Genus-specific quantitative PCR of thraustochytrid protists

Nakai, Ryosuke; Nakamura, Keiko; Jadoon, Waqar Azeem; Kashihara, Katsuhiko; Naganuma, Takeshi

doi:10.3354/meps10412

Cited by 12 publications

(3 citation statements)

References 30 publications

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“…The thalli-derived DNA samples (obtained in Section 2.2) were used for the PCR amplification of near full-length 16S rRNA gene sequences of the chloroplasts and prokaryotes, as well as the fungal and algal near full-length 18S rRNA genes and ITS regions (between small- and large-subunit ribosomal RNA genes), by using a TaKaRa Thermal Cycler Dice (TaKaRa Bio, Kusatsu, Japan). All PCR amplifications were conducted with an initial denaturation at 94 °C for 5 min; 30 cycles of 94 °C 30 s, 56 °C 40 s, and 72 °C for 1 min; and the final elongation at 72 °C for 5 min [32], with thraustochytrid-derived [33] and the below-mentioned Escherichia coli TOP10 competent cell-derived DNAs as the eukaryotic and prokaryotic positive controls, respectively, and the non-DNA-added reactions as the negative control.…”

Section: Methodsmentioning

confidence: 99%

Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica

et al. 2019

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Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.

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Section: Methodsmentioning

confidence: 99%

Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica

et al. 2019

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“…The MPN method using pine pollen likely underestimates cell number compared with the acriflavine direct detection (AfDD) method using epifluorescence microscopy (Raghukumar & Schaumann 1993, Raghukumar 2002, Li et al 2013, Nakai et al 2013; Table 1). In some samples, no thraustochytrids were detected, i.e.…”

Section: Estimation Of Thraustochytrid Cell Density By the Mpn Methodsmentioning

confidence: 99%

“…Moreover, little information is available on thraustochytrid species composition and succession (Bongiorni & Dini 2002, and recent studies on the sequences of thraustochytrids in environmental DNA reported unknown labyrinthulid and thraustochytrid lineages (Collado-Mercado et al 2010, Li et al 2013. A species-monitoring investigation using quantitative PCR (qPCR) was also recently conducted, but thraustochytrids were detected in only a few samples using this method (Nakai et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Seasonal dynamics of culturable thraustochytrids (Labyrinthulomycetes, Stramenopiles) in estuarine and coastal waters

Ueda¹,

Nomura²,

Doi³

et al. 2015

Aquat. Microb. Ecol.

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Regular monitoring of estuarine and coastal areas at fixed points was carried out to investigate changes in biomass and species composition of thraustochytrids, which are colorless heterotrophs in the class Labyrinthulomycetes, Stramenopiles. Cell number counts using the most probable number (MPN) method with pine pollen baiting showed that 1 or 2 conspicuous peaks in abundance (termed 'thraustochytrid spikes') occurred between spring and late summer in most sampling years. Changes in thraustochytrid biomass had no correlation with phytoplankton abundance, although spikes seemed to occur after reductions in salinity and associated rapid rises of water temperature. The average cell density at the estuary site, excluding values during spike periods, was 4670 cells l −1 . Although thraustochytrid biomass was only 1.59% that of bacterial biomass, the fixed energy (as biomass) transferred directly from thraustochytrids to zooplankton was estimated to be 15.9% of that transferred from bacterioplankton via phagotrophic protists. This is because, per the theory of energy efficiency, energy transfer between trophic levels only creates 10% of the net production in the next trophic level relative to the first. The phylogenetic identification of established strains revealed an unexpectedly high diversity of thraustochytrids, including 10 unidentified lineages. A similar seasonal succession of phylogenetic groups was observed in each year of sampling. The differences in thraustochytrids isolated at each monitoring site and date suggest that habitat segregation may occur as a result of differences in environmental factors such as water temperature, salinity, and nutrient sources.

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The Pelagic Ecosystem

Raghukumar¹

2017

Fungi in Coastal and Oceanic Marine Ecosystems

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Genus-specific quantitative PCR of thraustochytrid protists

Cited by 12 publications

References 30 publications

Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica

Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica

Seasonal dynamics of culturable thraustochytrids (Labyrinthulomycetes, Stramenopiles) in estuarine and coastal waters

The Pelagic Ecosystem

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