Grants

Research and restoration of giant kelp at Catalina Island

Builders Vision Walten Foundation – $600K | June 2023 – June 2026

PI: Sergey Nuzhdin; co-PI: Matt Edwards (SDSU)
The near-shore ecosystems of Catalina Island have been dominated by forests of giant kelp that provide home to fishes, invertebrates, marine mammals, and seabirds, and that support fishing, diving and tourism. Ocean warming has led to the loss of these iconic kelp forests and a rise in invasive Sargassum pastures, reducing biodiversity and ecosystem services. Our innovation will include reliance on macroalgal seed bank to develop and store strains required for success of kelp restoration in warming ocean. This work will compare the efficacy of using green gravel versus spore bags for scalable restoration of kelp in sargassum pastures within low wave action areas. Finally, we will control for kelp-associated microbiome, making sure it aids to kelp recruitment and growth.

Establishing healthy coastal ecosystems via captive breeding of sunflower sea stars

USC Sustainability – $32K | August 2023 – August 2024

PI: Andrew Gracey (USC); co-PI: Sergey Nuzhdin
Sunflower sea stars are the main predator of purple sea urchins. Sea star wasting disease which first appeared in 2013 has decimated populations of this sea star along the West Coast. As a result of their decline, numbers of purple urchins have rocketed, and these voracious herbivores have consumed vast swaths of kelp forest leading to ‘urchin-barrens’. One solution to this problem is to captive-rear sunflower sea stars for reintroduction to sites that used to host kelp. Through this grant, we aim to expand captive-rearing efforts through a partnership with an aquaculture practitioner, and engaging visitors of the Carlsbad Aquafarm farm tour on the role that aquaculture can play in environmental restoration.

America’s first boats: Securing knowledge of the Kelp Highway and California’s enduring, sustainable Indigenous maritime traditions

Library of Congress – $50K | January 2023 – December 2024

PI: Lynn Dodd (USC); co-PIs: Terry Tamminen (AltaSea), Amy Gusick (NHMLA), Sergey Nuzhdin
This project is led by Los Angeles Indigenous community members whose maritime coastal lifeways depended on human powered vessels, ti’ats (tee-ahtz), which people paddled while settling the Pacific coastline. This boat–making tradition thrived for millennia and then was suppressed until the last decade of the 20th century when an Indigenous group, The Ti’at Society, revived hand-crafted, sewn plank canoe-making. That pivotal cultural moment contributes to healing and growing culture confidence while building wider awareness of their lifeway focused on sustainable foods from coastal kelp forests. This project will build internal community capacity and pride by developing skills that support community creation of future archives. This foundational archival work secures a suppressed tradition that supported thriving communities, preserves a transformative moment in California history within our national institutions of memory, and cultivates intergenerational knowledge transfer about boatmaking as a central feature of past — and future — healthy, local food-gathering lifeways. [Source/More Info]

Developing sporeless (infertile) breeds of domesticated kelp species to reduce regulatory barriers for expanded kelp farming

Sea Grant – $750K | August 2022 – July 2025

PI: Sergey Nuzhdin; co-PI: Scott Lindell (WHOI)
Global seaweed aquaculture production is over 33 million metric tons (FW) with an annual value of ~$13 billion in 2018 (FAO 2020). Over 99 of the production is farmed in Asia. Of the varieties of macroalgae, kelp grows the fastest and largest (Krumhansl et al. 2016; Wernberg et al. 2018). Some kelps have well-established health benefits with the potential to become a competitive food, pharmaceutical, and biofuel crops (Hafting et al. 2015; Kim and Bhatnagar, 2011; Wells et al., 2017; Jahan et al. 2017). The goal of this project is to establish breeding practices that enable genetically improved (non-GMO) and infertile kelps to be adopted by farmers because they satisfy regulatory concerns about possible genetic changes of wild kelp. The life cycle of kelp has distinct, free-living haploid and diploid stages. The diploid sporophyte (SP) generation is the harvested crop (large blades), while the microscopic haploid gametophyte (GP) generation can be vegetatively propagated indefinitely and bulked up in culture. The kelp haplo-diplontic reproductive cycle is remarkably well suited to (i) intense and efficient genome-based breeding improvement and (ii) F1-based cultivation of infertile (“sporeless”) SPs. Kelp uni-clonal GPs can be efficiently propagated vegetatively en mass and induced to fuse as desired, resulting in juvenile SPs or “seed”. In the near future, the germplasm banks of GPs from this and other projects will be available to kelp nurseries/”seed companies” who will hold bulk GPs, and sell farmers F1 sporeless hybrid juvenile SPs. Note, none of these kelp species reproduce vegetatively as SPs. Taking advantage of haploid-phase GP breeding has the potential to dramatically accelerate multi-trait breeding domestication of infertile strains. This will enable environmentally responsible kelp farming, and establish businesses with improved kelp seed and farmed products. [Source/More Info]

Developing the native CA mussel (Mytilus californianus) as a new CA aquaculture product

Saltonstall-Kennedy – $300K | November 2022 – October 2024

PI: Nathan Churches (HFA); co-PIs: Diane Kim (USC/HFA), Sergey Nuzhdin
Our project seeks to develop a new sustainable seafood variety, the California Mussel (CM; Mytilus californianus), via fully life-cycle controlled aquaculture for US markets. Several questions and data gaps had prevented businesses from investing into a commercial scale effort with this species, centered around the amenability of CM to hatchery based longline production. We demonstrated that the CM will spawn en masse, will settle onto longlines in the hatchery, and will respond to re-socking. Related scientific work also demonstrated that the mutation rates in bivalves may considerably alter approaches for selective breeding in CM and other commercial species. This proposal, therefore, is primarily concerned with researching a full manufacturing pipeline for CM grow-out at commercial scales (several tons), and implementing synergistic outreach and scientific agendas.

Genomics breeding of giant kelp for growth, protein and sugar composition

ARPA-E Plus Up – $1.1M | May 2022 – April 2024

PI: Filipe Alberto (UWM); co-PIs: Dan Reed (UCSB), Bob Miller (UCSB), Sergey Nuzhdin
The University of Wisconsin-Milwaukee (UWM) will lead a MARINER Category 5 project to develop a breeding program and enable the development of macroalgae varieties that consistently produce high yields under farmed conditions. Controlled genetic improvements through crop breeding require establishing a bank of genetically homogeneous lines that are examined for markers and traits important for domestication and production. The researchers will sample giant sea kelp from the Southern California Bight, an area of high genetic diversity. The team will assess phenotypic performance of these samples at a real-world farm location at Catalina Island, which has oceanographic conditions that resemble the warm, offshore waters suitable for macroalgae farming. Traits such as survival, growth rate, temperature tolerance and photosynthetic efficiency will be measured at different stages. The team will establish genomic resources for giant kelp and utilize them in conjunction with the field performance observed to predict the best performing varieties from approximately 50,000 possible crosses. If successful, these germplasm lines will constitute a “seed stock” similar to that established for agricultural crops that can be used by breeders to stage model-based, efficient, cost-effective, and environmentally sound targeted genome-based selection. [Source/More Info]

USC – AltaSea – Industry partnership to sustainably farm our oceans

Strategic Provost Initiatives – $260K| January 2022 – September 2023

PI: Sergey Nuzhdin; co-PIs: Aroussiak Gabrielian (USC), Pat Lynnet (USC), Gale Sinatra (USC)

Aquaculture as a food sector has dramatically increased in recent decades with a global seaweed aquaculture market rapidly expanding in parallel. A recent shift towards aquaculture intensification can be largely attributed to historically deleterious farming methods that have left vast terrestrial ecosystems polluted and depleted of their once abundant natural diversity. This dramatic shift necessitates a prompt response from researchers, industry, and stakeholder groups to address and synthesize innovative pathways forward to expand aquaculture efforts to meet market demand while also reducing the industry’s environmental footprint. Despite seaweed aquaculture’s rise in popularity and potential to become a disruptive food and pharmaceutical crop, there are inherent regulatory and biological hurtles that foremost need to be overcome. The 2020 USC State of the University Address has highlighted the vital importance and utility of building-out the blue-green economy through major scientific innovations. To address this need, we at USC have built a team of uniquely diverse, and dedicated biologists, economists, political scientists, architects, educators and engineers who have come together to create this proposal with the goal of addressing critical issues and proposing new conduits towards transformative, environmentally friendly commercial aquaculture systems. We propose to address the inherent challenges of establishing ocean-based seaweed aquaculture through a comprehensive analysis of four sectors-economy, design, policy, technology/biology. The research aim in this proposal will look towards constructing narrative frameworks that identify key concepts, needs, and ecosystem service benefits of synergistic aquaculture techniques and drivers of the Blue-Green Economy. The systematic reviews described in this study will position USC, along with our collaborators, as a central hub for sustainable aquaculture systems design through multidimensional research while also competitively positioning our team for future research opportunities.

Research and Extension Experiences for Undergraduates: year-round aquaculture training and R&D engagement in professional setting

USDA REEU – $500K | August 2021 – July 2026

PI: Andrew Gracey (USC); co-PIs: Scott Applebaum (USC), Meredith Brooks (AltaSea), Sergey Nuzhdin

A Blue Economy offers potential to more sustainably produce biofuel, meet growing human population demands for animal proteins, and generate alternative livestock feeds from the ocean, while reducing fertilizers use and CO2 emission. Attaining these objectives necessitates recruitment and training of an expanded workforce of research and development, (R&D) professionals and aquaculture practitioners to bring about a ‘blue revolution’ that includes domesticating marine organisms and optimized ocean farming practices. In collaboration with Alta Sea Blue Economy Incubator, the University of Southern California is offering a training program in the science and practice of aquaculture and blue economy. [Source/More Info]

MCA: Genomic diversification and speciation along ecological gradients in a marine fish radiation

NSF – $500K | September 2021 – August 2024

PI: Andres Aguilar (CSULA); Mentor of a mid-career researcher: Sergey Nuzhdin

This research program will determine the genomic basis of divergence among closely related species and populations along latitudinal and depth gradients to determine the role of adaptation in the speciation process. Rockfish (Sebastes) are an ideal system to examine these questions as they are a diverse group of temperate fishes inhabiting a wide array of habitats, and they have been subject to numerous phylogenetic studies. This project will utilize genome scans and de novo genome assemblies to test for speciation histories of rockfish associated with divergence along ecological (depth) or geographic (latitude) gradients. These findings can be used to better understand the role of natural selection on the genome and how this contributes to the diversification of this group. Training opportunities will be provided to undergraduate and graduate students at Cal State LA, and data from this project will also serve as a resource for the management of rockfish, many of which are commercially important. [Source/More Info]

Developing non-reproductive kelp via a unique bioinformatic pipeline framework and genomic breeding

NOAA-MOF JOINT PROJECT – $100K | January 2021 – December 2026

PI: Sergey Nuzhdin; co-PI: Young Dae Kim 
Seaweed aquaculture is a 10 billion USD global industry, with Korea leading global production at approximately 5.8% (FAO 2018). Groundbreaking research in Korea and the U.S. has illuminated the great potential for further growth using available genomic aquaculture techniques (Hwang et al., 2011; Kim et al. 2017; Grandview Market Research 2016). The high market potential for wakame (Undaria pinnatifida) and the species, Saccharina as one of the most broadly consumed species of seaweed provides impetus to develop non-reproductive commercial strains. The utility of reproductively sterile strains includes increased cultivation efforts for a growing global market demand without compromising environmental protection from the species’ invasive nature (Yamanka et al., 1993). Our proposal seeks to utilize an extant bioinformatics pipeline that can be applied to screen for desirable traits in Undaria and Saccharina, specifically targeting reproductive sterility.  Our team will utilize data accessions of sequenced kelp strains from researchers at NIFS and Incheon International University to feed into an established in-house bioinformatics pipeline at USC that will allow researchers to discern functional knockout mutations with potential to sterilize strains for future commercial out-cropping. This collaboration will develop a channel to exchange cultivation resources (e.g., immortalized sterile seed stock) and cross-pollinate strategies to strengthen the seaweed industry in both countries. USC collaborators will also include a biodiversity assessment of California strains of each species. The trajectory of this research will culminate in the ability for aquaculture producers to completely sterilize sporophytes using naturally occurring alleles for the purpose of responsible commercial-scale aquaculture of kelp.