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Current issues of Microbes Scientist set to make Synthetic microbe
Effort to manufacture biofuel:
A scientist is poised to create the world's first man-made species, a synthetic microbe that could lead to an endless supply of biofuelCraig Venter, an American who cracked the human genome in 2000, has applied for a patent at more than 100 national offices to make a bacterium from laboratory-made DNA.It is part of an effort to create designer bugs to manufacture hydrogen and biofuels, as well as absorb carbon dioxide and other harmful greenhouse gasses. DNA contains the instructions to make the proteins that build and run and organism.The J Craig Venter Institute in Rockville, Maryland, is applying for worldwide patents on what it refers to as "Mycoplasma laboratorium "based on DNA assembled by scientists. Venter said: "it is only an application on methods". As for whether the world's first synthetic bug was thriving in a test tube in Rockville, all he would say was: "We are getting close".The Venter Institute's US Patent application Claims exclusive ownership of a set of essential genes and a synthetic "free-living organisms that can grow that replicate" that is made using those genes.To create the synthetic organism his team is making snippets of DNA, known as oligonucleotides or "oligos", of up to 100 letters of DNA.The Candian ETC Group, which tracks developments in biotechnology, believes that this development in synthetic biology is more significant than the cloning of Dolly the sheep a decade ago.On Wednesday, and ETC spokes man, Jim Thomas, called on the world's patent offices to reject the applications. He said: "These monopoly claims signal the start of high stakes commercial race to synthesise and privatise synthetic life forms. Will Venter's company become the 'Microbesoft' of synthetic biology?"A colleague, Pat Mooney, said: "For the first time, God has competition, Venter and his colleagues have breached a societal boundary, and the public hasn't even had a chance to debate the far-reaching social, ethical and environmental implications of synthetic life.
Source: Newspaper 'Sunday Star' 10 June, 2007

The history of microbial species definitions and conventions
One of the most exciting developments in biology in the past 100 years has been the transformation of bacterial systematics from a largely subjective area of study with little relevance to the rest of science into a rigorous and objective discipline that now provides a phylogenetic framework that supports research in all other areas of microbiology. The history of bacterial systematics can be divided into four distinct phases: the phase of "early description" between 1872 and 1900; a phase between 1900 and 1955 in which bacterial physiology and ecology were first explored and described; the era from 1955 until 1980, when many new approaches were developed; and the modern era, from 1980 until today, in which modern DNA technique were incorporated into the species description. Today, the prevailing opinion among microbiologist appears to be shifting away from demarcating bacterial species using arbitrary and artificial definitions and towards a description of species as ecologically or genetically meaningful entities with a shared phylogenetic heritage.

In 1872, Ferdinand Cohn demonstrated that bacteria could be divided into genera and species using the paradigm proposed for plants and animals by the father of modern taxonomy, Carl Linnaeus. During this early phase of microbial taxonomy, the field was largely dominated by the concerns of medical microbiology; most of the pathogenic bacteria known today were described before the end of the 19th century. At the time, the pattern of properties used to identify new species of bacteria included pathogenic potential, a chemical reaction, requirements for growth, and morphology, all of which are still in use today. Bringing order to the bacterial world proved difficult, however. Only two decades after the first bacterial species was described, K.B.Lehmann and R.Newmann denounced the state of bacterial taxonomy as "haphazard and non-scientific".

At the end of 19th century, bacterial physiology began to have an impact on taxonomy, but systematics still employed a typically "botanical" technique for naming new species; the classified bacteria according to the morphology first, and then used physiology to discriminate among the more closely aligned organisms- a mode of classification that did not began to change until the 1950s . Also during this time, in 1923, the Society of American Bacteriologists (which later became the American Society for microbiology) presented a report on the characterization and classification of bacterial types that became the basis for Bergey's Manual, a text that remain the primary reference in bacterial taxonomy even today.

By 1955, the field had adopted a pragmatic, arbitrary, and artificial definition for bacterial species: "the type culture together with such other cultures or strains of bacteria that are accepted by bacteriologist as sufficiently closely related". Although this definition was widely accepted, the meaning of "sufficiently closely related" could not be articulated as there was no effective way to determine relatedness at that time.

Between 1955 and the 1980s, bacterial taxonomists developed many new techniques for parsing the bacterial world. Chemotaxonomy, in which the chemical structures of cell constituents are used to different bacteria into relatedness groups, was integrated into species description. In 1961, McCarthy and Bolton presented a means of comparing genetic material through DNA-DNA hybridization, a method bacterial systematists rely on to this day to draw distinctions between closely related species. Numerical phenotypic analysis also emerged during this time, followed by the more sophisticated protein sequence analysis.

In 1965, Zuckerkandl and Pauling evaluated the fitness of various types of biological molecules for deriving the phylogeny of organisms. They concluded that the most appropriate molecules are the "semantide, "the molecules that carry genetic information and change slowly over time. In the 1970s, Carl Woese complied a database of partial rRNA gene sequence and used sequence comparison to derive a tree of life that put the Bacteria and Eukaryotes on distinctly different branches and uncovered the existence of a third Kingdom, the Archaea. This work explained the techniques used in protein sequence comparison that were developed in the preceding years. Methodological advances that enabled the cultivation of anaerobes also facilitated progress in developing the tree of life and in adding novel branches to the bacterial and archaeal trees. The combination of molecular, chemotaxonomic, physiological, and other cellular trait analyses also led to new insights into the relatedness among prokaryotic species and revolutionized microbial systematic. (The terms "prokaryotic and "prokaryote denote organisms that lack a nucleus. i.e., the Bacteria and Archeae). Although the term is not useful for biological classification, as it denotes the lack of a feature, it is commonly used to designate microscopic organisms that are neither eukaryotes (possessing a nucleus) nor viruses.

By the 1980s, the list of bacterial names had reached 40,000, a number that many systematic agreed was out of proportion with the sum of bacterial diversity described to date. In 1980, a group of invested microbiologist hewed the list of 40,000 down to trim 2,500 names designated as "validly published species".

In the following years, nucleic acid analysis, including 16SrRNA sequence analysis, protein-encoding gene sequence analysis, and gene profiling methods, influenced bacterial taxonomy. As new methods were developed, many were integrated into the requirements for defining new species. Today, fewer than 600 new species of bacteria are described every year, in part because of the onerous amount of testing required to ensure a bacteria can be discerned from neighboring species of the same genus.

In 2000, Hagstrom et al. reported their comparison of 16SrRNA sequence similarities with DNA-DNA reassociation values. They asserted that 97% 16SrRNA sequence identify or lower between two bacteria was sufficiently dissimilar to characterize those bacteria as different species. Later this value was increased to 99% sequence identify in light of new data.

In summary, molecular analyses have enabled bacterial taxonomists to decode the phylogeny of the bacterial world and the distinctions between different types of bacteria are being drawn with a finer and finer brush. However, there is still no consensus in the microbiology community about what exactly constitutes a bacterial species, what tests (and results) are required to identify a bacterium as a unique species, or how to classify those bacteria that cannot be cultivated in the lab.
SOURCE: Report From the American Academy of Microbiology www.asm.org
ENVIS CENTRE Newsletter Vol.5, July 2007 Back 
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