纳米孔测序技术在环境微生物研究中的应用

高通量测序技术是研究环境微生物的有效手段,而以纳米孔测序为代表的第三代测序技术以其测序读长长、测序速度快、测序数据实时监控、仪器方便携带、无GC偏好性、无需经过PCR扩增等显著优势有力推动了环境微生物研究的发展.本文对纳米孔测序技术的技术原理和特点进行了简要概述,重点介绍了纳米孔测序技术在环境微生物扩增子测序、宏基因组...     

Challenges in applying microarrays to environmental studies

Although DNA microarray technology has been used successfully to analyze global gene expression in pure cultures, it has not been rigorously tested and evaluated within the context of complex environmental samples. Adapting microarray hybridization for use in environmental studies faces several challenges associated with specificity, sensitivity and quantitation.     

Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints

Advances in our understanding of functional genomics are best addressed by integrative studies that include measurements of mRNA, proteins, and low molecular weight metabolites over time and varied conditions. Bioinformatics can then be used to relate this data to the genome. Current technology allows for comprehensive and rapid mRNA expression profiling and mass spectrophotometric measurement of low molecular weight intermediates and metabolic products. In prokaryotic organisms, this combination provides a potentially powerful tool for identifying gene function and regulatory networks even in the absence of a combined proteomic approach.     

Genomics for environmental microbiology

The utilization of natural microbial diversity in biotechnology is hindered by our inability to culture the vast majority of microorganisms and the observation that laboratory engineered bacteria rarely function in the wild. It is now clear that an understanding of the community structure, function and evolution of bacteria in their natural environments is required to meet the promise of microbial biotechnology. To meet these new challenges, microbiologists are applying the tools of genomics and related high-throughput technologies to both cultured microbes and environmental samples. This work will lead to new views on ecosystems and biological function together with the biotechnology enabled by this science.     

Listeria: growth,phenotypic differentiation and molecular microbiology

The identification of Listeria species is based on a limited number of biochemical markers, among which absence or presence of hemolysis and arylamidase are used to differentiate between L. monocytogenes and L. innocua. The CAMP (Christie, Atkins, Munch-Petersen) test must be interpreted with caution. Chromogenic media are based on both the specific chromogenic detection of phosphatidylinositol phospholipase C and the xylose fermentation and give specific and direct identification of L. monocytogenes and L. ivanovii. Isolates of L. monocytogenes with atypical properties require tools of molecular biology for final identification. Serotyping, although not allowing speciation, serves a useful purpose for confirming the genus diagnosis Listeria. Polymerase chain reaction is particularly useful when prior administration of antimicrobial agents compromises culture. For clinical specimens the importance of trying to isolate the pathogen as a prerequisite for an epidemiological work-up and finally for prevention of further cases cannot be overstressed.     

Proteomics in environmental and technical microbiology

Nowadays, the field of proteomics encompasses various techniques for the analysis of the entirety of proteins in biological samples. Not only 2D electrophoresis as the primary method, but also MS‐based workflows and bioinformatic tools are being increasingly applied. In particular, research in microbiology was significantly influenced by proteomics during the last few decades. Hence, this review presents results of proteomic studies carried out in areas, such as fundamental microbiological research and biotechnology. In addition, the emerging field of metaproteomics is addressed because high‐throughput genome sequencing and high‐performance MS facilitate the access to such complex samples from microbial communities as found in sludge from wastewater treatment plants and biogas plants. Both current technical limitations and new concepts in this growing and important area are discussed. Moreover, it was convincingly shown that future prospective applications of proteomics in technical and environmental microbiology might also be closely connected with other Omics approaches as well as bioinformatics for systems biology studies.     

Application of independent component analysis to microarrays

We apply linear and nonlinear independent component analysis (ICA) to project microarray data into statistically independent components that correspond to putative biological processes, and to cluster genes according to over- or under-expression in each component. We test the statistical significance of enrichment of gene annotations within clusters. ICA outperforms other leading methods, such as principal component analysis, k-means clustering and the Plaid model, in constructing functionally coherent clusters on microarray datasets from Saccharomyces cerevisiae, Caenorhabditis elegans and human.     

From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules

Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.     

Maternal effects provide phenotypic adaptation to local environmental conditions

In outcrossing plants, seed dispersal distance is often less than pollen movement. If the scale of environmental heterogeneity within a population is greater than typical seed dispersal distances but less than pollen movement, an individual's environment will be similar to that of its mother but not necessarily its father. Under these conditions, environmental maternal effects may evolve as a source of adaptive plasticity between generations, enhancing offspring fitness in the environment that they are likely to experience. This idea is illustrated using Campanula americana, an herb that grows in understory and light-gap habitats. Estimates of seed dispersal suggest that offspring typically experience the same light environment as their mother. In a field experiment testing the effect of open vs understory maternal light environments, maternal light directly influenced offspring germination rate and season, and indirectly affected germination season by altering maternal flowering time. Results to date indicate that these maternal effects are adaptive; further experimental tests are ongoing. Evaluating maternal environmental effects in an ecological context demonstrates that they may provide phenotypic adaptation to local environmental conditions.