Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR)
Quantification of feeding rates and selectivity of zooplankton is vital for understanding the mechanisms structuring marine ecosystems. However, methodological limitations have made many of these studies difficult. Recently, molecular based methods have demonstrated that DNA from prey species can be...
Published in: | Marine Biology |
---|---|
Main Authors: | , , , , |
Format: | Text |
Language: | English |
Published: |
Springer Berlin Heidelberg
2009
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477863/ https://doi.org/10.1007/s00227-008-1079-8 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:7477863 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:7477863 2023-05-15T15:48:01+02:00 Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) Troedsson, Christofer Simonelli, Paolo Nägele, Verena Nejstgaard, Jens C. Frischer, Marc E. 2009-02-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477863/ https://doi.org/10.1007/s00227-008-1079-8 en eng Springer Berlin Heidelberg http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477863/ http://dx.doi.org/10.1007/s00227-008-1079-8 © The Author(s) 2008 Open AccessThis is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License (https://creativecommons.org/licenses/by-nc/2.0), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. CC-BY-NC Mar Biol Original Paper Text 2009 ftpubmed https://doi.org/10.1007/s00227-008-1079-8 2020-09-13T00:26:49Z Quantification of feeding rates and selectivity of zooplankton is vital for understanding the mechanisms structuring marine ecosystems. However, methodological limitations have made many of these studies difficult. Recently, molecular based methods have demonstrated that DNA from prey species can be used to identify zooplankton gut contents, and further, quantitative gut content estimates by quantitative PCR (qPCR) assays targeted to the 18S rRNA gene have been used to estimate feeding rates in appendicularians and copepods. However, while standard single primer based qPCR assays were quantitative for the filter feeding appendicularian Oikopleura dioica, feeding rates were consistently underestimated in the copepod Calanus finmarchicus. In this study, we test the hypothesis that prey DNA is rapidly digested after ingestion by copepods and describe a qPCR-based assay, differential length amplification qPCR (dla-qPCR), to account for DNA digestion. The assay utilizes multiple primer sets that amplify different sized fragments of the prey 18S rRNA gene and, based on the differential amplification of these fragments, the degree of digestion is estimated and corrected for. Application of this approach to C. finmarchicus fed Rhodomonas marina significantly improved quantitative feeding estimates compared to standard qPCR. The development of dla-qPCR represents a significant advancement towards a quantitative method for assessing in situ copepod feeding rates without involving cultivation-based manipulation. Text Calanus finmarchicus Copepods PubMed Central (PMC) Marine Biology 156 3 253 259 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Original Paper |
spellingShingle |
Original Paper Troedsson, Christofer Simonelli, Paolo Nägele, Verena Nejstgaard, Jens C. Frischer, Marc E. Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) |
topic_facet |
Original Paper |
description |
Quantification of feeding rates and selectivity of zooplankton is vital for understanding the mechanisms structuring marine ecosystems. However, methodological limitations have made many of these studies difficult. Recently, molecular based methods have demonstrated that DNA from prey species can be used to identify zooplankton gut contents, and further, quantitative gut content estimates by quantitative PCR (qPCR) assays targeted to the 18S rRNA gene have been used to estimate feeding rates in appendicularians and copepods. However, while standard single primer based qPCR assays were quantitative for the filter feeding appendicularian Oikopleura dioica, feeding rates were consistently underestimated in the copepod Calanus finmarchicus. In this study, we test the hypothesis that prey DNA is rapidly digested after ingestion by copepods and describe a qPCR-based assay, differential length amplification qPCR (dla-qPCR), to account for DNA digestion. The assay utilizes multiple primer sets that amplify different sized fragments of the prey 18S rRNA gene and, based on the differential amplification of these fragments, the degree of digestion is estimated and corrected for. Application of this approach to C. finmarchicus fed Rhodomonas marina significantly improved quantitative feeding estimates compared to standard qPCR. The development of dla-qPCR represents a significant advancement towards a quantitative method for assessing in situ copepod feeding rates without involving cultivation-based manipulation. |
format |
Text |
author |
Troedsson, Christofer Simonelli, Paolo Nägele, Verena Nejstgaard, Jens C. Frischer, Marc E. |
author_facet |
Troedsson, Christofer Simonelli, Paolo Nägele, Verena Nejstgaard, Jens C. Frischer, Marc E. |
author_sort |
Troedsson, Christofer |
title |
Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) |
title_short |
Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) |
title_full |
Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) |
title_fullStr |
Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) |
title_full_unstemmed |
Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) |
title_sort |
quantification of copepod gut content by differential length amplification quantitative pcr (dla-qpcr) |
publisher |
Springer Berlin Heidelberg |
publishDate |
2009 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477863/ https://doi.org/10.1007/s00227-008-1079-8 |
genre |
Calanus finmarchicus Copepods |
genre_facet |
Calanus finmarchicus Copepods |
op_source |
Mar Biol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477863/ http://dx.doi.org/10.1007/s00227-008-1079-8 |
op_rights |
© The Author(s) 2008 Open AccessThis is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License (https://creativecommons.org/licenses/by-nc/2.0), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1007/s00227-008-1079-8 |
container_title |
Marine Biology |
container_volume |
156 |
container_issue |
3 |
container_start_page |
253 |
op_container_end_page |
259 |
_version_ |
1766383004737863680 |