Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC

This paper deals with the simulation of microbial degradation of organic matter in soil within the pore space at a microscopic scale. Pore space was analysed with micro-computed tomography and described using a sphere network coming from a geometrical modelling algorithm. The biological model was improved regarding previous work in order to include the transformation of dissolved organic compounds and diffusion processes. We tested our model using experimental results of a simple substrate decomposition experiment (fructose) within a simple medium (sand) in the presence of different bacterial strains. Separate incubations were carried out in microcosms using five different bacterial communities at two different water potentials of −10 and −100 cm of water. We calibrated the biological parameters by means of experimental data obtained at high water content, and we tested the model without changing any parameters at low water content. Same as for the experimental data, our simulation results showed that the decrease in water content caused a decrease of mineralization rate. The model was able to simulate the decrease of connectivity between substrate and microorganism due the decrease of water content

Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils

Pore-scale monitoring of the effect of microarchitecture on fungal growth in a two-dimensional soil-like micromodel

In spite of the very significant role that fungi are called to play in agricultural production and climate change over the next two decades, very little is known at this point about the parameters that control the spread of fungal hyphae in the pore space of soils. Monitoring of this process in 3 dimensions is not technically feasible at the moment. The use of transparent micromodels simulating the internal geometry of real soils affords an opportunity to approach the problem in 2 dimensions, provided it is confirmed that fungi would actually want to propagate in such artificial systems. In this context, the key objectives of the research described in this article are to ascertain, first, that the fungus Rhizoctonia solani can indeed grow in a micromodel of a sandy loam soil, and, second, to identify and analyze in detail the pattern by which it spreads in the tortuous pores of the micromodel. Experimental observations show that hyphae penetrate easily inside the micromodel, where they bend frequently to adapt to the confinement to which they are subjected, and branch at irregular intervals, unlike in current computer models of the growth of hyphae, which tend to describe them as series of straight tubular segments. A portion of the time, hyphae in the micromodels also exhibit thigmotropism, i.e., tend to follow solid surfaces closely. Sub-apical branching, which in unconfined situations seems to be controlled by the fungus, appears to be closely connected with the bending of the hyphae, resulting from their interactions with surfaces. These different observations not only indicate different directions to follow to modify current mesoscopic models of fungal growth, so they can apply to soils, but they also suggest a wealth of further experiments using the same set-up, involving for example competing fungal hyphae, or the coexistence of fungi and bacteria in the same pore space

Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil‐atmosphere exchange of greenhouse gases

Over the last two decades, the fact that soils are significant sources of greenhouse gases (GHG), e.g., carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and water vapor, has received considerable attention from the scientific community. Many laboratory and field experiments have been carried out to investigate the release of GHG by soils, and a wide range of computer modeling approaches have been explored to encapsulate what is known about the process, as well as to improve its prediction at various spatial and temporal scales

Nestemäisten jätteiden vastaanotto ja käsittely Tarastenjärven jätekeskuksessa : Selvitys vaihtoehtoisista menetelmistä

Nestemäiset jätteet ovat erilaisia loka-autoilla kuljetettavia jätteitä, jotka koostuvat nesteestä ja kiintoaineksesta. Tällaisia jätteitä ovat esimerkiksi hiekan- ja rasvanerotuskaivoista imetyt nesteet sekä teollisuudessa syntyvät jätevesilietteet. Nestemäisiä jätteitä ei ole Valtioneuvoston päätöksestä enää vuoden 2002 jälkeen saanut sijoittaa sellaisenaan kaatopaikkapenkkaan, vaan ne on tullut esikäsitellä nesteen poistamiseksi. Tähän asti nestemäiset jätteet on käsitelty Tarastenjärven jätekeskuksessa painovoimaisesti erottelemalla. Menetelmä on ollut toimiva, mutta on päivityksen tarpeessa. Tämän opinnäytetyön tarkoituksena olikin tutkia erilaisia vaihtoehtoja nestemäisten jätteiden vastaanotolle sekä käsittelylle Tarastenjärven jätekeskuksessa, sekä arvioida eri vaihtoehtojen kustannuksia mikäli mahdollista. Myös tarvetta haitta-aineiden, kuten metallien ja öljyjen poistamiselle tutkittiin. Työn laatimisessa hyödynnettiin olemassa olevaa tieteellistä kirjallisuutta sekä asiantuntijahaastatteluja. Työn tilaajana toimi Pirkanmaan Jätehuolto Oy. Selvitystyön tuloksena kävi ilmi, että yleisimmät menetelmät nesteiden ja kiinteiden ainesten erottamiseen ovat painovoimainen erottelu ja suodatus. Painovoimaiset erottelijat ovat useimmiten kiinteäseinäisiä altaita, joissa kiintoaines laskeutuu painovoimaisesti altaan pohjalle ja pinnalle jäänyt kirkastunut neste ohjataan ylivuotona jatkokäsittelyyn. Kiintoaineksen ollessa kevyempää kuin vesi, se erottuu nesteen pinnalle. Suodattimien toiminta taas perustuu puoliläpäisevään suodatusmediaan, joka päästää nesteen läpi, mutta jättää kiintoaineksen suodattimeen. Suodattimet voivat olla esimerkiksi paineistettuja tai painovoimalla toimivia. Geotuubit ovat eräänlaisia paineistettuja säkkisuodattimia, joita on käytössä myös jätekeskuksissa. Useissa käsittelymenetelmissä käytetään apuna myös saostuskemikaaleja, jotka edistävät kiintoaineksen erottumista nesteestä. Haitta-aineiden osalta helpoin ratkaisu on poistaa ne kiintoaineksen mukana ja käsitellä ne pilaantuneiden maiden kanssa jätekeskuksessa. Mikäli haitta-aineet ovat nesteessä liukoisessa muodossa, voidaan apuna käyttää saostuskemikaaleja, kuten alumiini- tai rautasuoloja. Öljyjen erottamisessa olisi mahdollista hyödyntää öljynerotuskaivoa. Kirjallisuuden sekä haastattelujen perusteella päivitetty versio painovoimaisesta erottelujärjestelmästä sekä geotuubimenetelmä vaikuttavat parhailta käytettävissä olevilta ratkaisuilta. Suurin haaste jätekeskuksen nestemäisten jätteiden käsittelyssä on kuitenkin se, että nesteiden ominaisuudet eroavat kuormittain hyvin paljon toisistaan. Tähän voitaisiin vaikuttaa jätteiden tarkemmalla lajittelulla vastaanottovaiheessa. Käsittelymenetelmää valittaessa tulee kuitenkin pohtia järjestelmän kuluja sekä hyötyjä pitkällä aikavälillä niin, että päästään parhaaseen mahdolliseen puhdistuslopputulokseen.Liquid wastes are solid-liquid mixtures such as wastes from sand and grease separation wells and industrial wastewaters. Since 2002 liquid wastes have no longer been allowed to be placed at a waste disposal site according to the decree 1049/1999 of the Finnish Council of State. Therefore liquid wastes have to be dewatered before final disposal. At the moment liquid wastes are treated at the Tarastenjärvi waste management centre with gravitational separation but the system needs updating. The aim of this study was to provide Pirkanmaan Jätehuolto Oy with different methods of liquid waste handling as well as evaluate the costs of a new system if possible. Also the need for contaminant removal was taken into consideration. The study was carried out by literature reviews and interviewing professionals of the industry. The results showed that the most common methods of solid-liquid separation are gravitational separation and filtration. Gravitational separators are usually containers in which the solid matter is allowed to separate either by sedimentation or flotation. Filters have a semi-permeable filter media which traps the solid matter but allows the liquid to flow through. Geotubes are an example of filters that are currently being used in several waste management centres. Many separation methods also require the use of polymers or flocculants to operate effectively. When contaminants are in a settleable form they are rather easy to be removed and treated with the solid matter. If the contaminants are dissolved in the liquid it might be possible to make them settle by adding aluminium or iron sulphate. Also an oil separation well could be used to separate oils from the liquid phase. Based on the literature reviews and interviews an upgraded gravitational system or the geotube method seem to be the best options. However, more tests should be conducted to see if these methods would work in practice. The biggest challenge is that the incoming liquid waste loads at Tarastenjärvi are not homogenous which makes it difficult to choose a solution that works well for all of them. The situation could be improved with more precise classification of the waste loads and handling them separately according to their characteristics. The most important aspect is to find a long-term cost-effective solution that can provide sufficient handling of the liquid wastes

Inhibición de los efectos coagulante, fosfolipasa A2 y proteolítico del veneno de Bothrops asper por plantas usadas tradicionalmente en Centroamérica

Existen pocos estudios científicos que demuestren el valor terapéutico de las plantas en la medicina tradicional centroamericana para tratar el envenenamiento ofídico. En este estudio se evaluó la capacidad de los extractos etanólicos de nueve plantas de uso etnomédico en Centroamérica (Acacia hindsii, Aristolochia maxima, Bursera simaruba, Cissampelos pareira, Eryngium foetidum, Hamelia patens, Pimenta dioica, Piper peltatum y Sansevieria hyacinthoides) para inhibir el efecto coagulante del veneno de Bothrops asper. Tres de ellas (B. simaruba, E. foetidum y P. dioica) también fueron evaluadas en cuanto a su capacidad inhibitoria de los efectos fosfolipasa A2 (PLA2) y proteolítico del veneno. Las plantas fueron colectadas en Guatemala, secadas, extraídas con etanol y los efectos inhibitorios evaluados in vitro después de preincubar concentraciones variables de extracto con concentraciones fijas de veneno. Los resultados demostraron que ninguno de los extractos logró inhibir los efectos coagulante y PLA2, pero los extractos clorofilados de P. dioica y E. foetidum inhibieron efectivamente la actividad proteolítica del veneno. El tamizaje fitoquímico, mediante ensayos macro y semimicrométricos de cromatografía en capa fina, demostró la presencia de metabolitos secundarios reportados con actividad antiproteolítica (flavonoides, antocianinas, catequinas y taninos) en la composición química de los extractos de E. foetidum y P. dioica. Su efecto sobre el veneno se evaluó mediante electroforesis SDS-PAGE, demostrándose que no está mediado por degradación proteolítica de los componentes del veneno. El aislamiento y caracterización específica de sus metabolitos secundarios en futuros estudios, permitirá determinar el mecanismo de acción inhibitoria ejercido por estos extractos

Emergent properties of microbial activity in heterogeneous soil microenvironments:Different research approaches are slowly converging, yet major challenges remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gases. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale). 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. In terms of microbial aspects, whereas 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 relevant experimental data are extremely scarce. For the overall research to move forward, it will be 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

Lessons from a landmark 1991 article on soil structure: distinct precedence of non-destructive assessment and benefits of fresh perspectives in soil research

In 1991, at the launch of a national symposium devoted to soil structure, the Australian Society of Soil Science invited Professor John Letey to deliver a keynote address, which was later published in the society’s journal. In his lecture, he shared the outcome of his reflexion about what the assessment of soil structure should amount to, in order to produce useful insight into the functioning of soils. His viewpoint was that the focus should be put on the openings present in the structure, rather than on the chunks of material resulting from its mechanical dismantlement. In the present article, we provide some historical background for Letey’s analysis, and try to explain why it took a number of years for the paradigm shift that he advocated to begin to occur. Over the last decade, his perspective that soil structure needs to be characterised via non-destructive methods appears to have gained significant momentum, which is likely to increase further in the near future, as we take advantage of recent technological advances. Other valuable lessons that one can derive from Letey’s pioneering article relate to the extreme value for everyone, even neophytes, to constantly ask questions about where research on given topics is heading, what its goals are, and whether the methods that are used at a certain time are optimal

De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs

Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this ‘siRNA omics’ approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense