Sequencing our way to more accurate community abundance
(2023) In Molecular Ecology Resources 23(1). p.13-15- Abstract
Over the last two decades, there has been a huge increase in our understanding of microbial diversity, structure and composition enabled by high-throughput sequencing technologies. Yet, it is unclear how the number of sequences translates to the number of cells or species within the community. In some cases, additional observational data may be required to ensure relative abundance patterns from sequence reads are biologically meaningful. The goal of DNA-based methods for biodiversity assessments is to obtain robust community abundance data, simultaneously, from environmental samples. In this issue of Molecular Ecology Resources, Pierella Karlusich et al. (2022) describe a new method for quantifying phytoplankton cell abundance. Using... (More)
Over the last two decades, there has been a huge increase in our understanding of microbial diversity, structure and composition enabled by high-throughput sequencing technologies. Yet, it is unclear how the number of sequences translates to the number of cells or species within the community. In some cases, additional observational data may be required to ensure relative abundance patterns from sequence reads are biologically meaningful. The goal of DNA-based methods for biodiversity assessments is to obtain robust community abundance data, simultaneously, from environmental samples. In this issue of Molecular Ecology Resources, Pierella Karlusich et al. (2022) describe a new method for quantifying phytoplankton cell abundance. Using Tara Oceans data sets, the authors propose the photosynthetic gene psbO for reporting accurate relative abundance of the entire phytoplankton community from metagenomic data. The authors demonstrate higher correlations with traditional optical methods (including microscopy and flow cytometry), using their new method, improving upon molecular abundance assessments using multicopy marker genes. Furthermore, to facilitate application of their approach, the authors curated a psbO gene database for accessible taxonomic queries. This is an important step towards improving species abundance estimates from molecular data and eventually reporting of absolute species abundance, enhancing our understanding of community dynamics.
(Less)
- author
- Brennan, Georgina L. LU
- publishing date
- 2023-01
- type
- Contribution to journal
- publication status
- published
- keywords
- Community Ecology, Metabarcoding, Metagenomics, phytoplankton
- in
- Molecular Ecology Resources
- volume
- 23
- issue
- 1
- pages
- 3 pages
- publisher
- Wiley-Blackwell
- external identifiers
-
- pmid:36197791
- scopus:85140222128
- ISSN
- 1755-098X
- DOI
- 10.1111/1755-0998.13717
- language
- English
- LU publication?
- no
- additional info
- Publisher Copyright: © 2022 The Author. Molecular Ecology Resources published by John Wiley & Sons Ltd.
- id
- a1da1b52-9088-402e-8ae7-5dd839a2b1e2
- date added to LUP
- 2024-10-15 14:47:52
- date last changed
- 2024-12-10 20:38:57
@article{a1da1b52-9088-402e-8ae7-5dd839a2b1e2,
abstract = {{<p>Over the last two decades, there has been a huge increase in our understanding of microbial diversity, structure and composition enabled by high-throughput sequencing technologies. Yet, it is unclear how the number of sequences translates to the number of cells or species within the community. In some cases, additional observational data may be required to ensure relative abundance patterns from sequence reads are biologically meaningful. The goal of DNA-based methods for biodiversity assessments is to obtain robust community abundance data, simultaneously, from environmental samples. In this issue of Molecular Ecology Resources, Pierella Karlusich et al. (2022) describe a new method for quantifying phytoplankton cell abundance. Using Tara Oceans data sets, the authors propose the photosynthetic gene psbO for reporting accurate relative abundance of the entire phytoplankton community from metagenomic data. The authors demonstrate higher correlations with traditional optical methods (including microscopy and flow cytometry), using their new method, improving upon molecular abundance assessments using multicopy marker genes. Furthermore, to facilitate application of their approach, the authors curated a psbO gene database for accessible taxonomic queries. This is an important step towards improving species abundance estimates from molecular data and eventually reporting of absolute species abundance, enhancing our understanding of community dynamics.</p>}},
author = {{Brennan, Georgina L.}},
issn = {{1755-098X}},
keywords = {{Community Ecology; Metabarcoding; Metagenomics; phytoplankton}},
language = {{eng}},
number = {{1}},
pages = {{13--15}},
publisher = {{Wiley-Blackwell}},
series = {{Molecular Ecology Resources}},
title = {{Sequencing our way to more accurate community abundance}},
url = {{http://dx.doi.org/10.1111/1755-0998.13717}},
doi = {{10.1111/1755-0998.13717}},
volume = {{23}},
year = {{2023}},
}