Alexandra Campbell

Seaweeds (marine macroalgae) are crucial to the functioning of healthy coastal ecosystems and global biogeochemical cycles, and sometimes provide novel solutions to help mitigate climate change. The red seaweed Asparagopsis taxiformis (Bonnemaisoniaceae, Rhodophyta) produces bioactive natural products that, when fed to cattle and sheep, can eradicate methane emissions from these livestock. However, in order to cultivate enough A. taxiformis to have a meaningful impact on global greenhouse gas emissions, we need to improve our understanding of the biology of this new crop. In this study, we used a domesticated diploid sporophyte (> 1.5 years in culture, with relatively low microbial diversity) to establish a high-quality draft nuclear genome for A. taxiformis from Queensland, Australia. The A. taxiformis lineage was confirmed as Lineage 6 (L6) based upon phylogenetic analysis (Cox2-3 spacer). The genome of A. taxiformis (L6) was 142 Mb in size with approximately 11,000 protein-coding genes, including those associated with secondary metabolism, photosynthesis and defence, and the assembly contained 70.67% repeat regions. Based on protein domain analysis, the most prominent lineage-specific duplications belonged to those containing WD repeat proteins, as well as bestrophin and N6_N4_Mtase domain proteins. Cultured (domesticated) A. taxiformis (L6) sporophytes contained 4-times more bromoform (the key anti-methanogenic natural product) compared to wild sporophytes. To obtain information regarding associated molecular differences, the genome was used as a reference to explore differential gene expression related to environment. Cultured sporophytes demonstrated an enrichment of regulatory factors (kinases, transcription factors), whereas wild sporophytes were enriched with defence and stress-related genes, including those involved in protein folding (heat shock proteins) and halogenated metabolite production. Wild sporophytes also expressed a relatively high level of novel secreted proteins, with similarity to collagen-alpha proteins (termed rhodophyte collagen-alpha-like proteins, RCAPs). Proteomic investigation of the genome of cultured sporophytes, resulting in the identification of over 400 proteins, including RCAPs, as well as numerous enzymes and phycobiliproteins, which will facilitate future functional characterisation. In summary, as the most comprehensive genomic resource for any Asparagopsis species, this resource provides a gateway for seaweed researchers to fast-track the development and production of Asparagopsis to meet demand by agriculture and do so with economic and environmental agility.

Zeta diversity provides the average number of shared species across n sites (or shared operational taxonomic units (OTUs) across n cases). It quantifies the variation in species composition of multiple assemblages in space and time to capture the contribution of the full suite of narrow, intermediate and wide-ranging species to biotic heterogeneity. Zeta diversity was proposed for measuring compositional turnover in plant and animal assemblages, but is equally relevant for application to any biological system that can be characterised by a row by column incidence matrix. Here we illustrate the application of zeta diversity to explore compositional change in empirical data, and how observed patterns may be interpreted. We use 10 datasets from a broad range of scales and levels of biological organisation, from DNA molecules to microbes, plants and birds, including one of the original data sets used by R.H. Whittaker in the 1960s to express compositional change and distance decay using beta diversity. The applications show (i) how different sampling schemes used during the calculation of zeta diversity may be appropriate for different data types and ecological questions, (ii) how higher orders of zeta may in some cases better detect shifts, transitions or periodicity, and importantly (iii) the relative roles of rare versus common species in driving patterns of compositional change. By exploring the application of zeta diversity across this broad range of contexts, our goal is to demonstrate its value as a tool for understanding continuous biodiversity turnover and as a metric for filling the empirical gap that exists on spatial or temporal change in compositional diversity.