Biology Reference
In-Depth Information
The resolution of Prochlorococcus
-
Synechococcus
by 16S rRNA-23S rRNA ITS regions:
Rocap
et
al
. (2002) resolved
Prochlorococcus
and
Synechococcus
ecotypes on the basis of 16S rRNA-23S rRNA
ITS sequence homology. They have examined 32
Prochlorococcus
strains and 25
Synechococcus
isolates
from all over the world. These exhibited a variation in length and G+C content of the spacer. All of
them uniformly possessed tRNA
Leu
and tRNA
Ala
genes. The results further justify the recognition of
high-B/A and low-B/A strains of
Prochlorococcus
and six clades of MC-A of
Synechococcus
.
Interestingly, three of them are associated with a particular phenotype (motility, chromatic adaptation
and lack of phycourobilin).
The diversity of marine
Synechococcus
strains occurring in Chesapeake Bay has been
determined by 16S rRNA-23S rRNA ITS sequences (Chen
et al
., 2006). A phylogenetic analysis of
82 picocyanobacterial ITS sequences revealed that the majority of the sequences were affi liated
with either MC-A or MC-B. Among the 22 environmental clones isolated from Chesapeake Bay
(CB) waters, 13 of them clustered with MC-A while the rest 9 clustered with MC-B. They further
identifi ed 16 sub-clusters (having more than 95% sequence identity) with a bootstrap value of 100 in
MC-B. Eleven of these sub-clusters overlapped with those already reported in literature (Rocap
et al
.,
2002; Ernst
et al.,
2003) whereas fi ve subclusters (CB1 to CB5) have been considered to be novel and
unique to Chesapeake Bay. Of these, at least two subclusters (CB4 and CB5) could be defi ned. The
subcluster CB-4 consisted of fi ve PE-rich
Synechococcus
strains (CB0206, CB0207, CB0208, CB 0209
and CB0210) that were closely related to PC-rich
Synechococcus
strains (CB0101, CB0102, CB0202 and
CB 0204). It is interesting to note that a close relationship between
Synechococcus
PE-rich and PC-
rich strains has also been derived from
rbcL
phylogeny. Further the separation of MC-A and MC-B
is also supported by
rbcL
phylogeny. The interoperon variation in
Synechococcus
is not problematic
because of the existence of two identical rRNA operons. However, the length of heterogeneity in
ITS region is suffi cient to distinguish the different
Synechococcus
strains. Based on ITS phylogeny
and GC content, they suggested that
Synechococcus
sp. strain
WH 8007 should serve as the reference
strain for MC-B but not
Synechococcus
sp. strain WH5701 as suggested earlier (Urbach
et al
., 1998;
Fuller
et al
., 2003).
The phylogeny of
Synechococcus
strains based on 16S rRNA gene sequences revealed that this
botanical form-genus is distributed into fi ve of the eight cyanobacterial lineages (Honda
et al
.,
1999; Robertson
et al
., 2001). Two or more strains of
Synechococcus
distributed into each of these fi ve
clusters exhibited 99.4-100% 16S rRNA sequence identity. One of these fi ve clades is represented
by picophytoplanktons in which along with PE-rich and PC-rich strains of
Synechococcus
, strains of
Prochlorococcus
have been clustered as revealed by the phylogenetic relationships drawn on the basis
of 16S rRNA gene sequences as well as DNA-dependent RNA polymerase gene sequences (Palenik
and Swift, 1996; Urbach
et al
., 1998). Strains of
Synechococcus,
i.e. WH7803, PCC 7001, PCC 6307 that
are representatives of oceanic, marine and freshwaters, respectively differ from one another in the
length of ITS of the rrn operon and also differ from
P.
marinus
subsp.
pastoris
PCC 9511. However,
these four cyanobacteria are closely related on the basis of 16S rDNA phylogeny. A comparison
of the sequences of the ITS region of these four strains with those available in the database for
Prochlorococcus
MED4 (CCMP 1378) and MIT9313 revealed that HL-adapted
Prochlorococcus
clade
differed from those of LL-adapted clade by the length of ITS (Laloui
et al
., 2002). Ernst
et al
. (2003)
studied the RFLP patterns of
psbA
genes of 19 picoplanktonic cyanobacteria and the phylogenetic
analysis is not consistent with the original distinction of isolates based on pigmentation. In view of
this, it was concluded that selection pressure plays a great role in shaping the populations and the
diversity in
Synechococcus
strains refl ects ecosystem-specifi c adaptations. On the basis of
cpcBA
-IGS
spacer region, Crosbie
et al
. (2003) showed that some closely related forms of picocyanobacteria are
