Control of P2X2 Channel Permeability by the Cytosolic Domain

ATP-gated P2X channels are the simplest of the three families of transmitter-gated ion channels. Some P2X channels display a time- and activation-dependent change in permeability as they undergo the transition from the relatively Na+-selective I1 state to the I2 state, which is also permeable to organic cations. We report that the previously reported permeability change of rat P2X2 (rP2X2) channels does not occur at mouse P2X2 (mP2X2) channels expressed in oocytes. Domain swaps, species chimeras, and point mutations were employed to determine that two specific amino acid residues in the cytosolic tail domain govern this difference in behavior between the two orthologous channels. The change in pore diameter was characterized using reversal potential measurements and excluded field theory for several organic ions; both rP2X2 and mP2X2 channels have a pore diameter of ~11 Å in the I1 state, but the transition to the I2 state increases the rP2X2 diameter by at least 3 Å. The I1 to I2 transition occurs with a rate constant of ~0.5 s^-1. The data focus attention on specific residues of P2X2 channel cytoplasmic domains as determinants of permeation in a state-specific manner

Control of pore geometry in soil microcosms and its effect on the growth and spread of <i>Pseudomonas </i>and <i>Bacillus</i> sp.

Simplified experimental systems, often referred to as microcosms, have played a central role in the development of modern ecological thinking on issues ranging from competitive exclusion to examination of spatial resources and competition mechanisms, with important model-driven insights to the field. It is widely recognized that soil architecture is the key driver of biological and physical processes underpinning ecosystem services, and the role of soil architecture and soil physical conditions is receiving growing interest. The difficulty to capture the architectural heterogeneity in microcosms means that we typically disrupt physical architecture when collecting soils. We then use surrogate measures of soil architecture such as aggregate size distribution and bulk-density, in an attempt to recreate conditions encountered in the field. These bulk-measures are too crude and do not describe the heterogeneity at microscopic scales where microorganisms operate. In the current paper we therefore ask the following questions: (i) To what extent can we control the pore geometry at microscopic scales in microcosm studies through manipulation of common variables such as density and aggregate size?; (ii) What is the effect of pore geometry on the growth and spread dynamics of bacteria following introduction into soil? To answer these questions, we focus on Pseudomonas sp. and Bacillus sp. We study the growth of populations introduced in replicated microcosms packed at densities ranging from 1.2 – 1.6 g cm-3, as well as packed with different aggregate sizes at identical bulk-density. We use X-ray CT and show how pore geometrical properties at microbial scales such as connectivity and solid-pore interface area, are affected by the way we prepare microcosms. At a bulk-density of 1.6 g cm-3 the average number of Pseudomonas was 63% lower than at a bulk-density of 1.3 g cm-3. For Bacillus this reduction was 66 %. Depending on the physical conditions, bacteria in half the samples took between 1.62 and 9.22 days to spread 1.5 cm. Bacillus did spread faster than Pseudomonas and both did spread faster at a lower bulk-density. Our results highlight the importance that soil physical properties be considered in greater detail in soil microbiological studies than is currently the case

Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales

To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescens was 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils

Influence of soil structure on the spread of <i>Pseudomonas fluorescens</i> in soil at microscale

For over a half a century, researchers have been aware of the fact that the physical and chemical characteristics of microenvironments in soils strongly influence the activity, growth, and metabolism of microorganisms. However, many aspects of the effect of soil physical characteristics, such as the pore geometry, remain poorly understood. Therefore, the objective of the present research was to determine the influence of soil pore characteristics on the spread of bacteria, observed at the scale relevant to microbes. Pseudomonas fluorescens was introduced in columns filled with 1–2 mm soil aggregates, packed at different bulk densities.. Soil microcosms were scanned at 10.87 μm voxel resolution using X‐ray computed tomography (CT) to characterize the geometry of pores. Thin sections were prepared to determine the spread and colonization of bacteria. The results showed that average bacterial cell density was 174 cells mm−2 in soil with bulk density of 1.3 g cm−3 and 99 cells mm−2 in soil with bulk density of 1.5 g cm−3. Soil porosity and solid‐pore interfaces influence the spread of bacteria and their colonization of the pore space at lower bulk density, resulting in relatively higher bacterial densities in larger pore spaces. The study also demonstrates that thin sectioning of resin impregnated soil samples can be combined with X‐ray CT to visualize bacterial colonization of a 3D pore volume. This research therefore represents a significant step towards understanding how environmental change and soil management impact bacterial diversity in soils

Der Einfluss von Reisstrohmanagement-Praktiken auf mikrobielle Prozesse in chinesischen Reisböden

Das Verbrennen von Reisstroh ist in China eine der gängigen Reisstrohmanagement-Praktiken, welche neben den Verlusten von Nährstoffen auch zu Umweltproblemen, wie der Emission von Treibhausgasen und der Produktion von Feinstaub führt. Eine Alternative zur Verbrennung ist das Einbringen des anfallenden Strohs in den Boden. Mit einem Mikrokosmenexperiment konnte der Einfluss der verschiedenen Reisstrohapplikationen auf die Aktivitäten unterschiedlicher mikrobieller Enzyme während der Vegetationsperiode im Nassreisanbau gezeigt werden. Zusätzlich wurden die Beziehungen zwischen der Pflanze, dem Stroh, bzw. der Strohasche, einerseits und der Produktion von Kohlendioxid und Methan sowie dem pH und dem Redoxpotential andererseits aufgezeigt

Räumlich-zeitliche Charakterisierung mikrobieller Gemeinschaften im Wurzelraum eines Nassreisbodens

Die lokal begrenzte Verfügbarkeit von Sauerstoff im anoxischen Wurzelraum von Nassreisböden induziert gegensätzliche physiko-chemische Rahmenbedingungen, deren Einfluss auf die räumlich-zeitliche Dynamik mikrobieller Populationen untersucht wurde. In einem Rhizotronexperiment wurden während einer Anbauphase von Nassreis (Oryza sativa L.) Bodenproben aus unterschiedlichen Bereichen im Wurzelraum entnommen, die mit Hilfe der molekularbio-logischen Methoden PCR-DGGE und CARD-FISH ausgewertet wurden. Die auf domänenspezifischer Ebene untersuchten mikrobiellen Gemeinschaften wiesen für die beprobten Bereiche deutliche Unterschiede hinsichtlich ihrer Struktur sowie ihrer Individuenzahl auf. Neben der Verfügbarkeit von Sauerstoff erwies sich die variierende Wurzelaktivität im Verlauf der Anbauphase als entscheidender Faktor für die Ausbildung einer heterogenen Verteilung mikrobieller Habitate im Wurzelraum von Nassreis

Monitoring des Wurzelraumes von Paddy Soils mit Hilfe von Rhizotronen und digitaler Bildanalyse

Chemische Eigenschaften im Wurzelraum von Nassreisböden Paddy Soils) werden signifikant durch die Aktivität der Reiswurzeln beeinflusst. Die partielle Freisetzung des zuvor über Aerenchyme zu den Wurzeln transportierten Sauerstoffs führt in der Rhizosphäre unter anoxischen Bedingungen zur Entstehung räumlicher Redoxgradienten. In einem Rhizotron-Experiment wurde die Entwicklung des Wurzelraumes eines Paddy Soils dokumentiert. Während einer Anbauphase von Nassreis (Oryza sativa L.) wurden hierfür täglich Rhizotron-Scans erstellt, die mit Hilfe digitaler Bildanalysemethoden ausgewertet wurden. Prägnant gefärbte reduzierte und oxidierte Bereiche im Wurzelraum wurden mit Farbschwellwerten detektiert und in Falschfarben diskret dargestellt. Über die Quantifizierung der detektierten Bereiche konnte die Dynamik reduzierter und oxidierter Flächen während der Anbauphase visualisiert und analysiert werden

Bewirtschaftungsinduzierte Populationsveränderungen von Archaeen in Paddy Soils

Die Produktion des Treibhausgases Methan durch Archaeen im Nassfeldanbau von Reis ist von großer Relevanz für das Weltklima. In einem Mikrokosmenexperiment wurden die Bewirtschaftungsphasen im Anbau von Nassreis simuliert und die Populationsdynamik der Archaeen in drei unterschiedlichen Reisböden untersucht. Die molekularbiologische Analyse ausgesuchter Bewirtschaftungszustände (flooded und drained) mit Hilfe von DGGE zeigte deutliche Populationsshifts der Archaeen. Chemische und strukturelle Veränderungen des Bodens wurden ebenfalls beobachtet

The distribution of organic contaminant in aged tar-oil contaminated soils

One of the most common soil contamination sources in Germany are former manufactured gas plants. Many of them were destroyed during the World War II or abandoned in late XXth century. As the result a lot of potentially fertile soils were contaminated with specific viscous tar oil wastes. We studied a small tar oil waste basin. The age of the contamination was assessed to be at least 30 years. Natural attenuation processes resulted in formation of three soil layers. The upper layer (about 7cm in thickness) was rooted by weak grass vegetation and had features of newly formed humic-like organic matter. The total petroleum hydrocarbon (TPH) content was 28 mg/g. Below this layer (7-15 cm) we observed the most contaminated stratum with 90 mg/g TPH. The layer underneath (15-22 cm) had smaller concentrations of 16 mg/g TPH. Underlying strata had no visual evidence of contamination. Microbial biomass analyses showed that the most contaminated layer had 2-3 times more bacteria than the control soils. We suppose that during the aging processes a new microbial consortium capable of transforming high-molecular weight hydrocarbons has developed. Optical and FTIR-microscopy allowed us to observe the microstructure of contaminated soils. The tar oil formed dense spherical aggregates within the soil, which contained almost no mineral phase. Root channels and macropores were identified as preferential pathflows for the viscous tar oil, as they seemed to be coated with hydrocarbons even in less contaminated underlayers. We presume that open pores could initially act as remediation spots with aerobic conditions. Future oil migration might clog these pores, cease oxidation processes and slow down the remediation. High contents of total Fe and both dithionite-extractable and oxalate-extractable Fe as well as the occurrence of large siderite crystals in the most contaminated layer suggested that there might be isolated zones with anaerobic conditions to support this assumption