ENVIRONMENTAL FUNCTIONAL GENOMICS

Biodiversity is fundamental to preserving the capacity of organisms to adapt to new environmental conditions. The accelerated loss of species and the diminution of diversity due to human activities is of growing concern, yet to tackle this major problem, society lacks a good understanding of the mechanisms underlying biodiversity at different levels. In its broadest sense, biodiversity embraces ecosystems as well as species and genetic diversity. Functional genomics provides a new means to study biodiversity and guide actions to preserve the highest possible level of diversity in natural populations in terrestrial and marine ecosystems. As environmental changes accelerate, it becomes ever more crucial to strengthen efforts to apply post-genomics technologies (eg metagenomics) to understand natural ecosystems better and to exploit their enormous capabilities to degrade pollutant products of human activities.

Metagenomics
Since over 99% of microbial species cannot be cultivated in the laboratory, most of the constituents of environmental samples remain unknown and the genetic and biological diversity of microorganisms, as the main component of the environment, becomes an important area of research. Metagenomics, the genomic analysis of uncultured microorganisms, attempts to identify and characterise the genetic material from environmental samples and apply that knowledge to an understanding of the properties of the corresponding systems. Progress is expected to produce new biotechnological products for environmental and public health, using the ability of microorganisms to degrade waste products, and screening for new drugs - new antibiotics and enzymes being among early metagenomics discoveries. Many other biotechnological possibilities are also under investigation, such as food ingredients and ‘friendly' plastics. Metagenomics is also able to provide strategic information on the vulnerability of humans, animals, plants and microbes to environmental insults and represents a powerful tool with which to access the biodiversity of native environmental samples.

The genetic diversity of microbial populations in natural ecosystems is highly complex, frequently including thousands of different species. Several techniques have been developed to grasp the genomic diversity of a population more selectively. These involve extraction of DNA from environmental samples for the construction of metagenomic libraries, which can be explored for the presence of specific genes or markers; similarly, high density DNA arrays can be designed to detect genes from environmental DNA samples. These methods are especially suited to characterisation of the degradation potential of ecosystems, since the presence of whole pathways and degradative enzymes can be detected. The direct approach to the sequencing of all the genomes is also possible, as recently demonstrated for Sargasso sea samples. The availability of this new type of large sequence collection requires a complex computational analysis, of which we have so far only seen the initial results.

Biodegradation by Microbial Populations
One of the interesting applications of metagenomics is in the assessment of the degradative capabilities of ecosystems. Soil microbial ecosystems, which are able to metabolise natural and xenobiotic compounds produced by plant material and animal excreta, can also degrade xenobiotic chemicals and other pollutant products of human activities. These communities present complex metabolic interdependencies and competition for restricted resources in the microbial food-web. The increasing information on the strains, compounds, enzymes and reactions implicated in microbial biodegradation provides the first view of what has been called the Global Biodegradation Network, a development of systems biology.

The interest in understanding the integrated metabolism of contaminants by microbial communities is close to practical problems afflicting contemporary societies. The rise of genomic technologies and systems biology provides fresh approaches to seemingly intractable biological processes that are the basis of serious environmental challenges. One formidable issue is the fate of the nearly 8 million new chemical compounds (predominantly ~40,000) which modern organic and industrial chemistry has deposited in the biosphere. Since the late 1960s, many reports have documented the isolation of microbial strains (now ~800) which can grow on given environmental pollutants. This was followed by cloning of the whole or part of the pathway in suitable vectors and/or the mutagenesis of selected strains, characterisation of the intermediate metabolites and correlation with given ORFs for identification. More recently, much of the ongoing research in biodegradation has focused on sequencing long DNA segments thought to be involved in a given metabolic process.  The Biodegradation database of the University of Minnesota has made a pioneering effort in putting together nearly every aspect of current knowledge on biodegradation pathways and operons. 

Nevertheless, most information available in the literature on microbial biodegradation of xenobiotics and recalcitrant chemicals deals with pairs comprising one pollutant and one strain and therefore lacks three essential aspects of natural scenarios. First, bacteria colonise polluted sites not as single species, but rather as consortia which can exchange genes and cooperate metabolically, so that a complete pathway for degradation of a certain compound may not be present in a single member. Secondly, pollutants seldom appear as single chemical species, and thirdly, only a tiny fraction of soil microbes are culturable with our current laboratory procedures. All these circumstances expose the need to represent information available in biodegradation databases such that the entire biodegradative potential of the microbial world can be crossed with the whole collection of compounds know to be degraded through bacterial action. A key aspect to this end is the need for a suitable format in which to compare and match results arising from different experimental systems and strains. It is necessary to envisage interactive integrated databases developed for three major purposes: (i) extracting, cataloguing and displaying existing genetic and enzymatic information on microbial biodegradation or biotransformations of environmental pollutants regardless of the specific microbial host; (ii) guiding strategies of metabolic engineering of superior catalysts; and (iii) assessing the environmental fate of compounds or mixtures for which degraders have not yet been isolated.