A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes
The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempte...
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MDPI AG
2021-04-01
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| Online Access: | https://www.mdpi.com/1424-2818/13/5/180 |
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| author | Ioulia Santi Panagiotis Kasapidis Ioannis Karakassis Paraskevi Pitta |
| author_facet | Ioulia Santi Panagiotis Kasapidis Ioannis Karakassis Paraskevi Pitta |
| author_sort | Ioulia Santi |
| collection | DOAJ |
| description | The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes. |
| first_indexed | 2024-03-10T12:01:31Z |
| format | Article |
| id | doaj.art-1002cf8f2f834da6a28895604ffc6444 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T12:01:31Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
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| spelling | doaj.art-1002cf8f2f834da6a28895604ffc64442023-11-21T16:54:58ZengMDPI AGDiversity1424-28182021-04-0113518010.3390/d13050180A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial EukaryotesIoulia Santi0Panagiotis Kasapidis1Ioannis Karakassis2Paraskevi Pitta3Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, GR71003 Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), P.O. Box 2214, GR71003 Heraklion, Crete, GreeceDepartment of Biology, Voutes Campus, University of Crete, 70013 Heraklion, Crete, GreeceHellenic Centre for Marine Research (HCMR), Institute of Oceanography, P.O. Box 2214, GR71003 Heraklion, Crete, GreeceThe procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.https://www.mdpi.com/1424-2818/13/5/180microbial eukaryotesDNA metabarcodingmicroscopymarine plankton18S rRNA |
| spellingShingle | Ioulia Santi Panagiotis Kasapidis Ioannis Karakassis Paraskevi Pitta A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes Diversity microbial eukaryotes DNA metabarcoding microscopy marine plankton 18S rRNA |
| title | A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes |
| title_full | A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes |
| title_fullStr | A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes |
| title_full_unstemmed | A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes |
| title_short | A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes |
| title_sort | comparison of dna metabarcoding and microscopy methodologies for the study of aquatic microbial eukaryotes |
| topic | microbial eukaryotes DNA metabarcoding microscopy marine plankton 18S rRNA |
| url | https://www.mdpi.com/1424-2818/13/5/180 |
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