Evaluating the interaction of biofilms, organic matter and soil structures at the pore scale

2021 ◽  
Author(s):  
Alexander Prechtel ◽  
Simon Zech ◽  
Alice Lieu ◽  
Raphael Schulz ◽  
Nadja Ray
Keyword(s):  
Organic Matter ◽  
Structural Changes ◽  
Effective Diffusivity ◽  
Computational Domain ◽  
Pore Scale ◽  
Gas Phases ◽  
Soil Structures ◽  
Ldg Method ◽  
Conventional Models ◽  
Diffusive Processes

<div class="description js-mathjax"> <p>Key functions of soils, such as permeability or habitat for microorganisms, are determined by structures at the microaggregate scale. The evolution of elemental distributions and dynamic processes can often not be assessed experimentally. So mechanistic models operating at the pore scale are needed.<br />We consider the complex coupling of biological, chemical, and physical processes in a hybrid discrete-continuum modeling approach. It integrates dynamic wetting (liquid) and non-wetting (gas) phases including biofilms, diffusive processes for solutes, mobile bacteria transforming into immobile biomass, and ions which are prescribed by means of partial differential equations. Furthermore the growth of biofilms as, e.g., mucilage exuded by roots, or the distribution of particulate organic matter in the system, is incorporated in a cellular automaton framework (CAM) presented in [1, 2]. It also allows for structural changes of the porous medium itself (see, e.g. [3]). As the evolving computational domain leads to discrete discontinuities, we apply the local discontinuous Galerkin (LDG) method for the transport part. Mathematical upscaling techniques incorporate the information from the pore to the macroscale [1,4].<br />The model is applied for two research questions: We model the incorporation and turnover of particulate OM influencing soil aggregation, including ‘gluing’ hotspots, and show scenarios varying of OM input, turnover, or particle size distribution. <br />Second, we quantify the effective diffusivity on 3D geometries from CT scans of a loamy and a sandy soil. Conventional models cannot account for natural pore geometries and varying phase properties. Upscaling allows also to quantify how root exudates (mucilage) can significantly alter the macroscopic soil hydraulic properties.</p> </div> <div id="field-23"> <p>[1]  Ray, Rupp, Prechtel (2017). AWR (107), 393-404.<br />[2] Rupp, Totsche, Prechtel, Ray (2018). Front. Env. Sci. (6) 96.<br />[3] Zech, Dultz, Guggenberger, Prechtel, Ray (2020). Appl. Clay Sci. 198, 105845.<br />[4] Ray, Rupp, Schulz, Knabner (2018). TPM 124(3), 803-824.</p> </div>

The impact of porosity on organic matter cycling in a two-dimensional porous medium 

2021 ◽  
Author(s):  
Hanbang Zou ◽  
Pelle Ohlsson ◽  
Edith Hammer
Keyword(s):  
Porous Medium ◽  
Organic Matter ◽  
Carbon Sequestration ◽  
Soil Carbon ◽  
Pore Network ◽  
Pore Scale ◽  
Decomposition Of Organic Matter ◽  
Organic Matter Cycling ◽  
The Impact

<p>Carbon sequestration has been a popular research topic in recent years as the rapid elevation of carbon emission has significantly impacted our climate. Apart from carbon capture and storage in e.g. oil reservoirs, soil carbon sequestration offers a long term and safe solution for the environment and human beings. The net soil carbon budget is determined by the balance between terrestrial ecosystem sink and sources of respiration to atmospheric carbon dioxide. Carbon can be long term stored as organic matters in the soil whereas it can be released from the decomposition of organic matter. The complex pore networks in the soil are believed to be able to "protect" microbial-derived organic matter from decomposition. Therefore, it is important to understand how soil structure impacts organic matter cycling at the pore scale. However, there are limited experimental studies on understanding the mechanism of physical stabilization of organic matter. Hence, my project plan is to create a heterogeneous microfluidic porous microenvironment to mimic the complex soil pore network which allows us to investigate the ability of organisms to access spaces starting from an initial ecophysiological precondition to changes of spatial accessibility mediated by interactions with the microbial community.</p><p>Microfluidics is a powerful tool that enables studies of fundamental physics, rapid measurements and real-time visualisation in a complex spatial microstructure that can be designed and controlled. Many complex processes can now be visualized enabled by the development of microfluidics and photolithography, such as microbial dynamics in pore-scale soil systems and pore network modification mimicking different soil environments – earlier considered impossible to achieve experimentally. The microfluidic channel used in this project contains a random distribution of cylindrical pillars of different sizes so as to mimic the variations found in real soil. The randomness in the design creates various spatial availability for microbes (preferential flow paths with dead-end or continuous flow) as an invasion of liquids proceeds into the pore with the lowest capillary entry pressure. In order to study the impact of different porosity in isolation of varying heterogeneity of the porous medium, different pore size chips that use the same randomly generated pore network is created. Those chips have the same location of the pillars, but the relative size of each pillar is scaled. The experiments will be carried out using sterile cultures of fluorescent bacteria, fungi and protists, synthetic communities of combinations of these, or a whole soil community inoculum. We will quantify the consumption of organic matter from the different areas via fluorescent substrates, and the bio-/necromass produced. We hypothesise that lower porosity will reduce the net decomposition of organic matter as the narrower pore throat limits the access, and that net decomposition rate at the main preferential path will be higher than inside branches</p>

scholarly journals Microbial diversity affects self-organization of the soil–microbe system with consequences for function

2011 ◽  
Vol 9 (71) ◽  
pp. 1302-1310 ◽  
Author(s):  
John W. Crawford ◽  
Lewis Deacon ◽  
Dmitri Grinev ◽  
James A. Harris ◽  
Karl Ritz ◽  
...  
Keyword(s):  
Structural Changes ◽  
Bacterial Biomass ◽  
Soil Nutrient ◽  
Physical Structure ◽  
Self Organization ◽  
Pore Scale ◽  
Lattice Boltzmann Simulation ◽  
Unique Material ◽  
Terrestrial Life ◽  
Measured Change

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.

Long-term organic fertilization effect on chernozem structure

2013 ◽  
Vol 27 (1) ◽  
pp. 81-87 ◽  
Author(s):  
A. Słowińska-Jurkiewicz ◽  
M. Bryk ◽  
V.V. Medvedev
Keyword(s):  
Organic Matter ◽  
Sugar Beet ◽  
Crop Rotation ◽  
Morphological Analysis ◽  
Ground Level ◽  
Organic Fertilization ◽  
Farm Yard Manure ◽  
Soil Structures ◽  
Fertilization Effect

Abstract The objective of the study was to examine the structure of typical Ukrainian chernozem developed on loess, which (I) had been fertilized by standard crop rotation since 1912 with farm yard manure at the rate of 16 t ha-1 and (II) had not been fertilized with farm yard manure by sugar beet monoculture since 1929. After harvest of winter wheat and sugar beet, the samples of undisturbed structure were taken from 5 layers of both profiles: 0-8, 10-18, 20-28, 30-38, and 40-48 cm. The morphological analysis of the structure of the investigated chernozem revealed that the most visible differences between the soil structures of the two pedons occurred in their superficial layers. The 0-18 cm layer of the soil in the experiment I had an aggregate structure, whereas analogous layer of the soil in experiment II was much more compacted. Below about 30 cm from the ground level both pedons had very similar structure. For the soil in the experiment I an appropriate crop rotation and regular supplies of organic matter allowed for preservation of a favourable structure even in the upper layers - in contrast to the soil in the experiment II.

scholarly journals Pore-scale investigation of selective plugging mechanism in immiscible two-phase flow using phase-field method

2019 ◽  
Vol 74 ◽  
pp. 78 ◽  
Author(s):  
Ehsan Sabooniha ◽  
Mohammad-Reza Rokhforouz ◽  
Shahab Ayatollahi
Keyword(s):  
Oil Recovery ◽  
Phase Field ◽  
Water Injection ◽  
Flow Patterns ◽  
Field Method ◽  
Phase Field Method ◽  
Phase Flow ◽  
Computational Domain ◽  
Pore Scale ◽  
The Matrix

Biotechnology has had a major effect on improving crude oil displacement to increase petroleum production. The role of biopolymers and bio cells for selective plugging of production zones through biofilm formation has been defined. The ability of microorganisms to improve the volumetric sweep efficiency and increase oil recovery by plugging off high-permeability layers and diverting injection fluid to lower-permeability was studied through experimental tests followed by multiple simulations. The main goal of this research was to examine the selective plugging effect of hydrophobic bacteria cell on secondary oil recovery performance. In the experimental section, water and aqua solution of purified Acinetobacter strain RAG-1 were injected into an oil-saturated heterogeneous micromodel porous media. Pure water injection could expel oil by 41%, while bacterial solution injection resulted in higher oil recovery efficiency; i.e., 59%. In the simulation section, a smaller part of the heterogeneous geometry was employed as a computational domain. A numerical model was developed using coupled Cahn–Hilliard phase-field method and Navier–Stokes equations, solved by a finite element solver. In the non-plugging model, approximately 50% of the matrix oil is recovered through water injection. Seven different models, which have different plugging distributions, were constructed to evaluate the influences of selective plugging mechanism on the flow patterns. Each plugging module represents a physical phenomenon which can resist the displacing phase flow in pores, throats, and walls during Microbial-Enhanced Oil Recovery (MEOR). After plugging of the main diameter route, displacing phase inevitably exit from sidelong routes located on the top and bottom of the matrix. Our results indicate that the number of plugs occurring in the medium could significantly affect the breakthrough time. It was also observed that increasing the number of plugging modules may not necessarily lead to higher ultimate oil recovery. Furthermore, it was shown that adjacent plugs to the inlet caused flow patterns similar to the non-plugging model, and higher oil recovery factor than the models with farther plugs from the inlet. The obtained results illustrated that the fluids distribution at the pore-scale and the ultimate oil recovery are strongly dependent on the plugging distribution.

Chemical-Structural Changes of Organic Matter in a Semi-Arid Soil After Organic Amendment

Pedosphere ◽  
2012 ◽  
Vol 22 (3) ◽  
pp. 283-293 ◽  
Author(s):  
C. NICOLÁS ◽  
G. MASCIANDARO ◽  
T. HERNÁNDEZ ◽  
C. GARCIA
Keyword(s):  
Organic Matter ◽  
Structural Changes ◽  
Organic Amendment ◽  
Arid Soil ◽  
Semi Arid

Properties of Heat Treatment Alkaline Pulping Black Liquor with Aluminum Chloride

2012 ◽  
Vol 610-613 ◽  
pp. 2220-2223
Author(s):  
Lan Ge ◽  
Jie Lu ◽  
Rui Feng Yang ◽  
Yan Jun Liu
Keyword(s):  
Heat Treatment ◽  
Organic Matter ◽  
Aluminum Chloride ◽  
Structural Changes ◽  
Heating Temperature ◽  
Lignin Content ◽  
Black Liquor ◽  
Organic Matter Content ◽  
Toxic Substances ◽  
Alkaline Pulping

The black liquor contains a large amount of suspended solids, organic pollutants and toxic substances, the black liquor discharged directly into water bodies will lead to serious pollution. So we regards the alkaline pulping black liquor as a research object, using autoclave to heat the mixture of aluminum chloride and soda black liquor lignin. By changing the heating temperature and the pH before the heat treatment, we analyze the lignin and carbohydrates in the cooking liquid to study cleavage situation and the corresponding structural changes. The results show that the lignin content accompanied the increase in temperature, organic matter content decreased and part of the decomposition of organic matter. Without adjusting pH, the lignin content is small and ash (inorganic) content is higher.

Microscale soil structures foster organic matter stabilization in permafrost soils

Geoderma ◽  
2017 ◽  
Vol 293 ◽  
pp. 44-53 ◽  
Author(s):  
Carsten W. Mueller ◽  
Carmen Hoeschen ◽  
Markus Steffens ◽  
Henning Buddenbaum ◽  
Kenneth Hinkel ◽  
...  
Keyword(s):  
Organic Matter ◽  
Organic Matter Stabilization ◽  
Soil Structures ◽  
Permafrost Soils

scholarly journals Structural changes and degradation of Red Latosols under different management systems for 20 years

2014 ◽  
Vol 38 (4) ◽  
pp. 1293-1303 ◽  
Author(s):  
João Tavares Filho ◽  
Thadeu Rodrigues de Melo ◽  
Wesley Machado ◽  
Bruno Vieira Maciel
Keyword(s):  
Organic Matter ◽  
Bulk Density ◽  
Crop Rotation ◽  
Structural Changes ◽  
Soil Depth ◽  
Conventional Tillage ◽  
No Tillage ◽  
Reference Area ◽  
Perennial Crop ◽  
Structural Units

Soils are the foundation of terrestrial ecosystems and their role in food production is fundamental, although physical degradation has been observed in recent years, caused by different cultural practices that modify structures and consequently the functioning of soils. The objective of this study was to evaluate possible structural changes and degradation in an Oxisol under different managements for 20 years: no-tillage cultivation with and without crop rotation, perennial crop and conventional tillage, plus a forested area (reference). Initially, the crop profile was described and subsequently, 10 samples per management system and forest soil were collected to quantify soil organic matter, flocculation degree, bulk density, and macroporosity. The results indicated structural changes down to a soil depth of 50 cm, with predominance of structural units ∆μ (intermediate compaction level) under perennial crop and no-tillage crop rotation, and of structural units ∆ (compacted) under conventional tillage and no-tillage. The soil was increasingly degraded in the increasing order: forest => no-tillage crop rotation => perennial crop => no-tillage without crop rotation => conventional tillage. In all managements, the values of organic matter and macroporosity were always below and bulk density always above those of the reference area (forest) and, under no-tillage crop rotation and perennial crop, the flocculation degree was proportionally equal to that of the reference area.

The biomolecular paleontology of continental fossils

Paleobiology ◽  
2000 ◽  
Vol 26 (S4) ◽  
pp. 169-193 ◽  
Author(s):  
Derek E. G. Briggs ◽  
Richard P. Evershed ◽  
Matthew J. Lockheart
Keyword(s):  
Organic Matter ◽  
Organic Material ◽  
Structural Changes ◽  
Environmental Data ◽  
Time Slice ◽  
Final Time ◽  
Biological Origin ◽  
Rapid Degradation ◽  
Substantial Modification ◽  
Living Organisms

The preservation of compounds of biological origin (nucleic acids, proteins, carbohydrates, lipids, and resistant biopolymers) in terrigenous fossils and the chemical and structural changes that they undergo during fossilization are discussed over three critical stratigraphic levels or “time slices.” The youngest of these is the archeological record (e.g., <10 k.y. B.P.), when organic matter from living organisms undergoes the preliminary stages of fossilization (certain classes of biomolecule are selectively preserved while others undergo rapid degradation). The second time slice is the Tertiary. Well-preserved fossils of this age retain diagenetically modified biomarkers and biopolymers for which a product-precursor relationship with the original biological materials can still be identified. The final time slice is the Carboniferous. Organic material of this age has generally undergone such extensive diagenetic degradation that only the most resistant biopolymers remain and these have undergone substantial modification. Trends through time in the taphonomy and utility of ancient biomolecules in terrigenous fossils affect their potential for studies that involve chemosystematic and environmental data.

Sign in / Sign up

Export Citation Format

Share Document