02866nas a2200313   4500008004100000020005900041022001300100245008300113210006900196300001100265490000700276520189000283653003302173653004302206653001702249653001702266100001402283700002002297700002302317700002502340700001302365700001802378700001502396700002102411700002002432700002302452700001902475856005802494       2010                        eng d  a1365-294X (Electronic)$\backslash$n0962-1083 (Linking)  a0962108300a{Ultrasequencing of the meiofaunal biosphere: Practice, pitfalls and promises}0 aUltrasequencing of the meiofaunal biosphere Practice pitfalls an  a4–200 v193 aBiodiversity 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.10a454 environmental sequencing10aMeiofaunal and eukaryotic biodiversity10aMetagenetics10aMetagenomics1 aCreer, S.1 aFonseca, V., G.1 aPorazinska, D., L.1 aGiblin-Davis, R., M.1 aSung, W.1 aPower, D., M.1 aPacker, M.1 aCarvalho, G., R.1 aBlaxter, M., L.1 aLambshead, P., J D1 aThomas, W., K.  uhttp://doi.wiley.com/10.1111/j.1365-294X.2009.04473.x