Invertebrate DNA Chip: Opportunities and Challenges in the Development and Application of Microarrays for Marine Biodiversity Studies

DNA microarrays for marine biodiversity studies have been developed and tested in several groups, spanning different applications. They are employed to characterize ecological communities circumventing uncertainties and challenges associated with the conventional techniques of taxonomy employed to characterize these communities. Examples come from identifications of fishes and phytoplankton to monitoring of harmful algae. Although DNA microchips support a great diversity of applications and provide a wealth of findings in functional genomics and environmental studies, limits in ecological applications are known. So far, DNA microarrays used in biodiversity studies provide only qualitative data in terms of presence or absence of the species and its usage is greatly limited in providing the quantitative measurement of environmental samples. Moreover, DNA microarrays are commonly restricted to identify only those species that are targeted by the probes implemented on the chip. In turn, developing a broad spectrum array has technological challenges in terms of probe designing, experimental optimization, and statistical analysis. In this book chapter, we provide a critical assessment on promises and pitfalls of DNA microarrays as tool for marine invertebrate species identification. We implemented a DNA-chip prototype to identify 15 species of marine invertebrates from European Seas, including crustaceans, molluscs, and polychaetes, based on the two mitochondrial markers, cytochrome oxidase subunit I and 16S rRNA. Challenges involved in oligonucleotide probe design, in silico evaluation, and difficulties encountered through hybridization experiments are here explored. Specificity and sensitivity of the probes have also been critically evaluated to verify the suitability of the selected markers for microarray probe design. Since ultimate application of DNA microarray to resolve complex environmental samples is a major challenge, we made an attempt to analyse gut contents of predator fishes. The problems encountered during this analysis, as the presence of target and not target species that could affect the specificity and the sensitivity of the DNA-chip to distinguish low and high abundant target species from a background of non-targets, were explored. We also reviewed advantages and disadvantages of DNA microarray technology compared to other molecular identification methods that recently spread, i.e. DNA barcoding and next generation sequencing. The outcome of the Invertebrate DNA Chip prototype served as a proof-of-concept for the identification of selected marine invertebrates and prey species of demersal fishes by DNA microarray. The potential of such microarrays can encompass several fields of scientific applications in marine biodiversity and ecosystem sciences, as marine ecosystem diversity and environmental monitoring, seafood quality control, and understanding food webs and ecosystem functioning.