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.     

贺兰山不同海拔典型植被带土壤微生物多样性

土壤微生物多样性在海拔梯度的分布格局研究近年来受到和植物动物一样的重视程度,但是干旱风沙区微生物多样性在海拔梯度上的多样性分布规律尚未揭示。本研究以处于干旱风沙区的贺兰山不同海拔的六个典型植被带（荒漠草原带、山地旱生灌丛带、温性针叶林带、针阔混交林带、寒温性针叶林带和亚高山草甸带）土壤为研究对象,利用Biolog微平板法和磷脂脂肪酸甲酯法(FAMEs)系统研究微生物多样性群落特征以及在不同植被带分布规律。结果表明：土壤微生物功能多样性随海拔增加发生变化,且微生物群落结构存在显著差异。Biolog分析显示土壤微生物群落代谢活性依次是：亚高山草甸>寒温性针叶林>针阔混交林>温性针叶林>山地旱生灌丛>荒漠草原,随海拔的升高土壤微生物群落物种丰富度指数（H）和均匀度指数（E）总体上均表现出增大的趋势,差异显著（P＜0.05）;FAMEs分析表明不同海拔的微生物区系发生了一定程度的变化,寒温性针叶林土壤微生物磷酸脂肪酸生物标记的数量和种类均最高,且细菌、真菌特征脂肪酸相对含量也最高;土壤微生物群落结构多样性次序是：寒温性针叶林带>针阔混交林带>温性针叶林带>亚高山草甸>山地旱生灌丛>荒漠草原。本研究结果表明贺兰山海拔梯度的微生物多样性分布规律不同于已有的植物多样性“中部膨胀”研究结果,这说明在高海拔地区有更多的适合该生境的微生物存在,这对维持干旱风沙区的生态系统功能稳定性具有重要意义。     

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.     

Microbial structural diversity estimated by dilution-extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient

The present work tested whether the relationship between functional traits and inoculum density reflected structural diversity in bacterial communities from a land-use intensification gradient applying a mathematical model. Terminal restriction fragment length polymorphism (T-RFLP) analysis was also performed to provide an independent assessment of species richness. Successive 10-fold dilutions of a soil suspension were inoculated onto Biolog GN(R) microplates. Soil bacterial density was determined by total cell and plate counts. The relationship between phenotypic traits and inoculum density fit the model, allowing the estimation of maximal phenotypic potential (Rmax) and inoculum density (KI) at which Rmax will be half-reduced. Though Rmax decreased with time elapsed since clearing of native vegetation, KI remained high in two of the disturbed sites. The genetic pool of bacterial community did not experience a significant reduction, but the active fraction responding in the Biolog assay was adversely affected, suggesting a reduction in the functional potential.     

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     

Anti-protozoal and anti-bacterial antibiotics that inhibit protein synthesis kill cancer subtypes enriched for stem cell-like properties

Key players in translational regulation such as ribosomes might represent powerful, but hitherto largely unexplored, targets to eliminate drug-refractory cancer stem cells (CSCs). A recent study by the Lisanti group has documented how puromycin, an old antibiotic derived from Streptomyces alboniger that inhibits ribosomal protein translation, can efficiently suppress CSC states in tumorspheres and monolayer cultures. We have used a closely related approach based on Biolog Phenotype Microarrays (PM), which contain tens of lyophilized antimicrobial drugs, to assess the chemosensitivity profiles of breast cancer cell lines enriched for stem cell-like properties. Antibiotics directly targeting active sites of the ribosome including emetine, puromycin and cycloheximide, inhibitors of ribosome biogenesis such as dactinomycin, ribotoxic stress agents such as daunorubicin, and indirect inhibitors of protein synthesis such as acriflavine, had the largest cytotoxic impact against claudin-low and basal-like breast cancer cells. Thus, biologically aggressive, treatment-resistant breast cancer subtypes enriched for stem cell-like properties exhibit exacerbated chemosensitivities to anti-protozoal and anti-bacterial antibiotics targeting protein synthesis. These results suggest that old/existing microbicides might be repurposed not only as new cancer therapeutics, but also might provide the tools and molecular understanding needed to develop second-generation inhibitors of ribosomal translation to eradicate CSC traits in tumor tissues.     

Sheep-urine-induced changes in soil microbial community structure

Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.