Diving into the soil microhabitat - Impacts of the soil physical structure on soil biota and vice-versa
This PICO session will gather most recent tools and experimental strategies to shed light on (i) the role of the soil physical structure on the soil biota on the one hand and (ii) focus on soil biota shaping soil physical structure and functionality on the other hand. Case studies linking soil structure to soil biota with respect to soil functions and the processing of organic matter will be described using novel techniques and approaches. Materials such as manufactured aggregates or synthetic polymers (Soil Chips) are used to re-create soil structure with defined characteristics and open unprecedented experimental possibilities in soil physics-soil ecology boundary line. Under natural conditions, cutting-edge imaging techniques, such as µCT (X-rays), neutron radiography and Nano-SIMS allow to finely characterise soil structures and link it to soil biological activity (isotopes, PLFA). Vice-versa, soil biota shapes soil physical structure, in particular through extracellular polymeric substances (EPS), excreted mainly by bacteria, fungi and plants. EPS are assumed to play a role in particle cohesion and thus in soil physical structure, besides the several functions they promote in microbial life, e.g. adhesion to surfaces; reduction of cellular desiccation; tolerance of excessive changes in temperature, pH, salinity. If and how this can be transferred to soil functionality such as soil hydrologic properties and under which condition significant EPS will be produced is still a pending question. The overview provided here mostly focus on microorganisms and microfauna, with some case studies reporting the effect of roots or larger organisms, such as earthworms. The PICO format will convey demonstration of new tools and approaches to study the soil physics - soil ecology interface.
The Keynote speaker of this session is Dr. Edith Hammer (Lund University, Sweden).
Edith Hammer, Micaela Paola Mafla Endara, Carlos G. C. Arellano, Kristin Aleklett, Milda Pucetaite, and Pelle Ohlsson
Many soil processes are governed by microbes, and biological and physical processes influence each other. We recently developed microfluidic model systems that simulate the spatial microstructure of soil microbial habitats in a transparent material, which we call Soil Chips. They allow us to study the impact of soil physical microstructures on microbes, and vice versa, the influence of microbes on soil physical properties: such as Microbial behavior and interactions in response to a spatially refined habitat, or wettability and water retention, soil aggregate formation and changes in the pore space.
We inoculated our chips with fluorescent lab cultures or natural whole soil inocula. Through the chips we observed via microscopy processes in real-time and at the scale of the microbial cells.
We could study fungi, bacteria, protists and nematodes as well as the distribution of soil minerals and soil solution in the chips. We subjected the adjacent soil to drying-rewetting processes, which was visible in water movements inside the chip. We studied the development of preferential water flow paths, and water retention in smaller pores and as a consequence of microbial exudates. Also the microbes themselves influenced the formation of microhabitats, where fungal hyphae both blocked connections and pushed through existing borders, and single-celled protozoa opened passages through existing aggregates. We found that the presence of fungal hyphae in a pore space system increased both the presence of bacteria and the likelihood of water in the pores, and thus allowing us to study fungal highways in a more realistic soil setting.
The chips act like a window into the soil, through which we can eaves-drop on a world that otherwise is largely hidden to us: Jostling protists, tsunami-like drying-rewetting events, and fungi with character. Beyond the scientific potential, the chips can also bring soils closer to people and hopefully increase engagement in soil health conservation.
How to cite:
Hammer, E., Mafla Endara, M. P., Arellano, C. G. C., Aleklett, K., Pucetaite, M., and Ohlsson, P.: Microbes meet Structure - Soil Ecology in Microengineered Soil Chips, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-18396, https://doi.org/10.5194/egusphere-egu2020-18396, 2020
Harry Harvey, Ricky Wildman, Sacha Mooney, and Simon Avery
Environmental perturbation, anthropogenic or otherwise, can have a profound effect on soil microbiota and essential biogeochemical processes. The general resistance and adaptation of yeasts and other fungi to stressors has been well studied in vitro however, the influence of key physical variables, such as how soil structure regulates fungal response to perturbation, is poorly understood. In this study, we developed an approach to manufacture soil macroaggregates that are characteristically similar to their natural counterpart (determined by X-ray CT) and with defined microbial composition. This new tool allowed us to examine the influence of soil aggregation on fungal stress response by manufacturing aggregates with yeast cells either within, or on, the aggregate surface. Environmental stressors including heavy metals, anoxia, and heat stress were applied to these aggregates to capture an array of environmental stressors and assay differences in survival between exo-and-endo aggregate cells. Results generated with this new tool indicate that the location of yeast cells in soil macroaggregates can impact on their survival, in a stressor- and time-dependent manner.
How to cite:
Harvey, H., Wildman, R., Mooney, S., and Avery, S.: Manufactured Soil Aggregates for Studying Microhabitats, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-9512, https://doi.org/10.5194/egusphere-egu2020-9512, 2020
Fabrizio De Cesare, Elena Di Mattia, and Antonella Macagnano
Soil structure is the organisation of soil particles in aggregates with increasing hierarchical levels, from nano- to macro-architectures. Several processes and the functioning of the entire soil ecosystem fundamentally depends on soil structure. Soil is also a very heterogeneous and complex matrix to study because of several components with different nature (mineral, organic and biological), physics and chemistry comprise it. Its study often involves techniques that profoundly alter its natural composition or destroy its original 3D arrangement, including the pore distribution and organisation, which is crucial in preserving a suitable habitat for soil ecology and functioning.
Microbial life has been discovered in the last decades to exist in biofilms, 3D spatial organisations of microbial communities adhering to solid surfaces. In these well-organised assemblages of one or more different microbial species, extracellular polymeric substances (EPS) play remarkable functions for microorganisms in biofilms and facilitate aggregation of soil particles.
As a model system, a self-standing polymer biodegradable nanostructured scaffolds (NS) composed of a mixture of nano- to microfibres and microbeads mimicking the fibrous materials and particles comprising the main morphological types of soil (organic matter and mineral particles) and the relative spatial architecture at the micro- and nanoscale were created by electrospinning. Electrospinning is a nanotechnology producing 2D and 3D nano- and microfibrous scaffolds under an electric field. The resulting NS were characterised by considerable porosity and extensive surface area. A PGPR species was employed as a model microbial type to test the capacity of similar NS of supporting the biofilm development. Incubation was performed under stirring to stimulate only stable interactions between microorganisms and the various morphological types of the NS, and also to assess the stability of the NS mimicking the soil aggregates. To shed some light into the nexus between microorganisms and soil structure and the reciprocal influence, combination of imaging techniques such as optical, SEM and TEM microscopy were used to observe “in situ” associations of microbes with mineral and organic materials at nano- and microscale and the consequent effects on porosity usually destroyed under investigations.
The typical phases of conditioning film release, initial and stable adhesion mediated by appendages and EPS release, micro- and macrocolony formation until a mature biofilm development were observed. Morphological modifications of bacteria and the involvement of other components in the mentioned stages were also detected. The bacteria growth rate, the overall respiratory activity and its spatial distribution throughout the NS were recorded.
Hence, the tools here proposed can have high potentials in reproducing the spatial and temporal dynamics of microbial hotspots of activity typically present in the rhizosphere, the sphere of soil surrounding roots, which is of central importance for the entire soil ecosystem functioning.
Similar 3D NS can also provide the opportunity of zooming in microbial lifestyle observing microbes at work, from the dynamics of interactions with organic matter and particle surfaces to their spatial distribution and colony formation, then linking biological processes to specific physical and chemical features of soil at different scales (from nm to mm).
How to cite:
De Cesare, F., Di Mattia, E., and Macagnano, A.: Developing 3D polymer nanostructured fabric as a soil-like model for studying interactions between microorganisms and soil structure - The case of bacterial biofilm development, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-19304, https://doi.org/10.5194/egusphere-egu2020-19304, 2020
Maik Lucas, Doris Vetterlein, Hans-Jörg Vogel, and Steffen Schlüter
An important parameter to quantify pore structure and link it to soil functions is connectivity. When quantifying connectivity with X-ray microtomography (X-ray-µCT), one of the major drawbacks is that high resolution can only be achieved in small samples. In these samples, the small pores can be described, but the connectivity of larger pores cannot be quantified reasonably.
Here we explore changes in pore connectivity with changing sample size covering a range of analyzed pore diameters of more than three orders of magnitude. Soil columns with a diameter of 10 cm were taken in two different depths (0 - 20 cm and 40 - 60 cm) at different sites of an agricultural chronosequence ranging in age from 0 to 24 years. X-ray CT was used for scanning the original columns as well as undisturbed subsamples of 3 and 0.7 cm diameter. This enabled us to detect characteristic traces in certain connectivity metrics on the chronosequence, caused by different pore types and thus different processes. In detail, we determined the connection probability of two random points within the pore system, i.e. the Γ-indicator and the Euler number, χ as a function of minimum pore diameter.
Our results revealed that scale artifacts in the connectivity functions overlap with characteristic signatures of certain pore types. For the very first time a new method for a joint-Γ-curve was developed that merges information from three samples sizes, as the Γ-indicator gives highly biased information in small samples. In contrast, χ does not require such a scale fusion and is helpful to define characteristic size ranges for pore types. Overall, findings suggest a joint evaluation of both connectivity metrics to identify the contribution of different pore types to the total pore connectivity with Γ and to disentangle different pore types with χ.
For the samples of the chronosequence such an evaluation revealed that biopores mainly connect pores of diameters between 0.1 and 0.5 mm. However, this was not necessarily coupled with increasing porosity. Tillage, conversely, lead to an increase in porosity due to a shift of pores of diameter >0.05 mm towards pores of diameter >0.20 mm and therefore increased connectivity of pores >0.20 mm.
The current study is part of the DFG-Project Soil Structure (AOBJ: 628683).
How to cite:
Lucas, M., Vetterlein, D., Vogel, H.-J., and Schlüter, S.: Pore connectivity across scales and resolutions , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-7588, https://doi.org/10.5194/egusphere-egu2020-7588, 2020
Genoveva Burca, Stephen Hillier, Pawala Ariyathilaka, Jumpei Fukumasu, Anke Herrmann, Mats Larsbo, Oxana Magdysyuk, and John Koestel
Soil organic carbon (SOC) is of key importance for soil functioning. It strongly impacts soil fertility, greenhouse gas emissions, nutrient retention, and contaminant degradation. The soil pore network determines how oxygen, water and nutrients are transported and exchanged in soil, and the architecture of the soil is therefore equally fundamental to soil functions. For a thorough understanding of the microbial habitat, the soil pore network architecture needs to be evaluated alongside with the spatial distribution of SOC, but the challenge ahead is the 3-D visualization of organic carbon at the micro-scale. At present, such visualizations are undertaken using staining agents, but their non-specific binding to other features in the soil aggravates evaluation of organic carbon at the micro-scale.
In the present study, we investigated the potential and limitations of using joint white-beam neutron and X-ray imaging for mapping the 3-dimensional organic carbon distribution in soil. This approach is viable because neutron and X-ray beams have complementary attenuation properties. Soil minerals consist to a large part of silicon and aluminium, elements which are relatively translucent to neutrons but attenuate X-rays. In contrast, attenuation of neutrons is strong for hydrogen, which is abundant in SOC, while hydrogen barely attenuates X-rays. When considering dried soil samples, the complementary attenuation for neutrons and X-rays may be used to quantify the fractions of air, SOC and minerals for any imaged voxel in a bi-modal 3-dimensional image, i.e. a combined neutron and X-ray image.
We collected neutron data at the IMAT beamline at the ISIS facility and X-ray data at the I12 beamline at the Diamond Light source, both located within the Rutherford Appleton Laboratory, Harwell, UK. The neutron image clearly showed variations in neutron attenuation within soil aggregates at approximately constant X-ray attenuations. This indicates a constant bulk density with varying organic matter and/or mineralogy. For samples with identical mineral composition, neutron attenuation data of sieved and repacked soil samples exhibited a large coefficient of determination (R2) in a regression between volumetric SOC content and neutron attenuation (0.9). Even larger R2 (0.93) were obtained when the volumetric clay content was also included into the regression. However, when comparing soil samples with different mineralogy, R2 dropped to 0.24 and 0.37, depending whether the clay content was considered or not. To improve the method, it is necessary to include specifics of the soil mineralogy. Here, analysing the time-of-flight neutron attenuation data collected at the IMAT beamline will provide further insights. In summary, our approach yielded promising results. We anticipate that quantitative 3-D imaging of organic carbon contents in soil will be possible in the near future.
How to cite:
Burca, G., Hillier, S., Ariyathilaka, P., Fukumasu, J., Herrmann, A., Larsbo, M., Magdysyuk, O., and Koestel, J.: Potential of combined neutron and X-ray imaging to quantify local carbon contents in soil, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-18948, https://doi.org/10.5194/egusphere-egu2020-18948, 2020
Guillaume Le Mer, Nicolas Bottinelli, Marie-France Dignac, Arnaud Mazurier, Laurent Caner, and Cornelia Rumpel
Plant residues are the main precursors of soil organic matter (SOM) and soil macrofauna is an important driver of ecological processes involved in the sequestration of carbon (C) in soils. In particular, earthworms are one of the largest contributors to soil matter formation in most terrestrial ecosystems. In the short term, they may increase the rate of OM turnover by mineralization, fragmentation and stimulation of microbial activity. On the other hand they may reduce OM degradability by forming stable aggregates and organo-mineral complexes protecting C from mineralization for longer time scales. Earthworms are classified in three main ecological groups depending on their behaviors and on their morpho-functional traits. However, their intra- or inter- ecological group effect on C stabilization needs to be investigated.
In this study, we explored the impact of earthworm diversity (composed of several species belonging to different ecological groups) on the physicochemical properties of casts, related to CO2 emissions. We hypothesized that C mineralization in casts would be related to the ecological category.
We studied casts of 6 species (2 anecic species: Lumbricus terrestris & Aporectodea nocturna, 2 endogeic species: Allolobophora icterica & Aporrectodea caliginosa and 2 epigeic species: Lumbricus castaneus & Eisenia fetida) produced in a silty subsoil with addition of plant litter. Casts were incubated for 140 days under similar laboratory conditions. We measured CO2 mineralization, pH, elemental composition and physical cast organization by X-ray microtomography (resolution of 9.49 µm voxel) at 7, 42, and 140 days.
Our results showed lower CO2 mineralization in aggregates produced without earthworms than all earthworm casts. In the beginning of the incubation casts showed similar CO2 emissions and specific physicochemical properties as OC content and pH. After 140 days, CO2 emissions were earthworm species specific with Aporectodea nocturna showing highest CO2 emissions, and Aporrectodea caliginosa the lowest values. Microtomographic analyses showed that this is due to an increase of cast porosity with increasing cast age coupled with a concurrent decrease particulate organic matter (POM) structures. Our first results seemed to suggest that earthworms belonging to the same ecological category influence similarly C mineralization through their impact on the cast organization.
How to cite:
Le Mer, G., Bottinelli, N., Dignac, M.-F., Mazurier, A., Caner, L., and Rumpel, C.: X-ray computed microtomography to predict CO2 emissions in casts of 6 earthworm species (Lumbricidae), EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-12324, https://doi.org/10.5194/egusphere-egu2020-12324, 2020
Kristina Witzgall, Alix Vidal, David Schubert, Carmen Höschen, Steffen Schweizer, Franz Bruegger, Valerie Pouteau, Hirte Juliane, Claire Chenu, and Mueller Carsten W
Soil texture and microorganisms are key drivers controlling the fate of organic matter (OM) originating from decaying plant litter, and thus the stabilization of soil organic matter (SOM). However, the understanding of the mutual interactions between microbial litter decay and soil structure formation controlled by different soil textures remains incomplete. We monitored the fate of litter-derived OM (using 13C isotopic enrichment) from decaying litter (shredded maize leaves) to microorganisms and SOM in two differently textured soils (sand and loam). The two soils were incubated with litter mixed in the top layer in microcosms for 95 days during which regular CO2 and 13CO2 measurements were conducted. After the incubation, each microcosm was divided in three to separate a top, center and bottom layer. Using a physical soil fractionation scheme, we assessed the fate of litter-derived OM to free and occluded particulate OM (POM), as well as mineral associated OM (MAOM). All SOM fractions were analysed with respect to their mass distribution, C, N, and 13C contents, and for their chemical composition using compound-specific 13C-CPMAS NMR spectroscopy. The effects of contrasting textures on the total microbial community structure were studied using phospholipid fatty acids (PLFA) and the incorporation of litter-derived C into individual PLFAs was assessed via 13C-PLFA. Lastly, scanning electron microscopy and nano scale secondary ion mass spectroscopy (NanoSIMS) analysis of free POM of both textures enabled qualitative insights directly at the biogeochemical interface of the microbial hot spot of decaying plant litter.
We were able to clearly demonstrate higher contents of litter-derived OM still residing as free POM in the loamy textured soil after the 95 day-incubation, while higher contents were found in occluded and MAOM in the sandy textured soil. This indicated that the overall litter decomposition was refrained in the finer-textured soil, whereas microbial alteration and allocation of litter-derived compounds was promoted in the coarser textured soil. This was further corroborated by higher respiration and higher amounts of respired litter-derived CO2-C in the sandy soil. The PLFA analysis showed a coherent pattern between the textures, with similar community structures in all treatments and significant increases in microbial abundance in the top layers induced by litter addition. This increase was found most pronounced in fungal biomarkers, which was in line with the 13C-PLFA measurements revealing over 90% of fungal biomarkers to be of litter-origin (compared to 30-40% in the other microbial groups). The labelled PLFA profiles also confirmed the importance of fungi as a vector for litter-derived OM into deeper layers of the soil columns, with significantly higher litter-derived fungal markers also in center and bottom layers. The NanoSIMS measurements verified the high 13C enrichment in fungal hyphae and further revealed clay minerals embedded in enriched microbial-derived extracellular polymeric substances and intertwined with hyphae directly on top of the POM. Based on this comprehensive data, we highlight that regardless of the texture, plant litter in association with microbial-derived products represent a hot spot for soil structure formation by harbouring a core for aggregation and MAOM formation.
How to cite:
Witzgall, K., Vidal, A., Schubert, D., Höschen, C., Schweizer, S., Bruegger, F., Pouteau, V., Juliane, H., Chenu, C., and Carsten W, M.: Soil texture determines the microbial processing from litter to POM and MAOM in the detritussphere, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-20330, https://doi.org/10.5194/egusphere-egu2020-20330, 2020
Jeroen Zethof, Antje Bettermann, Cordula Vogel, Doreen Babin, Erik Cammeraat, Albert Solé-Benet, Roberto Lázaro, Lourdes Luna, Joseph Nesme, Susanne Woche, Søren Sørensen, Kornelia Smalla, and Karsten Kalbitz
Individual plant species form so-called resource islands in the barren semiarid landscape, whereby many soil properties are enhanced including soil structure. Within the soil structure, mostly studied as soil aggregates, microaggregates (<250µm) form fundamental components, reducing potential erosion of finer particles and subsequent loss of nutrients. Extracellular polymeric substances (EPS) are considered an important glue determining aggregation in addition to inorganic binding agents such as carbonates and clay minerals. However, the role of the soil prokaryotic community in EPS formation and consequently for microaggregation in natural environments has not been clarified yet. EPS should be particularly important under semiarid conditions as they form a protection mechanism of the prokaryotes against desiccation. Therefore, we examined the influence of the prokaryotic community on soil EPS content and subsequently on soil aggregation in semiarid grasslands, with respect to the parent material of soil formation, common plant species and the distance to the plant.
During two sampling campaigns in spring 2017 and 2018, soil samples were taken over a distance gradient from two major semiarid grassland plant species in Southern Spain, the legume shrub Anthyllis cytisoides and the grass tussock Macrochloa tenacissima, to the surrounding bare soil. While topsoil was sampled in five distances to the plant during the first sampling campaign, the second one focused stronger on the root influence, hence rhizoplane and rhizosphere were sampled. Additionally, two sites with different parent materials were chosen to scale the effect of EPS on soil aggregation in the presence of inorganic binding agents (here carbonates). Total community DNA and EPS were extracted, followed by quantification of EPS-saccharides and bacterial abundance, as well as examination of the prokaryotic community composition by Illumina amplicon sequencing of the 16S rRNA genes. Further, the particle size distribution of (micro)aggregates in water was determined, with and without ultrasound treatment, as a measure of soil aggregate size distribution and stability.
Based on the first sampling campaign, we found that the overall prokaryotic community composition differed between the two sites, but not between plant species. Interdependencies between the community composition and EPS content were revealed, whereby soil organic matter (SOM) seems to be a regulating factor as increasing SOM contents resulted in more EPS-saccharides. Soil microaggregation in the topsoil was enhanced by the plant canopy, especially at the edge of Macrochloa tussocks. Contrary to the expectation that increasing inorganic C contents would diminish the importance of EPS, the parent material richest in inorganic C results in a significant effect of EPS-saccharides on microaggregation.
First results of the second sampling campaign indicate that even in the rhizoplane and rhizosphere, parent material had a dominating influence on the prokaryotic community composition. As EPS-saccharide contents and soil aggregation followed a similar decreasing trend with distance to the roots and canopy cover, interdependencies are expected.
From the outcomes until now, we can conclude that the availability of decomposable OM influences the prokaryotic community composition and thereby triggers EPS production, whereas large contents of polyvalent cations from carbonates promote the stabilizing effect of EPS on microaggregates.
How to cite:
Zethof, J., Bettermann, A., Vogel, C., Babin, D., Cammeraat, E., Solé-Benet, A., Lázaro, R., Luna, L., Nesme, J., Woche, S., Sørensen, S., Smalla, K., and Kalbitz, K.: The role of prokaryotes and their extracellular polymeric substances on soil aggregation in carbonate containing semiarid grasslands, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-13565, https://doi.org/10.5194/egusphere-egu2020-13565, 2020
Natalia Cortes Osorio, Robert Endrika, Karsten Kalbitz, and Cordula Vogel
In natural environments, bacteria can be found as multicellular communities exhibiting a high degree of structure, denominated biofilms. Biofilms are composed of microbial cells, often of multiple species, embedded within a matrix of extracellular polymeric substances (EPS). The exact composition, physical and chemical properties, and amounts of these components varies depending on their growth conditions. However, it remains unclear how nutrient availability drives the allocation into cell growth or EPS production, especially under conditions found in soils. Here we aimed to evaluate the effect of various C/N ratios on Bacillus subtilis biofilm growth (spatial expansion and structure) and their EPS composition. We hypothesized that the largest biofilm development and highest EPS production by Bacillus subtilis would be caused by a nutrient imbalance reflected in C/N ratios, especially high C availability. Biofilms were grown on membranes on MSgg agar plates with C/N ratios of 1:1, 10:1, 25:1 and 100:1. Several methods from macroscopic observations over EPS extraction and determination up to various microscopic visualisation techniques were used. The radial expansion of the biofilm was measured, followed by EPS extraction to quantify EPS-proteins and EPS-polysaccharides. Hydrated biofilm samples were studied regarding their biofilm structures by scanning electron microscopy (SEM) within the environmental mode at approximately 97% humidity. Fixed, dehydrated and embedded samples were used to evaluate the biofilm height and internal structure with SEM in high vacuum mode. Low C/N ratio (1:1) resulted in the smallest biofilms in terms of radial expansion and biofilm height, with densely packed layers of cells and low amounts of EPS. Our first results revealed that the highest biofilm productions were observed at C/N ratio of 10:1 and 25:1. The microscopic approaches indicated that biofilms growing at C/N ratios of 100:1 produced the highest amount of EPS. Furthermore, changes in the microscopical features of the biofilms were detected with different structures along the biofilm regions affected by the nutrient conditions. These results suggest that the C/N ratio has a large impact on the biofilm development and structure, with different allocations into microbial cells and EPS. Overall, the results obtained until now allowed us to accept the initial hypothesis, indicating that higher C/N ratios induce a higher EPS production. This suggests that environments containing a high ratio between carbon and the limiting nutrient, often nitrogen, may favour polysaccharide production, probably because energy from the carbon excess is used for polysaccharide biosynthesis.
How to cite:
Cortes Osorio, N., Endrika, R., Kalbitz, K., and Vogel, C.: Effects of carbon to nitrogen ratios on amounts and composition of Bacillus subtilis biofilms, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-10286, https://doi.org/10.5194/egusphere-egu2020-10286, 2020
Yan Jin, Saiqi Zeng, Fatema Kaniz, Wenjuan Zheng, Jacob LaManna, and Harsh Bais
Large communities of microbes are associated with plant roots in the rhizosphere, which is a critical interface supporting the exchange of water and nutrients between plants and their associated soil environment. The diverse communities of rhizobacteria mediate plant-soil feedback through a multitude of interactions including those that contribute to plant abiotic stresses. For example, enhancement of plant drought stress tolerance by plant growth promoting rhizobacteria (PGPR) has been increasingly documented in the literature, however, investigations to date have been largely focused on PGPR-root/plant interactions and related plant responses to PGPR activities that induce drought tolerance. Comparatively, much less is known about PGPR’s role in mediating physiochemical and hydrological changes in the rhizospheric soil that may also impact plant drought stress tolerance. Using UD1022, aka Bacillus subtilis FB17, as a model bacterium, we demonstrated via soil water characteristic measurements that UD1022-treated soil samples retained more water, had lower hydraulic conductivity than its controls. In addition, we investigated the effects of UD1022 on soil water evaporation via combined neutron radiography, neutron tomography, and X-ray tomography imaging techniques. Neutron radiography images confirmed greater water retention in UD1022-treated soil samples than their controls due to reduced water evaporation. Combined neutron and X-ray tomography 3D images revealed that water distribution in UD1022-treated soil samples was heterogeneous, i.e., there were more disconnected water pockets compared with the controls where water was distributed more uniformly. Our study provides pore-scale mechanistic explanation for increased water retention and reduced evaporation rate from UD1022-treated soil samples, which is mainly attributed to the production of extracellular polymeric substances (EPS) by UD1022 due to EPS’ hygroscopic and chemical properties (viscosity and surface tension). However, our latest experiments showed similar effects by a UD1022 mutant with eps-producing genes removed, suggesting that the beneficial impacts of rhizobacteria may not be limited to their ability to EPS production alone. These findings have practical implications in, for example, “rhizosphere engineering” to improve/restore soil structure, support sustainable agricultural production, and mitigate climate change.
How to cite:
Jin, Y., Zeng, S., Kaniz, F., Zheng, W., LaManna, J., and Bais, H.: Rhizobacteria Mediated Changes in Soil Physical and Hydrological Properties, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-11651, https://doi.org/10.5194/egusphere-egu2020-11651, 2020
Violeta Carmen Angulo Fernández, Mariet Hefting, and George Kowalchuk
Soil degradation represents a pressing worldwide problem that is being accelerated by processes of erosion, depletion of soil organic matter, soil compaction, acidification, salinization, and drought. Soil microorganisms can influence soil aggregation via a range of mechanisms such as the production of exopolysaccharides and other extracellular matrix polymers such those involved in biofilm formation. In this study, we south to use bacteria harboring specific traits to enhance soil aggregation. To this end, 120 bacterial strains were isolated from an experiment field under drought conditions and tested for their ability to grow under drought, salinity tolerance, rapid growth, biofilm, and exopolysacharides production. Based upon this trait assessment, 24 strains were further tested at two moisture levels for their ability to impact soil structure after 8 weeks of incubation at 25ºC. The mean weight diameter (MWD) of water-stable aggregates and carbohydrates were determined for treated soils. Three strains were shown to impact soil aggregate properties at the higher moisture content: one affiliated with Bacillus niacini, one affiliated with Paenarthrobacter nitroguajacolicus and one of unclear classification. The first of these strains also affected soil structure at the lower moisture level. This B. niacini strain also increased the carbohydrate content of the soil, as did two other strains, related to B. wiedmannii and B. aryabhattai, respectively. However, no positive correlation was observed between the MWD and the production of carbohydrates in soil. Our results suggest that soil inoculation with specific microbial strains can improve soil structure.
How to cite:
Angulo Fernández, V. C., Hefting, M., and Kowalchuk, G.: Inoculation of bacteria for the amelioration of sandy soil under drought, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-15917, https://doi.org/10.5194/egusphere-egu2020-15917, 2020
Andrea Carminati, Pascal Benard, Judith Schepers, Margherita Crosta, and Mohsen Zarebanadkouki
Bacteria alter the physical properties of soil hotspots by secreting extracellular polymeric substances EPS. Despite the biogeochemical importance of these alterations is well accepted, the physical mechanisms by which EPS shapes the properties of the soil solution and its interactions with the soil matrix are not well understood.
Here we show that upon drying in porous media EPS forms one-dimensional filaments and two-dimensional interconnected structures spanning across multiple pores. Unlike water, primarily shaped by surface tension, EPS remains connected upon drying thanks to its high extensional viscosity. The integrity of one-dimensional structures is explained by the interplay of viscosity and surface tension forces (characterized by the Ohnesorge number), while the formation of two-dimensional structures requires consideration of the interaction of EPS with the solid surfaces and external drivers, such as the drying rate. During drying, the viscosity of EPS increases and, at a critical point, when the friction between polymers and solid surfaces overcomes the water adsorption of the polymers, the concentration of the polymer solution at the liquid-gas interface increases asymptotically and the polymers can no longer follow the retreating gas-water interface. At this critical point the polymers do not move any longer and are deposited as two-dimensional surfaces, such as hollow cylinders or interconnected surfaces. EPS viscosity, specific soil surface and drying rates are the key parameters determining the transition from one- to two-dimensional structures.
The high viscosity of EPS maintains the connectivity of the liquid phase during drying in soil hotspots, such as bacterial colonies, the rhizosphere and biological soil crusts.
How to cite:
Carminati, A., Benard, P., Schepers, J., Crosta, M., and Zarebanadkouki, M.: Interplay between water adsorption and viscosity determines the spatial configuration of EPS during soil drying, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-4126, https://doi.org/10.5194/egusphere-egu2020-4126, 2020
Structural stability in agricultural soils is said to be maintained through production of ‘biological binding agents’, including temporary binding agents (fungi, roots), transient binding agents (EPS), and persistent binding agents (of less certain origin). We sampled soils from a long-term field trial, comprising previous grassland, arable and fallow land-uses in factorial combination with current land-uses of the same type: previous 3 land-uses x current 3 land-uses = 9 treatments (Redmile-Gordon et al., 2020). Total soil organic carbon (SOC), EPS (including protein, and polysaccharide fractions; Redmile-Gordon et al., 2014), and mean weight diameter (MWD) of water stable aggregates (Le Bissonnais, 1996) were quantified.
Both EPS and MWD were correlated, and were both strongly influenced by current land-use (implemented 2.5 years before sampling), but not by previous land-use (implemented > 50 years ago, terminated 2.5 years before sampling). While exopolysaccharides were significantly correlated to the soil’s structural stability (p = 0.027), proteinaceous EPS were more closely related to the associated gains in soil aggregate stability (p = 0.002).
In contrast to EPS and soil stability, total soil organic carbon (SOC) was strongly influenced by previous land-use. Importantly, this indicates that any capacity for relatively stable organic matter to contribute to the soil’s structural stability is overwhelmed by temporary/transient effects owed to current land-use. This is cause for optimism, as it seems the physical quality of soils might be improved by short-term application of managements that favour EPS production. This approach would represent a qualitative step beyond that of building total SOC, which can be difficult for land-managers to achieve. This study is the first to simultaneously assess the effects of land-use on proteinaceous and polysaccharide content of EPS, and link this to the structural stability of soils. Further understanding surrounding the ecology of EPS production, and disentangling the contributions of temporary (largely physical) vs. transient (biochemical) binding agents is hoped to contribute to the development of more efficient land-management strategies.
Le Bissonnais, Y., 1996. Aggregate stability and assessment of soil crustability and erodibility. 1. Theory and methodology. Eur. J. Soil Sci. 47, 425–437.
Redmile-Gordon, M., Brookes, P.C., Evershed, R.P., Goulding, K.W.T., Hirsch, P.R., 2014. Measuring the soil-microbial interface: extraction of extracellular polymeric substances (EPS) from soil biofilms. Soil Biol. Biochem. 72, 163–171.
Redmile-Gordon, M., Gregory, A.S., White, R.P., Watts, C.W. 2020. Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use. Geoderma, 363. https://doi.org/10.1016/j.geoderma.2019.114143
How to cite:
Redmile-Gordon, M.: Soil Structural Stability and Extracellular Polymeric Substances (EPS): transient binding agents affected by land-use., EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-5742, https://doi.org/10.5194/egusphere-egu2020-5742, 2020