The process of transformation of soil organic matter is dependent on functional traits of active microbial decomposers. Microbial functional traits, in turn are selected and driven by the local environmental conditions and can be subdivided into three groups. Microbial traits in the first group are very dynamic, for example, the size of the microbial fraction maintaining activity or alert state (active biomass) and the time required for dormant microorganisms to switch to active growth (i.e., lag time). The second group represents intrinsic functional traits of the microbial population, such as maximal specific growth rate (µ_m), generation time (T_g), and affinity of extracellular enzyme systems (K_m) to soil organic substrates used for microbial growth. The third group refers to phenotypic traits at the level of functional genes, for example, those related to internal microbial metabolism, extracellular resource acquisition, or stress tolerance. Recent developments in molecular approaches have provided potential for microbial trait differentiation based on information regarding genome size, number of ribosomal gene copies per genome, and quantification of functional marker genes or their transcripts by -omics approaches (Li et al., 2019; Malik et al., 2020). This enabled to reconsider the classical concepts of microbial life strategies with the goal of specifying functional groups according to their ecological relevance considering microbial yield, resource acquisition, and stress tolerance (Ho et al. 2017, Krause et al. 2014; Malik et al., 2020). However, it remains challenging to identify proxies for specific traits that can serve as quantitative measures of a category. Based on literature review and own experiments, we compared the specificity of microbial physiological and phenotypic functional traits in contrasting soil environments. We demonstrated that mechanical disturbance of soil structure by tillage rather than chemical properties were responsible for reduction of total biomass and growing microbial fraction, for slower activity of C- and N-acquiring enzymes under conventional versus minimal tillage. High nutrient availability ensured by fertilization generally selected the microbial strategy with low total biomass but high abundance of active microorganisms. Microbial community adapted to resource depletion with soil depth was characterized by low total and growing biomass, retarded activity of enzymes decomposing plant and microbial residues and by accelerated activity and altered affinity of enzyme systems responsible for nutrients acquisition. Thus, environmental selection resulted in the activation of populations with intrinsic functional traits that are mostly suited to the individual soil habitat. This calls for the studies linking genetic and metabolic potential with microbial functions. However, synchronization of experimental design by sampling time is required for correct comparisons of microbial growth rates obtained by different approaches. 

How to cite: Blagodatskaya, E.: Microbial functional traits and life strategies: Bridging physiological and molecular approaches, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-5987, https://doi.org/10.5194/egusphere-egu22-5987, 2022.

Soil microbial growth, respiration and carbon use efficiency (CUE) are essential parameters to understand, describe and model the soil carbon cycle. While seasonal dynamics of microbial respiration are well studied, little is known about how microbial growth and CUE change over the course of a year, especially outside the plant growing season. In this study we measured soil microbial respiration, growth and biomass in an agricultural field and a deciduous forest 16 times over the course of two years. We sampled plots, at which harvest residues or leaf litter were either incorporated or removed. We observed strong seasonal variations of microbial respiration, growth and biomass. All microbial parameters were significantly higher at the forest site, which contained 3.5% organic C compared to the agricultural site with 0.9% organic C. CUE also varied strongly but was overall significantly higher at the agricultural site ranging from 0.1 to 0.7 compared to the forest site where CUE ranged from 0.1 to 0.6. We found that microbial respiration and to a lesser extent microbial growth followed the seasonal dynamics of soil temperature. Microbial growth was further affected by plant or foliage presence. At low temperatures in winter, both microbial respiration and growth rates were lowest. Due to higher temperature sensitivity of microbial respiration, CUE showed the highest values in the coldest months. Microbial biomass C was also strongly increased in winter. Surprisingly, this winter peak was not connected to high microbial growth or an increase in DNA content. This suggests that microorganisms accumulated osmo- or cryoprotectants but did not divide. This microbial winter bloom and following decline, where C is released and can be stabilized, could constitute the main season for C sequestration in temperate soil systems.  Highly variable CUE, and the fact that CUE is calculated from independently controlled microbial respiration and growth, ask for great caution when CUE is used to describe soil microbial physiology, soil C dynamics or C sequestration. Instead, microbial respiration, microbial growth and biomass should rather be investigated individually to better understand the soil C cycle.

How to cite: Schnecker, J., Baldaszti, L., Gündler, P., Pleitner, M., Richter, A., Sandén, T., Simon, E., Spiegel, F., Spiegel, H., Urbina Malo, C., and Zechmeister-Boltenstern, S.: Seasonal dynamics of soil microbial respiration, growth, biomass, and carbon use efficiency, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-1179, https://doi.org/10.5194/egusphere-egu22-1179, 2022.

Microbial communities are a critical component of the soil carbon (C) cycle as they are responsible for the decomposition of both organic inputs from plants and of soil organic C. However, there is still no consensus about how to explicitly represent their role in terrestrial C cycling. The objective of the study was to determine how the properties of organic matter affect the metabolic response of the resident microbial communities in soils, using a bioenergetics approach. This was achieved by cross-amending six soils with excess water-soluble organic matter (WSOM) extracted from the same six soils and measuring heat dissipated due to the increase in microbial metabolic activity. The conditions of the experiment were chosen in order to replicate conditions in activity hotspots. The metabolic activity was then related to the potential return on investment (ROI) that the microbial communities could derive from the WSOM. The objective of the study was to determine how different energetic profiles in available organic avec the metabolic response of different microbial communities.

The ROI was calculated as the ratio between the total net energy available (ΔE) in the WSOM and the weighted average standard state Gibbs energies of oxidation half reactions of organic C (ΔG°Cox) of the molecules present in the WSOM. The ΔE was measured as the heat of combustion of the WSOM, which was measured using bomb calorimetry. ΔG°Cox was estimated from the average nominal oxidation state of C (NOSC), which itself was determined from the elemental composition of each molecular species in the organic matter amendments analyzed by Fourier transform ion cyclotron resonance mass spectrometry. The soil bacterial community structure was determined by 16S rRNA gene sequencing and using the weighted UniFrac distance of rarefied amplicon sequence variants data.

We found that the potential ROI that microbial communities could obtain from the consumption of the added organic matter was positively related to the overall metabolic response of microbial decomposers. However, the observed temporal differences in metabolism across soils indicate that bacterial communities do not exploit energetic return-on-investment in the same ways. Overall, our results suggest that microbial communities preferentially use organic matter with a high energetic return on investment.

How to cite: Nunan, N., Dufour, L., Herrmann, A., Leloup, J., Przybylski, C., Foti, L., and Abbadie, L.: Potential return on investment that microbial communities can obtain from the consumption of organic matter determines overall soil microbial activity, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-9981, https://doi.org/10.5194/egusphere-egu22-9981, 2022.

Arbuscular mycorrhizal fungi (AMF) efficiently take up mineral nutrients such as phosphorus and nitrogen (N) from the soil solution, and trade them for organic carbon with their host plants. Acquisition of nutrients bound in organic forms by the AMF under unsterile soil conditions has previously been reported, assuming an important role of soil prokaryotes, yet mostly without proper mechanistic understanding. Here we present a synthetic approach to study involvement of such inter-kingdom interactions in utilization of organic nitrogen by a mycorrhizal plant. We employ ¹⁵N-labelled chitin (as an organic N source) added to AM fungal (Rhizophagus irregularis) hyphosphere under in vitro conditions, with or without other microorganisms. Upon presence of Paenibacillus sp., the AMF and their associated host plant obtained several-fold larger quantities of N from the chitin than they did with other bacteria, whether chitinolytic or not. Moreover, upon adding a protist Polysphondylium pallidum to the hyphosphere with Paenibacillus sp., the gain of N from the chitin by the AMF and their associated plant further and significantly increased by another 60+%, pointing to soil microbial loop as the underlying mechanism.

This work will appear shortly in the ISME Journal.

Reference: Rozmoš M, Bukovská P, Hršelová H, Kotianová M, Dudáš M, Gančarčíková K, Jansa J (2022) Organic nitrogen utilization by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist. ISME Journal, in press. doi 10.1038/s41396-021-01112-8 .

How to cite: Jansa, J., Bukovská, P., and Rozmoš, M.: Arbuscular mycorrhizal hyphosphere as a soil nutrient turnover hotspot, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-4653, https://doi.org/10.5194/egusphere-egu22-4653, 2022.

Nitrogen (N) availability is a main constraint to plant productivity, especially when vegetation relies largely on subsoils, which contain considerable N resources but in low availability. Rhizodeposition can promote N cycling by stimulating microbial growth and activity and thus induces the release of mineral-bound nutrients and accelerates decomposition of soil organic matter (SOM). However, many specific processes how root exudates interact with distinct N forms altering their subsoil mobilization still remain unclear. We hypothesize that the lower microbial activity but higher sorption capacity of subsoils induces subsoil-specific N dynamics. To disentangle this, we added four N sources (free NH₄⁺, sorbed NH₄⁺, urea and plant residues with identical total N content) into top-and subsoils. We quantified microbial processes regulating mineral and organic N availability in top-and subsoils by simulating rhizosphere condition via application of collected root exudates in a well-controlled microcosm experiment. Our results showed that neither growth of the total microbial community, nor shift in the community composition occurs based on maize root exudate amendment resembling a daily exudation amount. However, we observed a clear increase in microbial activity and activation of organic nutrient mobilizing mechanisms (e.g. enzyme activation), which was in most cases higher in sub- than in topsoils. This suggests that root exudates may not be of highest relevance for topsoil nutrient mobilization. In contrast, high root exudation is of much higher relevance for crops, which aim to mobilize a significant proportion of their nutrients from subsoils. We could demonstrate that subsoil communities were well capable of using litter-derived N, especially if root exudates accelerate overall activity and N cycling in subsoils. N incorporated from plant litter is successively recycled in microbial bio-and necromass following the initial degradation. Consequently, if breeding for deep-rooting crops with nutrient uptake from subsoils shall be promoted in the future, it is essential to ensure that these crops deep roots have a high root exudation to activate the highly C limited microbial communities of the subsoil.

How to cite: Ai, J., Banfield, C., Shao, G., Zamanian, K., Spielvogel, S., and Dippold, M.: The role of maize root exudates to availability of N source in different forms in top- and subsoils, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-4304, https://doi.org/10.5194/egusphere-egu22-4304, 2022.

The rhizosphere is a dynamic region governed by the composition and pattern of root exudates, which in turn impact the beneficial or harmful relationships between the rhizosphere microbiome, which affect their function and plant performance. Successive wheat following wheat shows yield decline, hence, this rhizobox-study aims to illuminate and quantify the effects of subsequent wheat rotations for 3 years (W3) at different growth stages on glucose releasing rate and soil enzyme activity.

We hypothesized that the long-term wheat rotation leads to lower glucose release, which will result in lower microbial activity accompanied by the decline of enzyme production than the first year wheat rotation (W1) using soil samples collected from the experimental farm Hohenschulen, (CAU, Kiel) from 1^st and 3^rd wheat after break crop. Glucose Imaging was utilized for visualizing and localizing glucose exudation rate from wheat roots and β-glucosidase zymography, involved in the degradation of C substances, was applied for rhizoboxes at two growth stages (BBCH 31 (T1), BBCH 59(T2)).

Results showed that crop rotation affected glucose release from roots and β-glucosidase activity and this effect was more pronounced at the second sampling time at BBCH-59. The total hotspot area of enzyme activity declined at W3. Third wheat after break crop had the lowest hotspot percent for glucose release and β-glucosidase activity at BBCH-59 by 1.83 and 4.26 percent of total soil surface area, indicating 68.3 and 47 percent decline compared to W1, respectively. While rhizosphere extends for glucose release increased in W3 compared to W1 at the first sampling date, there was a strong decrease at the second sampling time by 60.2 percent. However, β-glucosidase activity extend around the wheat root at T1 had a decreasing trend from W1 toward W3 and there was a slight decrease at T2. Plants benefit from root exudates by stimulating beneficial microorganisms and improving nutrient acquisition. Decreasing glucose release, as a readily available energy source for microorganisms and declining C availability because of root senescence, leads to competition for C in rhizosphere among beneficial microbes and soil-borne pathogens. Continuous wheat cultivation accelerates root senescence, accompanied by more severe environment for soil microbes and higher abundancy of wheat pathogens which ultimately will affect wheat yield.

How to cite: Rashtbari, M.: Patterns of glucose release and enzyme activity affected by crop rotation and plant senescence, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-6074, https://doi.org/10.5194/egusphere-egu22-6074, 2022.

Soil microbiome is an important indicator of soil quality and it is related to various soil functions, including soil carbon cycling. Plant litter decomposition is a key process in carbon cycling, and the use of standardized plant litter for the comparison of decomposition rates between different conditions is a promising method. In this study, we aimed to investigate the difference in microbial community composition in long-term manure amended soils with different crop rotations, and its relationship with litter decomposition by using the Tea Bag Index (TBI) protocol. Green tea and rooibos tea bags were buried pairwise in three long-term experimental sites (LTEs) in Germany, Denmark and Sweden for three months. The TBI, i.e. decomposition rate and stabilization factor, was calculated from the weight loss of tea. The three LTEs have contrasting soil textures and had been manured between 20 and 127 years. The rotation elements in the LTEs include spring barley, winter wheat, winter oat, maize, and grass/clover. The microbial community composition was characterized by biomarkers (phospholipid fatty acids and neutral lipid fatty acids) and 16S and ITS sequencing. Enzyme activity was quantified by fluorescein diacetate hydrolysis analysis. The linkage between TBI and several microbial properties including microbial biomass, enzyme activity, the fungal:bacterial ratio, and the abundance and the diversity of the microbial community, will be discussed. The interactive effect of soil texture and management on the TBI and microbial properties will be addressed, which shall provide implications for soil quality and soil management.

How to cite: Fu, Y., Paradelo, M., Ravnskov, S., de Jonge, L. W., and Arthur, E.: Linking litter decomposition characterized by the Tea Bag Index to soil microbial characteristics under long term manure and crop rotation management, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-7721, https://doi.org/10.5194/egusphere-egu22-7721, 2022.

Root morphology and the composition of root exudates shape the spatial organization and various processes in the rhizosphere. For instance, root hairs are essential for plant nutrition, while secondary plant metabolites (i.e. benzoxazinoids) ensure plant defence from herbivore and fungal infection. Nevertheless, it is still unknown to which extent root hairs and benzoxazinoids may change the microbiome and enzymatic activities, as well as formation of rhizosphere hot- and coldspots.

To study the effect of root hairs and benzoxasinoids on the rhizosphere microbiome structure and its enzymatic activities we compared mutants with defective root hairs rth3 or with reduced benzoxazinoids bx1 with the corresponding wild-type (WT) maize.

Root hairs increased acid phosphatase activity by 80 % promoting mineralization of organic phosphorus sources to available forms in the hotspots. In the coldspots, broken root hairs in WT facilitated the intensive microbial hotspots with up to two times higher β-glucosidase and chitinase activities, compared to rth3.

The presence of benzoxazinoids in root exudates strongly supported plant defence against pathogenic fungi (i.e., genus Fusarium and Gibberella) while the total microbial biomass remained unaffected. In response to the presence of pathogenic fungi, bx1 exuded 70 % more chitinase for defence purpose to partly compensate for benzoxazinoids deficiency, which was however, less efficient against pathogens than the presence of benzoxazinoids.

Overall, we conclude that: i) root hairs facilitate better plant nutrition at the shortage of available nutrients (i.e., coldspots), while; ii) the presence of benzoxazinoids in exudates protect plant from pathogenic microorganisms. This two root traits are promising for plant breeding of genotypes suitable for sustainable agriculture and organic farming.

How to cite: Bilyera, N., Waelchli, J., Shi, L., Caggia, V., Zhang, X., Shlaeppi, K., Dippold, M. A., Razavi, B. S., and Spielvogel, S.: Effect of root hairs and benzoxazinoids on maize microbiome and its enzymatic activity in the rhizosphere, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-8562, https://doi.org/10.5194/egusphere-egu22-8562, 2022.

Interactions between plants, soil, and microbiota makes the rhizosphere of central importance for ecosystem functioning. Although non-pathogenic organism dominate this rhizobiome, plant pathogens have an important functional role for plant performance. In fact, plant pathogens trigger plant defence and alter the metabolism, nutrient flow and survival of the host, leading to changes in overall plant performance which feeds-back to the rhizobiome. However, the links between soil-borne pathogens and the rhizobiome are only starting to be explored. Here we focus on the clubroot pathogen Plasmodiophora brassicae, a pathogen that forces farmers to abandon cultivation of Brassica species for more than a decade, to decipher pathogen impact on the rhizobiome. Furthermore, we aim to identify potentially disease suppressive and disease conducive microbiome members, including bacteria, fungi, protists and animals. We are performing complex plant and soil physicochemical analyses to decipher underlying drivers of taxonomic and functional changes in the rhizobiome to clubroot infection including the impact of the detritusphere. The results of this studies will give an important insight of the ecological role of plasmodiophorid species on the plants and its rhizobiome. Additionally, by identifying pathogen suppressive and conducive soil biota new biocontrol applications can be developed that will also be useful to control other soil-borne pathogens. In this presentation we will provide the framework of the research and initial findings that provide first ideas on the importance of the plant-clubroot-rhizobiome connections.

How to cite: Schwelm, A. and Geisen, S.: Clubroot and soil biology – from ecology to biocontrol?, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-10214, https://doi.org/10.5194/egusphere-egu22-10214, 2022.

Soil extracellular enzyme stoichiometry (EES) reflects the biogeochemical balance between microbial metabolic requirements and environmental nutrient availability. Previous studies have focused on the perspective of nutrient acquisition, while soil microbial metabolic limitations (SMML) were minor in the focus of those studies. Therefore, how grassland succession drives SMML has mainly been under explored. Here, we used EES models to identify the response of SMML during grassland restoration while also investigating potential implications of microbial nutritional limitations across the time series (herbaceous succession) and with space (transformation interface soil and underlying topsoil layer) in a grassland restoration series. The results showed that soil microorganisms were generally limited by C, both in the transformation interface soil (TIS) and the underlying topsoil layer (UTS). During herbaceous succession, microbial P-limitation was more substantial than that by N-limitation. Microbial C-limitation displayed a uni-modal direction, peaking in intermediate successional stages. However, microbial P-limitation presented the opposite trend. In the TIS layer, SMML gradually transferred from P- to N- and back to P-limitation at later successional stages. Biotic factors, together with soil basic index, and soil nutrients, explained 92.2% of the variation in microbial C-limitation and 84.4% of the variation in microbial P-limitation. Multi-interaction factors show the most significant relative influences of 65.11% (TIS) and 43% (UTS) of the SMML, respectively. Microbial C-limitation was induced by the imbalance between C supply and microbial C demand, while the changes in microbial P-limitation were due to changes in the competition for P between plants and microorganisms. Therefore, the impacts of long-term grassland succession on SMML resulted from the concerted changes in vegetation composition, soil properties, and the nutritional demands of the soil microorganisms.

How to cite: Xue, Z., Liu, C., and Wolfgang, W.: Extracellular enzyme stoichiometry reflects the C-and P- microbial metabolic limitations along a grassland succession on the Loess Plateau in China., EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-3020, https://doi.org/10.5194/egusphere-egu22-3020, 2022.

Soil microbiome is the most diverse ecosystem in the world and carries out some of the most important soil functions through nutrient cycling. Agroecosystem health and sustainability are strongly connected to understanding soil microbiome and its composition, yet unknown in many agricultural areas. In this study we compared in a rainfed almond orchard in Spain the long-term effect of intensive tillage (IT), reduced-tillage (RT) and reduced-tillage with alley cropping (RTAC) on soil fungal and bacterial communities and their interrelationship with soil physicochemical properties and almond yield. Fungi and bacteria population were characterized using next-generation sequencing technology. Soil organic C, total N and particulate organic C were were significantly higher in RT and RTAC treatments compared to IT, with no significant differences concerning cation exchange capacity, ammonium or nitrates. RTAC showed the highest proportion of macro-aggregates (>250 µm). Richness and diversity indices showed no significant differences among treatments for fungal and bacterial communities. Within bacterial genera, we observed higher abundance of Sphingomonas, Streptomyces, Blastococcus, and Nocardioides in RT and RTAC treatments. Within fungi genera, Mortierella, Coprinopsis and Chaetomium showed higher abundance in IT. Multivariate analysis showed that soil fungal and bacterial communities were different depending on the treatment, mostly associated to changes in soil organic C. Deep identification of bacterial and fungal taxa may give light to the understanding of soil microbiome and functions in almond orchards, and brings the producers one step closer to make productive areas more sustainable related to soil C sequestration and fertility.

How to cite: Ozbolat, O., Zornoza, R., Sánchez-Navarro, V., Cuartero, J., Ros, M., Canfora, L., Orrù, L., Martínez-Mena, M., Boix-Fayos, C., and Almagro, M.: Composition of Soil Fungal and Bacterial Communities and their Relation with Soil Physicochemical Properties under different Agricultural managements in a Mediterranean Almond Orchard, EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-12827, https://doi.org/10.5194/egusphere-egu22-12827, 2022.