Determination of substrate utilization patterns of soil microbial communities: An approach to assess population changes after hydrocarbon pollution

Abstract: Changes in hydrocarbon content in soils resulted in characteristic shifts of the substrate utilization patterns as tested with the Biolog system. The altered patterns of substrate utilization corresponded to similar changes in abundance of hydrocarbon-utilizing bacteria and the occurrence of specific bacterial groups in the soils. Substrate utilization patterns as recorded with the Biolog system are suitable for rapidly assessing dynamics of autochthonous soil communities and evaluating their biodegradative potential.     

A Microplate Assay to Assess Chemical Effects on RBL-2H3 Mast Cell Degranulation: Effects of Triclosan without Use of an Organic Solvent

Mast cells play important roles in allergic disease and immune defense against parasites. Once activated (e.g. by an allergen), they degranulate, a process that results in the exocytosis of allergic mediators. Modulation of mast cell degranulation by drugs and toxicants may have positive or adverse effects on human health. Mast cell function has been dissected in detail with the use of rat basophilic leukemia mast cells (RBL-2H3), a widely accepted model of human mucosal mast cells^3-5. Mast cell granule component and the allergic mediator β-hexosaminidase, which is released linearly in tandem with histamine from mast cells⁶, can easily and reliably be measured through reaction with a fluorogenic substrate, yielding measurable fluorescence intensity in a microplate assay that is amenable to high-throughput studies¹. Originally published by Naal et al.¹, we have adapted this degranulation assay for the screening of drugs and toxicants and demonstrate its use here.Triclosan is a broad-spectrum antibacterial agent that is present in many consumer products and has been found to be a therapeutic aid in human allergic skin disease^7-11, although the mechanism for this effect is unknown. Here we demonstrate an assay for the effect of triclosan on mast cell degranulation. We recently showed that triclosan strongly affects mast cell function². In an effort to avoid use of an organic solvent, triclosan is dissolved directly into aqueous buffer with heat and stirring, and resultant concentration is confirmed using UV-Vis spectrophotometry (using ε₂₈₀ = 4,200 L/M/cm)¹². This protocol has the potential to be used with a variety of chemicals to determine their effects on mast cell degranulation, and more broadly, their allergic potential.     

Microplates as a microreactor platform for microalgae research

High‐throughput platforms for microalgae screening are not yet commercially available. In this study, the feasibility of 96‐well microplates was analyzed for microalgae research. Equivalence among wells, as culture microreactors, was investigated in controlled high CO₂ conditions. Specific growth rates of two microalgae species, Scenedesmus sp. UTEX1589 and an environmental isolate, were significantly higher in border wells than in internal positions. Furthermore, growth rate gradients analyzed as contours throughout the platform were observed for Scenedesmus sp. However, the output variable exhibited high precision associated with a low coefficient of variation (CV), between 6.8 and 7.8%. In a demonstrative experiment to determine the effect of culture media dilution on six microalgae species, treatments were randomized in the central subset of a microplate. Results were consistent and statistically sound (CV 9.4–12.9%), and showed that microalgae species could grow with no detrimental effect in 50% (v/v) dilution of the culture medium. Provided border wells exclusion and a randomized design, 96‐well microplates are a practical and statistical robust platform for microalgae research. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:638–644, 2013     

Development of a micelle‐enhanced high‐throughput fluorometric method for determination of niclosamide using a microplate reader

The present paper describes the development and validation of a simple and sensitive micelle‐enhanced high‐throughput fluorometric method for the determination of niclosamide (NIC) in 96‐microwell plates. The proposed method is based on the reduction of the nitro group of niclosamide to an amino group using Zn/HCl to give a highly fluorescent derivative that was developed simultaneously and measured at λ_em 444 nm after excitation at λ_ex 275 nm. Tween‐80 and carboxymethylcellulose (CMC) have been used as fluorescence enhancers and greatly enhanced the fluorescence by factors of 100–150%. The different experimental conditions affecting the fluorescence reaction were carefully investigated and optimized. The proposed method showed good linearity (r²≥ 0.9997) over the concentration ranges of 1–5 and 0.5–5 μg/ml with lower detection limits of 0.01 and 0.008 μg/ml and lower quantification limits of 0.04 and 0.03 μg/ml on using Tween‐80 and or CMC, respectively. The developed high‐throughput method was successfully applied for the determination of niclosamide in both tablets and spiked plasma. The capability of the method for measuring microvolume samples made it convenient for handling a very large number of samples simultaneously. In addition, it is considered an environmentally friendly method with lower consumption of chemicals and solvents.     

Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback

Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here, we quantified the suite of elements in individuals (i.e., ionome) and differences in the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony plating is associated with changes in the ionome and nutrient recycling. More broadly, we find that adaptation of marine stickleback to freshwater conditions shifts the ionomes of natural populations and populations raised in common gardens. In both cases ionomic divergence between populations was primarily driven by differences in trace elements rather than elements typically associated with bone. These findings demonstrate the utility of ecological stoichiometry and the importance of ionome‐wide data in understanding eco‐evolutionary dynamics.     

Functional diversity and community structure of microorganisms in rhizosphere and non-rhizosphere Canadian arctic soils

Functional diversities of microorganisms in arctic soil samples at three incubation temperatures were assessed using sole-carbon-source-utilization (SCSU). Soil samples from four sites were collected from the rhizosphere and non-rhizosphere soils. Microorganisms were extracted from samples and inoculated into ECO-Biolog plates and incubated at 4, 10 and 28 °C. Calculations of Shannon–Weaver diversity and Shannon–Weaver evenness were based on the substrate utilization in the Biolog plates. Shannon–Weaver diversities (H) in rhizosphere samples were significantly greater ( _H = 3.023 ± 0.197; P < 0.005) than in non-rhizosphere samples ( _H = 2.770 ± 0.154). Similarly, the evenness (E) of the inoculated microbial cells exhibited significant differences (P < 0.005) between the rhizosphere and non-rhizosphere soil samples ( _E = 0.880 ± 0.057 for soils with rhizosphere; _E = 0.807 ± 0.044 for non-rhizosphere samples). Higher microbial diversity and evenness were observed in samples incubated at 4 °C than at 28 °C [least significant difference (lsd) = 0.29], and evenness indices were higher in rhizosphere samples than in non-rhizosphere soils incubated at all three temperatures (lsd = 0.02). Principal component analysis (PCA) of the multivariate data set differentiated the soil samples on the relatively gross scale of microbial communities isolated from rhizosphere and non-rhizosphere soils at all three temperatures.     

乐陵金丝小枣区生态环境地质特征

乐陵金丝小枣区生态环境地质研究表明,层状沉积的河流相及其变异体,心、底土层层位为壤质、粘壤质的土体构型,以不稳定原生矿物为主的土壤,中性或微碱性的重碳酸盐型地球化学环境,钾素丰富、理化性状良好的潮土、褐土化潮土、盐化潮土为该枣区生态环境地质特征的重要标志．对枣生长发育适宜区进行了划分．     

Metabolic characterisation of fifteen atrazine-degrading microbial communities

Fifteen atrazine-degrading microbial communities obtained from different sources were able to degrade atrazine in a liquid mineral medium as the main organic substrate at high rates (atrazine half-lives ranging from 20 to 164 h). Hydroxyatrazine was the sole metabolite detected. This metabolite was always transient but its maximum level varied from 4 to 67% of the parent compound. Communities originating from subsurface sediments degraded atrazine at similar rates (half-lives between 56 and 62 h). A Biolog characterisation revealed a wide diversity of substrate utilisation by the communities originating either from the surface or the subsurface environments. Twenty-four Biolog carbon sources were degraded by the fifteen communities. A multiple regression analysis established a statistically significant relationship between the atrazine DT50 values of thirteen communities and their responses to four Biolog carbon sources. Received 12 June 1998/ Accepted in revised form 9 October 1998