Biological processes in modelling soil functions – a balancing act between too complex and too simple

2021 ◽  
Author(s):  
Sara König ◽  
Ulrich Weller ◽  
Thomas Reitz ◽  
Bibiana Betancur-Corredor ◽  
Birgit Lang ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Microbial Activity ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Simulation Models ◽  
Microbial Processes ◽  
Biological Processes ◽  
Soil Functions ◽  
Management Options ◽  
The Impact

<p>Mechanistic simulation models are an essential tool for predicting soil functions such as nutrient cycling, water filtering and storage, productivity and carbon storage as well as the complex interactions between these functions. Most soil functions are driven or affected by soil organisms. Yet, biological processes are often neglected in soil function models or implicitly described by rate parameters. This can be explained by the high complexity of the soil ecosystem with its dynamic and heterogeneous environment, and by the range of temporal and spatial scales these processes are taking place at. On the other hand, the technical capabilities to explore microbial activity and communities in soil has greatly improved, resulting in new possibilities to understand soil microbial processes on various scales.</p><p>However, to integrate such biological processes in soil modelling, we need to find the right level of detail. Here, we present a systemic soil model approach to simulate the impact of different management options and changing climate on soil functions integrating biological activity on the profile scale. We use stoichiometric considerations to simulate microbial processes involved in different soil functions without explicitly describing community dynamics or functional groups. With this approach we are able to mechanistically describe microbial activity and its impact on the turnover of organic matter and nutrient cycling as driven by agricultural soil management.</p><p>Further, we discuss general challenges and ongoing developments to additionally consider, e.g., microbe-fauna-interactions or microbial feedback with soil structure dynamics.</p>

Systemic modelling of soil functions under the impact of agricultural management

2020 ◽  
Author(s):  
Sara König ◽  
Ulrich Weller ◽  
Birgit Lang ◽  
Mareike Ließ ◽  
Stefanie Mayer ◽  
...  
Keyword(s):  
Soil Structure ◽  
Water Distribution ◽  
Management Strategies ◽  
Simulation Models ◽  
Crop Growth ◽  
Soil Productivity ◽  
Soil Functions ◽  
Management Options ◽  
Soil Organic Matter Turnover ◽  
The Impact

<p>The increasing demand for food and bio-energy gives need to optimize soil productivity, while securing other soil functions such as nutrient cycling and buffer capacity, carbon storage, biological activity, and water filter and storage. Mechanistic simulation models are an essential tool to fully understand and predict the complex interactions between physical, biological and chemical processes of soil with those functions, as well as the feedbacks between these functions.</p><p>We developed a systemic soil model to simulate the impact of different management options and changing climate on the named soil functions by integrating them within a simplified system. The model operates on a 1d soil profile consisting of dynamic nodes, which may represent the different soil horizons, and integrates different processes including dynamic water distribution, soil organic matter turnover, crop growth, nitrogen cycling, and root growth.</p><p>We present the main features of our model by simulating crop growth under various climatic scenarios on different soil types including management strategies affecting the soil structure. We show the relevance of soil structure for the main soil functions and discuss different model outcome variables as possible measures for these functions.</p><p>Further, we discuss ongoing model extensions, especially regarding the integration of biological processes, and possible applications.</p>

Fish-mediated nutrient cycling and benthic microbial processes: can consumers influence stream nutrient cycling at multiple spatial scales?

2012 ◽  
Vol 31 (3) ◽  
pp. 928-944 ◽  
Author(s):  
Jason M. Taylor ◽  
Jeffrey A. Back ◽  
Theodore W. Valenti ◽  
Ryan S. King
Keyword(s):  
Nutrient Cycling ◽  
Spatial Scales ◽  
Microbial Processes ◽  
Multiple Spatial Scales

Impact of land-use on soil structure and soil ecological properties in a long-term field experiment

2021 ◽  
Author(s):  
Steffen Schlüter ◽  
Tim Roussety ◽  
Lena Rohe ◽  
Vusal Guliyev ◽  
Evgenia Blagodatskaya ◽  
...  
Keyword(s):  
Land Use ◽  
Field Experiment ◽  
Soil Properties ◽  
Microbial Activity ◽  
Structural Properties ◽  
Soil Structure ◽  
Basal Respiration ◽  
Soil Functions ◽  
Substrate Induced Respiration ◽  
The Impact

<p>Land use is known to exert a dominant impact on a range of essential soil functions like water retention, carbon sequestration, matter cycling and plant growth. In addition, land use management is known to have a strong influence on soil structure, e.g. through tillage and compaction. While the difference in topsoil structure between grassland and agricultural soil is huge, differences among different farming or grassland management practices can be more subtle. At the same time, soil structure is known to be a suitable indicator for many soil functions. That is, differences in carbon content or plant-available field capacity between different land uses can often be explained by different structural properties.</p><p>This impact of land use on the relationship between soil structure and biological indicators for soil processes was explored in the Global Change Exploratory Facility, a well-established (>5 years) field experiment in Bad Lauchstädt, Germany, comprising five land use types (conventional farming, organic farming, intensive meadow, extensive meadow, extensive pasture). 15 intact topsoil cores were sampled from each land use type in spring 2020 and soil structure and microbial activity were measured using X-ray CT and respirometry, respectively. Microbial activity was estimated by basal respiration at field moisture and by substrate-induced respiration with glucose solution under wet conditions. The aims of this study were to (1) quantify the impact of land use on these structural and biological soil properties and (2) to assess in how far microbial activity can be predicted by the structural properties.</p><p>Surprisingly, image-derived macroporosity did not differ between farming and grassland plots mainly due to the huge variability among compacted and non-compacted samples in the farming plots. Other pore metrics like pore distance and pore connectivity followed the same trend, whereas mean pore size was larger in the grassland plots due to more large biopores. Basal respiration increased in the order farming < meadow < pasture, whereas the order was reversed for substrate-induced respiration. The predictability of basal respiration (R<sup>2</sup>=0.29) and substrate-induced respiration (R<sup>2</sup>=0.5) with explanatory variables based on pore metrics and bulk soil properties was rather low, with root mass and bulk density being the best predictors.</p>

scholarly journals Simulating impact of climatic variability and extreme climatic events on crop production

MAUSAM ◽  
2021 ◽  
Vol 67 (1) ◽  
pp. 113-130
Author(s):  
K. K. SINGH ◽  
NAVEEN KALRA
Keyword(s):  
Remote Sensing ◽  
Climatic Variability ◽  
Simulation Models ◽  
Management Options ◽  
Advisory Services ◽  
Extreme Climatic Events ◽  
Crop Simulation ◽  
Crop Simulation Models ◽  
Wide Range ◽  
The Impact

Wide range of inter-annual climatic variability and frequent occurrence of extreme climatic events in Indian context is a great concern. There is a need to assess the impact of these events on agriculture production as well suggest the agri-management options for sustenance. The appropriate region specific agro-advisory needs to be established for the farmers and other stake holders. Crop simulation models are effective tools for assessing the crops’ response to these climate related events and for suggesting suitable adaptation procedures for ensuring higher agricultural production. Remote sensing and GIS are effective tools in this regard to prepare the regional based agro-advisories, by linking with the crop simulation models and relational database layers of bio-physical and socio-economic aspects. For effective agro-advisory services, there is a need to link the other biotic and abiotic stresses for accurate estimates and generating window of suitable agri-management options. Crop simulation models can effectively integrate these stresses for crop and soil processes understanding and ultimate yield formation. In this review article, we have discussed about the inter-annual/ seasonal climatic variability and occurrence of extreme climatic events in India and demonstrated the potential of crop models viz., INFOCROP, WTGROWS, DSSAT to assess the impact of these events (also including climate change) on growth and yield of crops and cropping systems and thereby suggesting appropriate adaptation strategies for sustenance. The potential of remote sensing for crop condition assessment and regional/national yield forecast has been demonstrated. Crop simulation tools coupled with remote sensing inputs through GIS can play an important role in evolving this unique operational platform of designing weather based agro-advisory services for India.

Fluorescent potentiometric dyes for membrane-potential imaging

1994 ◽  
Vol 52 ◽  
pp. 166-167
Author(s):  
Leslie M. Loew
Keyword(s):  
Membrane Potential ◽  
Single Cells ◽  
Quantitative Imaging ◽  
Optical Recording ◽  
Biological Processes ◽  
Major Focus ◽  
The Past ◽  
Excitable Systems ◽  
Major Application ◽  
The Impact

A major application of potentiometric dyes has been the multisite optical recording of electrical activity in excitable systems. After being championed by L.B. Cohen and his colleagues for the past 20 years, the impact of this technology is rapidly being felt and is spreading to an increasing number of neuroscience laboratories. A second class of experiments involves using dyes to image membrane potential distributions in single cells by digital imaging microscopy - a major focus of this lab. These studies usually do not require the temporal resolution of multisite optical recording, being primarily focussed on slow cell biological processes, and therefore can achieve much higher spatial resolution. We have developed 2 methods for quantitative imaging of membrane potential. One method uses dual wavelength imaging of membrane-staining dyes and the other uses quantitative 3D imaging of a fluorescent lipophilic cation; the dyes used in each case were synthesized for this purpose in this laboratory.

Maternal-Fetal Management in Trombophilia Related and Placenta-Mediated Pregnancy Complications

2018 ◽  
Vol 69 (9) ◽  
pp. 2396-2401
Author(s):  
Costin Berceanu ◽  
Elena Loredana Ciurea ◽  
Monica Mihaela Cirstoiu ◽  
Sabina Berceanu ◽  
Anca Maria Ofiteru ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Pregnancy Complications ◽  
Case Control Study ◽  
Case Control ◽  
Placental Insufficiency ◽  
Management Options ◽  
Specific Therapy ◽  
Pregnancy Morbidity ◽  
The Impact ◽  
Control Study

It is widely accepted that thrombophilia in pregnancy greatly increases the risk of venous thromboembolism. Pregnancy complications arise, at least partly, from placental insufficiency. Any change in the functioning of the gestational transient biological system, such as inherited or acquired thrombophilia, might lead to placental insufficiency. In this research we included 64 pregnant women with trombophilia and 70 cases non-trombophilic pregnant women, with or without PMPC, over a two-year period. The purpose of this multicenter case-control study is to analyze the maternal-fetal management options in obstetric thrombophilia, the impact of this pathology on the placental structure and possible correlations with placenta-mediated pregnancy complications. Maternal-fetal management in obstetric thrombophilia means preconceptional or early diagnosis, prevention of pregnancy morbidity, specific therapy as quickly as possible and fetal systematic surveilance to identify the possible occurrence of placenta-mediated pregnancy complications.

Plant Community Dynamics, Nutrient Cycling, and Alternative Stable Equilibria in Peatlands

2002 ◽  
Vol 160 (5) ◽  
pp. 553
Author(s):  
Pastor ◽  
Peckham ◽  
Bridgham ◽  
Weltzin ◽  
Chen
Keyword(s):  
Nutrient Cycling ◽  
Plant Community ◽  
Community Dynamics ◽  
Plant Community Dynamics ◽  
Stable Equilibria

scholarly journals Scale dependence of galaxy biasing investigated by weak gravitational lensing: An assessment using semi-analytic galaxies and simulated lensing data

2018 ◽  
Vol 613 ◽  
pp. A15 ◽  
Author(s):  
Patrick Simon ◽  
Stefan Hilbert
Keyword(s):  
Gravitational Lensing ◽  
Spatial Scales ◽  
Scale Dependence ◽  
Reconstruction Technique ◽  
Weak Gravitational Lensing ◽  
Physical Scale ◽  
The Galaxy ◽  
Galaxy Bias ◽  
The Impact ◽  
Lens Galaxies

Galaxies are biased tracers of the matter density on cosmological scales. For future tests of galaxy models, we refine and assess a method to measure galaxy biasing as a function of physical scalekwith weak gravitational lensing. This method enables us to reconstruct the galaxy bias factorb(k) as well as the galaxy-matter correlationr(k) on spatial scales between 0.01hMpc−1≲k≲ 10hMpc−1for redshift-binned lens galaxies below redshiftz≲ 0.6. In the refinement, we account for an intrinsic alignment of source ellipticities, and we correct for the magnification bias of the lens galaxies, relevant for the galaxy-galaxy lensing signal, to improve the accuracy of the reconstructedr(k). For simulated data, the reconstructions achieve an accuracy of 3–7% (68% confidence level) over the abovek-range for a survey area and a typical depth of contemporary ground-based surveys. Realistically the accuracy is, however, probably reduced to about 10–15%, mainly by systematic uncertainties in the assumed intrinsic source alignment, the fiducial cosmology, and the redshift distributions of lens and source galaxies (in that order). Furthermore, our reconstruction technique employs physical templates forb(k) andr(k) that elucidate the impact of central galaxies and the halo-occupation statistics of satellite galaxies on the scale-dependence of galaxy bias, which we discuss in the paper. In a first demonstration, we apply this method to previous measurements in the Garching-Bonn Deep Survey and give a physical interpretation of the lens population.

scholarly journals Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Rameen Shakur ◽  
Juan Pablo Ochoa ◽  
Alan J. Robinson ◽  
Abhishek Niroula ◽  
Aneesh Chandran ◽  
...  
Keyword(s):  
Heart Failure ◽  
Systems Biology ◽  
Sudden Cardiac Death ◽  
Risk Stratification ◽  
Clinical Data ◽  
Cardiac Death ◽  
Troponin T ◽  
Management Options ◽  
Familial Cardiomyopathy ◽  
The Impact

AbstractThe cardiac troponin T variations have often been used as an example of the application of clinical genotyping for prognostication and risk stratification measures for the management of patients with a family history of sudden cardiac death or familial cardiomyopathy. Given the disparity in patient outcomes and therapy options, we investigated the impact of variations on the intermolecular interactions across the thin filament complex as an example of an unbiased systems biology method to better define clinical prognosis to aid future management options. We present a novel unbiased dynamic model to define and analyse the functional, structural and physico-chemical consequences of genetic variations among the troponins. This was subsequently integrated with clinical data from accessible global multi-centre systematic reviews of familial cardiomyopathy cases from 106 articles of the literature: 136 disease-causing variations pertaining to 981 global clinical cases. Troponin T variations showed distinct pathogenic hotspots for dilated and hypertrophic cardiomyopathies; considering the causes of cardiovascular death separately, there was a worse survival in terms of sudden cardiac death for patients with a variation at regions 90–129 and 130–179 when compared to amino acids 1–89 and 200–288. Our data support variations among 90–130 as being a hotspot for sudden cardiac death and the region 131–179 for heart failure death/transplantation outcomes wherein the most common phenotype was dilated cardiomyopathy. Survival analysis into regions of high risk (regions 90–129 and 130–180) and low risk (regions 1–89 and 200–288) was significant for sudden cardiac death (p = 0.011) and for heart failure death/transplant (p = 0.028). Our integrative genomic, structural, model from genotype to clinical data integration has implications for enhancing clinical genomics methodologies to improve risk stratification.

scholarly journals Phony peach disease: past and present impact on the peach industry in the southeastern U.S.A

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Kendall A. Johnson ◽  
Clive H. Bock ◽  
Phillip M. Brannen
Keyword(s):  
New Technologies ◽  
Current Knowledge ◽  
Future Research ◽  
Management Options ◽  
Disease Epidemiology ◽  
Pathogen Diversity ◽  
Foundational Research ◽  
Global Threat ◽  
And Control ◽  
The Impact

Abstract Background Phony peach disease (PPD) is caused by the plant pathogenic bacterium Xylella fastidiosa subsp. multiplex (Xfm). Historically, the disease has caused severe yield loss in Georgia and elsewhere in the southeastern United States, with millions of PPD trees being removed from peach orchards over the last century. The disease remains a production constraint, and management options are few. Limited research has been conducted on PPD since the 1980s, but the advent of new technologies offers the opportunity for new, foundational research to form a basis for informed management of PPD in the U.S. Furthermore, considering the global threat of Xylella to many plant species, preventing import of Xfm to other regions, particularly where peach is grown, should be considered an important phytosanitary endeavor. Main topics We review PPD, its history and impact on peach production, and the eradication efforts that were conducted for 42 years. Additionally, we review the current knowledge of the pathogen, Xfm, and how that knowledge relates to our understanding of the peach—Xylella pathosystem, including the epidemiology of the disease and consideration of the vectors. Methods used to detect the pathogen in peach are discussed, and ramifications of detection in relation to management and control of PPD are considered. Control options for PPD are limited. Our current knowledge of the pathogen diversity and disease epidemiology are described, and based on this, some potential areas for future research are also considered. Conclusion There is a lack of recent foundational research on PPD and the associated strain of Xfm. More research is needed to reduce the impact of this pathogen on peach production in the southeastern U.S., and, should it spread internationally, wherever peaches are grown.

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