Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
Biodiversity assessment is the key to understanding the relationship between biodiversity
and ecosystem functioning, but there is a well-acknowledged biodiversity identification
gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is
confounded by the small size of taxa, morphological convergence and intraspecific
variation. However, the most important restricting factor in meiofaunal ecological
research is the mismatch between diversity and the number of taxonomists that are able
to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular
operational taxonomic unit (MOTU)-based approach has been advocated for en mass
meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput
afforded by chain termination sequencing. Contemporary pyrosequencing offers a
solution to this problem in the form of environmental metagenetic analyses, but this
represents a novel field of biodiversity assessment. Here, we provide an overview of
meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction
to PCR, sequencing and the bioinformatic interrogation of multiple, independent
samples using 454 Roche sequencing platforms. We report two examples of environmental
metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical
rainforest habitats and provide critical appraisals of the level of putative recombinant
DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control
measures, environmental metagenetic analyses achieve MOTU formation across the
eukaryote domain of life at a fraction of the time and cost of traditional approaches. The
effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to
elucidate the molecular genetic richness of not only meiofaunal, but also all complex
eukaryotic communities.
4-20
Creer, S.
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Fonseca, V.G.
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Porazinska, D.L.
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Giblin-Davis, R.M.
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Sung, W.
c93c6368-70a5-4210-a093-4bc09ab97015
Power, D.M.
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Packer, M.
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Carvalho, G.R.
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Blaxter, M.L.
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Lambshead, P.J.D.
fe845f6c-a28f-4e4b-b64f-cee2f83bdffc
Thomas, W.K.
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February 2010
Creer, S.
78dbe97c-480f-46b3-9b7a-2c69c8608a79
Fonseca, V.G.
bb3ffa28-fb0b-4d05-addf-66a78e28f5f8
Porazinska, D.L.
4f9fbd5d-ad8b-40ac-912f-c1cb830bc8b0
Giblin-Davis, R.M.
152939e6-1e62-43a7-8d59-d7f29981d95b
Sung, W.
c93c6368-70a5-4210-a093-4bc09ab97015
Power, D.M.
87fa460b-57ef-4ab3-8810-1511a1ab4bb9
Packer, M.
74b2dc48-a36d-474c-9811-81606476438c
Carvalho, G.R.
18ee4b9f-5314-46d7-8e69-e43089e7ed08
Blaxter, M.L.
84af8139-8923-45a1-9ed0-0f49b69ef752
Lambshead, P.J.D.
fe845f6c-a28f-4e4b-b64f-cee2f83bdffc
Thomas, W.K.
54147135-9c90-486f-892e-12b92d336650
Creer, S., Fonseca, V.G., Porazinska, D.L., Giblin-Davis, R.M., Sung, W., Power, D.M., Packer, M., Carvalho, G.R., Blaxter, M.L., Lambshead, P.J.D. and Thomas, W.K.
(2010)
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.
Molecular Ecology, 19 (Suppl. 1), .
(doi:10.1111/j.1365-294X.2009.04473.x).
Abstract
Biodiversity assessment is the key to understanding the relationship between biodiversity
and ecosystem functioning, but there is a well-acknowledged biodiversity identification
gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is
confounded by the small size of taxa, morphological convergence and intraspecific
variation. However, the most important restricting factor in meiofaunal ecological
research is the mismatch between diversity and the number of taxonomists that are able
to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular
operational taxonomic unit (MOTU)-based approach has been advocated for en mass
meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput
afforded by chain termination sequencing. Contemporary pyrosequencing offers a
solution to this problem in the form of environmental metagenetic analyses, but this
represents a novel field of biodiversity assessment. Here, we provide an overview of
meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction
to PCR, sequencing and the bioinformatic interrogation of multiple, independent
samples using 454 Roche sequencing platforms. We report two examples of environmental
metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical
rainforest habitats and provide critical appraisals of the level of putative recombinant
DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control
measures, environmental metagenetic analyses achieve MOTU formation across the
eukaryote domain of life at a fraction of the time and cost of traditional approaches. The
effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to
elucidate the molecular genetic richness of not only meiofaunal, but also all complex
eukaryotic communities.
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Published date: February 2010
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Local EPrints ID: 79682
URI: http://eprints.soton.ac.uk/id/eprint/79682
ISSN: 0962-1083
PURE UUID: 91560379-62d8-470c-99cb-536da79d241f
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Date deposited: 18 Mar 2010
Last modified: 14 Mar 2024 00:32
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Contributors
Author:
S. Creer
Author:
V.G. Fonseca
Author:
D.L. Porazinska
Author:
R.M. Giblin-Davis
Author:
W. Sung
Author:
D.M. Power
Author:
M. Packer
Author:
G.R. Carvalho
Author:
M.L. Blaxter
Author:
P.J.D. Lambshead
Author:
W.K. Thomas
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