Biology Reference
In-Depth Information
By these efforts it has now been possible to identify a number of heterotrophic bacteria that have
not been cultured hitherto. In the study of uncultured microorganisms, metagenomics occupies a
central place. The term 'Metagenomics', was coined by Handelsman
et al
. (1998), to represent the
analysis of gene sequences of uncultured microorganisms. This involves direct isolation of DNA
sample from the environment, cloning of it into a suitable vector, followed by the transformation
of host bacterium like
E
.
coli
by this vector and screening the transformant for the respective trait.
The transformed clones of
E
.
coli
can be maintained as a metagenomic library. Metagenomics has
also been alternatively called as community genomics, environmental genomics and population
genomics.
Two types of approaches have been followed in the study of such cloned genes, i.e. (i) function-
driven analysis and (ii) sequence-driven analysis. Function-driven analysis involves heterologous
gene expression and identifying the protein synthesized from such a gene sequence. In sequence-
driven analysis cloned DNA preparation is identifi ed by sequence analysis of phylogenetic markers
such as 'anchor' sequences (16S rRNA and
recA
) or for other conserved genes by hybridization or
by PCR or random sequencing. With the help of sequence based screening for small molecules it
has now been possible to discover new antibiotics (such as turbomycin A, turbomycin B, violacein,
deoxyviolacein, terragine A, indirubin and a number of long-chain N-acyl amino acid antibiotics).
This subject has been reviewed (Handelsman, 2004; Schloss and Handelsman, 2005). The diversity of
viruses in a particular sample can be estimated by either employing the amplifi cation and sequencing
of conserved genes or partially sequencing shotgun libraries. Metagenomic analysis deals with the
discovery of the uncultured marine viral communities by the latter technique (Breitbart
et al
., 2002;
Hendrix, 2003; Pedulla
et al
., 2003) and those of marine cyanophages by the former. The sequencing
of shotgun libraries of 168 viral assemblages collected from four oceanic regions revealed that several
hundred thousand distinct viral species are dispersed in these waters. Most of these sequences do
not resemble any of the previously reported sequences suggesting that much of the viral diversity
remains unexplored and uncharacterized. From these studies it is concluded that it is through
the selective pressure prevailing in a particular environment that selects a certain viral type to be
an effective infectious agent (Angly
et al
., 2006). The diversity of marine cyanophages has been
determined with the help of the amplifi cation of conserved
psbA
and
psbD
genes from diverse marine
habitats (Venter
et al
., 2004; Angly
et al
., 2006; Zeidner
et al
., 2005; DeLong
et al
., 2006; Sharon
et al
.,
2007; Bench
et al
., 2007) and
g20
gene sequence (Wilson
et al
., 1999, 2000; Zhong
et al
., 2002; Marston
and Sallee, 2003; Frederickson
et al
., 2003; Dorigo
et al
., 2004; Wang and Chen, 2004; Mühling
et al
.,
2005; McDaniel
et al
., 2006; Baker
et al
., 2006; Wilhelm
et al
., 2006).
LITERATURE CITED
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