Life in soil: spatial and temporal heterogeneity and consequences for soil functioning



Soil is a highly heterogeneous environment, both regarding space and time. From the spatial point of view, soil comprises a myriad of microhabitats that host an unparalleled biodiversity, from micro- to macrobiota. Several physical and chemical parameters define the soil microhabitat: the geometry of the pore space, its connectivity, the water micro-distribution and the nature, distribution and association of organic compounds within the soil mineral matrix (organo-mineral associations, soil aggregates). Variations in these parameters result in micro-gradients of oxygen, moisture, nutrients and organic compounds, acting as ecological filters for soil biota, usually promoting the co-existence of contrasting ecological strategies, with consequences for soil functioning. From a dynamic point of view, micro-scale heterogeneity is related to patterns of activity in soil, notably at the microbial level. Areas with high activity and fast process rates are defined as microbial hotspots (e.g rhizosphere, detritusphere, biopores, hyphasphere, aggregate surfaces, etc.). These hotspots show accelerated turnover of soil organic matter and other microbial functions (e.g. nutrient mobilization, litter decomposition, respiration, organic matter stabilization, greenhouse gas emission, acidification, etc.). The intensity of microbial and SOM turnover as well as nutrient cycling in such hotspots is at least one order of magnitude higher than in the bulk soil, and this can further affect the activity of other soil biota. In addition, microhabitats and soil hotspots are highly variable in time, being constantly re-modelled by numerous factors such as the alternation of wet and dry cycles, the activity of soil biota, especially plant roots and ecosystem engineers, and the input of fresh organic matter.
In this session we gather contributions on: (i) deciphering the main drivers of the formation and spatiotemporal variability of soil microhabitats (ii) quantifying the role of the soil microhabitat in determining soil ecology, and (iii) studies assessing the variability in soil activity within the soil matrix, notably at soil microbial hotspots. In particular, we tackle various aspects of microbial activity, interactions, community composition and distribution in hotspots, and factors influencing (micro)biological nutrient (re)cycling, including biotic and abiotic controls. The session presents a combination of field, experimental and modeling approaches.

Convener: Amandine ErktanECSECS | Co-conveners: Bettina Weber, Bahar Razavi, Claire Chenu, Naoise Nunan
vPICO presentations
| Thu, 29 Apr, 09:00–11:45 (CEST)

vPICO presentations: Thu, 29 Apr

Chairpersons: Bahar Razavi, Claire Chenu, Amandine Erktan
Tancredi Caruso

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,, 2021.

Pierre Ganault, Johanne Nahmani, Yvan Capowiez, Isabelle Bertrand, Bruno Buatois, Ammar Shihan, Nathalie Fromin, and Alexandru Milcu

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,, 2021.

Henny Omosigho, Liz Shaw, Tom Sizmur, David Spurgeon, and Claus Svendsen

Earthworms are dominant members of soil invertebrate communities that play a key role in soil ecosystems' functioning directly through impacts on soil structure and through the stimulation of soil microbial decompositional activities in bipores and as a result of soil ingestion and gut passage. The earthworm gut microbiome, mainly derived from ingested soil, is hypothesised to influence host physiology, for example, by enhancing nutrition through provision of assimilable nutrients via depolymerisation, or alleviation of chemical stress by detoxification. However, few studies have examined the nature of the relationship between earthworm health and function and their soil-derived gut microbiome's diversity and composition.

 We first used a novel antibiotic-based procedure to suppress Lumbricus terrestris earthworms' gut microbiome. We then investigated the influence of earthworm microbiome (antibiotic-treated or untreated) and soil microbiome (autoclaved or unautoclaved), and their interaction on L. terrestris feeding on, and preference for, three plant species litters (Lolium multiflorum, Quercus robur and Fraxinus excelsior). Finally, in a soil microbial diversity manipulation experiment, we examined if more subtle perturbations to microbial community richness and structure influenced earthworm health and function by determining the fate of crop residue C added to the soil.  

 The use of antibiotics significantly reduced the abundance of L. terrestris-associated culturable microorganisms (P < 0.05), but 16S rRNA gene amplicon analysis showed no effect on earthworm microbiome alpha diversity and only subtle effects on beta diversity despite the pronounced knockdown of bacterial colony-forming units. Across all earthworm microbiome x soil microbiome treatments, L. terrestris showed a greater preference for F. excelsior litter (P < 0.05) when compared to L. multiflorum and Q. robur litter: a preference which may relate to differences in litter quality parameters (C: N and polyphenol content). However, disruption of either the soil microbiome, earthworm microbiome or soil and earthworm microbiome all resulted in significantly (P < 0.05) reduced overall consumption of litter and a shift in litter preference to consume less Q. robur litter.

 The outcome of the diversity manipulation experiment suggested that only the soil treatment with the most eroded microbial diversity (by one order of magnitude compared to the intact soil) impacted earthworm energy reserves ( protein, carbohydrate and lipid), which were lowered by 0.307 %, 0.22% and 0.265% respectively.

Examining the effect of the presence of earthworm and soil microbial diversity revealed an influence on the rate of soil respiration. The diversity*earthworm interaction also revealed an influence on soil respiration rate. Our results highlight the importance of the soil microbiome for earthworm function; particularly organic matter decomposition. Further experiments examine whether residue C's fate is altered by earthworm presence and/or the soil microbial community's diversity.

This presentation will highlight the evidence underpinning the detailed effects of earthworm microbiome and soil microbial diversity on earthworm physiology and function.  

Keywords: earthworm, microbiome, Fraxinus excelsior, Lumbricus terrestris, preference,16S rRNA, health and function, litter decomposition, diversity.

How to cite: Omosigho, H., Shaw, L., Sizmur, T., Spurgeon, D., and Svendsen, C.: The role of soil bacterial community diversity and composition in earthworm health and function, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-12981,, 2021.

Peter Lehmann, Pascal Benard, Anders Kaestner, and Andrea Carminati

Water flow dynamics and hydraulic properties of the rhizosphere are influenced by the exudation of mucilage and microbial extracellular polymeric substances (EPS). Upon drying, mucilage becomes hydrophobic and it impacts the rewetting kinetics of the rhizosphere. The effect of deposited mucilage on rewetting depends on the spatial distribution of the hydrophobic structures, which is a result of the drying rate, soil texture and mucilage concentration. To predict the role of deposited mucilage on rewetting, we simulate the deposition and rewetting process using a morphological pore network model that takes into account the spatial distribution of pores sizes and hydrophobic and hydrophilic structures. We show that the simulated water distribution is controlled by the amount, size and connectivity of the deposited material. The simulated water distribution is compared to neutron imaging experiments conducted in soils with different mucilage content. Comparison of simulations and measurements reveals the governing mechanisms of mucilage deposition and its impact on the environmental conditions in the rhizosphere.

How to cite: Lehmann, P., Benard, P., Kaestner, A., and Carminati, A.: Simulating the effect of mucilage deposition on rhizosphere rewetting using a morphological pore network model, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8767,, 2021.

Kazumichi Fujii, Chie Hayakawa, and Tininsih Sukar

Tropical forests can develop by roots foraging nutrients in the highly weathered soils. In rhizosphere, soil volume affected by roots, tree species modify carbon (C) and nutrient cycles directly through root exudation and indirectly through increased microbial activity. We test whether root exudation and rhizosphere C fluxes of organic acids and sugars differ between dominant dipterocarp trees and pioneer trees (Macaranga gigantea). To quantify the C fluxes of organic acids in the rhizosphere soils, we measured in situ root exudation from mature trees, concentrations of monosaccharides and organic acids (acetate, oxalate, malate, and citrate) in the rhizosphere and bulk soil fractions, and mineralization kinetics of 14C-radiolabelled substrates. Organic acid exudation increases with increasing root surface area. Dipterocarp roots release greater amounts of malate, while monosaccharides are dominant exudates of pioneer trees. Microbial activities of malate mineralization increase in the rhizosphere soil both under dipterocarp and pioneer trees. The greater C fluxes of malate mineralization, compared to root exudation, suggests rhizosphere microbes are another malate producer under dipterocarp trees. Both root exudation composition and rhizosphere microbes increase malate production with increasing phosphorus demands and with increasing soil acidity.

How to cite: Fujii, K., Hayakawa, C., and Sukar, T.: Effects of tree species on root exudation and mineralization of organic acids in a tropical forest, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2131,, 2021.

Kyungmin Kim, Jenie Gil, Nathaniel Ostrom, Hasand Gandhi, Maxwell Oerther, Yakov Kuzyakov, Andrey Guber, and Alexandra Kravchenko

High temporal and spatial variability of nitrous oxide (N2O) emission from soils has been a challenge for the systematic prediction of global climate change. It is attributed to multiple hotspots occurring simultaneously and affecting the N dynamics cumulatively on an ecosystem scale. Understanding the mechanisms and contributing factors of N2O emission in single hotspots is a prerequisite to overcoming this problem.

We investigated the decomposing switchgrass roots as N2O hotspots, using isotope dual-labeling (15N and 13C) and zymography. Our main objectives were i) to quantify the contribution of decomposing roots to N2O emission along with the N contents in the soil (total, organic, and inorganic N) and microbial pools, and ii) to differentiate the extracellular enzyme activity in decomposing roots from the bulk soil, and test if the ‘spatially differentiated’ hotspot enzyme activity indeed related to ‘isotopically differentiated’ hotspot N2O emissions. We treated the soils of the same origin to have different moisture contents (40% and 70% water-filled pore space, WFPS) and pore size distributions (dominant pores of >30 Ø and < 10 mm Ø, referred to as coarse and fine soil), to evaluate how these variables change the contribution of decomposing roots to the N2O production.

Our results showed that up to 0.4 % of the root driven N can be emitted as N2O gas, only within 21 days of the decomposition. Approximately 21 ~35% of root N was transformed to dissolved organic N, while less than 1 % of the root N remained as ammonium (NH4+) and nitrate (NO3-) during the incubation. Decreasing NH4+ and increasing NO3- suggested nitrification. Surprisingly, both inorganic and organic N content was greater in coarse soil, which likely led to intense hotspots of enzyme activity and N2O emission. However, there was no difference in microbial biomass between the soil materials. Higher chitinase activity and relatively large pores in coarse soils suggest that the fungal activity was higher in coarse soils compared to the fine soils. Root chitinase activity was positively correlated with the root driven N2O emission rate (p< 0.01, R2=0.22), supporting that the microbial hotspot formed near the root is the hotspots of N2O emission.

Our study showed that the intensity of root driven N2O hotspots can highly depend on the soil physical characteristics, being mediated by decomposed substances, and enzyme activity. Tracking the fate of N during the plant root decomposition can provide a new perspective on the strategies to minimize N2O emissions in bioenergy systems.

How to cite: Kim, K., Gil, J., Ostrom, N., Gandhi, H., Oerther, M., Kuzyakov, Y., Guber, A., and Kravchenko, A.: Decomposing in-situ grown switchgrass roots as hotspots of microbial activity and N2O emission: the combination of dual-isotope labeling and zymography, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13272,, 2021.

Jenie Gil, Kyungmin Kim, Hasand Gandhi, Maxwell Oerther, Nathaniel Ostrom, and Alexandra Kravchenko

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 (δ15Nbulk, site preference (SP), 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 SP  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,, 2021.

Apsara Amarasinghe, Oliver G G Knox, Christine Fyfe, Lisa A Lobry de Bruyn, and Brian R Wilson

Native trees and shrubs planted in large contiguous blocks (environmental plantings) have been established on agricultural lands in Australia to reinstate ecosystem functions and protect the biodiversity that has been degraded by agricultural activities. Limited work exists on the extent of the ecosystem recovery, but the assessment of microbial attributes (i.e. microbial activity and functional diversity) in these plantings may provide an indication of status. This study investigated how environmental plantings, and time since their establishment, affects aforementioned soil microbial attributes,  to determine if the recovery to conditions found under extant remnant woodland were achievable. We compared changes in microbial functional diversity and activity along with total organic carbon (TOC), total nitrogen (TN), extractable phosphorous (P), soil pH, and electrical conductivity (EC) between environmental plantings established for 16 and 26 years, a paired adjacent pasture, and nearby remnant native woodland at Gunnedah, New South Wales. The results indicated that microbial activity under the trees, compared to that of pasture, increased by 20%–93% with increasing tree age. The ordination distance of microbial functional diversity declined between environmental plantings and remnant woodland as the age of the environmental planting increased, which was indicative of microbial functions becoming similar to that in the remnant vegetation with time. Soil P levels under trees were significantly higher compared to pasture and also increased with increasing planting age. However, TOC and TN levels under environmental plantings remained similar to pasture. These results suggest that microbial attributes and soil nutrient status of the investigated environmental plantings were on a trajectory of change from that of the pasture systems toward that of the remnant vegetation, but that full ecosystem recovery had not yet been achieved, even after 26 years.

Keywords: Environmental plantings, Microbial activity, Microbial functional diversity, Soil organic carbon, Soil nutrients

How to cite: Amarasinghe, A., Knox, O. G. G., Fyfe, C., Lobry de Bruyn, L. A., and Wilson, B. R.: Environmental plantings’ influence on microbial attributes and soil properties in Australia., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1014,, 2021.

Xin Shu, Yiran Zou, Liz Shaw, Lindsay Todman, Mark Tibbett, and Tom Sizmur

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,, 2021.

Xiu Dong and Yan Zhang

On the way towards conservation tillage on the activities of soil enzymes related to carbon cycle in a multi-sequence maize-wheat-soybean rotation system

Authors: Xiu Dong1,2, Yan Zhang1,2, Yuying Shen1,2*


1State key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou 730020, PR China

2College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, PR China


Designing and developing sustainable cropping systems and reasonable cultivation measures have become the major focuses in the semiarid Loess Plateau region of China. However, long-term conservation tillage practices on the activities of soil enzymes related to carbon cycle in maize-wheat-soybean rotation system are still unclear. This study aimed to investigate the effects of 19 years of conservation tillage practices on the cellobiohydrolase (CBH), β-1,4-glucosidase (BG) and β-1,4-xylosidase (BXYL) activities in the 0-20 cm soil depth under a two-year cycle spring maize (Zea mays L.)-winter wheat (Triticum aestivum L.) -summer soybean (Glycine max L.) rotation cropping system. Treatments included conventional tillage (T), conventional tillage followed by straw mulching (TS), no tillage (NT), and no tillage followed by straw mulching (NTS). We found that conservation tillage practices could increase soil enzyme activities significantly, the highest soil CBH and BG activities were in NTS (1.25 and 5.72 nmol·g-1·h-1), the highest soil BX activities were in TS (2.13 nmol·g-1·h-1). Compared to T, no tillage had no effect on soil enzymes activities. The effects of conservation tillage practices on soil enzyme activities varied with soil depth, higher soil enzyme activities were showed in the 0-5 cm than in 5-20 cm soil depths. In addition, our results indicated that the key factors driving the changes in soil enzyme activities were soil microbial biomass carbon and organic carbon. This finding highlighted the importance of conversation tillage practices on maintaining the soil carbon pool in rotation ecosystem.

How to cite: Dong, X. and Zhang, Y.: On the way towards conservation tillage on the activities of soil enzymes related to carbon cycle in a multi-sequence maize-wheat-soybean rotation system, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-10622,, 2021.

Haining Tao, Jianqiang Deng, and Yuan Li

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,, 2021.

Archana Juyal, Andrey Guber, and Alexandra Kravchenko

Extracellular enzymes play an important role in soil biochemical processes as they are the key regulators of litter and soil organic matter degradation. However, understanding of the factors influencing their activity and fate in soil is still limited. In this study, we examined the relationship between soil pores and spatial patterns of extracellular enzyme activity in soils from two bioenergy cropping systems: monoculture switchgrass (Panicum virgatum L.) and restored prairie. Intact soil cores (5 cm Ø x 5 cm height) were collected at two contrasting topographical positions (depression and slope) within large topographically diverse fields where the switchgrass and prairie were grown since 2008. The cores were subjected to X-ray computed tomography scanning at 18 µm resolution. After the scanning, a switchgrass seedling was planted in these cores and allowed to grow for three months. Then the plants were terminated and the cores were rescanned. Pore characteristics were assessed using the image information, and b-glucosidase activity was characterized via 2D zymography. Preliminary results showed that soil of the prairie system had greater volumes of 60-180 mm Ø size pores compared to monoculture switchgrass system. However, enzyme activity was higher in the soil of monoculture switchgrass. Our preliminary results indicate that the soil pore size distribution and enzyme activity differ depending on the type of the bioenergy cropping system. Further analysis is conducted to determine microbial abundance, total C in soil and microbial biomass in these cropping systems to understand the effect of pores on microbial activity associated with C processes in soil.

How to cite: Juyal, A., Guber, A., and Kravchenko, A.: Soil pore effects on spatial patterns of extracellular enzymes: combined X-ray computed tomography and 2D zymography, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13205,, 2021.

Chang Tian, Jiao Xi, Mengchen Ju, Yahong Li, Qi Guo, Le Yao, Chun Wang, Yanbin Lin, Qiang Li, Wendy J. Williams, and Chongfeng Bu

Biocrusts (Biological soil crusts) are a living ground cover widely distributed in arid and semi-arid regions worldwide and provide important ecological functions in ecosystems. As an important part of biocrusts, the microorganisms in the formation and succession of biocrusts should not be underestimated. However, the microbial processes among different types of biocrusts are poorly understood. We used high-throughput sequencing to identify soil bacteria and fungal community in two types of biocrusts, lichen crust and moss crust, in the Mu Us Sandland. The aims were to explore the composition, diversity, and ecological function of the microbial community in two types of biocrusts. Our study found that (1) The diversity of bacterial and fungal communities was significantly different between the two types of biocrusts. The Shannon index (6.18) of fungi in moss crust was higher than that (5.75) in lichen crust, and the operational taxonomic units of bacteria and fungi in moss crust were also higher than those in lichen crust by 3.22% and 30.61%, respectively. The bacteria and fungi community structure in two types of biocrusts were significantly different, while the differences were not significant. (2) In the microbiomes of lichen and moss biocrusts, Actinomycetes, Cyanobacteria, and Proteobacteria, the sum of which accounted for 68.01% in lichen crust and 59.88% in moss crust at operational taxonomic units level, were dominant phylum of bacteria, while the dominant phylum of fungi was mainly Ascomycota. Microcoleus (11.10%) and Exophiala (7.37%) were dominant genera in lichen crust, while the dominant genus in moss crust was RB41 (5.16%). (3) The pH, soil dissolved organic carbon, and soil organic carbon were the top three factors that correlated with both bacterial and fungal community structures. (4) The metabolic function of the bacterial community in two types of biocrusts was quite different. The relative abundances of metabolic pathways in moss crust, such as chemoheterotrophy, ureolysis, aromatic compound degradation, and nitrate reduction, were significantly higher than those in lichen crust, however, the relative abundances of cyanobacteria, oxygenic photoautotrophy, photoautotrophy, and phototrophy were significantly lower (ANOVA, P<0.05). Altogether, our study suggests that the biocrust types have significant effects on the pH, taxonomic, and metabolic diversity, providing a theoretical basis for improving the physicochemical properties of the surface soil in the desertification land ecosystem.

How to cite: Tian, C., Xi, J., Ju, M., Li, Y., Guo, Q., Yao, L., Wang, C., Lin, Y., Li, Q., Williams, W. J., and Bu, C.: Microbial community structure and function prediction of two typical biocrusts in the Mu Us Sandland, Northwest China, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1638,, 2021.

Jens Weber, Stefanie Maier, Alexandra Kratz, Maria Prass, Liu Fobang, Adam T. Clark, Raeid M. M. Abed, Eckhard Thines, Christopher Pöhlker, Hang Su, Yafang Cheng, Thilo Eickhorst, Sabine Fiedler, Ulrich Pöschl, and Bettina Weber

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 (Nr) per year, corresponding to ~20% of the global nitrogen oxide emissions from soils under natural vegetation. The underlying mechanisms of Nr 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 Nr emissions along a full wetting and drying cycle. Therefore, Nr fluxes were analyzed at three key hydration stages, i.e., immediately after wetting (T1), prior to (T2), and after maximum Nr 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 Nr 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 Nr 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,, 2021.

Pavel Ivanov, Karin Eusterhues, and Kai Uwe Totsche

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,, 2021.

Chairpersons: Bettina Weber, Naoise Nunan, Amandine Erktan
Carlos Arellano-Caicedo, Pelle Ohlsson, and Edith C. Hammer

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,, 2021.

Jan Zawallich, Daria Frohloff, Tobias Spanner, Marcus A. Horn, Peter Dörsch, and Olaf Ippisch

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,, 2021.

Simon Zech, Nadja Ray, Thomas Ritschel, Kai Uwe Totsche, and Alexander Prechtel

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,, 2021.

Hanbang Zou, Pelle Ohlsson, and Edith Hammer

Carbon sequestration has been a popular research topic in recent years as the rapid elevation of carbon emission has significantly impacted our climate. Apart from carbon capture and storage in e.g. oil reservoirs, soil carbon sequestration offers a long term and safe solution for the environment and human beings. The net soil carbon budget is determined by the balance between terrestrial ecosystem sink and sources of respiration to atmospheric carbon dioxide. Carbon can be long term stored as organic matters in the soil whereas it can be released from the decomposition of organic matter. The complex pore networks in the soil are believed to be able to "protect" microbial-derived organic matter from decomposition. Therefore, it is important to understand how soil structure impacts organic matter cycling at the pore scale. However, there are limited experimental studies on understanding the mechanism of physical stabilization of organic matter. Hence, my project plan is to create a heterogeneous microfluidic porous microenvironment to mimic the complex soil pore network which allows us to investigate the ability of organisms to access spaces starting from an initial ecophysiological precondition to changes of spatial accessibility mediated by interactions with the microbial community.

Microfluidics is a powerful tool that enables studies of fundamental physics, rapid measurements and real-time visualisation in a complex spatial microstructure that can be designed and controlled. Many complex processes can now be visualized enabled by the development of microfluidics and photolithography, such as microbial dynamics in pore-scale soil systems and pore network modification mimicking different soil environments – earlier considered impossible to achieve experimentally. The microfluidic channel used in this project contains a random distribution of cylindrical pillars of different sizes so as to mimic the variations found in real soil. The randomness in the design creates various spatial availability for microbes (preferential flow paths with dead-end or continuous flow) as an invasion of liquids proceeds into the pore with the lowest capillary entry pressure. In order to study the impact of different porosity in isolation of varying heterogeneity of the porous medium, different pore size chips that use the same randomly generated pore network is created. Those chips have the same location of the pillars, but the relative size of each pillar is scaled. The experiments will be carried out using sterile cultures of fluorescent bacteria, fungi and protists, synthetic communities of combinations of these, or a whole soil community inoculum. We will quantify the consumption of organic matter from the different areas via fluorescent substrates, and the bio-/necromass produced. We hypothesise that lower porosity will reduce the net decomposition of organic matter as the narrower pore throat limits the access, and that net decomposition rate at the main preferential path will be higher than inside branches

How to cite: Zou, H., Ohlsson, P., and Hammer, E.: The impact of porosity on organic matter cycling in a two-dimensional porous medium, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9432,, 2021.

Fabrizio De Cesare, Elena Di Mattia, and Antonella Macagnano

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,, 2021.

Daquan Sun, Gerrit Angst, and Jan Frouz

The stability of soil organic carbon is empirically believed to relate to the location of soil microorganisms inside or between aggregates. However, there are knowledge gaps about how micro-niches shape the microbial community composition and activity and how these effects vary between various soils. Here, we investigate fungal and bacterial community structures (composition and biomass), networks, and respiration in individual micro-niches between and inside soil aggregates using seven different chronosequences (both primary and secondary successions covering sites from pioneer stages to well-developed ecosystems) from a maritime climate in Belgium to a more continental climate in Hungary. We show that while the sampling site is the most crucial factor in shaping microbial community structures, soil aggregates are often more important than succession age and vegetation in differentiating major microbial taxa. Soil fractions are also the dominant factor affecting microbial biomass along the individual chronosequences. Specifically, macro-aggregates often have more variable α-diversities and high microbial community stability, accompanied by low microbial respiration rates. Although the other isolated soil fractions have similar microbial diversities as macro-aggregates, they feature unstable microbial communities with a higher respiration rate. The isolated primary particles have more stable bacterial communities in secondary than primary successions. We, thus, provide a mechanism for interpreting the links between soil microsite heterogeneity, microbial community stability, and microbial respiration. 

How to cite: Sun, D., Angst, G., and Frouz, J.: Microbial communities in soil macro-aggregates respire less, are more diverse and stable across successional and geographical gradients, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-16011,, 2021.

Grigory Gladkov, Anastasiia Kimeklis, Rustam Tembotov, Arina Kichko, Evgeny Andronov, and Evgeny Abakumov

The soil microbiome is critical to the restoration of soils , destroyed by human activity. The dynamics of changes in the soil microbiome was investigated from the two overgrown gravel-sand quarry dumps in the North Caucasus (Kabardino-Balkaria, Russia). Samples were taken in the quarries of contrasting soil types (Calcareous Chernozem and Umbric Gleyic soils) under the various types of reclamation. Samples were taken from 10 points from a quarry with meadow soil and from 11 points from the Chernozem. The 16S ssu gene libraries were sequenced from soil DNA.The difference in microbiomes between the control points and the points where the soil is restored was statistically significant. The disturbed Gleyic soil is characterized by an increase in the representatives of Acidobacteria, for Chernozem of the genera Niastella, Ramlibacter, Microvirga. On the Umbric  Gleyic soil without reclamation, significant heterogeneity was shown, in contrast to Chernozem with different types of reclamation. In different soil types, the response of the soil microbiome to soil restoration was significantly different, which in turn should influence the choice of the strategy for the restoration of anthropogenically diturbed soils.

How to cite: Gladkov, G., Kimeklis, A., Tembotov, R., Kichko, A., Andronov, E., and Abakumov, E.: Soil microbiome from postmining ecosystems from Kabardino-Balkaria, Russia, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2100,, 2021.

Anastasiia Kimeklis, Grigory Gladkov, Aleksei Zverev, Arina Kichko, Evgeny Andronov, Elena Ergina, Igor Kostenko, and Evgeny Abakumov

Pedogenesis depends on multiple factors, such as climate, vegetation, topography, parent material. Some of these factors are zonal, meaning they are determined by climate zone. But some factors are intrazonal, meaning that it has the same impact on soil formation in different climate zones. One example is parent material. The other peculiar feature of a parent material is that it determines the rates of pedogenesis. In this regard, Rendzic Leptosols – are intrazonal slowly developing soils formed on a limestone bedrock. In this study we approached the dynamics of microbiome formation in a chronosequence of these soils collected in Crimean Peninsula using analysis of 16S rRNA gene libraries and quantitative PCR. The chronosequence included benchmark soil, 700 year-old soil from the ancient city of Eski-Kermen, 70 year-old soil from WWII trenches and 50 year-old soil from the open quarry screenings. Our research demonstrated that soil type on a limestone rock is the driving force behind microbiome shaping, without any apparent influence of its age. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the nutrients associated with the soil horizon, and our analysis showed that the reactive component of the soil microbiome shifted simultaneously in both soil horizons between different soil sites.

The work was supported by the grant of the Russian Scientific Foundation, project 17-16-01030.

How to cite: Kimeklis, A., Gladkov, G., Zverev, A., Kichko, A., Andronov, E., Ergina, E., Kostenko, I., and Abakumov, E.: Influence of soil factors on the microbiome of Rendzic Leptosols chronosequence in the Crimean Peninsula, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1767,, 2021.

Alejandro Javier Criado Monleon

Soil Treatment units (STU) receiving domestic wastewater from on-site wastewater treatment systems (ONWTS), such as septic tanks, rely on the development of microbial biomat at the infiltrative surface.  Community ecology analysis was conducted on two separate STUs, each receiving both primary (SE) and secondary effluent (SE) in parallel trenches under identical hydrogeological and environmental conditions.  At Site A SE was produced by a Ecoflo Coco Filter (Premier Tech Aqua Ltd., Ireland) and in Site B SE was produced from a Rotating Biodisc Contactor (Klargester BioDisc,Kingspan Ltd., UK). A total 92 samples were taken from both STU locations, (n= 51) samples were taken at the infiltrative surface of the STUs and (n=24) subsurface samples were taken above the STU system across a range distances and depths for both effluent types. Additional samples were taken of PE and SE effluent (n=5), distribution boxes (n=2), and of adjacent control soils (n=10).

Samples were characterized by 16S rRNA gene sequencing analysis. Data from water quality (ammonia, chloride, E. coli, nitrate, nitrite, non-purgeable organic carbon, phosphate, sulphate) were also taken on this sampling day using lysimeters installed at both sites. Inter-site phylogenetic analysis showed that there was little to no difference in phylogenetic composition between the control microcosm soil samples at each site. The impact of effluent characteristics on the microbial community’s present within the STU microcosms resulted in the STU receiving SE at Site A being richer in species (ACE) and a greater diversity in species (Shannon) when compared to the SE in Site B.  Further analysis of Site A showed that both species richness and diversity were at their highest in the SE trench at the sampling point closest to the effluent inlet, whereas for PE the opposite was noted as richness and diversity increased downstream of the inlet. This was confirmed with principle component analysis (PCOA) showing a clustering of PE STU samples located at the inlet of the trench. The STU receiving SE at Site B showed a notable lack of species and richness when compared to the PE counterpart across all distances and depth. Again, clear clustering of SE STU samples was present in PCOA results.

Samples were screened for the abundances of particular sequences corresponding to target organisms (i.e. nitrifiers, denitrifiers, methanotrophs, denitrifying methanotrophs, gut flora, Extracellular Polymeric Substances producing bacteria). STUs in both sites contained a greater abundance of target sequences than the controls. In the case of denitrifiers, EPS producers, methanogens and methanotrophs these sequences were absent from the deep soil control samples taken at both sites. In Site B the number of denitrifying bacteria, EPS bacteria and methanogens sequences counted in the STU receiving SE was on average by an order of magnitude of 2, 3, 2, and 1 greater than its PE STU counterpart respectively, and by an order of magnitude of 2 respectively when compared to SE STU in Site A. It is evident, therefore, that the application of secondary effluent is conferring phylogenetic changes to the composition of the microbiomes within the studied biomats.  

How to cite: Criado Monleon, A. J.: The impact of pre-treatment on microbiome within soil treatment units in a temperate region, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13229,, 2021.

Diego Leiva, Fernando Fernández-Mendoza, José Acevedo, Margarita Carú, Martin Grube, and Julieta Orlando

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,, 2021.

Claudio Zaccone, Edoardo Puglisi, Fabio Terribile, and Andrea Squartini

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,, 2021.