The driving role of microhabitats in soil ecology: rebuilding artificial 3D soil-like nanostructured microhabitats for experimental reproducible works

2021 ◽  
Author(s):  
Fabrizio De Cesare ◽  
Elena Di Mattia ◽  
Antonella Macagnano
Keyword(s):  
Soil Ph ◽  
Model Systems ◽  
Natural Soil ◽  
Phenotypic Traits ◽  
Local Concentration ◽  
Bacterial Populations ◽  
Soil Features ◽  
Soil Mesocosms ◽  
Soil Ecosystems ◽  
Soil Components

<p>Soil ecosystems are composed of microhabitats that often differ in composition and ecological strategies at the microscale. Besides, the assumption that soil organism behaviour at the ecosystem level is similar to that at microscale may drive unexpected findings. Soil pH at microsites either can differ significantly from whole soil pH. Moreover, the large porosity measured in the whole soil can contrast with water, nutrient, air and waste flow limitations and dramatic constraints to microbial mobility and access to food, when analysed at the microscale, consequent to local pore geometry, connectivity and tortuosity. Incidentally, soil microorganisms, which are present in billions of individuals per gram of soil, have micrometre sizes and prevalently interact with the other soil components at the nano-to-microscale. They colonise soil microhabitat based on the local concentration and composition of air, nutrients and materials. Finally, different organic materials and minerals in the soil induce distinct interactions at microsites, generating diverse organo-mineral associations and different microbial populations. </p><p>The study of soil microhabitats can enable comprehending how the microsites' dynamics can drive to ecosystems' macroscale behaviours. However, the study of soil microhabitats in real conditions, even when investigated in soil mesocosms and microcosms, can be challenging or require complicated and expensive instrumentations to achieve such outcomes. </p><p>The rebuilding of soil microhabitats in model systems can help study the microhabitats' mutual interactions at the microscale. However, it is impossible to reproduce any possible combination of soil components to replicate the multitude of microhabitats existing in natural soil ecosystems. Then, approximations are necessary. </p><p>The present study proposes to recreate an artificial model 3D soil-like microhabitat resulting from the aggregation of the major classes of soil components (mineral particles, organic polymeric components, and microorganisms) in nano- to macro-architectures to study organo-mineral-microbe interactions at the microscale, and enable reproducible works. Electrospinning/electrospraying technologies were chosen for their extreme versatility in creating self-standing 3D complex, porous and functional structures and their proven capacity to permit microbes to grow on the resulting composite fibrous frameworks.</p><p>Bacteria strains of <em>Pseudomonas fluorescens</em> and <em>Burkholderia terricola</em>, typical microbial species populating the rhizosphere soils, will be utilised as microhabitat microbial components for generating a simplified microbiome in the 3D soil-like nanostructures. At first instance, we intended to use microscopy (e.g. SEM, TEM, confocal) as the tool of choice to investigate over time the spatial distribution of bacterial populations throughout the artificial nanostructured soil microhabitat here reproduced, the release of EPS by the bacterial populations and possible interactions. The proposed 3D soil-like nanostructures are supposed to provide the possibility of investigating the microbial lifestyle in microhabitats at different scales, from nm to mm, then linking microbial phenotypic traits to specific soil features.</p>

scholarly journals Cerebrospinal fluid (CSF) augments metabolism and virulence expression factors in Acinetobacter baumannii

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jasmine Martinez ◽  
Chelsea Razo-Gutierrez ◽  
Casin Le ◽  
Robert Courville ◽  
Camila Pimentel ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Acinetobacter Baumannii ◽  
Virulence Factors ◽  
Atp Synthesis ◽  
Bloodstream Infections ◽  
Model Systems ◽  
Phenotypic Traits ◽  
Virulence Determinants ◽  
Expression Of Genes

AbstractIn a recent report by the Centers for Disease Control and Prevention (CDC), multidrug resistant (MDR) Acinetobacter baumannii is a pathogen described as an “urgent threat.” Infection with this bacterium manifests as different diseases such as community and nosocomial pneumonia, bloodstream infections, endocarditis, infections of the urinary tract, wound infections, burn infections, skin and soft tissue infections, and meningitis. In particular, nosocomial meningitis, an unwelcome complication of neurosurgery caused by extensively-drug resistant (XDR) A. baumannii, is extremely challenging to manage. Therefore, understanding how A. baumannii adapts to different host environments, such as cerebrospinal fluid (CSF) that may trigger changes in expression of virulence factors that are associated with the successful establishment and progress of this infection is necessary. The present in-vitro work describes, the genetic changes that occur during A. baumannii infiltration into CSF and displays A. baumannii’s expansive versatility to persist in a nutrient limited environment while enhancing several virulence factors to survive and persist. While a hypervirulent A. baumannii strain did not show changes in its transcriptome when incubated in the presence of CSF, a low-virulence isolate showed significant differences in gene expression and phenotypic traits. Exposure to 4% CSF caused increased expression of virulence factors such as fimbriae, pilins, and iron chelators, and other virulence determinants that was confirmed in various model systems. Furthermore, although CSF's presence did not enhance bacterial growth, an increase of expression of genes encoding transcription, translation, and the ATP synthesis machinery was observed. This work also explores A. baumannii’s response to an essential component, human serum albumin (HSA), within CSF to trigger the differential expression of genes associated with its pathoadaptibility in this environment.

scholarly journals Influence of Cry1Ac Toxin From Bt Cotton on the Soil Microbiota

2019 ◽  
Vol 11 (4) ◽  
pp. 364
Author(s):  
Marcos Gino Fernandes ◽  
Renata Pires de Araújo ◽  
Eduardo Neves Costa ◽  
Ana Claudia Terumi Abe Zangirolymo ◽  
Rodrigo Matheus Pereira
Keyword(s):  
Soil Bacteria ◽  
Marker Gene ◽  
First Record ◽  
Transgenic Cotton ◽  
Natural Soil ◽  
Bt Cotton ◽  
Bacterial Populations ◽  
Soil Microbiota ◽  
Cry1ac Toxin ◽  
Gene 16S Rrna

The first record of transgenic cotton cultivation in Brazil was in 2005, of that of the cultivar MON 531, possessing the cry1Ac gene. Since then, no evaluation has been performed to understand whether the cultivation of Bt cotton has caused any interference with the soil microbiota, including bacteria. In this context, our research was aimed to assess whether the cultivation of Bt cotton negatively affects the community of soil bacteria, through quantitative and metagenomic analyses (marker gene 16S rRNA) for phylum identification. Samples of bacterial populations obtained from the soil cultivated with Bt cotton expressing the Cry1Ac toxin were compared with soil samples from the area cultivated with conventional cotton. Significant differences were not observed in the measure of colony-forming units of bacteria between the soils cultivated with Bt and non-Bt cotton; however, differences were detected only when comparing samples from different collection times of the Bt treatment. Cultivation of Bt cotton did not affect the diversity of the soil bacterial population. Overall, our study shows that, similar to most of the works that have been reported worldwide, cultivation of transgenic cotton does not seem to affect the quantity and diversity of natural soil bacteria.

scholarly journals USE OF HYDROGEN PEROXIDE AND PERCARBONATE TO TREAT CHLORINATED AROMATIC HYDROCARBON-CONTAMINATED SOIL

2014 ◽  
Vol 22 (1) ◽  
pp. 30-39 ◽  
Author(s):  
Marika Viisimaa ◽  
Anna Goi
Keyword(s):  
Hydrogen Peroxide ◽  
Soil Ph ◽  
Liquid Hydrogen ◽  
Natural Soil ◽  
Contaminant Removal ◽  
Contaminant Degradation ◽  
Solid Carrier ◽  
Liquid Carrier ◽  
Initial Ph ◽  
Ph Conditions

This study compared treatment methods that utilised a liquid carrier of hydrogen peroxide and a solid carrier, percarbonate, for p-dichlorobenzene, p-chloro-m-cresol and p-chlorothymol degradation in the soil. The targeted chlorinated aromatic contaminants in the soil degraded to a certain level when treated with the liquid hydrogen peroxide, but the removal efficacy was not dependent on the dosage. In contrast, an increase in the percarbonate dosage enhanced the contaminant removal. Supplementary ferrous iron was more effective for the treatment that employed the liquid carrier of hydrogen peroxide than the treatment employing the solid carrier. Although acidic pH conditions (initial pH of 2.5) favoured contaminant degradation using liquid hydrogen peroxide, the treatment involving percarbonate resulted in more effective contaminant removal without any soil pH preadjustment. Therefore, the solid carrier of hydrogen peroxide, percarbonate, was concluded to be an effective alternative to the liquid carrier, resulting in greater contaminant removal at natural soil pH values.

What do we know about how the terrestrial multicellular soil fauna reacts to microplastic?

2020 ◽  
Author(s):  
Frederick Büks ◽  
Loes van Schaik ◽  
Martin Kaupenjohann
Keyword(s):  
Adverse Effects ◽  
Contaminated Soils ◽  
Model Organisms ◽  
Natural Soil ◽  
Soil Food Webs ◽  
Soil Ecosystems ◽  
Plastic Type ◽  
Wide Range ◽  
High Concentrations ◽  
Using Data

<p><span>The ubiquitous accumulation of microplastic particles across all global ecosystems comes along with the uptake into soil food webs. In this work, we evaluated studies on passive translocation, active ingestion, bioaccumulation and adverse effects within the phylogenetic tree of multicellular soil faunal life. The representativity of these studies for natural soil ecosystems was assessed using data on the type of plastic, shape, composition, concentration and time of exposure.</span></p><p><span>Available studies cover a wide range of soil organisms, with emphasis on earthworms, nematodes, springtails, beetles and lugworms, each focused on well known model organisms. Most of the studies applied microplastic concentrations similar to amounts in slightly to very heavily polluted soils. In many cases, however, polystyrene microspheres have been used, a combination of plastic type and shape, that is easily available, but do not represent the main plastic input into soil ecosystems. In turn, microplastic fibres are strongly underrepresented compared to their high abundance within contaminated soils. Further properties of plastic such as aging, coating and additives were insufficiently documented. Despite of these limitations, there is a recurring pattern of active intake followed by a population shift within the gut microbiome and adverse effects on motility, growth, metabolism, reproduction and mortality in various combinations, especially at high concentrations and small particle sizes.</span></p><p><span>For future experiments<span>, we recommend a </span><span>modus operandi</span><span> that takes into account </span><span>the</span> <span>type, shape, grade of aging and specific concentrations of microplastic </span><span>fractions</span><span> in natural and contaminated soils </span><span>as well as long-term incubation within</span><span> soil </span><span>meso</span><span>cosms.</span></span></p>

Persistence and nontarget effects of Bacillusthuringiensis in soil: a review

1993 ◽  
Vol 23 (11) ◽  
pp. 2329-2342 ◽  
Author(s):  
J.A. Addison
Keyword(s):  
Forest Ecosystems ◽  
Soil Microflora ◽  
Natural Soil ◽  
Ecological Role ◽  
Laboratory Studies ◽  
Soil Ecosystem ◽  
Bacterial Populations ◽  
Nontarget Effects

This review presents information on the occurrence, persistence and nontarget effects of Bacillusthuringiensis Berliner (B.t.) in soil, with particular emphasis on forest ecosystems. Both field and laboratory studies have confirmed that B.t. is able to survive for several years after spraying, but studies on long-term persistence and possible accumulation of spores in soils are inadequate. The ecological role of B.t. in the soil ecosystem is poorly understood; we do not even know where and under what conditions B.t. multiplies in nature. Information on the effects of B.t. on soil microflora is contradictory, with studies variously suggesting that B.t. caused an increase, a decrease, or did not affect indigenous bacterial populations. Toxicity of B.t. to species of several invertebrate taxa (Acarina, Nematoda, Collembola, Annelida, Hymenoptera) inhabiting the soil has been demonstrated, but only rarely is it possible to relate dosage information to field situations, and in many cases the B.t. subspecies tested are not currently used for pest control in North America. There is an urgent need for further research to elucidate the relationships between B.t. and the natural soil microflora and fauna.

scholarly journals Percolation properties of 3-D multiscale pore networks: how connectivity controls soil filtration processes

2010 ◽  
Vol 7 (2) ◽  
pp. 2997-3018 ◽  
Author(s):  
E. M. A. Perrier ◽  
N. R. A. Bird ◽  
T. B. Rieutord
Keyword(s):  
Pore Size ◽  
Scaling Laws ◽  
Fractal Dimensions ◽  
Natural Soil ◽  
Pore Networks ◽  
Multi Scale ◽  
Soil Ecosystems ◽  
Pore Size Distributions ◽  
Soil Structures ◽  
Soil Filtration

Abstract. Quantifying the connectivity of pore networks is a key issue not only for modelling fluid flow and solute transport in porous media but also for assessing the ability of soil ecosystems to filter bacteria, viruses and any type of living microorganisms as well inert particles which pose a contamination risk. Straining is the main mechanical component of filtration processes: it is due to size effects, when a given soil retains a conveyed entity larger than the pores through which it is attempting to pass. We postulate that the range of sizes of entities which can be trapped inside soils has to be associated with the large range of scales involved in natural soil structures and that information on the pore size distribution has to be complemented by information on a Critical Filtration Size (CFS) delimiting the transition between percolating and non percolating regimes in multiscale pore networks. We show that the mass fractal dimensions which are classically used in soil science to quantify scaling laws in observed pore size distributions can also be used to build 3-D multiscale models of pore networks exhibiting such a critical transition. We extend to the 3-D case a new theoretical approach recently developed to address the connectivity of 2-D fractal networks (Bird and Perrier, 2009). Theoretical arguments based on renormalisation functions provide insight into multi-scale connectivity and a first estimation of CFS. Numerical experiments on 3-D prefractal media confirm the qualitative theory. These results open the way towards a new methodology to estimate soil filtration efficiency from the construction of soil structural models to be calibrated on available multiscale data.

scholarly journals N2O Fluxes and Related Processes of Denitrification in Acidified Soil

2020 ◽  
Author(s):  
Qian Zheng ◽  
Junjun Ding ◽  
Qiaozhen Li ◽  
Chunying Xu ◽  
Wei Lin ◽  
...  
Keyword(s):  
Soil Ph ◽  
Irrigation Water ◽  
Soil Acidification ◽  
N Fertilizer ◽  
Soil Conditions ◽  
Natural Soil ◽  
Large Contribution ◽  
Total N ◽  
Mapping Approach ◽  
The Impact

Abstract In North China, high levels of N fertilizer and irrigation water are used in fields, which cause considerable N2O fluxes via several pathways, especially anaerobic denitrification. Anaerobic denitrification is regarded as an important microbial process for N2O production in soils with a low O2 level and high N and labile C availability (the typical soil conditions caused by high levels of N fertilizer and irrigation water in the field). We conducted an anaerobic incubation experiment to determine the impact of soil acidification (with a series of soil pH levels, pH 6.2, pH 7.1, and pH 8.7) on N2O source partitioning with the addition of KNO3 and glucose. Natural abundance isotope techniques and gas inhibitor technique were applied to analyze the N2O flux derived from fungal denitrification and bacterial denitrification and its isotopocule characteristics emitted from soils after the addition of NO- 3 and glucose. A mapping approach was used to obtain further insight into the N2O production processes. Our findings confirmed that soil pH strongly controlled the N2O production and reduction rates of denitrification. Soil acidification significantly increased N2O emissions varied from 0.76 mg N kg-1 for natural soil (pH 8.7), to 1.88 mg N kg-1 for pH 7.1, and to 2.35 mg N kg-1 for pH 6.2, and had a blockage effect on the reduction of N2O to N2. The addition of carbon sources promoted complete denitrification. We assumed a higher contribution of fungal denitrification to N2O production compared to total N2O emission associated with acidified soil. A promotion of the contribution of fungal denitrification-derived N2O was indeed observed with decreasing pH, increasing from 0.28 mg N kg-1 for pH 8.7 to 0.94 mg N kg-1 for pH 6.2. The addition of glucose further increased the contribution of fungal denitrification to N2O production from 0.99 mg N kg-1 for pH 8.7 to 3.66 mg N kg-1 for pH 6.2. The mapping approach provided rational results for correcting N2O reduction compared with the acetylene inhibition method. The results calculated by both methods indicated a reasonably large contribution of fungal denitrification to total N2O production in acidified soils.

scholarly journals Lipooligosaccharides Containing Phosphorylcholine Delay Pulmonary Clearance of Nontypeable Haemophilus influenzae

2008 ◽  
Vol 76 (5) ◽  
pp. 2037-2043 ◽  
Author(s):  
Bing Pang ◽  
Dana Winn ◽  
Ryan Johnson ◽  
Wenzhou Hong ◽  
Shayla West-Barnette ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Bacterial Resistance ◽  
Serial Passage ◽  
Model Systems ◽  
Immunofluorescent Staining ◽  
Mouse Lung ◽  
Chronic Obstructive ◽  
Nontypeable Haemophilus Influenzae ◽  
Bacterial Populations ◽  
Pulmonary Clearance

ABSTRACT Nontypeable Haemophilus influenzae (NTHi) causes pulmonary infections in patients with chronic obstructive pulmonary disease and other mucociliary clearance defects. Like many bacteria inhabiting mucosal surfaces, NTHi produces lipooligosaccharide (LOS) endotoxins that lack the O side chain. Persistent NTHi populations express a discrete subset of LOS glycoforms, including those containing phosphorylcholine (PCho). In this study, we compared two NTHi strains with isogenic mutants lacking PCho for clearance from mice following pulmonary infection. Consistent with data from other model systems, populations of the strains NTHi 2019 and NTHi 86-028NP recovered from mouse lung contained an increased proportion of PCho+ variants compared to that in the inocula. PCho− mutants were more rapidly cleared. Serial passage of NTHi increased both PCho content and bacterial resistance to clearance, and no such increases were observed for PCho− mutants. Increased PCho content was also observed in NTHi populations within non-endotoxin-responsive C3H/HeJ and Toll-like receptor 4 null (TLR4−/−) mice, albeit at later times postinfection. Changes in bacterial subpopulations and clearance were unaffected in TLR2−/− mice compared to the subpopulations in and clearance from mice of the parental strain. The clearance of PCho− mutants occurred at earlier time points in both strain backgrounds and in all types of mice. Comparison of bacterial populations in lung tissue cryosections by immunofluorescent staining showed sparse bacteria within the air spaces of C57BL/6 mice and large bacterial aggregates within the lungs of MyD88−/− mice. These results indicate that PCho promotes bacterial resistance to pulmonary clearance early in infection in a manner that is at least partially independent of the TLR4 pathway.

scholarly journals Cerebrospinal fluid (CSF) boosts metabolism and virulence expression factors in Acinetobacter baumannii

2020 ◽  
Author(s):  
Jasmine Martinez ◽  
Chelsea Razo-Gutierrez ◽  
Casin Le ◽  
Robert Courville ◽  
Camila Pimentel ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Acinetobacter Baumannii ◽  
Virulence Factors ◽  
Respiratory Infections ◽  
Atp Synthesis ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Model Systems ◽  
Phenotypic Traits ◽  
Expression Of Genes

AbstractIn a recent report by the Centers for Disease Control and Prevention (CDC), multidrug resistant (MDR) Acinetobacter baumannii is a pathogen described as an “urgent threat”. Infection with this bacterium manifests as different diseases such as community and nosocomial pneumonia, bloodstream infections, endocarditis, urinary tract, wound infections, burn infections, skin and soft tissue infections, and meningitis. In particular, nosocomial meningitis, a common complication of neurosurgery caused by extensively-drug resistant (XDR) A. baumannii, is extremely challenging to manage. Therefore, it is necessary to identify signals, such as exposure to cerebrospinal fluid (CSF), that trigger expression of virulence factors that are associated with the successful establishment and progress of this infection. While a hypervirulent A. baumannii strain did not show changes in its transcriptome when incubated in the presence of CSF, a low-virulence isolate showed significant differences in gene expression and phenotypic traits. Exposure to 4% CSF caused increased expression of virulence factors such as fimbriae, pilins, and iron chelators, and virulence as determined in various model systems. Furthermore, although CSF’s presence did not enhance bacterial growth, it was associated with an increase of expression of genes encoding transcription, translation, and the ATP synthesis machinery. Experiments to identify the active CSF component pointed to human serum albumin (HSA).ImportanceAcinetobacter baumannii, notorious for its multidrug resistant phenotype, overcomes nutrient deprived and desiccated conditions through its metabolic flexibility, pathogenic and physiological adaptability. Although this pathogen is commonly associated with respiratory infections, there have been a considerable amount of cases of A. baumannii bacterial meningitis. These infections are usually post-neurological surgery complications associated with high mortality rates ranging from 40 to 70%. This work describes interactions that may occur during A. baumannii infection of human cerebrospinal fluid (CSF). A. baumannii’s displays capabilities to persist and thrive in a nutrient-limited environment, which also triggers the expression of virulence factors. This work also further explores A. baumannii’s utilization of an essential component within CSF to trigger enhanced expression of genes associated with its pathoadaptibility in this environment.

scholarly journals Base Neutralizing Capacity of Agricultural Soils in a Quaternary Landscape of North-East Germany and Its Relationship to Best Management Practices in Lime Requirement Determination

Agronomy ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 877
Author(s):  
Sebastian Vogel ◽  
Eric Bönecke ◽  
Charlotte Kling ◽  
Eckart Kramer ◽  
Katrin Lück ◽  
...  
Keyword(s):  
Soil Properties ◽  
Soil Ph ◽  
Soil Acidification ◽  
Titration Curve ◽  
Soil Acidity ◽  
Management Practices ◽  
Natural Soil ◽  
Natural Processes ◽  
North East ◽  
Neutralizing Capacity

Despite being a natural soil-forming process, soil acidification is a major agronomic challenge under humid climate conditions, as soil acidity influences several yield-relevant soil properties. It can be counterbalanced by the regular application of agricultural lime to maintain or re-establish soil fertility and to optimize plant growth and yield. To avoid underdose as well as overdose, lime rates need to be calculated carefully. The lime rate should be determined by the optimum soil pH (target pH) and the response of the soil to lime, which is described by the base neutralizing capacity (BNC). Several methods exist to determine the lime requirement (LR) to raise the soil pH to its optimum. They range from extremely time-consuming equilibration methods, which mimic the natural processes in the soil, to quick tests, which rely on some approximations and are designed to provide farmers with timely and cost-efficient data. Due to the higher analytical efforts, only limited information is available on the real BNC of particular soils. In the present paper, we report the BNC of 420 topsoil samples from Central Europe (north-east Germany), developed on sediments from the last ice age 10,000 years ago under Holocene conditions. These soils are predominantly sandy and low in humus, but they exhibit a huge spatial variability in soil properties on a small scale. The BNC was determined by adding various concentrations of Ca(OH)2 and fitting an exponential model to derive a titration curve for each sample. The coefficients of the BNC titration curve were well correlated with soil properties affecting soil acidity and pH buffer capacity, i.e., pH, soil texture and soil organic matter (SOM). From the BNC model, the LRs (LRBNC) were derived and compared with LRVDLUFA based on the standard protocol in Germany as established by the Association of German Agricultural Analytic and Research Institutes (VDLUFA). The LRBNC and LRVDLUFA correlated well but the LRVDLUFA were generally by approximately one order of magnitude higher. This is partly due to the VDLUFA concept to recommend a maintenance or conservation liming, even though the pH value is in the optimum range, to keep it there until the next lime application during the following rotation. Furthermore, the VDLUFA method was primarily developed from field experiments where natural soil acidification and management practices depressed the effect of lime treatment. The BNC method, on the other hand, is solely based on laboratory analysis with standardized soil samples. This indicates the demand for further research to develop a sound scientific algorithm that complements LRBNC with realistic values of annual Ca2+ removal and acidification by natural processes and N fertilization.

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