Caister Academic Press

Environmental Microbiology

Metagenomics: Current Advances and Emerging Concepts
Edited by: Diana Marco
Cutting-edge and emerging conceptual and methodological tools used in metagenomics

Environmental Microbiology

Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganisms that exist in artificial environments such as bioreactors.

Molecular biology has revolutionized the study of microorganisms in the environment and improved our understanding of the composition, phylogeny, and physiology of microbial communities. The current molecular toolbox encompasses a range of DNA-based technologies and new methods for the study of RNA and proteins extracted from environmental samples. Currently there is a major emphasis on the application of "omics" approaches to determine the identities and functions of microbes inhabiting different environments.

Microbial life is amazingly diverse and microorganisms literally cover the planet. It is estimated that we know fewer than 1% of the microbial species on Earth. Microorganisms can survive in some of the most extreme environments on the planet and some can survive high temperatures, often above 100°C, as found in geysers, black smokers, and oil wells. Some are found in very cold habitats and others in highly salt|saline, acidic, or alkaline water.

An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species. Microorganisms have special impact on the whole biosphere. They are the backbone of ecosystems of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. So, microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance in the sense that their symbiotic relationship (either positive or negative) have special effects on the ecosystem.

Microorganisms are cost effective agents for in-situ remediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since most sites are typically comprised of multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species/strains, each specific to the degradation of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacterial consortium in order to evaluate the activity level of the bacteria, and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.

Oil Biodegradation
Petroleum oil is toxic and pollution of the environment by oil causes major ecological concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult, however much of the oil can be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remediate the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastics and biocatalysis.

Degradation of Aromatic Compounds by Acinetobacter
Acinetobacter strains isolated from the environment are capable of the degradation of a wide range of aromatic compounds. The predominant route for the final stages of assimilation to central metabolites is through catechol or protocatechuate (3,4-dihydroxybenzoate) and the beta-ketoadipate pathway, and the diversity within the genus lies in the channelling of growth substrates, most of which are natural products of plant origin, into this pathway.

Analysis of Waste Biotreatment
Biotreatment, the processing of wastes using living organisms, is an environmentally friendly alternative to other options. Bioreactors have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.

Environmental Genomics of Cyanobacteria
The application of molecular biology and genomics to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting, and functional interrogation of natural populations have become common, enabled by a battery of molecular and bioinformatics techniques. Recent studies on the ecology of Cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological, and geochemical techniques have combined in the study of natural communities of these bacteria.

Further reading