Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts
Oxford Nanopore Technologies has recently launched a duplex sequencing strategy and announced an improved error rate which is in a similar order of magnitude as Illumina sequencing. We therefore conducted a pilot study to assess whether Nanopore duplex sequencing has potential to be used as a techno...
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ftdoajarticles:oai:doaj.org/article:ab8db4960d014f7a97a78233475756cc 2024-09-15T17:56:29+00:00 Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts Thorsten Stoeck Sven Nicolai Katzenmeier Hans-Werner Breiner Verena Rubel 2024-05-01T00:00:00Z https://doi.org/10.3897/mbmg.8.121817 https://doaj.org/article/ab8db4960d014f7a97a78233475756cc EN eng Pensoft Publishers https://mbmg.pensoft.net/article/121817/download/pdf/ https://mbmg.pensoft.net/article/121817/download/xml/ https://mbmg.pensoft.net/article/121817/ https://doaj.org/toc/2534-9708 doi:10.3897/mbmg.8.121817 2534-9708 https://doaj.org/article/ab8db4960d014f7a97a78233475756cc Metabarcoding and Metagenomics, Vol 8, Iss , Pp 45-68 (2024) Ecology QH540-549.5 article 2024 ftdoajarticles https://doi.org/10.3897/mbmg.8.121817 2024-08-05T17:49:18Z Oxford Nanopore Technologies has recently launched a duplex sequencing strategy and announced an improved error rate which is in a similar order of magnitude as Illumina sequencing. We therefore conducted a pilot study to assess whether Nanopore duplex sequencing has potential to be used as a technology in eDNA-based marine biomonitoring. Specifically, we investigated bacterial communities of sediment samples collected from Atlantic salmon (Salmo salar) aquaculture installations and compared the ecological trends obtained from short Illumina (V3-V4 region of the 16S rRNA gene) and long Nanopore (full length 16S rRNA gene) sequence reads. The obtained duplex rate of Nanopore amplicon reads with a Phred score ≥ 30 was 36%, notably higher compared to previous reports from bacterial genome sequencing. When inferring alpha- and beta-diversity from Illumina ASVs and Nanopore OTUs, we found highly congruent ecological patterns. Only when collating ASVs and OTUs across taxonomic ranks, beta-diversity analyses of Illumina-data slightly changed, due to the difficulties to assign a taxonomy to short sequence reads. While on family rank, both sequence datasets had good agreement, genus-assignments of Illumina data were critical, resulting in higher disagreement between the two protocols. Our data provide evidence that eDNA-based monitoring of aquaculture-related environmental impacts could equally well be conducted with the improved Nanopore duplex sequencing. We discuss to what extent eDNA-based biomonitoring could benefit from long-read information. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles Metabarcoding and Metagenomics 8 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Ecology QH540-549.5 |
spellingShingle |
Ecology QH540-549.5 Thorsten Stoeck Sven Nicolai Katzenmeier Hans-Werner Breiner Verena Rubel Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts |
topic_facet |
Ecology QH540-549.5 |
description |
Oxford Nanopore Technologies has recently launched a duplex sequencing strategy and announced an improved error rate which is in a similar order of magnitude as Illumina sequencing. We therefore conducted a pilot study to assess whether Nanopore duplex sequencing has potential to be used as a technology in eDNA-based marine biomonitoring. Specifically, we investigated bacterial communities of sediment samples collected from Atlantic salmon (Salmo salar) aquaculture installations and compared the ecological trends obtained from short Illumina (V3-V4 region of the 16S rRNA gene) and long Nanopore (full length 16S rRNA gene) sequence reads. The obtained duplex rate of Nanopore amplicon reads with a Phred score ≥ 30 was 36%, notably higher compared to previous reports from bacterial genome sequencing. When inferring alpha- and beta-diversity from Illumina ASVs and Nanopore OTUs, we found highly congruent ecological patterns. Only when collating ASVs and OTUs across taxonomic ranks, beta-diversity analyses of Illumina-data slightly changed, due to the difficulties to assign a taxonomy to short sequence reads. While on family rank, both sequence datasets had good agreement, genus-assignments of Illumina data were critical, resulting in higher disagreement between the two protocols. Our data provide evidence that eDNA-based monitoring of aquaculture-related environmental impacts could equally well be conducted with the improved Nanopore duplex sequencing. We discuss to what extent eDNA-based biomonitoring could benefit from long-read information. |
format |
Article in Journal/Newspaper |
author |
Thorsten Stoeck Sven Nicolai Katzenmeier Hans-Werner Breiner Verena Rubel |
author_facet |
Thorsten Stoeck Sven Nicolai Katzenmeier Hans-Werner Breiner Verena Rubel |
author_sort |
Thorsten Stoeck |
title |
Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts |
title_short |
Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts |
title_full |
Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts |
title_fullStr |
Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts |
title_full_unstemmed |
Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts |
title_sort |
nanopore duplex sequencing as an alternative to illumina miseq sequencing for edna-based biomonitoring of coastal aquaculture impacts |
publisher |
Pensoft Publishers |
publishDate |
2024 |
url |
https://doi.org/10.3897/mbmg.8.121817 https://doaj.org/article/ab8db4960d014f7a97a78233475756cc |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Metabarcoding and Metagenomics, Vol 8, Iss , Pp 45-68 (2024) |
op_relation |
https://mbmg.pensoft.net/article/121817/download/pdf/ https://mbmg.pensoft.net/article/121817/download/xml/ https://mbmg.pensoft.net/article/121817/ https://doaj.org/toc/2534-9708 doi:10.3897/mbmg.8.121817 2534-9708 https://doaj.org/article/ab8db4960d014f7a97a78233475756cc |
op_doi |
https://doi.org/10.3897/mbmg.8.121817 |
container_title |
Metabarcoding and Metagenomics |
container_volume |
8 |
_version_ |
1810432688409018368 |