CERES :: Browsing by Author "Otten, Wilfred"

Browsing by Author "Otten, Wilfred"

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Open Access
Accounting for soil architecture and microbial dynamics in microscale models: current practices in soil science and the path ahead
(Wiley, 2021-07-04) Pot, Valérie; Portell, Xavier; Otten, Wilfred; Garnier, Patricia; Monga, Olivier; Baveye, Philippe C.
Macroscopic models of soil organic matter (SOM) turnover have faced difficulties in reproducing SOM dynamics or in predicting the spatial distribution of carbon stocks. These models are based on a largely inadequate linear response of soil microorganisms to bulk concentrations of nutrients and it is clear that a new approach to SOM modelling is required. Introducing explicit microbial activity and organic matter (OM) reactivity in macroscopic models represents a challenge because of the fine spatial scales at which the processes occur. To get a better grasp on interactions that take place at the microscale, a new generation of SOM models have been developed at the spatial scale of the soil microenvironments where microorganisms evolve. These models are well adapted to challenge traditional hypotheses about the influence of soil architecture on soil microbial activity. Soil architecture provides the stage for a dynamic spatial accessibility of resources to microbes and the emergence of interactions between the actors in SOM decomposition. In this context, we review microscale models of microbial activity that have been designed for soils and soil analogues. To understand how these models account for spatial accessibility, we look in detail at how soil microenvironments are described in the different approaches and how microbial colonies are spatialized in these microenvironments. We present the advantages and disadvantages of the developed strategies and we discuss their limits.
Open Access
Analysis of physical pore space characteristics of two pyrolytic biochars and potential as microhabitat
(Springer Verlag, 2016-03-02) Schnee, Laura S.; Knath, Stefan; Hapca, Simona; Otten, Wilfred; Eickhorst, Thilo
Background and Aims Biochar amendment to soil is a promising practice of enhancing productivity of agricultural systems. The positive effects on crop are often attributed to a promotion of beneficial soil microorganisms while suppressing pathogens e.g. This study aims to determine the influence of biochar feedstock on (i) spontaneous and fungi inoculated microbial colonisation of biochar particles and (ii) physical pore space characteristics of native and fungi colonised biochar particles which impact microbial habitat quality. Methods Pyrolytic biochars from mixed woods and Miscanthus were investigated towards spontaneous colonisation by classical microbiological isolation, phylogenetic identification of bacterial and fungal strains, and microbial respiration analysis. Physical pore space characteristics of biochar particles were determined by X-ray μ-CT. Subsequent 3D image analysis included porosity, surface area, connectivities, and pore size distribution. Results Microorganisms isolated from Wood biochar were more abundant and proliferated faster than those from the Miscanthus biochar. All isolated bacteria belonged to gram-positive bacteria and were feedstock specific. Respiration analysis revealed higher microbial activity for Wood biochar after water and substrate amendment while basal respiration was on the same low level for both biochars. Differences in porosity and physical surface area were detected only in interaction with biochar-specific colonisation. Miscanthus biochar was shown to have higher connectivity values in surface, volume and transmission than Wood biochars as well as larger pores as observed by pore size distribution. Differences in physical properties between colonised and non-colonised particles were larger in Miscanthus biochar than in Wood biochar. Conclusions Vigorous colonisation was found on Wood biochar compared to Miscanthus biochar. This is contrasted by our findings from physical pore space analysis which suggests better habitat quality in Miscanthus biochar than in Wood biochar. We conclude that (i) the selected feedstocks display large differences in microbial habitat quality as well as physical pore space characteristics and (ii) physical description of biochars alone does not suffice for the reliable prediction of microbial habitat quality and recommend that physical and surface chemical data should be linked for this purpose.
Open Access
Bacterial distribution in soil microhabitats at different spatial scales
(Cranfield University, 2018-08-08 16:11) Otten, Wilfred; Eickhorst, Thilo; Juyal, Archana; Falconer, Ruth; Hapca, Simona; Schmidt, Hannes; C Baveye, Philippe
The data underpin the results described in the Geoderma paper by Juyal et al (2018) https://doi.org/10.1016/j.geoderma.2018.07.031 entitled 'Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales'. The data are represented in an Excel file and show counts of bacteria in individual sections of soil blocks and their corresponding pore geometry as determined by Xray CT at three different spatial scales. The data underpin the summary data described in the paper where a detailed method description is also provided.
Open Access
Building soil sustainability from root–soil interface traits
(Elsevier - Cell Press, 2022-02-12) Hallett, Paul D.; Marin, Maria; Bending, Gary D.; George, Timothy S.; Collins, Chris D.; Otten, Wilfred
Great potential exists to harness plant traits at the root–soil interface, mainly rhizodeposition and root hairs, to ‘build’ soils with better structure that can trap more carbon and resources, resist climate stresses, and promote a healthy microbiome. These traits appear to have been preserved in modern crop varieties, but scope exists to improve them further because they vary considerably between genotypes and respond to environmental conditions. From emerging evidence, rhizodeposition can act as a disperser, aggregator, and/or hydrogel in soil, and root hairs expand rhizosheath size. Future research should explore impacts of selecting these traits on plants and soils concurrently, expanding from model plants to commercial genotypes, and observing whether impacts currently limited to glasshouse studies occur in the field.
Open Access
Challenges in imaging and predictive modeling of rhizosphere process
(Springer, 2016-04-08) Roose, T.; Keyes, S. D.; Daly, K. R.; Carminati, A.; Otten, Wilfred; Vetterlein, D.; Peth, S.
Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.
Open Access
Changes in soil surface properties under simulated rainfall and the effect of surface roughness on runoff, infiltration and soil loss
(Elsevier, 2023-02-03) Bahddou, Sophia; Otten, Wilfred; Whalley, W. Richard; Shin, Ho-Chul; El Gharous, Mohamed; Rickson, R. Jane
Soil erosion by water is a result of detachment of particles or small aggregates from the soil surface followed by transport of the detached material. One of the elements that affects surface runoff and soil erosion is the soil surface roughness (SSR). Prior research reports that increasing SSR reduces generation of runoff and soil loss. In addition to that, it is widely reported that across-slope oriented roughness is better at controlling soil and water losses. However, to date there have been few studies into the effect of both magnitude and orientation of SSR on runoff, infiltration and soil erosion at the sub process level (i.e. by raindrop splash and overland flow), occurring simultaneously. In this study, the effects of up-down-slope oriented SSR (Treatment A), across-slope oriented SSR (Treatment B) and random SSR (Treatment C) were compared, along with a smooth surface (Treatment D). A moderate slope gradient of 10 %, a simulated rainfall intensity of 90 mm hr−1 and storm durations of 15 or 30 min were considered. The SSR was measured using the chain method, before and after the rainfall event. Images of the soil surface were taken using a hand-held laser scanner to monitor the effect of rainfall on the surface morphology. The outcome of this study shows that rainfall erosivity increases the SSR of the initially smooth surface, but decreases that of the initially rough surface, particularly in the random SSR treatment, where the decrease in SSR was 64 % of the pre-rainfall condition. This was due to the effects of raindrop impacts and overland flow. The random SSR treatment generated significantly more runoff and soil loss, and less infiltration than all other treatments (p < 0.001), but for raindrop splash erosion, there was no significant difference between random SSR and the other treatments. Contrary to expectations, the across-slope oriented SSR did not always reduce runoff and soil erosion compared to the up-down-slope orientation. This can be explained by degradation of surface microtopography by rainfall and runoff, as confirmed by the post-rainfall SSR measurements.
Open Access
Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales
(Elsevier, 2018-04-08) Juyal, Archana; Otten, Wilfred; Falconer, Ruth; Hapca, Simona; Schmidt, Hannes; Baveye, Philippe C.; Eickhorst, Thilo
To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescens was 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.
Open Access
Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp.
(Frontiers, 2018-07-13) Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Baveye, Philippe C.; Spiers, Andrew; Otten, Wilfred
Simplified experimental systems, often referred to as microcosms, have played a central role in the development of modern ecological thinking on issues ranging from competitive exclusion to examination of spatial resources and competition mechanisms, with important model-driven insights to the field. It is widely recognized that soil architecture is the key driver of biological and physical processes underpinning ecosystem services, and the role of soil architecture and soil physical conditions is receiving growing interest. The difficulty to capture the architectural heterogeneity in microcosms means that we typically disrupt physical architecture when collecting soils. We then use surrogate measures of soil architecture such as aggregate size distribution and bulk-density, in an attempt to recreate conditions encountered in the field. These bulk-measures are too crude and do not describe the heterogeneity at microscopic scales where microorganisms operate. In the current paper we therefore ask the following questions: (i) To what extent can we control the pore geometry at microscopic scales in microcosm studies through manipulation of common variables such as density and aggregate size?; (ii) What is the effect of pore geometry on the growth and spread dynamics of bacteria following introduction into soil? To answer these questions, we focus on Pseudomonas sp. and Bacillus sp. We study the growth of populations introduced in replicated microcosms packed at densities ranging from 1.2 to 1.6 g cm−3, as well as packed with different aggregate sizes at identical bulk-density. We use X-ray CT and show how pore geometrical properties at microbial scales such as connectivity and solid-pore interface area, are affected by the way we prepare microcosms. At a bulk-density of 1.6 g cm−3 the average number of Pseudomonas was 63% lower than at a bulk-density of 1.3 g cm−3. For Bacillus this reduction was 66%. Depending on the physical conditions, bacteria in half the samples took between 1.62 and 9.22 days to spread 1.5 cm. Bacillus did spread faster than Pseudomonas and both did spread faster at a lower bulk-density. Our results highlight the importance that soil physical properties be considered in greater detail in soil microbiological studies than is currently the case.
Open Access
Data for spread of bacteria in soil
(Cranfield University, 2020-04-20 14:34) Otten, Wilfred; Eickhorst, Thilo; Juyal, Archana; C Baveye, Philippe
Data set related to the paper 'Influence of soil structure on the spread of Pseudomonas fluorescens in soil at microscale' the objective of the study was to determine the influence of soil pore characteristics on the spread of bacteria in soil. Bacteria were introduced and locally and allowed to spread through soil. Soil was resin impregnated and the location of bacteria was observed in thin sections. X-ray CT was used to determine the physical characteristics of the pore space. The data set contains the raw data published in the accompanying paper. Treatment refers to the bulk density of the soil and 2 thin sections were counted for each sample. at each micro-site in soil pore characteristics are given in the table and the number of bacterial cells found in that section through observation and counting under the microscope. Counts are converted to cell densities. The data relate to the spread of bacteria and further analysis of the data is described in the paper
Open Access
Data supporting 'Functional root trait-based classification of cover crops to improve soil physical properties'
(Cranfield University, 2023-02-15 10:20) Hudek, Csilla; Otten, Wilfred; De Baets, Sarah; Putinica, Cristinel
Supporting data for the publication "Functional root trait-based classification of cover crops to improve soil physical properties".
Open Access
Data underpinning "Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations"
(Cranfield University, 2018-07-30 11:12) Portell-Canal, Xavier; Pot, Valérie; Garnier, Patricia; Otten, Wilfred; Baveye, Philippe
Figures and data used in the paper "Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations". See readme.txt file in the compressed files (.7z) for a description of the files included in the folder.
Open Access
Data underpinning "Three-Dimensional Study of F. graminearum Colonisation of Stored Wheat: Post-Harvest Growth Patterns, Dry Matter Losses and Mycotoxin Contamination"
(Cranfield University, 2020-08-07 08:19) Portell-Canal, Xavier; Garcia Cela, Esther; Verheecke, Carol; Medina Vaya, Angel; Otten, Wilfred; Magan, Naresh; Torrelles-RÃfales, Rosa
Data used in the paper "Three-Dimensional Study of F. graminearum Colonisation of Stored Wheat: Post-Harvest Growth Patterns, Dry Matter Losses and Mycotoxin Contamination". Data is found in comma separated values files (e.g., "data1.csv") and the data content explained in text files (e.g., "data2_Readme.txt").
Open Access
Development of a defined compost system for the study of plant-microbe interactions
(Nature Publishing Group, 2020-05-05) Masters-Clark, Emily; Shone, E.; Paradelo, M.; Hirsch, Penny R.; Clark, Ian M.; Otten, Wilfred; Brennan, Feargal P.; Mauchline, T. H.
Plant growth promoting rhizobacteria can improve plant health by providing enhanced nutrition, disease suppression and abiotic stress resistance, and have potential to contribute to sustainable agriculture. We have developed a sphagnum peat-based compost platform for investigating plant-microbe interactions. The chemical, physical and biological status of the system can be manipulated to understand the relative importance of these factors for plant health, demonstrated using three case studies: 1. Nutrient depleted compost retained its structure, but plants grown in this medium were severely stunted in growth due to removal of essential soluble nutrients - particularly, nitrogen, phosphorus and potassium. Compost nutrient status was replenished with the addition of selected soluble nutrients, validated by plant biomass; 2. When comparing milled and unmilled compost, we found nutrient status to be more important than matrix structure for plant growth; 3. In compost deficient in soluble P, supplemented with an insoluble inorganic form of P (Ca3(PO4)2), application of a phosphate solubilising Pseudomonas strain to plant roots provides a significant growth boost when compared with a Pseudomonas strain incapable of solubilising Ca3(PO4)2. Our findings show that the compost system can be manipulated to impose biotic and abiotic stresses for testing how microbial inoculants influence plant growth.
Open Access
Editorial: A profile of 70 years of soil research
(Wiley, 2018-01-18) Otten, Wilfred; Haygarth, P. M.; Baggs, E. M.
As current and recent presidents it has been a privilege and a pleasure on behalf of the British Society of Soil Science to assemble articles for the special anniversary issue of the European Journal of Soil Science (EJSS) and Soil Use and Management (SUM). The papers assembled reflect the spectrum of contemporary issues in soil science, which also serve as a reminder of how our soil science has changed over the years, letting us peer into the past and reflect on 70 years of the Society. In addition to being a celebration of soil science, this is also an opportunity to celebrate and reflect upon the British Society of Soil Science itself and its two journals.
Open Access
Effect of surface roughness on runoff, infiltration and soil loss
(Cranfield University, 2023-02-06 12:12) Bahddou, Sophia; Otten, Wilfred; Rickson, Jane; Whalley, Richard; Shin, Ho-Chul; El Gharous, Mohamed
The excel spreadsheet presents the raw data generated from the experiments quantifying soil erosion that are described in the paper by Bahddou et al., 2023, published in Geoderma (Bahddou et al., 2023. Changes in soil surface properties under simulated rainfall and the effect of surface roughness on runoff, infiltration and soil loss). The experimental design and the statistical method are mentioned in the methodology section of the paper. The soil surface roughness data is expressed in two columns (E-F) presenting the measurements before and after the rainfall event (Table 3 and Figure 4 of the paper by Bahddou et al). The variables of the runoff, infiltrate, soil loss and sediment concentration are expressed in the columns G-R, where each variable is expressed in three columns presenting the 1st fifteen minutes of the rainfall event, the 2nd fifteen minutes of the rainfall event and the total 30 minutes of the rainfall event (Table 4 and Figures 6 and 7 in the paper by Bahddou et al., 2023). The columns S-U present the splash erosion after 30 minutes of rainfall, including the measurements on the ridges and in the furrows of Treatment B. More details are in the Materials and Methods section and the Results sections of the publication.
Open Access
Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain
(Frontiers Media, 2018-08-27) Baveye, Philippe C.; Otten, Wilfred; Kravchenko, Alexandra; Balseiro-Romero, María; Beckers, Éléonore; Chalhoub, Maha; Darnault, Christophe; Eickhorst, Thilo; Garnier, Patricia; Hapca, Simona; Kiranyaz, Serkan; Monga, Olivier; Mueller, Carsten W.; Nunan, Naoise; Pot, Valérie; Schlüter, Steffen; Schmidt, Hannes; Vogel, Hans-Jörg
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
Open Access
Evaluating phosphorus availability from sewage sludge derived pyrochar and hydrochar on spring wheat
(Cranfield University, 2021-09) Pimenta Da Costa Ocampo, Maria; Sakrabani, Ruben; Otten, Wilfred; Gasco Guerrero, Gabriel; Mendez Lazaro, Ana Maria
The production of sewage sludge is expected to increase as the population continuously develops worldwide. Being a source of nutrients, the re-use of this material as soil amendment could address the current unstable situation. Sewage sludge could be an alternative source of available phosphorus to chemical fertilisers that could help to remediate the growing demand of mineral phosphorus reserves. In parallel, it also acts as a good source of organic matter for low fertile soils resulting from overexploitation and erosion events. Even though recent studies have been focusing on the use of sewage sludge on land application, there is still a stigma attached to this practice as its use in agriculture has to be managed carefully due to its variability in physical-chemical properties. The perception of sewage sludge as a source of pollutants relies on current research and it´s tampered by the huge diversity of feedstocks and the variability of it depending on the sampling. Thermal treatments are assessed as route towards the production of alternative P fertilisers from sewage sludge. Two pyrochars were produced though pyrolysis at 400⁰C (P400-1) and 300⁰C (P300-1) for 1h using pre-oven dried (105⁰C-48h) sewage sludge from Spain (SSES). Two hydrochars were obtained through Hydrothermal Carbonization at 180⁰C (H180-4) and 240⁰C (H240-4) for 4h, using SSES adjusted to 20% dry matter. P availability changes of SSES were evaluated after thermal treatments and its effect on soil available P content when added on their own (5, 10, 20 t ha⁻¹) and in combination with a commercialized sewage sludge from UK (SSUK) as soil amendment (50% char 50% SSUK, at 10, 20, 40 t ha⁻¹). Single and combined amendment were carried out at the same time, comprising a total of 136 pots (H:50 cm; D:10.5 cm). Thermal treatments reduced available-P in all derivatives H180-4 (45.9%), H240-4 (57.5%), P300-1 (76.2%), P400-1 (83.6%) from 150.4 mg kg⁻¹SSES. Nonetheless, one single application over two cropping seasons of spring wheat in a glasshouse increased available-P to 23.7-26.7 mg kg⁻¹ from 1.5 mg kg⁻¹in control soil when combined at 40 t ha⁻¹. No significant improvement was observed in grain yield over two seasons among the treatments, but the nutrient balance and heavy metals assessment indicated an evolution of these materials in the soil over time. The use of pyrochars, produced a buffering effect that lasted two seasons preventing an acidification of the loamy sandy soil that couldn’t be achieved though hydrothermal carbonisation. This study shows the potential of thermal treatments as pre-treatment, and its limitations. Sewage sludge in agriculture must be managed carefully due to its variability in physical-chemical properties and their content of Al, Fe and heavy metals. Acidification of the soil should be avoided in order to obtain better results on P availability. Pyrolysis of sewage sludge may not replace mineral fertilisers, but it could be used to prevent acidification if used as a pre-treatment of sewage sludge, increasing carbon stability and organic matter in loamy sandy soil, immobilizing heavy metals, and providing a slow release of P.
Open Access
Evaluation of pedotransfer functions to estimate some of soil hydraulic characteristics in North Africa: a case study from Morocco
(Frontiers, 2023-02-08) Beniaich, Adnane; Otten, Wilfred; Shin, Ho-Chul; Cooper, Hannah; Rickson, R. Jane; Soulaimani, Azia; El Gharous, Mohamed
Soil hydraulic properties are an important factor to optimize and adapt water management for a given crop. Pedotransfer functions (PTFs) present a solution to predict soil variables such as hydraulic properties, using fundamental soil properties. In this research, we compared two sources of soil information: iSDAsoil data and field data, in four regions in Morocco. We then used this data to evaluate published data and developed new PTFs using soil information to estimate soil gravimetric moisture content at saturation (w0), field capacity (w330) and permanent wilting point (w15000). A total of 331 samples were collected from four regions: Doukkala, Gharb-Loukous, Moulouya and Tadla. The data was divided into calibration and validation datasets. For development of different PTFs, we used simple linear regression, multiple linear regression, regression tree, Cubist algorithm, and random forest approaches. PTFs developed by Dijkerman (Geoderma, 1988, 42, 29–49) presented the best performance, showing lower RMSE, Bias and MAE compared to other PTFs. Using multiple linear regression to develop PTFs, models based on clay, silt and soil organic matter as input variables showed the best performance after calibration (R2 of 0.590, 0.785, 0.786 for w0, w330, and w15000, respectively). Regarding the techniques based on machine learning, random forest showed the best performance after calibration compared with other algorithms (R2 of 0.930, 0.955, 0.954 for w0, w330, and w15000, respectively). PTFs represent a low cost and easy technique to estimate soil hydraulic properties, to improve water management efficiency for the farmers.
Open Access
Exploiting mycorrhizal selection of beneficial rhizosphere bacteria from the soil microbiome.
(Cranfield University, 2021-09) Masters-Clark, Emily; Mauchline, Tim; Otten, Wilfred; Hirsch, Penny; Brennan, Fiona; Clark, Ian; Harris, Jim A.
Soil health is dependent on its diverse communities of microbes. Many of these microorganisms enhance plant growth and enrich the soil. However, the interactions between communities of beneficial microbes remain unclear. Arbuscular mycorrhizal fungi (AMF) are responsible for the most prolific beneficial plant-fungal interaction. However, their influence on the diverse range of plant growth promoting rhizobacteria (PGPR) that also associate with plant roots is yet to be fully elucidated. This research investigates the tripartite interactions between host plant-AMF-PGPR using next-generation sequencing and culture- dependent methodology to define the effect of AMF inoculation on the taxonomic and functional characteristics of the bacterial assemblage of the root microbiome of white clover (Trifolium repens). Soil from two land use types (grassland and bare fallow) amended with fertiliser and/or AMF inoculants are used to describe the effect of these management components on the function of beneficial microbes in cropping systems. The AMF Funneliformis geosporum affected the taxonomic composition of bacteria in the rhizosphere but not the rhizoplane. However, soil type and fertiliser were more influential determinants of bacterial taxa and function. Using split-root microcosm experiments with root exclusion meshes, the dispersal of bacteria was observed in the absence of AMF hyphae. The approaches were combined to show that root microbiome establishment is independent of AMF hyphal facilitation or selection of beneficial bacterial traits or taxa. In vitro predictive measures were used to design a putative Phosphorus solubilising consortium comprised of synergistic P-solubilising rhizobacteria and AMF. Plant health parameters were influenced by the addition of Ca₃PO₄ but were unaffected by any microbial combination. The performance of a putative bioinoculant is dependent on many external factors which can negatively impact the intended function. This work is an important indicator of the complexity of the soil microbiome and demonstrates the profound influence of agronomic inputs on microbial function.
Open Access
A field system for measuring plant and soil carbon fluxes using stable isotope methods
(Wiley, 2020-06-21) McCloskey, Christopher S.; Otten, Wilfred; Paterson, Eric; Ingram, Benjamin R.; Kirk, Guy J. D.
There is a lack of field methods for measuring plant and soil processes controlling soil organic matter (SOM) turnover over diurnal, seasonal, and longer time-scales with which to develop datasets for modelling. We describe an automated field system for measuring plant and soil carbon fluxes over such time-scales using stable isotope methods, and we assess its performance. The system comprises 24 large (1-m deep, 0.8-m diameter) cylindrical lysimeters connected to gas-flux chambers and instruments. The lysimeters contain intact, naturally-structured C3 soil planted with a C4 grass. Fluxes of CO2 and their 13C isotope composition are measured 3-times daily in each lysimeter, and the isotope composition is used to partition the fluxes between plant and soil sources. We investigate the following potential sources of error in the measurement system and show they do not significantly affect the measured CO2 fluxes or isotope signatures: gas leaks; the rate of gas flow through sampling loops; instrument precision and drift; the concentration-dependence of isotope measurements; and the linearity of CO2 accumulation in the chambers and associated isotope fractionation resulting from different rates of 13CO2 and 12CO2 diffusion from the soil. For the loamy grassland soil and US prairie grass (Bouteloua dactyloides) tested, the precision of CO2 flux measurements was ± 0.04 % and that of the flux partitioning ± 0.40 %. We give examples of diurnal and seasonal patterns of plant and soil C fluxes and soil temperature and moisture. We discuss the limitations of the isotope methodology for partitioning fluxes as applied in our system. We conclude the system is suitable for measuring net ecosystem respiration fluxes and their plant and soil components with sufficient precision to resolve diurnal and seasonal patterns

Browsing by Author "Otten, Wilfred"

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