Reliability of qPCR for quantitative gut content estimation in the circumglobally abundant pelagic tunicate Dolioletta gegenbauri (Tunicata, Thaliacea)

Frischer, Marc E.; Sanchez, Christy A.; Walters, Tina L.; Thompson, Michael; Frazier, L.; Paffenhöfer, Gustav‐Adolf

doi:10.1016/j.fooweb.2014.11.001

Cited by 12 publications

(19 citation statements)

References 45 publications

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“…The use of PCR‐based assays for qualitative detection of prey consumed by predatory species has become nearly routine in the study of trophic ecology (Pompanon et al, ). Increasingly, these methods are also being used to quantify prey consumption although quantification can be considerably more challenging (Frischer et al, ; Nejstgaard et al, ). Results from NGS studies are particularly prone to systematic bias associated with library preparation, sequencing and bioinformatics procedures, and thus, it is recommended that NGS data be interpreted qualitatively unless appropriate controls or complimentary orthogonal methods are also applied (Bista et al, ; Hardwick, Deveson, & Mercer, ).…”

Section: Discussionmentioning

confidence: 99%

“…Utilizing a blocking PNA assay (Troedsson et al, ; Von Wintzingerode, Landt, Ehrlich, & Göbel, ) specific to D. gegenbauri in conjunction with a general (universal) 18S rDNA‐targeted PCR primer set, it was possible to directly determine the diversity of prey ingested by D. gegenbauri in both laboratory and field studies. Because prey DNA is poorly digested by D. gegenbauri (Frischer et al, ), it was also possible to quantify diatoms utilizing a real‐time quantitative PCR approach with a diatom group‐specific primer set. Comparison of NGS 18S rDNA amplicon libraries from continental shelf water (available prey field) with wild‐caught animals and cultured animals exposed to shelf water yielded new insights into the diet of D. gegenbauri .…”

Section: Discussionmentioning

confidence: 99%

“…Reference lines (---) indicate 1 standard deviation from the mean of the gut to water ratio for each prey and parasite type. be considerably more challenging (Frischer et al, 2014;Nejstgaard et al, 2008). Results from NGS studies are particularly prone to systematic bias associated with library preparation, sequencing and bioinformatics procedures, and thus, it is recommended that NGS data be interpreted qualitatively unless appropriate controls or complimentary orthogonal methods are also applied (Bista et al, 2018;Hardwick, Deveson, & Mercer, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Because prey DNA is poorly digested by D. gegenbauri (Frischer et al, 2014), it was also possible to quantify diatoms utilizing a real-time quantitative PCR approach with a diatom group-specific primer set.…”

Section: The Diet Of D Gegenbaurimentioning

confidence: 99%

“…Recently, PCR‐based assays for detection of prey content in the gut of a variety of marine mesozooplankton species including the larvacean Oikopleura dioica (Troedsson et al, ) and the doliolid D. gegenbauri (Frischer et al, ) have been developed. In the case of both these pelagic tunicate species, prey DNA digestion appears to be minimal and therefore prey ingestion can be quantitatively estimated using quantitative PCR approaches (Frischer et al, ). The availability of such methods provides a culture independent means to assess the diet of these delicate and cryptic marine animals.…”

Section: Introductionmentioning

confidence: 99%

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Diet and trophic interactions of a circumglobally significant gelatinous marine zooplankter,Dolioletta gegenbauri(Uljanin, 1884)

et al. 2018

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Gelatinous zooplankton play a crucial role in marine planktonic food webs. However, primarily due to methodological challenges, the in situ diet of zooplankton remains poorly investigated and little is known about their trophic interactions including feeding behaviour, prey selection and in situ feeding rates. This is particularly true for gelatinous zooplankton including the marine pelagic tunicate, Dolioletta gegenbauri. In this study, we applied an 18S rRNA amplicon metabarcoding approach to identify the diet of captive‐fed and wild‐caught D. gegenbauri on the midcontinental shelf of the South Atlantic Bight, USA. Sequencing‐based approaches were complimented with targeted quantitative real‐time polymerase chain reaction (PCR) analyses. Captive‐fed D. gegenbauri gut content was dominated by pico‐, nano‐ and micro‐plankton including pico‐dinoflagellates (picozoa) and diatoms. These results suggested that diatoms were concentrated by D. gegenbauri relative to their concentration in the water column. Analysis of wild‐caught doliolids by quantitative real‐time PCR utilizing a group‐specific diatom primer set confirmed that diatoms were concentrated by D. gegenbauri, particularly by the gonozooid life stage associated with actively developing blooms. Sequences derived from larger metazoans were frequently observed in wild‐caught animals but not in captive‐fed animals suggesting experimental bias associated with captive feeding. These studies revealed that the diet of D. gegenbauri is considerably more diverse than previously described, that parasites are common in wild populations, and that prey quality, quantity and parasites are likely all important factors in regulating doliolid population dynamics in continental shelf environments.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: The Diet Of D Gegenbaurimentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Diet and trophic interactions of a circumglobally significant gelatinous marine zooplankter,Dolioletta gegenbauri(Uljanin, 1884)

et al. 2018

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Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea

Martini

Neuer

Hamill

et al. 2017

Limnology & Oceanography

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The marine picocyanobacteria Prochlorococcus and Synechococcus dominate primary production in oligotrophic oceans, but their role in the particulate organic carbon (POC) flux into the deeper ocean remains unresolved. Here, we present for the first‐time data on the absolute clade and strain‐specific contribution to POC flux of two of the most abundant clades of Synechococcus (II and III) and strains of Prochlorococcus (high‐light strain MIT 9312 and low‐light strain MIT 9313) in the Sargasso Sea, by targeting the 23S‐16S rDNA internally transcribed spacer region using quantitative Polymerase Chain Reaction. We collected seawater samples and sinking particles using shallow sediment traps during winter and summer 2012 around the Bermuda Atlantic Time Series station. Both clades of Synechococcus had a higher contribution to the total POC flux during winter compared to the summer, with both clades contributing up to 2.7% to the total winter POC flux. Prochlorococcus was more abundant during the summer, but both strains of Prochlorococcus contributed less than 0.2% to the POC flux in both seasons. We found these differences in the contribution to flux to be mainly due to the smaller size of the Prochlorococcus. In addition, the flux of Synechococcus clade III, and Prochlorococcus MIT9312 was enhanced relative to their standing stock in a cyclonic eddy sampled during winter 2012. Using quantification of genetic markers, this study establishes distinct clade‐and strain specific patterns in POC flux among the most abundant picophytoplankton groups in the Atlantic Ocean.

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Selective feeding and linkages to the microbial food web by the doliolidDolioletta gegenbauri

Frischer

Lamboley

Walters

et al. 2021

Limnology & Oceanography

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Gelatinous zooplankton play a crucial role in pelagic marine food webs, however, due to methodological challenges and persistent misconceptions of their importance, the trophic role of gelatinous zooplankton remains poorly investigated. This is particularly true for small gelatinous zooplankton including the marine pelagic tunicate, Dolioletta gegenbauri. D. gegenbauri and other doliolid species occur persistently on wide subtropical shelves where they often produce massive blooms in association with shelf upwelling conditions. As efficient filter feeders and prodigious producers of relatively low-density organic-rich aggregates, doliolids are understood to contribute significantly to shelf production, pelagic ecology, and pelagic-benthic coupling. Utilizing molecular gut content analysis and stable isotope analysis approaches, the trophic interactions of doliolids were explored during bloom and nonbloom conditions on the South Atlantic Bight continental shelf in the Western North Atlantic. Based on molecular gut content analysis, relative ingestion selectivity varied with D. gegenbauri life stage. At all life stages, doliolids ingested a wide range of prey types and sizes, but exhibited selectivity for larger prey types including diatoms, ciliates, and metazoans. Experimental growth studies confirmed that metazoan prey were ingested, but indicated that they were not digested and assimilated. Stable isotopic composition (δ 13 C and δ 15 N) of wild-caught doliolids, during bloom and non-bloom conditions, were most consistent with a detrital-supplemented diet. These observations suggest that the feeding ecology of D. gegenbauri is more complex than previously reported, and have strong and unusual linkages to the microbial food web.

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Reliability of qPCR for quantitative gut content estimation in the circumglobally abundant pelagic tunicate Dolioletta gegenbauri (Tunicata, Thaliacea)

Cited by 12 publications

References 45 publications

Diet and trophic interactions of a circumglobally significant gelatinous marine zooplankter,Dolioletta gegenbauri(Uljanin, 1884)

Diet and trophic interactions of a circumglobally significant gelatinous marine zooplankter,Dolioletta gegenbauri(Uljanin, 1884)

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea

Selective feeding and linkages to the microbial food web by the doliolidDolioletta gegenbauri

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