Advances in seagrass’ omics research

Abstract

Seagrasses are submerged marine macrophytes, they form highly productive ecosystems that play a critical role in climate change mitigation. Seagrass meadows are known to stabilise coastal sediments, recycle nutrients, and provide nursery grounds and food sources for fishes and megafauna. However, nearly 30% of seagrass habitats have been lost worldwide because of global climate change and sustained negative pressure from coastal developments, as well as eutrophication and dredging. This global decline and ongoing threat from climate change have weakened their capacity to support coastal productivity. This alarming decline highlights a global urgency for the implementation of effective seagrass management strategies to prevent their decline. Until now, the physiological indicators used to monitor seagrass health, including seagrass species composition, above ground biomass, and spatial coverage, have failed to provide any insights into the intensity of environmental stress at the physiological and/or molecular level, which has led to their decline. Therefore, seagrass restoration efforts require highly accurate and novel tools for monitoring seagrass health and effective management strategies. In the era of systems biology, omics (transcriptomics, proteomics, and metabolomics) and their integration have shown promise in the identification of biomarkers of phenotypic plasticity of an organism under specific environmental conditions. Recently, with the influx of genomic information regarding seagrasses, omics have emerged as a new frontier in seagrass research and have deepened our understanding of their adaptation and underlying tolerance mechanisms to environmental stresses. This review article provides a state-of-art on seagrass’ omics and discusses their potential to discover stress biomarkers, and thereby aid in developing robust diagnostic tools for monitoring seagrass’ health and their management for protection and conservation. We discuss how omics platforms are advancing in technology, such as whole-genome shotgun, RNA-seq, 2-DE, and multidimensional GC- and MS-based platforms, which helps in developing high-throughput protocols for possible implementation in seagrass research. This article further discusses how such innovations can provide knowledge on: (1) Molecular adaptation and acclimatisation mechanisms in seagrass responses to light, salinity, thermal, carbon dioxide, eutrophication, and heavy metal concentration, (2) their genetic diversity and evolution, and (3) seagrass reproduction and development. Moreover, we discuss the organelle, such as the chloroplast, based omics frontier to explore its potential in seagrass research to better understand the biological processes at the organelle level and how it may help determine the role of different organelles in providing tolerance against various environmental stresses. Lastly, we discuss the do’s and don’ts of the experimental designs, methodological procedures, and analytical tools learned from higher plant studies to facilitate multi-omics studies and data integration in seagrass research. Creating an online user friendly database sourced from multi-omics studies and a suite of tools for analysis will attract seagrass molecular biologists and ecologists working on seagrass ecology, restoration, development, and evolution, and will improve the molecular horizons of seagrass research.