S. Creer and V. G. Fonseca are joint first authors of this work.
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
Article first published online: 10 FEB 2010
© 2010 Blackwell Publishing Ltd
Special Issue: Next Generation Molecular Ecology
Volume 19, Issue Supplement s1, pages 4–20, March 2010
How to Cite
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: 4–20. doi: 10.1111/j.1365-294X.2009.04473.x
SC is a molecular ecologist with broad interests in the spheres of ecology and evolution. Current research foci include understanding the mechanisms underpinning the role, origins and dynamics of biodiversity in ecosystem processes, environmental genomics, molecular phylogenetics and population genetics. VGF’s research interests focus on functional and environmental genomic aspects of differential gene expression under normal and pathological conditions, the analysis of marine biodiversity from a taxonomic and evolutionary perspective, and ecology and management of marine ecosystems. DP and RGD are interested in the patterns of terrestrial microbiotic diversity and their role in ecosystem functioning using ultrasequencing approaches as well as in molecular phylogeny of terrestrial and entomophilic nematodes for linking metagenetics with traditional taxonomy. DMP is interested in molecular evolution traced using gene families, particularly those regulating whole animal homeostasis. MP is an ecologist specializing in marine benthic biodiversity. PJD is a nematologist interested in the quantitative analysis of biodiversity and its origins. GRC’s research is aimed at the elucidation of fundamental aspects of a species’ biology such as patterns of dispersal and gene flow, evolution of life histories and behaviour, response to environmental stress, and mechanisms of speciation. MB is a genomics biologist, with major interests in the genomics and molecular identification of “neglected” animal phyla. WKT and WS are interested in patterns and processes of genomic change and how these relate to our understanding of genetic diversity and evolution, in addition to the analysis and interpretation of metagenetic data.
- Issue published online: 10 FEB 2010
- Article first published online: 10 FEB 2010
- Received 19 June 2009; revision received 19 August 2009; accepted 21 August 2009
- 454 environmental sequencing;
- meiofaunal and eukaryotic biodiversity;
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.