Modeling the effect of microscale heterogeneities on soil bacterial dynamics and the impact on soil functions

2021 ◽  
Author(s):  
Simon Zech ◽  
Nadja Ray ◽  
Thomas Ritschel ◽  
Kai Uwe Totsche ◽  
Alexander Prechtel
Keyword(s):  
Organic Matter ◽  
Liquid Phase ◽  
Reactive Transport ◽  
Geodesic Distance ◽  
Mechanistic Model ◽  
Bacterial Species ◽  
Soil Samples ◽  
Multiphase Model ◽  
Order Kinetic ◽  
The Impact

<p><span>There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly diverse as they are. Mathematically based modeling can facilitate the understanding of their development and function in soils, e.g. with respect to habitat </span><span>and carbon cycling</span><span>.</span></p><p><span>Our mechanistic model is based on [1,2] and allows studying the spatiotemporal dynamics of bacteria in unsaturated soil samples. In this presentation, different levels of saturation are investigated, for which the fluid (liquid and gas) distributions are calculated according to a morphological model</span><span>.</span> <span>As in [3] various bacteria strains and organic matter are heterogeneously distributed in CT scans of various soil samples.</span></p><p><span>The bacteria strains grow based on Michaelis-Menten kinetics due to the uptake of oxygen and dissolved organic carbon (DOC) present in the liquid phase. The development of bacterial colonies is realized in a cellular automaton framework (CAM) as presented in [1,2]. DOC is either present as a carbonaceous solution or hydrolized by a first order kinetic from heterogeneously distributed particulate organic matter (POM) sources. The diffusion of both nutrients oxygen and DOC are described by means of reactive transport equations, which include a Henry conditions for the transfer from/into the gas phase. We apply the local discontinuous Galerkin (LDG) method as a discretization scheme.</span></p><p><span>Our simulations show that the impact heterogeneity in nutrient and bacteria distribution has on overall biodegradation kinetics strongly depends on the scale of interest. On the scale of soil microaggregates (</span><span><em><</em></span><span>250 μm), only very specific cases can be distinguished </span><span>globally</span><span>, e.g. when nutrient sources are isolated from bacteria due to a disconnected liquid phase. </span><span>Locally </span><span>however</span><span>, heterogeneities in nutrient distribution impact </span><span>the </span><span>development of bacteria populations, </span><span>e.g. a lower geodesic distance of bacteria to nutrient promotes bacteria growth locally. Such local effects can have an important role for competing bacterial species. </span></p><p><span>O</span><span>n larger scales (millimeter scale), such heterogeneities can </span><span>also </span><span>have a large impact. </span><span>We conclude that the heterogeneous spatial structure must be resolved scale-dependently.</span></p><p> </p><p> </p><p><span>[1] </span><span>N. Ray, A. Rupp and A. Prechtel. </span><span><em>Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media</em></span><span>, Adv. </span>Water Resour. 107, 393-404 (2017), doi:10.1016/j.advwatres.2017.04.001.</p><p>[2] A. Rupp, K. Totsche, A. Prechtel and N. Ray. <span><em>Discrete-continuum multiphase model for structure formation in soils including electrostatic effects</em></span><span>, Front. </span>Environ. Sci. 6:96 (2018), doi:10.3389/fenvs.2018.00096.</p><p><span>[3] </span><span>X. Portell, V. Pot, P. Garnier, W. Otten and P.C. Baveye. </span><span><em>Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: insights from computer simulations.</em></span><span>, Front. </span>Microbiol. 9:1583 (2018), doi:10.3389/fmicb.2018.01583.</p>

scholarly journals ORGANIC MATTER FRACTIONS IN A QUARTZIPSAMMENT UNDER CULTIVATION OF IRRIGATED MANGO IN THE LOWER SÃO FRANCISCO VALLEY REGION, BRAZIL

2015 ◽  
Vol 39 (4) ◽  
pp. 1068-1078 ◽  
Author(s):  
José Alberto Ferreira Cardoso ◽  
Augusto Miguel Nascimento Lima ◽  
Tony Jarbas Ferreira Cunha ◽  
Marcos Sales Rodrigues ◽  
Luis Carlos Hernani ◽  
...  
Keyword(s):  
Organic Matter ◽  
Humic Acid ◽  
Soil Organic Matter ◽  
Fulvic Acid ◽  
Agricultural Production ◽  
Soil Layer ◽  
Soil Samples ◽  
C Stocks ◽  
Organic Matter Fractions ◽  
The Impact

Improper land use has lead to deterioration and depletion of natural resources, as well as a significant decline in agricultural production, due to decreased soil quality. Removal of native vegetation to make way for agricultural crops, often managed inadequately, results in soil disruption, decreased nutrient availability, and decomposition of soil organic matter, making sustainable agricultural production unviable. Thus, the aim of the present study was to evaluate the impact of growing irrigated mango (over a 20 year period) on the organic carbon (OC) stocks and on the fractions of soil organic matter (SOM) in relation to the native caatinga (xeric shrubland) vegetation in the Lower São Francisco Valley region, Brazil. The study was carried out on the Boa Esperança Farm located in Petrolina, Pernambuco, Brazil. In areas under irrigated mango and native caatinga, soil samples were collected at the 0-10 and 10-20 cm depths. After preparing the soil samples, we determined the OC stocks, carbon of humic substances (fulvic acid fractions, humic acid fractions, and humin fractions), and the light and heavy SOM fractions. Growing irrigated mango resulted in higher OC stocks; higher C stocks in the fulvic acid, humic acid, and humin fractions; and higher C stocks in the heavy and light SOM fraction in comparison to nativecaatinga, especially in the uppermost soil layer.

Carbon mineralisation and pore size classes in undisturbed soil cores

Soil Research ◽  
2013 ◽  
Vol 51 (1) ◽  
pp. 14 ◽  
Author(s):  
Liesbeth Bouckaert ◽  
Steven Sleutel ◽  
Denis Van Loo ◽  
Loes Brabant ◽  
Veerle Cnudde ◽  
...  
Keyword(s):  
Organic Matter ◽  
Pore Network ◽  
Order Kinetic ◽  
Soil Cores ◽  
Undisturbed Soil ◽  
Soil Matrix ◽  
X Ray ◽  
C Mineralisation ◽  
The Impact ◽  
Undisturbed Soil Cores

Soil pore network effects on organic matter turnover have, until now, been studied indirectly because of lack of data on the 3D structure of the pore network. Application of X-ray computed tomography (X-ray CT) to quantify the distribution of pore neck size and related pore sizes from undisturbed soil cores, with simultaneous assessment of carbon (C) mineralisation, could establish a relationship between soil organic matter (SOM) decomposition and soil pore volumes. Eighteen miniature soil cores (diameter 1.2 cm, height 1.2 cm) covering a range of bulk densities were incubated at 20°C for 35 days. Respiration was modelled with a parallel first- and zero-order kinetic model. The cores were scanned at 9.44 µm resolution using an X-ray CT scanner developed in-house. Correlation analysis between the slow pool C mineralisation rate, ks, and pore volume per pore neck class yielded significant (P < 0.05) positive correlations: r = 0.572, 0.598, and 0.516 for the 150–250, 250–350, and >350 µm pore neck classes, respectively. Because larger pores are most probably mainly air-filled, a positive relation with ks was ascribed to enhanced aeration of smaller pores surrounding large pores. The weak and insignificant relationship between the smallest pore neck class (<9.44 µm) and ks could be explained by obstructed microbial activity and mobility or diffusion of exo-enzymes and hydrolysis products as a result of limited oxygen availability. This study supports the hypothesis that the impact of soil structure on microbial processes occurs primarily via its determination of soil water distribution, which is possibly the main driver for the location of C mineralisation in the soil matrix.

scholarly journals Biodeterioration mechanisms and kinetics of SCM and aluminate based cements and AAM in the liquid phase of an anaerobic digestion

2018 ◽  
Vol 199 ◽  
pp. 02003 ◽  
Author(s):  
Marie Giroudon ◽  
Matthieu Peyre Lavigne ◽  
Cédric Patapy ◽  
Alexandra Bertron
Keyword(s):  
Organic Matter ◽  
Anaerobic Digestion ◽  
Liquid Phase ◽  
Biological Activities ◽  
Concrete Durability ◽  
Slag Cement ◽  
Cement Pastes ◽  
The Impact ◽  
Kinetics Of ◽  
Aluminate Cement

In biogas structures, concrete faces aggressive media during anaerobic digestion. Biological activities allow the conversion of organic matter into biogas, leading to a medium characterized by a variability of composition in time and space. In order to ensure the sustainability of this expanding industry, solutions for increasing concrete durability are needed. This study aims to analyse the deterioration mechanisms of different binders focusing on the impact of the binder nature on the medium (biochemical composition) during the digestion. Binders with favourable composition to chemically aggressive media were tested: slag cement (CEM III/B), calcium aluminate cement (CAC) and metakaolin-based alkaliactivated material (MKAA), and a reference binder: OPC (CEM I). They were exposed to three anaerobic digestion cycles in liquid phase in laboratory bioreactors. The organic acids and ammonium concentrations of the liquid phase were monitored by GC and HPIC. For OPC and slag cement pastes, the chemical and mineralogical changes were characterized by SEM/EDS and XRD. Locally, the presence of binder materials has an impact on the kinetics of the digestion reaction, and therefore on the quantities of gas produced. Ammonium concentrations were above the XA3 class range. Under the conditions explored, biodeterioration mainly led to the carbonation of cement pastes.

scholarly journals Small variations of soil properties control fire-induced water repellency .

2014 ◽  
Vol 4 ◽  
Author(s):  
Jorge Mataix-Solera ◽  
Lorena M. Zavala ◽  
Antonio Jordán ◽  
Gema Bárcenas-Moreno ◽  
Elena Lozano ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Properties ◽  
Plant Species ◽  
Water Repellency ◽  
Soil Samples ◽  
Soil Types ◽  
Water Repellent ◽  
Key Factors ◽  
The Impact

Fire induced soil water repellency (WR) is controlled by many different factors (temperature reached, amount and type of fuel, etc.). Soil properties may determine the occurrence and intensity of this property in burned soils. The objectives of this paper are to make advances in the study of soil properties as key factors controlling the behaviour of fire-induced WR, and to study the impact of pre-fire SOM content and SOM quality in fire-induced soil WR. In this research, experimental laboratory burnings were carried out using soil samples from different sites with different lithologies, soil types and plant species. Soil samples taken from the same site differ only in quantity and quality of soil organic matter, as they were collected from under different plant species. All soil samples were heated in a muffle furnace at 200, 250, 300 and 350 ºC without the addition of any fuel load. WR was measured using the water drop penetration time test (WDPT). The results showed significant differences between soil types and plant species, indicating that small differences in soil properties may act as key factors controlling the development and persistence of WR reached, with burned soil samples ranging from wettable to extremely water repellent. The main soil property controlling the response was texture, specifically sand content. The quality of organic matter was also observed to have an effect, since soil samples from the same site with similar organic matter contents, but taken from beneath different plant species, showed different WR values after burning.

scholarly journals Enzymatic Activity and Its Relationship with Organic Matter Characterization and Ecotoxicity to Aliivibrio fischeri of Soil Samples Exposed to Tetrabutylphosphonium Bromide

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1565
Author(s):  
Arkadiusz Telesiński ◽  
Barbara Pawłowska ◽  
Robert Biczak ◽  
Marek Śnieg ◽  
Jacek Wróbel ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Samples ◽  
Quantitative Composition ◽  
Phosphorus Cycle ◽  
Tetrabutylphosphonium Bromide ◽  
Ft Ir ◽  
Activity Of Enzymes ◽  
Aliivibrio Fischeri ◽  
The Impact ◽  
Higher Doses

This study aimed to determine the impact of tetrabutylphosphonium bromide [TBP][Br] on the soil environment through an experiment on loamy sand samples. The tested salt was added to soil samples at doses of 0 (control), 1, 10, 100, and 1000 mg kg−1 dry matter (DM). During the experiment, the activity of selected enzymes involved in carbon, phosphorus, and nitrogen cycles, characteristics of organic matter with Fourier-transform infrared (FT-IR) spectroscopy, and toxicity of soil samples in relation to Aliivibrio fischeri were determined at weekly intervals. The results showed that low doses of [TBP][Br] (1 and 10 mg kg−1 DM) did not have much influence on the analyzed parameters. However, the addition of higher doses of the salt into the soil samples (100 and 1000 mg kg−1 DM) resulted in a decrease in the activity of enzymes participating in the carbon and phosphorus cycle and affected the activation of those enzymes involved in the nitrogen cycle. This may be due to changes in aerobic conditions and in the qualitative and quantitative composition of soil microorganisms. It was also observed that the hydrophobicity of soil organic matter was increased. Moreover, the findings suggested that the soil samples containing the highest dose of [TBP][Br] (1000 mg kg−1 DM) can be characterized as acute environmental hazard based on their toxicity to Aliivibrio fischeri bacteria. The increased hydrophobicity and ecotoxicity of the soil samples exposed to the tested salt were also positively correlated with the activity of dehydrogenases, proteases, and nitrate reductase. Observed changes may indicate a disturbance of the soil ecochemical state caused by the presence of [TBP][Br].

scholarly journals Seasonal Variation in Physicochemical Properties of Soil within the Vicinity of an Iron Smelting Factory - Implication on Standing Vegetation

2016 ◽  
Vol 8 (2) ◽  
pp. 220-225 ◽  
Author(s):  
Olusanya Abiodun OLATUNJI ◽  
Emmanuel Timilehin KOMOLAFE ◽  
Samson Olajide OKE
Keyword(s):  
Organic Matter ◽  
Physicochemical Properties ◽  
Soil Nutrient ◽  
Soil Samples ◽  
Iron Smelting ◽  
Top Soil ◽  
Dry Seasons ◽  
High Level ◽  
The Impact ◽  
Properties Of Soil

This study examined the seasonal variations in the physicochemical properties of soil around the vicinity of an iron smelting factory in Fashina area, Ile-Ife, with the aim of monitoring the impact on the soil characteristics, nutrient availability and its possible consequence on the surrounding vegetation. Four study plots, each measuring 50 × 50 m were selected around the iron and smelting Factory. Soil samples were collected randomly and analysed during the rainy and dry seasons at a depth of 0-20 cm, representing the top soil using soil auger. The soil samples were analysed for particle size, soil texture, pH and availability of some basic soil nutrient such as nitrogen, organic carbon, potassium, phosphorus, etc. The study revealed that the physicochemical properties of soil in focus varied across the plots, which may be a consequence of the gradient created by the citing of iron smelting factory, but the data obtained did not significantly varied within the seasons. Furthermore, high organic matter was recorded in all the plots under study; this might be due to the fact that the study area was rich in clay. More clayey soils generally tend to contain higher levels of organic matter, mainly because of the tendency of clays to slow down microbial degradation of organic matter, as clays form clay-humus complexes with organic matter. Also, the heavy metal distribution varied within the two seasons, as most of the metals showed high level of concentration in the rainy season.

The impact of fertilization regime and land use change on the SOM after 60 years of maize cropping

2020 ◽  
Author(s):  
Zoltán Szalai ◽  
Ujházy Noémi ◽  
Anna Vancsik ◽  
Azer Hallabi ◽  
Gergely Jakab ◽  
...  
Keyword(s):  
Land Use ◽  
Organic Matter ◽  
Land Use Change ◽  
Microbial Diversity ◽  
Arable Land ◽  
Soil Samples ◽  
Size Exclusion ◽  
Rrna Gene ◽  
Arable Soils ◽  
The Impact

&lt;p&gt;The top metre of the soil is one of the largest terrestrial carbon reservoirs. More than 50% of the soil carbon is stored as soil organic matter (SOM). Several papers report about the SOM losses due to tillage and land-use change. On the other hand, a huge amount of papers focus on the environmental potential of various min-till, no-till and other techniques for regenerative agriculture. The change of the fertilization regime also has an influence on SOM so it also can influence the humus status of the soils. This presentation focuses on the effects of different kinds of fertilization and abandonment of arable lands on the quantity and quality of the SOM.&lt;br&gt;The present study is based on Martonv&amp;#225;s&amp;#225;r Experimental Station (Hungary) which was established in 1958. The research focused on maize monoculture with the following treatments: (a) no fertilization, (b) NPK, (c) NPK with manure addition. The soil of the plots is Chernozem. Two controls were selected: (a) a natural Grassland and a secondary grassland. The secondary grassland was an arable land until 1990. Five repetitions of soil samples were taken from each plot and times. Soils were fractionated to silt and clay associated OM (s+c), aggregate associated OM (S+A), dissolved organic matter (DOM) and particulate organic matter (POM) according to Zimmermann&amp;#8217;s method (4). Quality parameters of the DOM were studied by CN analyser, UV-Vis spectrometer, spectrofluorometer, zetasizer and size exclusion chromatograph. Solid SOM fractions were studied by CHNS analyser, ATR-FTIR and DRIFT FTIR. The V3-V4 regions of the 16S rRNA gene obtained from the soil samples were sequenced on the Illuma platform for the description of microbial diversity.&lt;br&gt;Twenty years were enough to restore the natural SOM content of the soils (land-use change from arable land to grassland). Labile fractions of the SOM were higher in case of secondary than the primary grasslands. We have found differences in weight ratios of SOM fractions between fertilization regimes, as well. The proportion of microbial contribution to SOM were higher in the arable soils than the grasslands based on the C:N ratios of the SOM. However, the predominance of phyla Proteobacteria, Acidobacteria, Bacteriodetes, Actinobacteria and Verrucomicrobia in all studied soils, microbial diversity is generally higher in the grasslands than in the arable plots. The DOM of different fertilization regimes and land uses have shown the most characteristic differences. The difference between arable plots (with various fertilization regimes) and grasslands can be characterized by humic substances (HS) with higher condensation degree and molecular mass. The application of manure has result same proportion of peptide-like components and HS with lower molecular as the DOM of grassland soils.&lt;br&gt;The microbial diversity of abandoned arable land remained similar to that of the arable lands over twenty years. The major part of the growth of SOM occurred in the labile fractions. The change of the fertilization regime also has limited potential to grow a total mass of SOM.&lt;br&gt;Support of the GINOP 2.3.2-15-2016-00056 and National Research, Development and Innovation Office under contracts K123953 are gratefully acknowledged.&lt;/p&gt;

Organic matter release in low temperature thermal treatment of biological sludge for reduction of excess sludge production

2006 ◽  
Vol 54 (5) ◽  
pp. 59-68 ◽  
Author(s):  
E. Paul ◽  
P. Camacho ◽  
D. Lefebvre ◽  
P. Ginestet
Keyword(s):  
Heat Treatment ◽  
Organic Matter ◽  
Thermal Treatment ◽  
Activated Sludge ◽  
Order Kinetic ◽  
Excess Sludge ◽  
Digested Sludge ◽  
Significant Difference ◽  
The Impact ◽  
Sludge Production

Thermal treatment applied in association with a biological system allows for a significant reduction in excess sludge production (∼50%). In general, heat treatment is described as a sludge disintegration technique. This paper offers a thorough study on the impact of heat treatment, at temperatures below 100 °C, on the solubilisation of the sludge COD and its biodegradability. Discontinuous heating experiments were performed on activated and digested sludge. At all temperatures tested the released COD for digested sludge was systematically higher than that for activated sludge (15 and 40%, respectively, at 95 °C for 40 min of contact time). For the first 30 min, a 1st order kinetic, with respect to the residual COD, was systematically found. In the range of 40–95 °C, digested sludge had a lower activation energy than activated sludge (26 kcal/mol compared to 70–160 kcal/mol). COD solubilisation is thus more positively influenced by temperature in the case of activated sludge. This may be due to the significant difference in the ratio of protein/carbohydrate in digested and activated sludge (1–5 and 0.2–0.7, respectively). The increase in the COD/TKN ratio in the solubilised fraction after thermal treatment of activated sludge suggests a preferential solubilisation of proteins over carbohydrates. Respirometric tests performed on the solubilised COD showed that whatever the sludge origin, only 40–50% of released COD is biodegradable at a conventional hydraulic retention time (i.e. 24 h). Hence, heat treatment would act more through organic matter solubilisation rather than by a biodegradability increase.

scholarly journals Concentration of lead and the proportion of sedimentary organic matter , clay minerals , non-clay minerals and soil gradation , City of Nasiriyah , Southern Iraq

2018 ◽  
Vol 12 (1) ◽  
pp. 34-39
Author(s):  
Baghdad Science Journal
Keyword(s):  
Organic Matter ◽  
Clay Minerals ◽  
Organic Matter Content ◽  
Average Concentration ◽  
Matter Content ◽  
Soil Samples ◽  
Sedimentary Organic Matter ◽  
Pollution Levels ◽  
Natural Factors ◽  
The Impact

The present research included sampling and analysis of 41 soil samples , the samples cover various areas of Nasiriyah city (industrial,commercial,residential and agricultural ) to estimate pollution levels of lead element and determine the correlation between lead concentration and natural factors in soil which represent sedimentary organic matter content, granular gradient, clay minerals and non-clay minerals . The results of the current study showed that the average concentration of lead in the soil samples was 61.12 ppm , it was noticed an increase in the concentration of lead in environmental components in the area of this study especially in residential , industrial and commercial location and the impact of natural factors of the soil was limited and the main factors of pollution is resulting from human activities

scholarly journals Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling

2020 ◽  
Author(s):  
Hyun-Seob Song ◽  
James C. Stegen ◽  
Emily B. Graham ◽  
Joon-Yong Lee ◽  
Vanessa A. Garayburu-Caruso ◽  
...  
Keyword(s):  
Organic Matter ◽  
Reactive Transport ◽  
Oxidative Degradation ◽  
Reaction Rates ◽  
Ecosystem Dynamics ◽  
Thermodynamic Efficiency ◽  
Specific Response ◽  
Biogeochemical Modeling ◽  
Biogeochemical Models ◽  
The Impact

AbstractPredictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation into biogeochemical models is often prohibited due to an over-simplified description of reaction networks. To fill this gap, we proposed a new concept of biogeochemical modeling—termed substrate-explicit modeling—that enables parameterizing OM-specific oxidative degradation pathways and reaction rates based on the thermodynamic properties of OM pools. The resulting kinetic models are characterized by only two parameters regardless of the complexity of OM profiles, which can greatly facilitate the integration with reactive transport models for ecosystem simulations by alleviating the difficulty in parameter identification. For every detected organic molecule in a given sample, our approach provides a systematic way to formulate reaction kinetics from chemical formula, which enables the evaluation of the impact of OM character on biogeochemical processes across conditions. In a case study of two sites with distinct OM thermodynamics, our method not only predicted oxidative degradation to be primarily driven by thermodynamic efficiency of OM consistent with experimental rate measurements, but also revealed previously unknown critically important aspects of biogeochemical reactions, including their condition-specific response to carbon and/or oxygen limitations. Lastly, we showed that the proposed substrate-explicit modeling approach can be synergistically combined with enzyme-explicit approach to provide improved predictions. This result led us to present integrative biogeochemical modeling as a unifying framework that can ideally describe the dynamic interplay among microbes, enzymes, and substrates to address advanced questions and hypotheses in future studies. Altogether, the new modeling concept we propose in this work provides a foundational platform for unprecedented predictions of biogeochemical and ecosystem dynamics through enhanced integration with diverse experimental data and extant modeling approaches.

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