technologies were chosen for their extreme versatility in creating self-standing 3D complex, porous and functional structures and their proven capacity to permit microbes to grow on the resulting composite fibrous frameworks.

Bacteria strains of Pseudomonas fluorescens and Burkholderia terricola, typical microbial species populating the rhizosphere soils, will be utilised as microhabitat microbial components for generating a simplified microbiome in the 3D soil-like nanostructures. At first instance, we intended to use microscopy (e.g. SEM, TEM, confocal) as the tool of choice to investigate over time the spatial distribution of bacterial populations throughout the artificial nanostructured soil microhabitat here reproduced, the release of EPS by the bacterial populations and possible interactions. The proposed 3D soil-like nanostructures are supposed to provide the possibility of investigating the microbial lifestyle in microhabitats at different scales, from nm to mm, then linking microbial phenotypic traits to specific soil features.

How to cite: De Cesare, F., Di Mattia, E., and Macagnano, A.: The driving role of microhabitats in soil ecology: rebuilding artificial 3D soil-like nanostructured microhabitats for experimental reproducible works, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-12421, https://doi.org/10.5194/egusphere-egu21-12421, 2021.

The lichen microbiome includes a diverse community of organisms, spanning widely across the bacterial tree of life. Lichens have been proposed to form partially open symbiotic systems, in which some microorganisms may be transmitted along within lichen propagules, while others are acquired from the surrounding environmental community.

In this survey, we discuss the extent to which the lichen microbiome is connected to that of its immediate substrate. For this we sampled ten specimens of the Patagonian foliose cyanolichen Peltigera frigida and their underlying soil substrates in two forest sites of the Coyhaique National Reserve (Aysén Region, Chile). Using 16S metabarcoding with primers that exclude cyanobacteria, we identified a significant taxonomic divergence between the bacterial communities of lichens and substrates.

At the Phylum level, Proteobacteria (37% of relative abundance) are most abundant within lichens, while soil substrates are dominated by Acidobacteriota (39%). At the Genus level, some bacteria are significantly more abundant in lichens, such as Sphingomonas (8% in lichens vs 0.2% in substrates) or an unassigned genus of Chitinophagaceae (10% vs 2%). Conversely, genera like the unassigned acidobacterial genus SCN-69-37 (0.9% vs 12%) are more abundant in substrates.

Overall, our results are consistent with the idea that lichens shape their microbiome obtaining components from various sources, including reproductive propagules and the substrate on which they grow. Further experimental and ecological approaches are needed to assess the contribution of these microorganisms to the fitness of the symbiotic system.

Funding: FONDECYT 1181510.

How to cite: Leiva, D., Fernández-Mendoza, F., Acevedo, J., Carú, M., Grube, M., and Orlando, J.: Comparative analysis of the bacterial community of the Patagonian lichen Peltigera frigida and its soil substrate, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7277, https://doi.org/10.5194/egusphere-egu21-7277, 2021.

A 3-m thick sediment was found in a limestone mine located in the southern part of the Gargano Promontory, Apulia region (south of Italy), at a depth of ca. 25-30 m from the current ground level.

Samples from 5 layers were analysed by X-ray diffraction (XRD), elementar analysis (CHNS), and Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Microbial DNA was also extracted and bacterial diversity analysed by PCR amplification and Illumina High-Throughput Sequencing (HTS) of the V3-V4 hypervariable regions of 16S rRNA.

Preliminary data showed that these sediments formed by subsequent weathering of carbonates and silicates, either by in situ oxidation or by dissolution followed by migration and reprecipitation, rather than during the accumulation of shallow marine sediments occurring between the middle Pliocene and the lower Pleistocene, when the extreme western sectors of the Apulian foreland underwent strong subsidence.

The main mineral compounds occurring in the 5 layers, from the top to the bottom, were the following: calcite (80%) and clay minerals in sample #1, goethite (75%) and hematite in sample #2, manganese (66%) and iron oxides in sample #3, almost exclusively goethite in sample #4, and calcite (71%) and clay minerals in sample #5.

From the microbiological point of view, drawn from a 16S metabarcoding amplicons sequencing analysis, these 5 layers appear to cluster in three groups: a) the uppermost layer (sample #1), dominated by a single and abundant taxon of Arthrobacter sp., which includes species known for  the capability of calcite precipitation; b) a middle layer (including samples #2 and #3), without prevailing abundances and less consistent occurrences across replicates, which featured members of the Oxalobacteraceae family and of the Methylophilus genus. Their closest matches in Genbank subjects included isolates from habitats such as calcium carbonate (moonmilk) muds in percolating waters within caves, mine tailings and other groundwater microcosms; c) a bottom layer (samples #4 and #5), showing an oligarchic situation and high abundances of bacteria but different from the ones that prevailed in the top layer and including members of the Nocardioidacaeae family. Also for these sequence queries, the closest GenBank subjects include cases with calcium carbonate-precipitating capabilities isolated from cave and groundwater sediments or former mining sites in studies on iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations.

Overall, such a distribution suggests that, both in the top and bottom layer, different communities would have undergone in situ-reproduction and colonization exploiting metabolically the substrate, whereas the mid layers would have received bacterial convection by passive transport of percolating waters.

How to cite: Zaccone, C., Puglisi, E., Terribile, F., and Squartini, A.: Bacterial in situ-reproduction and colonization of sediments occurring in a limestone mine, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14414, https://doi.org/10.5194/egusphere-egu21-14414, 2021.