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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. [ABSTRACT FROM AUTHOR]

Marine nematodes, which play an important role in many ecosystems, include a number of apparently cosmopolitan taxa that exhibit broad biogeographic ranges even though there is no obvious dispersal phase in their lifecycle. In this study, standard taxonomic approaches to marine nematode identification in conjunction with multivariate statistical analysis of morphometric data were compared with molecular techniques. Specimens of the marine nematode Terschellingia longicaudata that had been identified by their morphological features were investigated from a range of localities (East and West Atlantic, Bahrain, Malaysia) and habitats (estuarine, intertidal, subtidal) using molecular approaches based on the amplification and sequencing of the small subunit ribosomal RNA (18S rRNA). The study revealed that the majority of the morphologically defined T. longicaudata specimens share a single 18S rRNA sequence and apparently belong to a single taxon distributed from the British Isles to Malaysia. In addition, 18S rRNA analysis also revealed two additional sequences. One of these sequences was found in both the British Isles and Mexico, the other was recorded only from British waters. Individuals collected in Bahrain and identified from their morphology as T. longicaudata had two highly divergent 18S rRNA sequences. Separate morphological and morphometric approaches to identification of specimens from the same sites that had been formalin-preserved did not support evidence of multiple genotypes revealed previously by molecular analysis. Current taxonomy based on morphological characters detected using light-microscopy may be unable to discriminate possible species complexes. Biodiversity of marine nematodes may often be underestimated due to the presence of morphologically cryptic species complexes. High-throughput techniques such as DNA barcoding would aid in species identification but may require thorough analysis of multiple nuclear and mitochondrial molecular markers. [ABSTRACT FROM AUTHOR]

Small metazoans such as marine nematodes are increasingly identified using both molecular and morphological techniques. Formalin is the preferred fixative for morphological analysis but specimens become unsuitable for molecular study due to formalin-induced modification of DNA. Nematodes fixed in ethanol work well for molecular studies but become unsuitable for taxonomy due to shrinkage. Here we show for the first time that formalin can be used as a short-term fixative (≤ 7 days) for marine nematodes, allowing both morphological and molecular work to be conducted on the same individual. No sequence ambiguities were detected in polymerase chain reaction (PCR) amplifications of 18S ribosomal DNA (rDNA) following short-term formalin preservation. [ABSTRACT FROM AUTHOR]