Detection of a novel ecotype of Pfiesteria piscicida (Dinophyceae) in an Antarctic saline lake by real-time PCR

Park, Tae-Gyu; Bell, Elanor M.; Pearce, Imojen; Rublee, Parke A.; Bolch, Christopher J. S.; Hallegraeff, Gustaaf M.

doi:10.1007/s00300-006-0244-0

Cited by 14 publications

(9 citation statements)

References 34 publications

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“…In addition, local bacterial occupants further diversified local environmental characters interactively; ultimately each lake was a unique variation on the meromictic lake theme [ 13 , 16 , 53 ]. Distinct bacterial community compositions in the two layers were attributed to different mixing regimes, as well as disparate physicochemical milieus [ 8 , 20 , 54 , 55 ]. Therefore, this may also explain why bacterial communities and physicochemical characteristics frequently differ between oxic and anoxic layers of meromictic lakes, regardless of their similarities in lake profile.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

et al. 2016

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Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

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Section: Discussionmentioning

confidence: 99%

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

et al. 2016

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“…Rublee et al, 1999Rublee et al, , 2001Rublee et al, , 2004Rublee et al, , 2005Rublee et al, , 2006Burkholder et al, 2001a;Jakobsen et al, 2002;Rhodes et al, 2002Rhodes et al, , 2006Lin et al, 2006;Park et al, 2007). Both species are euryhaline (optimum, mesohaline at $10 to 15; range $0.5 to $50- Burkholder et al, 2001a;Sullivan and Andersen, 2001;Baek et al, 2010; note that P. shumwayae has also been reported to adapt to freshwater conditions - Baek et al, 2010) and eurythermal (e.g.…”

Section: Global Distributionmentioning

confidence: 88%

Toxigenic Pfiesteria species—Updates on biology, ecology, toxins, and impacts

Burkholder¹,

Marshall²

2012

Harmful Algae

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“…But given that DNA extracted from environmental samples can vary in quantity and quality, dilution alone may not be adequate to overcome this problem reliably. Recently, several approaches for removing inhibitory substances associated with genomic DNA from HAB species is to use extraction buffers containing CTAB (cetyltrimethylammonium bromide) or specialized DNA extraction kits such as the DNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) and PowerSoil DNA Isolation Kit (MO Bio, California, USA) [6], [9], [10], [11], [12], [13], [15], [20], [21], [22], [23], [25]. In this study, we extracted and purified the genomic DNA from the samples by using DNeasy Plant Mini Kit in order to minimize effects of PCR inhibitory substances in the samples.…”

Section: Discussionmentioning

confidence: 99%

“…For HAB species, qPCR methods have been developed for a variety of Alexandrium [6], [7], [8], [9], Aureococcus [10], Chattonella [11], [12], [13], [14], [15], Heterosigma [11], [12], [13], [14], [15], Gambierdiscus [ 16 ], Karenia [17], Lingulodinium [18], Ostreopsis [ 19 ] and Pfiesteria [18], [20], [21], [22], [23], [24], [25] species. The cell quantification methods by qPCR are broadly classified as “relative” and “absolute” methods [26].…”

Section: Introductionmentioning

confidence: 99%

Quantitative PCR Method for Enumeration of Cells of Cryptic Species of the Toxic Marine Dinoflagellate Ostreopsis spp. in Coastal Waters of Japan

et al. 2013

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Monitoring of harmful algal bloom (HAB) species in coastal waters is important for assessment of environmental impacts associated with HABs. Co-occurrence of multiple cryptic species such as toxic dinoflagellate Ostreopsis species make reliable microscopic identification difficult, so the employment of molecular tools is often necessary. Here we developed new qPCR method by which cells of cryptic species can be enumerated based on actual gene number of target species. The qPCR assay targets the LSU rDNA of Ostreopsis spp. from Japan. First, we constructed standard curves with a linearized plasmid containing the target rDNA. We then determined the number of rDNA copies per cell of target species from a single cell isolated from environmental samples using the qPCR assay. Differences in the DNA recovery efficiency was calculated by adding exogenous plasmid to a portion of the sample lysate before and after DNA extraction followed by qPCR. Then, the number of cells of each species was calculated by division of the total number of rDNA copies of each species in the samples by the number of rDNA copies per cell. To test our procedure, we determined the total number of rDNA copies using environmental samples containing no target cells but spiked with cultured cells of several species of Ostreopsis. The numbers estimated by the qPCR method closely approximated total numbers of cells added. Finally, the numbers of cells of target species in environmental samples containing cryptic species were enumerated by the qPCR method and the total numbers also closely approximated the microscopy cell counts. We developed a qPCR method that provides accurate enumeration of each cryptic species in environments. This method is expected to be a powerful tool for monitoring the various HAB species that occur as cryptic species in coastal waters.

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Detection of a novel ecotype of Pfiesteria piscicida (Dinophyceae) in an Antarctic saline lake by real-time PCR

Cited by 14 publications

References 34 publications

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

Toxigenic Pfiesteria species—Updates on biology, ecology, toxins, and impacts

Quantitative PCR Method for Enumeration of Cells of Cryptic Species of the Toxic Marine Dinoflagellate Ostreopsis spp. in Coastal Waters of Japan

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