Abstract
Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. 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. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. 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. 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. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.
Highlights
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. 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
Most evaluations of marine ecological status rely on biological quality element (BQE) assessments, such as monitoring of invertebrates, fishes, or phytoplankton
The call for integrated monitoring recognizes that isolated BQE measures may not capture ecological status adequately (Table 1) and instead should include multiple taxonomic groups and life stages (Aylagas et al, 2016; Thompson et al, 2016; Trivedi et al, 2016)
Summary
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. 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. Marine monitoring and impact assessment programs are developed to respond to sustainability requirements Such programs may evaluate marine ecological quality to inform management actions, such as establishment of harvest guidelines, habitat and species conservation plans, and setting of requirements and practices to minimize pollutants and invasive species. Holistic approaches require integrated monitoring and assessment of both abiotic and biotic parameters, including multiple species (Arkema et al, 2006; Day et al, 2008; Curtin and Prellezo, 2010; Möllmann et al, 2014) and, ideally, multiple trophic levels to capture Biodiversity and Ecosystem Function (BEF) relationships (Strong et al, 2015)
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