Genomics Applications for the Developing World (Advances in Microbial Ecology)

Advances in Microbial Ecology J. Advances in Microbial Ecology Bernhard Schink.

Advances in Microbial Ecology Martin Alexander. Advances in Microbial Ecology M. Nutrient Cycles and Energy Flow. Ecological Constraints of the Microhabitat. Nutrient Transport and Turnover. Population Structure and Dynamics.

Freshwater and Polluted Ecosystems. The Surface Microlayer s. Sampling Devices for Collection of the Surface Microlayers. Bacterial Accumulation at the Surface Lipid Film. Availiability of Nutrients for Bacterial Growth. Biochemical Activity of Neustonic Bacteria. Factors Affecting Rhizobial Survival. Observed Persistence in the Field. Stimulation of Rhizobium in the Rhizosphere. Organisms Inhabiting the Floodwater. N2 Fixation by Photoautotrophs. Nitrification at the Surface Soil Layer. Nature of Aerobic and Anaerobic Bacteria. Water Percolation and Microbial Activity.

However, a comparison between the genomes of bacteria isolated from soil environments where bioremediation activity was detected and the metagenome of that environment indicates that the genes responsible for remediation in the environment are different to those accessible through cultivation [[ 1 ]. Through metagenomics it is possible to learn more about the diverse xenobiotic degradation pathways used by prokaryotes in the environment [[ 2 ].

One of the main areas of metagenomic research from the beginning has been its application in the discovery of novel biocatalysts. Considering the high diversity of prokaroytic life in soil environments, soil metagenomic libraries offer one of the best sources when searching for a wide range of biocatalysts. Such libraries can be searched using direct sequencing of clones and comparison of sequences with the databases, or by functional analysis, screening for a specific activity [[ 6 ].

A diverse range of biocatalysts have been obtained from metagenomic libraries [[ 4 ,[ 6 ,[ 7 ]. As well as the diversity of enzyme classes found in metagenomic libraries there are also variations in functional characteristics within the classes which makes them of particular interest to biotechnology.

For example, recently in our research group two esterases were detected and characterised at the molecular and biochemical level. They displayed overlapping, but quite different, substrate profiles, and one had a much higher activity than the other unpublished data. When enzymes are required which have specific optimal conditions for functioning such as higher temperature, pH extremes or elevated salinity then metagenomic libraries derived from prokaryotic populations growing under those conditions can be targetted.

Using this strategy it was possible to isolate and characterise a novel, thermostable esterase [[ 7 ].

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This esterase had a narrower pH range 5. Considering the range of activities and functional optima displayed by these three characterised metagenome derived esterases, and the fact that many more esterases have been detected in libraries, this indicates a great natural diversity which could be applied in a broad range of biotechnological situations is just waiting to be tapped by metagenomic researchers. Metagenomics enables the detection and characterisation of a wide range of biocatalysts. However, often thousands of clones must be analysed before even a small number of positive clones can be detected.

Advances in Microbial Ecology : Martin Alexander :

One development which enables rapid screening of large numbers of clones is the use of DNA microarrays [[ 9 ]. Using this approach it is possible to identify clones generated from non-cultivated microorganisms, thus narrowing the range of clones to be sequenced and analysed further. A similar, highly sensitive, microarray development at the protein level allows the detection of enzyme activity in hundreds of samples simultaneously [[ 0 ].

One innovative approach to screening is substrate induced gene expression screening for catabolic genes [[ 1 ]. This is obtained by using an operon-trap gfp-expression vector for generating the metagenomic library, growing the library in liquid medium supplemented with the substrate of interest and using fluorescence-activated cell sorting to find the fluorescing cells containing the genes of interest [[ 1 ].

The application of these methods for screening metagenomic libraries will make the discovery of positive clones much more rapid and allow screening for a greater diversity of genes and their products.

The full range of potentially interesting gene products made available in metagenomic libraries has not yet been fully investigated. For example, the complexity of interaction between cell signalling molecules and gene regulation mechanisms could now be reconstructed and elucidated for mixed species biofilms which would provide valuable data of ecological and medical importance.

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A further example is the genomic analysis of 1 g of soil. The coding capacity of the soil metagenome is greater than that of the human genome. If equivalent funding was channeled into metagenomics this would unlock valuable information and provide the basis for major developments in key areas of ecology, medicine and biotechnology. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide.

Sign In or Create an Account. Close mobile search navigation Article navigation. Advances in ecology and biotechnology Helen L. Abstract This review highlights the significant advances which have been made in prokaryotic ecology and biotechnology due to the application of metagenomic techniques. View large Download slide. Molecular biological access to the chemistry of unknown soil microbes: Approaches to prokaryotic biodiversity: Ecotypes of planktonic actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical and tropical freshwater habitats.

Ecological significance of microdiversity: Introducing DOTUR, a computer programme for defining operational taxonomic units and estimating species richness. Integration of microbial ecology and statistics: Isolation and analysis of a kilobase-pair genome fragment from a planktonic marine archaeon. Characterisation of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments.

Community structure and metabolism through reconstruction of microbial genomes from the environment. Phylogeny-function analysis of meta genomic libraries: Cloning the soil metagenome: Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Quantifying the accessibility of the metagenome by random expression cloning techniques. Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts.

Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. One would have hoped that by now the technologies and approaches would have been adapted on a far greater scale. In addition to this, the associated information is not always easily accessible, and is not disseminated in a format that can become a useful reference for scientists, students and others who reside in developing countries.

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Environmental Microbiology

Advances in Microbial Ecology J. Advances in Microbial Ecology Bernhard Schink. Advances in Microbial Ecology Martin Alexander.