Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a “microbes to mammals” or “barcodes to biomes” approach. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. 6Marine and Environmental Sciences Centre (MARE), c/o DCV, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal.5Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA, USA. 4Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.3Marine and Environmental Sciences Centre (MARE), Faculty of Sciences, University of Lisbon, Lisbon, Portugal.2Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.1Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory (stationed at NOAA/NMFS/SWFSC/La Jolla, CA), National Oceanic and Atmospheric Administration, Miami, FL, USA.Thompson 1,2, Bernardo Duarte 3, Tim Kahlke 4, Andrew R.
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