Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

Abstract

Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment.

eDNA and specific primers for early detection of invasive species – A case study on the bivalve Rangia cuneata, currently spreading in Europe

“…for sparsely distributed marine species). This is particularly important in the current moment of diminishing budgets, when national monitoring networks carefully consider survey expenses and aim at cost-effective approaches (Aylagas et al, 2014).…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…This causes a bottleneck in sample throughput because manual sorting and visual identification is labor-intensive and slow. Identification demands a high degree of specialized taxonomic knowledge, such expertise is required for each BQE target separately, and juvenile and cryptic species can nonetheless be misidentified (Bourlat et al, 2013;Aylagas et al, 2014Aylagas et al, , 2016Pawlowski et al, 2014;Carugati et al, 2015;Thomsen and Willerslev, 2015;Bowers et al, 2016;Bucklin et al, 2016;Danovaro et al, 2016). Estimates suggest that between 24 and 98% of marine eukaryotic species are yet to be described (Leray and Knowlton, 2016).…”

“…High-throughput sequencing allows faster and more accurate species identification and decreases dependence on morphological taxonomic expertise (Bourlat et al, 2013;Aylagas et al, 2014). Advantages extend to taxa traditionally monitored in marine assessment programs, such as invertebrates and fish, investigated either as individuals or assemblages (Ardura et al, 2013;Bourlat et al, 2013;Carugati et al, 2015;Harada et al, 2015;Tan et al, 2015;Zimmermann et al, 2015;Aylagas et al, 2016;Borja et al, 2016;Caruso et al, 2016;Danovaro et al, 2016;Lewis et al, 2016;Thompson et al, 2016).…”

“…For example, molecular approaches were found to be more time-efficient compared to visual census (Yamamoto et al, 2017) and were successfully used to identify nonindigenous species in marine waters and to retrieve taxa from benthic samples that were not identified by morphological analysis (Zaiko et al, 2015;Aylagas et al, 2016). Progress moving molecular assessments into formal monitoring is being made as evidenced by adaptation of the AZTI Marine Biotic Index (AMBI), determined by traditional manual sorting and visual identification of benthic macroinvertebrates, to an index based on genetics (gAMBI) (Aylagas et al, 2014(Aylagas et al, , 2016. Success with this approach was extended to bacterial assemblages (Aylagas et al, 2017).…”

“…Studies demonstrate DNA metabarcoding to be a reliable method for biodiversity assessment with potential for inferring biotic indices for marine ecosystem quality assessment (Aylagas et al, 2014;Pawlowski et al, 2014;Cowart et al, 2015;Elbrecht and Leese, 2015;Visco et al, 2015;Ferrera et al, 2016). Comparable results between molecular and traditional approaches are reported in a number of studies (Hirai et al, 2015a;Lejzerowicz et al, 2015;Aylagas et al, 2016Aylagas et al, , 2017Valentini et al, 2016), suggesting that assessment programs that require manually intensive sorting and visual inspection will be among the first to formally integrate molecular techniques.…”