Genomics in marine monitoring: New opportunities for assessing marine health status

Abstract

This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

“…Bourlat et al 2013;Darling and Mahon 2011;Geller et al 2010;Karp et al 1997). In the marine environment, molecular methods can reveal patterns of We investigated the changes in the planktonic microbiome diversity of a lagoon habitat probably driven by the invasion and proliferation of a nonindigenous jellyfish (Aurelia sp.).…”

“…As defined by Thomas et al (2012), metagenomics represent the direct genetic analysis of genomes contained in an environmental sample, without isolation or culture of individual organisms. The metagenomic approach is experiencing an explosive improvement since the advent of high-throughput Next-Generation Sequencing (NGS) technologies, which allow an unprecedented largescale identification of organisms and communities S. Scorrano Dipartimento di Scienze Ecologiche e Biologiche (DEB), Università della Tuscia, Largo dell' Università, 01100 Viterbo, Italy L. Stabili Istituto per l'Ambiente Marino Costiero (IAMC), CNR, Via Roma 3, 74100 Taranto, Italy through the production of an enormous amount of genetic data (Bourlat et al 2013). Either of two experimental strategies can be applied starting from the total extracted DNA: (1) the entire metagenome is sequenced by a shotgun approach, or (2) gene markers specific for a given taxon are selectively sequenced after their amplification by PCR primer pairs able to function over a broad taxonomic range (ampliconbased approach).…”

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

“…These constraints have limited our ability to investigate patterns of diversity beyond a few indicator groups (4), most often conspicuous macroinvertebrates and fish. For this reason, molecular methods, particularly high-throughput sequencing (HTS) approaches, hold considerable promise not only for fundamental understanding of diversity but also for biodiversity monitoring in the context of global change (5).…”

Perspectives on a Global Observing System to Assess Ocean Health

“…That similarly powerful integrated platforms to assess ocean health are yet to be developed should not be considered acceptable. A global system to observe ocean health should involve ambitious targets to guide the development of revolutionary technologies including observing eEOV's from space and autonomous marine vehicles such as sea gliders, ocean robots or sensors mounted on marine organisms (Figure 1) loaded with miniaturized technologies to assess marine life, such as those emerging from the use of environmental DNA (Bourlat et al, 2013), combined with forthcoming in situ sequencing technologies and molecular chips for high-throughput screening of microbial activities (Tu et al, 2014), as a remote sensing tool (Bohmann et al, 2014;Valentini et al, 2016). Yet, a system that measures everything will not be either feasible nor useful.…”