Three clades of Pseudo-nitzschia pungens,
determined by the internal transcribed space (ITS)
regi... more Three clades of Pseudo-nitzschia pungens, determined by the internal transcribed space (ITS) region, are distributed throughout the world. We studied 15 P. pungens clones from various geographical locations and confirmed the existence of the three clades within P. pungens, based on ITS sequencing and described the three subgroups (IIIaa, IIIab, and IIIb) of clade III. Clade III (clade IIIaa) populations were reported for the first time in Korean coastal waters and the East China Sea. In morphometric analysis, we found the ultrastructural differences in the number of fibulae, striae, and poroids that separate the three clades. We carried out physiological tests on nine clones belonging to the three clades growing under various culture conditions. In temperature tests, only clade III clones could not grow at lower temperatures (10°C and 15°C), although clade I and II clones grew well. The estimated optimal growth range of clade I clones was wider than that of clades II and III. Clade II clones were considered to be adapted to lower temperatures and clade III to higher temperatures. In salinity tests, clade II and III clones did not grow well at a salinity of 40. Clade I clones were regarded as euryhaline and clade II and III clones were stenohaline. This supports the hypothesis that P. pungens clades have different ecophysiological characteristics based on their habitats. Our data show that physiological and morphological features are correlated with genetic intraspecific differentiation in P. pungens.
While the toxic dinoflagellate Cochlodinium polykrikoides is known to form blooms that are mainta... more While the toxic dinoflagellate Cochlodinium polykrikoides is known to form blooms that are maintained for extended periods, the genetic differentiation of these blooms are currently unknown. To assess this, we developed a real-time PCR assay to quantify C. polykrikoides at the intra-specific level, and applied this assay to field samples collected in Korean coastal waters from summer through fall. Assays were successfully developed to target the large-subunit ribosomal RNA region of the three major ribotypes of C. polykrikoides: Philippines, East Asian, and American/Malaysian. Significant linear relationships (r2 0.995) were established between Ct and the log of the copy number for each ribotype qPCR assay. Using these assays, C. polykrikoides blooms in Korean coastal waters were found to be comprised of Philippines and East Asian ribotypes but not the American/Malaysian ribotype. The Philippines ribotype was found to be highly abundant during summer bloom initiation and peak, whereas the East Asian ribotype became the dominant ribotype in the fall. As such, this newly developed qPCR assay can be used to quantify the cryptic ecological succession of sub-populations of C. polykrikoides during blooms that light microscopy and previously developed qPCR assays cannot resolve.
Amphora Ehrenberg ex Kützing sensu lato is a common and widespread benthic diatom genus with a ta... more Amphora Ehrenberg ex Kützing sensu lato is a common and widespread benthic diatom genus with a taxonomy that has been under continual revision, particularly based on molecular analyses. Although Amphora species have been studied using modern microscopy in recent years, there has not been much progress on molecular characterization of the species, especially in Asia. In this study of Amphora, sampling was carried out from September 2009 to August 2010 in Korean coastal waters. The morphological and molecular characteristics of eight Amphora sensu lato were examined: Amphora marina, A. proteus, Halamphora costata, H. coffeaeformis, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. Based on previous accounts, morphology suggested that A. marina and A. proteus belong to the subgenus Amphora Cleve, which have smooth girdle bands and rather coarse and very distinct areolae on the valve. The other species, H. coffeaeformis, H. costata, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. belong to the subgenus Halamphora Cleve, which was recently elevated to generic status by Levkov 2009, have plicate girdle bands, puncta which do not form straight longitudinal lines, valves which have a narrow ventral portion and apices that are generally rostrate-capitate and recurved. In agreement with analysis based on morphological characteristics, phylogenetic analysis based on small subunit rDNA suggested that the eight Amphora sensu lato species were not a monophyletic group as the morphological classification. Also, the results of molecular work and statistical analysis on all these Amphora sensu lato combined with phylogenic analysis on our geographically representative samples give strong evidence that Halamphora Levkov is independent of Amphora Cleve. Furthermore, in this study, Amphora terroris was transferred Halamphora as Halamphora terroris (Ehrenberg) Wang comb. nov. and Amphora marina was recorded for the first time in Korea.
Three clades of Pseudo-nitzschia pungens,
determined by the internal transcribed space (ITS)
regi... more Three clades of Pseudo-nitzschia pungens, determined by the internal transcribed space (ITS) region, are distributed throughout the world. We studied 15 P. pungens clones from various geographical locations and confirmed the existence of the three clades within P. pungens, based on ITS sequencing and described the three subgroups (IIIaa, IIIab, and IIIb) of clade III. Clade III (clade IIIaa) populations were reported for the first time in Korean coastal waters and the East China Sea. In morphometric analysis, we found the ultrastructural differences in the number of fibulae, striae, and poroids that separate the three clades. We carried out physiological tests on nine clones belonging to the three clades growing under various culture conditions. In temperature tests, only clade III clones could not grow at lower temperatures (10°C and 15°C), although clade I and II clones grew well. The estimated optimal growth range of clade I clones was wider than that of clades II and III. Clade II clones were considered to be adapted to lower temperatures and clade III to higher temperatures. In salinity tests, clade II and III clones did not grow well at a salinity of 40. Clade I clones were regarded as euryhaline and clade II and III clones were stenohaline. This supports the hypothesis that P. pungens clades have different ecophysiological characteristics based on their habitats. Our data show that physiological and morphological features are correlated with genetic intraspecific differentiation in P. pungens.
While the toxic dinoflagellate Cochlodinium polykrikoides is known to form blooms that are mainta... more While the toxic dinoflagellate Cochlodinium polykrikoides is known to form blooms that are maintained for extended periods, the genetic differentiation of these blooms are currently unknown. To assess this, we developed a real-time PCR assay to quantify C. polykrikoides at the intra-specific level, and applied this assay to field samples collected in Korean coastal waters from summer through fall. Assays were successfully developed to target the large-subunit ribosomal RNA region of the three major ribotypes of C. polykrikoides: Philippines, East Asian, and American/Malaysian. Significant linear relationships (r2 0.995) were established between Ct and the log of the copy number for each ribotype qPCR assay. Using these assays, C. polykrikoides blooms in Korean coastal waters were found to be comprised of Philippines and East Asian ribotypes but not the American/Malaysian ribotype. The Philippines ribotype was found to be highly abundant during summer bloom initiation and peak, whereas the East Asian ribotype became the dominant ribotype in the fall. As such, this newly developed qPCR assay can be used to quantify the cryptic ecological succession of sub-populations of C. polykrikoides during blooms that light microscopy and previously developed qPCR assays cannot resolve.
Amphora Ehrenberg ex Kützing sensu lato is a common and widespread benthic diatom genus with a ta... more Amphora Ehrenberg ex Kützing sensu lato is a common and widespread benthic diatom genus with a taxonomy that has been under continual revision, particularly based on molecular analyses. Although Amphora species have been studied using modern microscopy in recent years, there has not been much progress on molecular characterization of the species, especially in Asia. In this study of Amphora, sampling was carried out from September 2009 to August 2010 in Korean coastal waters. The morphological and molecular characteristics of eight Amphora sensu lato were examined: Amphora marina, A. proteus, Halamphora costata, H. coffeaeformis, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. Based on previous accounts, morphology suggested that A. marina and A. proteus belong to the subgenus Amphora Cleve, which have smooth girdle bands and rather coarse and very distinct areolae on the valve. The other species, H. coffeaeformis, H. costata, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. belong to the subgenus Halamphora Cleve, which was recently elevated to generic status by Levkov 2009, have plicate girdle bands, puncta which do not form straight longitudinal lines, valves which have a narrow ventral portion and apices that are generally rostrate-capitate and recurved. In agreement with analysis based on morphological characteristics, phylogenetic analysis based on small subunit rDNA suggested that the eight Amphora sensu lato species were not a monophyletic group as the morphological classification. Also, the results of molecular work and statistical analysis on all these Amphora sensu lato combined with phylogenic analysis on our geographically representative samples give strong evidence that Halamphora Levkov is independent of Amphora Cleve. Furthermore, in this study, Amphora terroris was transferred Halamphora as Halamphora terroris (Ehrenberg) Wang comb. nov. and Amphora marina was recorded for the first time in Korea.
Uploads
determined by the internal transcribed space (ITS)
region, are distributed throughout the world. We
studied 15 P. pungens clones from various
geographical locations and confirmed the existence
of the three clades within P. pungens, based on ITS
sequencing and described the three subgroups
(IIIaa, IIIab, and IIIb) of clade III. Clade III (clade
IIIaa) populations were reported for the first time
in Korean coastal waters and the East China Sea. In
morphometric analysis, we found the ultrastructural
differences in the number of fibulae, striae, and
poroids that separate the three clades. We carried
out physiological tests on nine clones belonging to
the three clades growing under various culture
conditions. In temperature tests, only clade III
clones could not grow at lower temperatures (10°C
and 15°C), although clade I and II clones grew well.
The estimated optimal growth range of clade I
clones was wider than that of clades II and III.
Clade II clones were considered to be adapted to
lower temperatures and clade III to higher
temperatures. In salinity tests, clade II and III
clones did not grow well at a salinity of 40. Clade I
clones were regarded as euryhaline and clade II and
III clones were stenohaline. This supports the
hypothesis that P. pungens clades have different
ecophysiological characteristics based on their
habitats. Our data show that physiological and
morphological features are correlated with genetic
intraspecific differentiation in P. pungens.
for extended periods, the genetic differentiation of these blooms are currently unknown. To assess this,
we developed a real-time PCR assay to quantify C. polykrikoides at the intra-specific level, and applied
this assay to field samples collected in Korean coastal waters from summer through fall. Assays were
successfully developed to target the large-subunit ribosomal RNA region of the three major ribotypes of
C. polykrikoides: Philippines, East Asian, and American/Malaysian. Significant linear relationships
(r2 0.995) were established between Ct and the log of the copy number for each ribotype qPCR assay.
Using these assays, C. polykrikoides blooms in Korean coastal waters were found to be comprised of
Philippines and East Asian ribotypes but not the American/Malaysian ribotype. The Philippines ribotype
was found to be highly abundant during summer bloom initiation and peak, whereas the East Asian
ribotype became the dominant ribotype in the fall. As such, this newly developed qPCR assay can be used
to quantify the cryptic ecological succession of sub-populations of C. polykrikoides during blooms that
light microscopy and previously developed qPCR assays cannot resolve.
has been under continual revision, particularly based on molecular analyses. Although Amphora species have been studied
using modern microscopy in recent years, there has not been much progress on molecular characterization of the
species, especially in Asia. In this study of Amphora, sampling was carried out from September 2009 to August 2010 in
Korean coastal waters. The morphological and molecular characteristics of eight Amphora sensu lato were examined:
Amphora marina, A. proteus, Halamphora costata, H. coffeaeformis, H. eunotia, H. holsatica, H. terroris, and Halamphora
sp. Based on previous accounts, morphology suggested that A. marina and A. proteus belong to the subgenus Amphora
Cleve, which have smooth girdle bands and rather coarse and very distinct areolae on the valve. The other species, H.
coffeaeformis, H. costata, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. belong to the subgenus Halamphora
Cleve, which was recently elevated to generic status by Levkov 2009, have plicate girdle bands, puncta which do not form
straight longitudinal lines, valves which have a narrow ventral portion and apices that are generally rostrate-capitate
and recurved. In agreement with analysis based on morphological characteristics, phylogenetic analysis based on small
subunit rDNA suggested that the eight Amphora sensu lato species were not a monophyletic group as the morphological
classification. Also, the results of molecular work and statistical analysis on all these Amphora sensu lato combined with
phylogenic analysis on our geographically representative samples give strong evidence that Halamphora Levkov is independent
of Amphora Cleve. Furthermore, in this study, Amphora terroris was transferred Halamphora as Halamphora
terroris (Ehrenberg) Wang comb. nov. and Amphora marina was recorded for the first time in Korea.
determined by the internal transcribed space (ITS)
region, are distributed throughout the world. We
studied 15 P. pungens clones from various
geographical locations and confirmed the existence
of the three clades within P. pungens, based on ITS
sequencing and described the three subgroups
(IIIaa, IIIab, and IIIb) of clade III. Clade III (clade
IIIaa) populations were reported for the first time
in Korean coastal waters and the East China Sea. In
morphometric analysis, we found the ultrastructural
differences in the number of fibulae, striae, and
poroids that separate the three clades. We carried
out physiological tests on nine clones belonging to
the three clades growing under various culture
conditions. In temperature tests, only clade III
clones could not grow at lower temperatures (10°C
and 15°C), although clade I and II clones grew well.
The estimated optimal growth range of clade I
clones was wider than that of clades II and III.
Clade II clones were considered to be adapted to
lower temperatures and clade III to higher
temperatures. In salinity tests, clade II and III
clones did not grow well at a salinity of 40. Clade I
clones were regarded as euryhaline and clade II and
III clones were stenohaline. This supports the
hypothesis that P. pungens clades have different
ecophysiological characteristics based on their
habitats. Our data show that physiological and
morphological features are correlated with genetic
intraspecific differentiation in P. pungens.
for extended periods, the genetic differentiation of these blooms are currently unknown. To assess this,
we developed a real-time PCR assay to quantify C. polykrikoides at the intra-specific level, and applied
this assay to field samples collected in Korean coastal waters from summer through fall. Assays were
successfully developed to target the large-subunit ribosomal RNA region of the three major ribotypes of
C. polykrikoides: Philippines, East Asian, and American/Malaysian. Significant linear relationships
(r2 0.995) were established between Ct and the log of the copy number for each ribotype qPCR assay.
Using these assays, C. polykrikoides blooms in Korean coastal waters were found to be comprised of
Philippines and East Asian ribotypes but not the American/Malaysian ribotype. The Philippines ribotype
was found to be highly abundant during summer bloom initiation and peak, whereas the East Asian
ribotype became the dominant ribotype in the fall. As such, this newly developed qPCR assay can be used
to quantify the cryptic ecological succession of sub-populations of C. polykrikoides during blooms that
light microscopy and previously developed qPCR assays cannot resolve.
has been under continual revision, particularly based on molecular analyses. Although Amphora species have been studied
using modern microscopy in recent years, there has not been much progress on molecular characterization of the
species, especially in Asia. In this study of Amphora, sampling was carried out from September 2009 to August 2010 in
Korean coastal waters. The morphological and molecular characteristics of eight Amphora sensu lato were examined:
Amphora marina, A. proteus, Halamphora costata, H. coffeaeformis, H. eunotia, H. holsatica, H. terroris, and Halamphora
sp. Based on previous accounts, morphology suggested that A. marina and A. proteus belong to the subgenus Amphora
Cleve, which have smooth girdle bands and rather coarse and very distinct areolae on the valve. The other species, H.
coffeaeformis, H. costata, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. belong to the subgenus Halamphora
Cleve, which was recently elevated to generic status by Levkov 2009, have plicate girdle bands, puncta which do not form
straight longitudinal lines, valves which have a narrow ventral portion and apices that are generally rostrate-capitate
and recurved. In agreement with analysis based on morphological characteristics, phylogenetic analysis based on small
subunit rDNA suggested that the eight Amphora sensu lato species were not a monophyletic group as the morphological
classification. Also, the results of molecular work and statistical analysis on all these Amphora sensu lato combined with
phylogenic analysis on our geographically representative samples give strong evidence that Halamphora Levkov is independent
of Amphora Cleve. Furthermore, in this study, Amphora terroris was transferred Halamphora as Halamphora
terroris (Ehrenberg) Wang comb. nov. and Amphora marina was recorded for the first time in Korea.