Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement

Abstract

Omics" techniques (including genomics, transcriptomics, metabolomics, proteomics, and metagenomics) have been employed with huge success in the improvement of agricultural crops. As marine aquaculture of macroalgae expands globally, biologists are working to domesticate species of macroalgae by applying these techniques tested in agriculture to wild macroalgae species. Metabolomics has revealed metabolites and pathways that influence agriculturally relevant traits in crops, allowing for informed crop crossing schemes and genomic improvement strategies that would be pivotal to inform selection on macroalgae for domestication. Advances in metagenomics have improved understanding of host-symbiont interactions and the potential for microbial organisms to improve crop outcomes. There is much room in the field of macroalgal biology for further research toward improvement of macroalgae cultivars in aquaculture using metabolomic and metagenomic analyses.To this end, this review discusses the application and necessary expansion of the omics tool kit for macroalgae domestication as we move to enhance seaweed farming worldwide.Kelly J. DeWeese and Melisa G. Osborne contributed equally to this work.

Natural variation of Macrocystis pyrifera gametophyte germplasm culture microbiomes and applications for improving yield in offshore farms

“…Although there is a wealth of research on the exploitation of host–microbe associations to improve plant fitness, most work has focused on land plants and agricultural crops. Building off the knowledge that host–microbe associations in aquatic plants, such as seaweeds, similarly impact fitness, there is an exciting opportunity to extend existing research into seaweed aquaculture (Osborne & DeWeese, 2021).…”

“…Overall, this work provides a valuable knowledge base for host–microbe associations in seaweed aquaculture and the development of early‐stage microbial inoculants that produce high‐biomass M. pyrifera cultivars to ultimately be used as biofuel feedstocks. As the industry moves toward large‐scale production, this work will complement other tools being developed to improve seaweed farming techniques and revolutionize the production of seaweed‐based biofuels (Gao et al, 2020; Leyton et al, 2020; Navarrete et al, 2021; Osborne & DeWeese, 2021; Purcell‐Meyerink et al, 2021).…”

The next era of crop domestication starts now

“…Domestication of new plant species in the twenty-first century has been initiated despite resource constraints, and these efforts span plant families and types: bioenergy crops ( 150 ), cacti ( 151 ), ferns ( 152 ), halophytes ( 153 – 160 ), tree fruits and nuts ( 161 , 162 ), macroalgae ( 163 – 166 ), marine grasses ( 141 , 167 ), microalgae ( 168 ), palms ( 169 , 170 ), perennial grasses ( 171 – 173 ), perennial groundcovers ( 174 ), perennial oilseeds ( 90 , 175 , 176 ), and perennial tree and grain legumes ( 177 – 179 ).…”

Host genotype and microbiome associations in co‐occurring clonal and non‐clonal kelp, Ecklonia radiata

“…Recent research has provided strong evidence for the importance of the relationships between host organisms and their associated microbiota in forming functional ecological units or ‘holobionts’ (Dittami et al, 2021). Holobionts are composed of multiple microbial communities that interact with the host and can determine and regulate multiple processes that support the host's performance, development, survival, and resilience to changing environments and different stressors (Egan et al, 2013; DeWeese & Osborne, 2021). Holobionts have been studied in multiple models from single‐cell interactions (Sallinger et al, 2021) to larger and more complex systems that include invertebrates, vertebrates and plants (Rosenberg & Zilber‐Rosenberg, 2014).…”