A DNA-based approach for assessing and monitoring benthic communities

Compositional changes in benthic invertebrate communities are commonly used to monitor and assess sedimentary marine environments. For the most part, sampling is restricted to a relatively small number of benthic organisms (<50 taxa), including taxa such as polychaetes, crustaceans and molluscs. The selection of taxa is predominately determined by size, ease of extraction from the sediment and regional taxonomic expertise. However, there are several significant limitations associated with this approach: 1) a large number of samples are required to produce informative data; 2) benthic programs are costly; 3) there is often a turnaround time of 6-12 months; and 4) assumptions about an ecosystem's health are being derived from a minute fraction of the total biodiversity. Recent innovations in DNA sequencing and computation now make it viable to obtain biodiversity information on potentially all organisms residing within a sediment sample (>1000 taxa in some studies). This can include traditionally examined organisms (e.g. polychaetes and bivalves), as well as micro- and meio-faunal taxa such as fungi, diatoms and bacteria. This ecogenomic approach not only produces comprehensive ecological information, but also, requires a small amount sediment; has a fairly rapid turnaround time; is cost competitive with traditional approaches; and can produce ecological data from poorly examined systems or those where taxonomic knowledge is limited. Here we provide an overview of the fundamentals behind a DNA-based monitoring program for marine sediments and present relevant examples of where this approach has been applied. In addition, we will discuss some of the advantages associated with the approach, as well as the limitations. Also described are some new technologies that have the potential to vastly bolster the ecological data obtained from DNA based ecological monitoring programs.