Biology Reference
In-Depth Information
(Binder and Liu, 1998). So this method would be ideally suited for estimating the growth rates of
such organisms
in situ
as well. Another approach for
in situ
identifi cation is the use of peptide-
nucleic acid (PNA) probes. PNA possesses a homomorphous pseudopeptide backbone instead of
sugarphosphate backbone of DNA (Egholm
et al
., 1993; Sen and Nilsson, 1998). The hybridization
product of PNA and RNA exhibits higher thermal stability than the DNA-RNA duplex. Due to
this inherent advantage, Worden
et al
. (2000) used PNA probes to detect rRNA in intact cells of
Prochlorococcus
and
Synechococcus
in combination with fl ow cytometry. It would thus be easier to
detect these cells in mixed microbial communities during fi eld studies.
Rudi
et al
. (2000) employed oligonucleotide labelled probes targeting 16S rDNA followed by
hybridization of these probes to their respective complements spotted on to a solid support (DNA
array). With the help of 10 such species-specifi c probes developed, it was possible to identify relative
abundance of cyanobacteria occurring in mesotrophic and eutrophic lakes. There was a good
correlation between the diversity of cyanobacterial species determined as per traditional taxonomy
and by molecular methods of analysis. Likewise, Wilson
et al
. (2000) designed species-specifi c primers
for the amplifi cation of a 609-bp region of
rpoC1
gene by PCR from 19 cultured isolates of
C. raciborskii
.
Sequence analysis revealed that all isolates belonged to the same species. Further, RAPD and STRR
sequence profi les revealed a greater heterogeneity among
C
.
raciborskii
strains. The identifi cation of
C
.
raciborskii
alone from purifi ed DNA samples as well as environmental samples was quite possible
by the amplifi cation of specifi c region of
rpoC1
gene. This would be greatly helpful in the identifi cation
of this toxin-producing cyanobacterium from natural waters. Abed
et al
. (2002a) studied the diversity
of benthic cyanobacterial mats inhabiting polluted waters of Wadi Gaza (Gaza Strip, Palestine)
and monitored community changes of these mats in the laboratory consequent upon degradation
of petroleum compounds. PCR amplifi ed products of 16S rRNA gene, with cyanobacteria-specifi c
primers CYA 359F (with 40 nucleotide clamp at 5'-end) and CYA 781R, were subjected to DGGE at
60
o
C. DNA from these bands was sequenced, aligned and phylogenetic tree construction made by
different methods in the ARB software.
Phormidium
and
Oscillatoria
-like cyanobacterial morphotypes
dominated the polluted habitats and the
in vitro
samples were dominated by a
Phormidium
-like new
cyanobacterium named as
Halomicronema.
Samples collected from microbial mats, maintained in
artifi cial ponds in Eilat (Israel), when subjected to DGGE also revealed the existence of
Halomicronema
in large numbers. By adopting a polyphasic taxonomic approach (morphology, ultrastucture,
16S rRNA-based phylogeny, temperature and salinity physiology and chemotaxonomic markers like
the presence of special carotenoids and mycosporine-like amino acids)
Halomicronema excentricum
gen. et sp. nov.
has further been characterized (Abed
et al
., 2002b).
Taton
et al
. (2003) presented cyanobacterial diversity patterns in natural and artifi cial microbial
mats of Lake Fryxell (McMurdo Dry Valleys, Antarctica) on the basis of morphological and
molecular methods. DNA isolated from environmental samples was subjected to ARDRA analysis
after PCR amplifi cation of 16S rDNA and fragments of 422 bp long generated by seminested PCR
have been subjected to DGGE, followed by sequencing. They have identifi ed 16S rRNA-23S rRNA
ITS sequences from environmental samples for the fi rst time. Molecular diversity appeared to be
more than microscopic diversity. Phylogenetic analysis revealed 11 lineages of which 3 have been
found to be exclusive to Antarctica and two of these were found to be novel. Microscopy revealed 8
morphotypes (
Nostoc
,
Nodularia
cf.
harveyana
,
Oscillatoria
cf.
subproboscidea
,
Phormidium
cf.
autumnale
,
Schizothrix
sp.,
Leptolyngbya
1 and
Leptolyngbya
2 with rare presence of
Hydrocoryne
cf.
spongiosa
and
Phormidium
cf.
autumnale
).
Phormidium
cf.
autumnale
has been observed as a minor component of
microbial mats
in vivo
but dominated
in vitro
with the absence of other heterocystous members like
