Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica
Environmental DNA is a powerful tool for monitoring biodiversity. Although environmental DNA surveys have successfully been implemented in various environments, protocol choice has been shown to affect results and inferences. Thus far, few method comparison studies for soil have been undertaken. Her...
Published in: | Antarctic Science |
---|---|
Main Authors: | , , , , , , |
Format: | Text |
Language: | unknown |
Published: |
Research Online
2023
|
Subjects: | |
Online Access: | https://ro.uow.edu.au/test2021/8009 https://doi.org/10.1017/S0954102022000384 |
id |
ftunivwollongong:oai:ro.uow.edu.au:test2021-13556 |
---|---|
record_format |
openpolar |
spelling |
ftunivwollongong:oai:ro.uow.edu.au:test2021-13556 2023-06-11T04:04:42+02:00 Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica Olmedo-Rojas, Pamela Jeunen, Gert Jan Lamare, Miles Turnbull, Johanna Terauds, Aleks Gemmell, Neil Fraser, Ceridwen I. 2023-02-06T08:00:00Z https://ro.uow.edu.au/test2021/8009 https://doi.org/10.1017/S0954102022000384 unknown Research Online https://ro.uow.edu.au/test2021/8009 doi:10.1017/S0954102022000384 https://doi.org/10.1017/S0954102022000384 Scopus Harvesting Series 18S biodiversity biogeography desert eDNA operational taxonomic unit remote environments text 2023 ftunivwollongong https://doi.org/10.1017/S0954102022000384 2023-05-15T22:24:53Z Environmental DNA is a powerful tool for monitoring biodiversity. Although environmental DNA surveys have successfully been implemented in various environments, protocol choice has been shown to affect results and inferences. Thus far, few method comparison studies for soil have been undertaken. Here, we optimized the workflow for soil metabarcoding through a comparative study encompassing variation in sampling strategy (individual and combined samples), DNA extraction (PowerSoil®, NucleoSpin® Soil, PowerSoil® + phosphate buffer and NucleoSpin® Soil + phosphate buffer) and library preparation (one-step and two-step quantitative polymerase chain reaction methods). Using a partial 18S rRNA marker, a total of 309 eukaryotic taxa across 21 phyla were identified from Antarctic soil from one site in the Larsemann Hills. Our optimized workflow was effective with no notable reduction in data quality for a considerable increase in time and cost efficiency. The NucleoSpin® Soil + phosphate buffer was the best-performing extraction method. Compared to similar studies in other regions, we obtained low taxonomic coverage, perhaps because of the paucity of Antarctic terrestrial organisms in genetic reference databases. Our findings provide useful methodological insights for maximizing efficiency in soil metabarcoding studies in Antarctica and other low-biomass environments. Text Antarc* Antarctic Antarctica University of Wollongong, Australia: Research Online Antarctic Larsemann Hills ENVELOPE(76.217,76.217,-69.400,-69.400) Antarctic Science 35 1 15 30 |
institution |
Open Polar |
collection |
University of Wollongong, Australia: Research Online |
op_collection_id |
ftunivwollongong |
language |
unknown |
topic |
18S biodiversity biogeography desert eDNA operational taxonomic unit remote environments |
spellingShingle |
18S biodiversity biogeography desert eDNA operational taxonomic unit remote environments Olmedo-Rojas, Pamela Jeunen, Gert Jan Lamare, Miles Turnbull, Johanna Terauds, Aleks Gemmell, Neil Fraser, Ceridwen I. Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica |
topic_facet |
18S biodiversity biogeography desert eDNA operational taxonomic unit remote environments |
description |
Environmental DNA is a powerful tool for monitoring biodiversity. Although environmental DNA surveys have successfully been implemented in various environments, protocol choice has been shown to affect results and inferences. Thus far, few method comparison studies for soil have been undertaken. Here, we optimized the workflow for soil metabarcoding through a comparative study encompassing variation in sampling strategy (individual and combined samples), DNA extraction (PowerSoil®, NucleoSpin® Soil, PowerSoil® + phosphate buffer and NucleoSpin® Soil + phosphate buffer) and library preparation (one-step and two-step quantitative polymerase chain reaction methods). Using a partial 18S rRNA marker, a total of 309 eukaryotic taxa across 21 phyla were identified from Antarctic soil from one site in the Larsemann Hills. Our optimized workflow was effective with no notable reduction in data quality for a considerable increase in time and cost efficiency. The NucleoSpin® Soil + phosphate buffer was the best-performing extraction method. Compared to similar studies in other regions, we obtained low taxonomic coverage, perhaps because of the paucity of Antarctic terrestrial organisms in genetic reference databases. Our findings provide useful methodological insights for maximizing efficiency in soil metabarcoding studies in Antarctica and other low-biomass environments. |
format |
Text |
author |
Olmedo-Rojas, Pamela Jeunen, Gert Jan Lamare, Miles Turnbull, Johanna Terauds, Aleks Gemmell, Neil Fraser, Ceridwen I. |
author_facet |
Olmedo-Rojas, Pamela Jeunen, Gert Jan Lamare, Miles Turnbull, Johanna Terauds, Aleks Gemmell, Neil Fraser, Ceridwen I. |
author_sort |
Olmedo-Rojas, Pamela |
title |
Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica |
title_short |
Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica |
title_full |
Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica |
title_fullStr |
Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica |
title_full_unstemmed |
Soil environmental DNA metabarcoding in low-biomass regions requires protocol optimization: a case study in Antarctica |
title_sort |
soil environmental dna metabarcoding in low-biomass regions requires protocol optimization: a case study in antarctica |
publisher |
Research Online |
publishDate |
2023 |
url |
https://ro.uow.edu.au/test2021/8009 https://doi.org/10.1017/S0954102022000384 |
long_lat |
ENVELOPE(76.217,76.217,-69.400,-69.400) |
geographic |
Antarctic Larsemann Hills |
geographic_facet |
Antarctic Larsemann Hills |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
Scopus Harvesting Series |
op_relation |
https://ro.uow.edu.au/test2021/8009 doi:10.1017/S0954102022000384 https://doi.org/10.1017/S0954102022000384 |
op_doi |
https://doi.org/10.1017/S0954102022000384 |
container_title |
Antarctic Science |
container_volume |
35 |
container_issue |
1 |
container_start_page |
15 |
op_container_end_page |
30 |
_version_ |
1768389915888844800 |