Implementing and Innovating Marine Monitoring Approaches for Assessing Marine Environmental Status

Abstract

Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labor intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine monitoring and design monitoring networks. This can be achieved by developing and testing innovative and cost-effective monitoring systems, as well as indicators of environmental status. Here, we present several recently developed methodologies and technologies to improve marine biodiversity indicators and monitoring methods. The innovative tools are discussed concerning the technologies presently utilized as well as the advantages and disadvantages of their use in routine monitoring. In particular, the present analysis focuses on: (i) molecular approaches, including microarray, Real Time quantitative PCR (qPCR), and metagenetic (metabarcoding) tools; (ii) optical (remote) sensing and acoustic methods; and (iii) in situ monitoring instruments. We also discuss Danovaro et al. Innovative Approaches in Marine Monitoring their applications in marine monitoring within the MSFD through the analysis of case studies in order to evaluate their potential utilization in future routine marine monitoring. We show that these recently-developed technologies can present clear advantages in accuracy, efficiency and cost.

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

“…This technique, albeit still subject to some limitations, will likely become a cornerstone in decision making of management bodies in the near future (Kelly et al, 2014a;Danovaro et al, 2016). In the marine realm, eukaryotic diversity has been analysed using metabarcoding in plankton and sediment communities (reviewed in Carugati et al, 2015;Bucklin et al, 2016;Sinniger et al, 2016).…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…Examples include the United Nations Convention on the Law of the Sea, Australia's Oceans Policy, the Canada Oceans Act and Oceans Strategy, the United States Oceans Act of 2000 and National Ocean Policy Implementation Plan, the European Union Marine Strategy Framework Directive (MSFD), and the South African National Water Act. A main objective of such policies is maintenance of good ecological status (GES) in marine waters, habitats, and resources using integrated or "holistic" approaches (Borja et al, 2008Karsenti et al, 2011;Duffy et al, 2013;Danovaro et al, 2016). For example, an Ecosystem-Based Management (EBM) approach to marine resources considers a suite of natural physical, chemical, biological, geographic, and climatic factors in context of anthropogenic activities and impacts.…”

“…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). Information about higher trophic levels also can be gleaned from DNA extracted from filtered seawater via capture of sloughed or excreted cells, rather than direct extraction from tissue (Foote et al, 2012;Kelly et al, 2014;Kelly, 2016).…”

“…Work initiated in the area of standardizing laboratory procedures includes much-needed development of reference materials and improved DNA extraction methods, as exemplified by establishment of the International Metagenomics and Microbiome Standards Alliance (IMMSA) (NIST, 2016). Controls used to assess artifacts and bias introduced by sample preparation, PCR, and sequencing are reviewed elsewhere (Pinto and Raskin, 2012;Elbrecht and Leese, 2015;Pedersen et al, 2015;Tan et al, 2015;Zhou et al, 2015;Aylagas et al, 2016;Danovaro et al, 2016) and should be used in conjunction with standard quality control pipelines for sequence quality, including chimeric removal (Smyth et al, 2010;Teeling and Glöckner, 2012;Zhou et al, 2014;Escobar-Zepeda et al, 2015;Jeon et al, 2015). Including mock communities in DNA sequencing efforts can assess technical issues such as incomplete DNA extraction or library preparation, PCR, and sequencing errors (Schirmer et al, 2015) and provide correction factors (Tan et al, 2015;Aylagas et al, 2016).…”