Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties.     

Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil

The Verrucomicrobia constitute a newly discovered division of the Bacteria identified as a numerically abundant component of soil microbial communities in numerous sites around the world. The relative abundance of rRNA from Verrucomicrobia was investigated in the soil to examine the influence of specific environmental factors on the distribution of Verrucomicrobia and to better understand the distribution of this group in terrestrial ecosystems. The abundance of the verrucomicrobial rRNA was determined by using a novel oligonucleotide probe that is specific for verrucomicrobial 16S rRNA. The abundance of verrucomicrobial 16S rRNA in soil microbial communities was determined in relation to plant community composition and soil management history over a period of 2 years. Additional samples were analyzed to determine if verrucomicrobial rRNA relative abundance changes in relation to either soil depth or soil moisture content. The Verrucomicrobia composed 1.9+/-0.2% of the microbial community rRNA present in the 85 soil samples examined. The distribution of verrucomicrobial rRNA in the soil reveals that Verrucomicrobia are significantly affected by environmental characteristics that change in relation to time, soil history, and soil depth, and reveals that a statistically significant amount of the variation in verrucomicrobial rRNA abundance can be explained by changes in soil moisture content.     

Immobilised activated sludge based biosensor for biochemical oxygen demand measurement

A biochemical oxygen demand (BOD) sensor, based on an immobilised mixed culture of microorganisms in combination with a dissolved oxygen electrode, has been developed for the purpose of on-line monitoring of the biological treatment process for waste and wastewater. The sensor was designed for easy replacement of the biomembrane, thereby making it suitable for short-term use. The drawbacks of activated sludge based sensor, such as short sensor lifetime, were thereby circumvented. The sensor BOD measurements were carried out in the kinetic mode using a flow injection system, resulting in 25 s for one measurement followed by 4–8 min recovery time. Based on the results of normalised sensor responses, the OECD synthetic wastewater was considered to be a more suitable calibration solution in comparison with the GGA solution. Good agreement was achieved between the results of the sensor BOD measurement and those obtained from BOD₅ analysis of a wastewater sample from a food-processing factory. Reproducibility of responses using one sensor was below ±5.6% standard deviation. Reproducibility of responses using different sensors was within acceptable bias limits, viz. ±15% standard deviation.     

Freshwater ecology: changes, requirements, and future demands

The past development and evolution of limnology as a discipline has demonstrated that experimentally controlled disturbances of parts of aquatic ecosystems are essential for quantitative evaluation of causal mechanisms governing their operation. Correlative analyses and modeling only establish hypotheses, not causality, and allow only therapeutic management applications. Rather than constantly searching for differences, commonality must be sought. Among the large diversity of species, communities, and biogeochemical processes controlling growth and reproduction, commonality emerges at the levels of regulation of metabolism. Five areas of current and future limnological research are discussed in relation to greatest needs and promise to yield insights into material and energy flows in freshwater ecosystems and their effective management: (1) coupled metabolic mutualism in the physiological ecology of microbes (viruses, bacteria, fungi, and protists) and their biogeochemical, especially organic, couplings with the environment; (2) biochemical regulation of collective metabolism, recycling, and bioavailability of nutrients and growth regulators; (3) application of genetic and molecular techniques to addressing biogeochemical, evolutionary, and pollution remediation problems; (4) recognition that the metabolism within lakes and streams is dependent upon and regulated to a major extent by organic matter of the drainage basin and especially by the land-water interface biogeochemistry; and (5) recognition that food-web alterations ("biomanipulation") are short-term, expensive therapeutic tools that may minimize effects of eutrophication but will not solve or control eutrophication. Received: October 30, 1999 / Accepted: December 6, 1999     

Random amplification of polymorphic DNA versus pulsed field gel electrophoresis of SmaI DNA macrorestriction fragments for typing strains of vancomycin-resistant enterococci

Genetic typing of vancomycin-resistant enterococci (VRE) can be performed using a variety of methods, but comparative analyses of the quality of these methods are still relatively scarce. We here compare random amplification of polymorphic DNA (RAPD) analysis with pulsed field gel electrophoresis (PFGE) of DNA macrorestriction fragments as examples of two of the recent and well-accepted molecular typing methods. For the latter method, empirical guidelines for the interpretation of the DNA fingerprints have been proposed in the international literature. Based on our experimental analyses, we define similar criteria for RAPD fingerprinting. A collection of 100 strains of VRE, comprising Enterococcus faecium, Enterococcus faecalis, Enterococcus avium, Enterococcus gallinarum and Enterococcus casseliflavus, was assembled. Fifty isolates were Dutch, another 50 were isolated in the UK. Strains were selected on the basis of previously determined putative identity, close relatedness or uniqueness. The strains were analysed using well-standardised RAPD and PFGE protocols. Resulting fingerprints were interpreted with computerised methods involving band positioning and we show that typing of VRE by PFGE and RAPD generates highly congruent DNA fingerprint clustering. When the proposed international criteria for interpretation of PFGE fingerprints were applied in our case, 86% PFGE homology as discriminating value between close relatedness and uniqueness, a 75% homology cut-off for the comparison of the RAPD-generated DNA fingerprints revealed essentially identical strain clusters. As a spin-off it is revealed that strains from the different species can be efficiently discriminated, that strains from the UK and The Netherlands form separate clusters and that strains from veterinary origin can be identified separately as well.     

Comparative analyses in aquatic microbial ecology: how far do they go?

Methodological developments in recent years have led to an increase in empirical databases on the abundance and functions of aquatic microbes, now allowing synthesis studies. Most of these studies have adopted a comparative approach, such that comparative analyses are now available for most aspects of aquatic microbial food webs (more than 50 papers published in the last 15 years). Some of these analyses apparently yield conflicting results, introducing confusion and unnecessary disputes in the field. We briefly review the comparative analyses so far produced and we highlight generalities, show that some of the perceived discrepancies largely derive from partial analyses of a general underlying trend and formulate predictions based on these general trends that provide new avenues for research.     

Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies

The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.     

Characterization of the microbial community of lotic organic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecular methods

Aerobic and anaerobic cultivation techniques, 16S rDNA-based phylogeny, and fluorescent in situ hybridization were used to describe the phylogenetic diversity and physiological versatility of lotic microbial aggregates ('river snow') obtained from the river Elbe. In the course of the year the 'river snow' community changed. It was characterized by a great bacterial diversity in spring, the predominant occurrence of algae in summer and reduction of the total bacterial cell count in autumn and winter. In all 'river snow' samples, more than 70% of the bacteria counted with the general DNA stain DAPI also hybridized with the Bacteria-specific probe EUB338. In situ analysis of the bacterial 'river snow' community with a comprehensive suite of specific rRNA-targeted probes revealed population dynamics to be governed by seasonal factors. During all seasons, beta-Proteobacteria constituted the numerically most important bacterial group forming up to 54% of the total cell counts. In contrast to this, the relative abundance of other major bacterial lineages ranged from 2% for the order Planctomycetales to 36% for Cytophaga-Flavobacteria. Cultivation of 'river snow' under aerobic and anaerobic conditions with a variety of different media resulted in the isolation of 40 new bacterial strains. Phenotypic and phylogenetic analyses revealed these new strains to be mostly unknown organisms affiliated to different bacterial phyla. Application of newly developed specific oligonucleotide probes proved the cultivated bacteria, including clostridia and the numerically abundant beta-Proteobacteria, as relevant in situ members of the 'river snow' community.     

Short chain fatty acid esters synthesis by commercial lipases in low-water systems and by resting microbial cells in aqueous medium

Thirteen commercial lipases in hexane and seventeen bacterial cell suspensions in aqueous media were screened for the production of ethyl valerate and ethyl butyrate. The highest esterifying activity was obtained with commercial Pancrealipase (Biozymes Inc.) and Candida rugosa lipase (Amano Enzyme Ltd) and with bacterial cell suspension from Pseudomonas fragi CRDA 446. Commercial enzymes gave molar conversion yield of 68% over 24 h as compared to 17% with whole cells in aqueous medium. However, a comparison of both sources of biocatalyst i.e. whole microbial cells and commercial lipases, based on the amount of ester produced per g of protein for a complete reaction, indicated similar activities. © Rapid Science Ltd. 1998     

对-氯代苯胺(PCA)在填充床生物反应器中的降解作用

以氯代苯胺(PCA)为选择基质,用驯化技术从降解对二氯苯(p-DCB)的富集培养物中得到了以同化PCA为唯一碳源和氮源的混合微生物。将这种固定在填充床反应器中的微生物用于PCA的降解作用研究中。在该反应器里,PCA的生物降解遵循Logistic方程q=q_max/(1+e^α-βU_v).由方程求出了主要的动力学常数,K_s(半速率常数)和q_max(最大比基质降解速率).于PCA降解的同时,释放氯离子到培养基中。在水力停留时间3h, 进水PCA浓度为360mg·L^-1情况下,基质的体积降解率达到125mg·L^-1·h^-1;基质的百分去除率为91%.