Brown Macroalgal Research

 

Current Research Areas

Branching patterns in brown macroalgae. Branching patterns are a major contributor to organismal form.  Most orders of brown algae exhibit planar branching, producing relatively ‘flat’ organisms. Only one family – the Sargasseaceae (order Fucales) – exhibits radial branching leading to fuller, bushier organisms. But exactly how prevalent is radial branching in the Sargasseaceae? When did it evolve? And how is it patterned and executed? Here are some of the things we are up to!

      • Mapping branching patterns in extant Sargasseaceae species from around the world using living and herbarium specimens. *Siobhan in collaboration with Dr. Kathy Ann Miller (University Herbarium, Berkeley).
      • Exploring when branching patterns may have evolved and what they looked like using existing and new fossil evidence. *Dean Lewis (UG) & Siobhan with collaborators Dr. Austin Hendy (LA NHM), the Raymond M. Alf Museum of Paleonotology, and Diane Erwin (UCMP).
      • Working to build a strong phylogeny for the Sargasseaceae, including many Californian species for the first time, by using RNAseq and de novo transcriptome assembly to identify ~50 markers. *Naomi Barber-Choi (UG), Siobhan, Kate Alley (MS), and in collaboration with Dr. Filipe Zapata (UCLA EEB).
      • Adding to existing morphological keys for native Californian Sargasseaceae species (Sargassum and Steohanocystis). *Savvanah Ruiz (UG) and Siobhan.
      • Investigating the cell & molecular biology underlying branch patterning at apical tips using histology, microscopy, and laser-capture-microdissection + RNAseq. *Siobhan with amazing help from Lauren Dedow.
      • Building computational models for planar and radial branching patterning in Fucales. *Jessica Echarte (UG), Sreeja Polkampally (UG), and Siobhan.

Embryo patterning & growth in brown macroalgae. Like many other sexually reproducing eukaryotes, brown algal embryos have internal patterning mechanisms. However, their growth and development happen outside of a parent body in close interaction with the environment. How is polarity established in embryos? When/how do they differentiate tissues and cell types? What programs are shared between species and when/how do their morphologies begin to diverge? Just how responsive are these programs to changes in the environment? And what does the cell wall have to do with it? Here are some of the things we are up to!

        • Exploring how embryos grow and develop in the Fucales using histology, microscopy, and transcriptomics; investigating the role of the cell wall in regulating cell elongation in embyros. *Kate Alley (MS)
        • Comparing embryo development and patterning between California kelps using histology, microscopy, and transcriptomic. *Siobhan with help from Leo Wall (UG)

The brown algal cell wall and the microbiome.  The cell wall is the organism’s major interface with the external biotic and abiotic environment. It plays host to microbes, providing food (carbon) to some while inhibiting others. How do microbes interact with the brown algal cell wall? What is the nature of the various host-microbe interactions & how might they impact development? What role do cell wall polysaccharides & microbes play in carbon sequestration and cycling? Here are some of the things we are up to!

        • Characterizing the cell wall composition of Californian brown algae using biochemical extraction, antibody reactivity, biochemical tests, and structural analyses. *Jess Carstens-Kass (PhD), Kieran Johnson (UG), Pepper Diaz (UG), with funding from the Phycological Society of America.
        • Characterizing the brown algal microbiome in Californian species using 16S and metagenomic sequencing. *Jess Carstens-Kass (PhD) with collaborator Dr. Sean Cokus (UCLA Collaboratory) and funding from the UCLA Goodman Luskin Microbiome Center.
        • Exploring how bacterial isolates interact with brown algal cell wall polysaccharides using culture methods, metagenomics, and transcriptomic. *Jess Carstens-Kass (PhD) with collaborator Dr. Sean Cokus (UCLA Collaboratory)
        • Investigating possible roles for algal microbes in development using culture expertiments, microscopy, and metagenomic sequencing.

The brown algal cell wall and heavy metals. The brown algal cell wall is rich with negatively charged groups, primed to interact with cations from the environment. Some of these cations, like Ca2+, are integral for cell wall mechanics & algal growth and development. But other cations, like heavy metals, may also accumulate in cell walls. Do algal cell walls help confer heavy metal tolerance? Are there patterns in heavy metal accumulation during the organism’s life? In its body? How do heavy metals alter cell wall mechanics and thus growth/development? Could brown algae be bioremediators? And how could understanding heavy metal accumulation influence industry and policy? Here are some of the things we are up to!

Investigating how heavy metals accumulate in giant kelp (M. pyrifera) using biochemical methods and spectroscopy on wild harvested kelp and in culture experiments; including after recent wildfires. *Hugh Knopp (PhD) with collaborators in the Moment Lab @ UCLA  and the Cavanaugh Lab @ UCLA.

Exploring how heavy metal exposure impacts the growth & development of microscopic giant kelp life stages using culture experiments, microscopy, and transcriptomic. *Hugh Knopp (PhD)

Examining how heavy metals change cell wall mechanics in living algae and cell wall material mimics. *Siobhan and Hugh Knopp (PhD)

Thermotolerance and growth in California kelps. As our environment changes over time, changes in ocean temperature may occur faster than organisms can adapt. Understanding how temperature impacts the microscopic stages of kelp is essential to ensure a resilient ocean future. How does thermo-susceptibility affect the growth and development of kelp? What is the thermotolerance range of microscopic kelp life stages? Is thermotolerance underlain by genetic variance?  And what molecular mechanisms might underlie tolerance?  *Lauren Dedow, Kaitlyn Kim (UG), Abby Krause (UG), Mia Bramante (UG), in collaboration with The Smith Lab at UCSD/SIO and the Michael Lab at UCSD/Salk.

      • Exploring how the microscopic life stages of giant kelp respond to temperature using culture experiments, microscopy, and transcriptomics.
      • Exploring how the microscopic life stages of 5 other Californian kelps respond to temperature using culture experiments, microscopy, and transcriptomics.

Methods & tool development for brown macroalgae. Brown macroalgae are tough, and they don’t make molecular biology easy – but we think they are worth careful, patient, persistent effort. Together with a small-but-mighty research community we are optimizing, adapting, and developing methods and tools needed for modern molecular biology in brown algae. Examples in our lab include: quality, purpose-driven, nucleic acid extraction methods; advanced imaging methods with confocal & AFM; RNAseq for de novo transcriptome assembly & gene expression analyses; laser capture microdissection; and RNAi and CRISPR-gene editing.