Microbial population genetics examines the spatial and temporal patterns of genetic variation across diverse geographic scales and ecological niches. With the arrival of molecular biological techniques, the past 40 years have seen tremendous progresses in microbial population genetics. However, in recent years, the analyses of genetic materials directly from natural environments have revolutionized our approaches and understandings of the diversity, function, and inter-relationships among microorganisms in diverse natural ecological niches (Xu, 2010).

The emergence and development of this expanding new field, that of metagenomics, has been primarily driven by technical and analytical methods developed from high throughput platforms for cloning, microfluidics, DNA sequencing, robotics, high-density microarrays, 2D-gel electrophoresis, and mass spectrometry as well as associated bioinformatics softwares. Molecular tools are used for identifying the diversity and function of microorganisms in natural biological communities. Of special notes are the potential impacts of recent developments in single cell isolation, whole-genome amplification, pyrosequencing, and database warehousing on our understanding of microbial population structures in nature. These exciting developments are bringing significant opportunities as well as new challenges to the field of microbial population genetics (Xu, 2010).

References:
Xu, J. (2010) Microbial Population Genetics. Caister Academic Press, Norfolk, UK.
Marco, D. (2010) Metagenomics: Theory, Methods and Applications. Caister Academic Press, Norfolk, UK.
Liu, W.-T. and Jansson, J.K. (2010) Environmental Molecular Microbiology. Caister Academic Press, Norfolk, UK.

Labels: metagenomics, Microbial Population Genetics, population genetics

The interactions between microbes and plants make the major contribution to the biotic components of soils, the most diverse habitats on Earth. Plants play central roles in providing nutrient input into the soil, both through microbially-mediated decomposition of plant matter, and through the direct provision of photosynthate derived root exudates. These nutrients support large and diverse microbial communities, many of which provide direct benefit to the plant. The interplay between plants and their microbial co-habitants is regulated by extensive chemical signalling. Most of what we know about these complex community interactions has been derived through study of organisms in pure culture, but it is well known that the vast majority of microbes have not been cultivated. We now have the opportunity to explore the interactions between plants and microbes through cultivation-independent study of the microbial communities. While high-throughput DNA sequence analysis is an important tool for these studies, the immense richness and diversity of such communities present a strong mandate for the use of functional metagenomics strategies that involve a broad variety of screening methodologies to discover and study the currently unknown key biological processes.

Further reading

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: Biotic components of soils, metagenomics, microbial communities, plant-microbe interactions

The advent of metagenomics has had a dramatic effect in the way we view and study the microbial world. By allowing the direct investigation of the vast majority of bacteria, as well as viruses and fungi, irrespective of their culturability and taxonomic identities, metagenomics has not only changed microbiological theory and methods but also has challenged the classical concept of species. This newly evolved biological field has proven to be rich and comprehensive and is making important contributions to microbial ecology, biodiversity, bioremediation, bioprospection of natural products, medicine, and many other fields. The diversity of facets of metagenomics as well as the multiplicity of its potential applications makes it difficult to find an ample but at the same time ordered account of this new discipline.

Further reading

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: metagenomics

A new update on research in Microbial Ecology

Microbial Diversity and Phylogeny
Genomics and Metagenomics
Metaproteomics
Nucleic-Acid-based Characterization
Microarrays in Microbial Ecology
The Soil Environment
Plant Microbial Communities
Marine Microbial Environments
Ocean microbial communities
Human Microbial Environment
Wastewater Treatment
Bacterial Biofilms

Read more at: Microbial Ecology

Labels: Bacterial Biofilms, ecology, genomics, metagenomics, Metaproteomics, microarrays, microbial communities, Microbial Diversity, Microbial Environments, Phylogeny, Soil Environment, Wastewater

The early genomics studies that began appearing in the 1980s progressed exponentially to the current state where the genome sequences of several hundred microbes, numerous eukaryotics, and thousands of viruses are available. Current estimates are that there are hundreds of partial genomes available and many other genome sequencing projects are also in progress. The real launch of the genomic era, however, began in the early 1990s with the availability of the complete genome sequence of Haemophilus influenzae.

This study which was mind shattering at the time has now become routine protocol in many laboratories.

Genomics really came of age when we began to witness a greater level of microbial diversity within species than previously anticipated, lateral gene transfer, and the significance of phage and viral genomics. The field of genomics which gave us the first genome of a free living organism also laid the foundation for generating genomic sequence data from whole environments without first using a culturing step, a field of research now known as 'metagenomics'.

The term metagenomics was first used in the late 1990s, and was defined as the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The availability of 'next generation' sequencing technologies such as 454 pyrosequencing have made it such that a cloning step is no longer essential for metagenomic projects.

Further reading:

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications

Labels: genomics, metagenomics

Metagenomics is a rapidly growing field of research that has had a dramatic effect on the way we view and study the microbial world. By permitting the direct investigation of bacteria, viruses and fungi irrespective of their culturability and taxonomic identities, metagenomics has changed microbiological theory and methods and has also challenged the classical concept of species. This new field of biology has proven to be rich and comprehensive and is making important contributions in many areas including ecology, biodiversity, bioremediation, bioprospection of natural products, and in medicine.

from Diana Marco in Metagenomics: Theory, Methods and Applications

Labels: archaea, archaeal metagenomics, bioremediation, horizontal gene transfer, metagenomics, microbial communities, microbiome, plant-microbe interactions

Metagenomics, which can be defined as the science of biological diversity, consists of the genomic analysis of a microbial population with similar but not identical members, by the use of genetic and molecular analysis. A comprehensive metagenomic study provides understanding of the dynamics of a microbial population and includes analysis of nucleotide sequence, structure, regulation and function. Metagenomics has applications in a broad range of areas. For example the metagenomics approach has been used to study the intestinal microflora (Norin et al 2009 in Lactobacillus Molecular Biology), in studies of bioremediation and biodegradation (Díaz 2008 Microbial Biodegradation), and in the study of bacteriophage in the environment (Weinbauer et al 2007 in Bacteriophage: Genetics and Molecular Biology).

Further reading: Metagenomics: Theory, Methods and Applications

Labels: metagenomics