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...
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Online Access: | http://www.osti.gov/servlets/purl/1816631 https://www.osti.gov/biblio/1816631 https://doi.org/10.1007/s00227-008-1079-8 |
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ftosti:oai:osti.gov:1816631 2023-07-30T04:02:46+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. 2023-07-04 application/pdf http://www.osti.gov/servlets/purl/1816631 https://www.osti.gov/biblio/1816631 https://doi.org/10.1007/s00227-008-1079-8 unknown http://www.osti.gov/servlets/purl/1816631 https://www.osti.gov/biblio/1816631 https://doi.org/10.1007/s00227-008-1079-8 doi:10.1007/s00227-008-1079-8 59 BASIC BIOLOGICAL SCIENCES 2023 ftosti https://doi.org/10.1007/s00227-008-1079-8 2023-07-11T10:06:30Z 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. Other/Unknown Material Calanus finmarchicus Copepods SciTec Connect (Office of Scientific and Technical Information - OSTI, U.S. Department of Energy) Marine Biology 156 3 253 259 |
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Open Polar |
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SciTec Connect (Office of Scientific and Technical Information - OSTI, U.S. Department of Energy) |
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language |
unknown |
topic |
59 BASIC BIOLOGICAL SCIENCES |
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59 BASIC BIOLOGICAL SCIENCES 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 |
59 BASIC BIOLOGICAL SCIENCES |
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. |
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) |
publishDate |
2023 |
url |
http://www.osti.gov/servlets/purl/1816631 https://www.osti.gov/biblio/1816631 https://doi.org/10.1007/s00227-008-1079-8 |
genre |
Calanus finmarchicus Copepods |
genre_facet |
Calanus finmarchicus Copepods |
op_relation |
http://www.osti.gov/servlets/purl/1816631 https://www.osti.gov/biblio/1816631 https://doi.org/10.1007/s00227-008-1079-8 doi:10.1007/s00227-008-1079-8 |
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_ |
1772813586132893696 |