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Open Access Publications from the University of California


To meet the challenges of marine conservation, the Center for Marine Biodiversity and Conservation (CMBC) was established at the Scripps Institution of Oceanography (SIO) in May 2001. Its goals are:

- Investigation: Assess the state of marine ecosystems now and in the past and develop predictive models for the future
- Education: Train new marine biodiversity and conservation scientists in the United States and around the world
- Integration: Develop novel interdisciplinary approaches linking the biological, physical, social and informatic sciences
- Communication: Increase public understanding of scientific issues and provide sound scientific analyses to policy makers
- Application: Design technically sophisticated, regionally appropriate strategies to prevent and reverse biodiversity collapse

Dr. Lisa Levin, Director

Center for Marine Biodiversity and Conservation

There are 461 publications in this collection, published between 2001 and 2022.
Capstone Projects (245)

The Issues of Solid Waste Management on Small Islands: Malapascua Island Philippines as a Case Study

The issues, that small islands face, regarding the disposal and management of their solid waste are serious. Although not all small islands face the same problems, it is worth looking at one island in particular as a case study to get a better understanding of some of these issues. Malapascua Island in the Philippines, a small island, has over a very short time gone through a period of rapid development due to tourism. Malapascua Island’s solid waste disposal

infrastructure has not kept up with this rapid development. The management and disposal of solid waste has now become a serious issue that needs addressing. Malapascua’s current issues create a platform for the study of the causes as well as possible solutions to the issue of solid waste management. The approach taken is to describe well-developed solid waste management systems contrasted with the current problems faced on Malapascua to examine if there is any way of adapting modern systems to serve Malapascua’s current and future needs.

A Scientist’s Guide to Philanthropy: Bridging the Gap between Marine Conservation Biologists & Funding

This capstone report involves the relationship between marine conservation biologists and funding. The goal is to help scientists pitch their projects in a way that compels potential philanthropists dedicated to ocean conservation to financially contribute by investigating transferable communication tools that scientists can utilize. This has been done through conducting interviews with various marine foundations and institutions’ program departments. Upon conducting extensive research in marine fundraising, it becomes clear that there has been a shift in the philanthropic landscape that requires scientists and labs to think differently about cultivating relationships with donors. Ocean science research has been reliant upon now dwindling large scale financial support from federal agencies. This research highlights the importance of cultivating relationships with philanthropists and marine conservation foundations through new and different communication approaches.

"CONNECTIVITY": A Documentary/Series of Transmedia Research Projects

This project is a transmedia research series that is captured in the stunning format of Ultra-High Definition, or 4k. We explore how life on Planet Ocean, and specifically around the Pacific basin, is inseparably intertwined. Scripps scientists are interviewed about their respective fields of research, and weigh in on their interests, concerns, and the broader scale implications of their work in oceanography. Common anthropogenic stressors take many forms but for this documentary will include (1) Near coastal land development can increase siltation and nutrient loading, which can smother sensitive coral reefs (2) Unsustainable fishing practices are depleting fish stocks in many areas around the Pacific (3) Plastic micro-particles are accumulating in the subtropical oceanic gyres, and overall ocean health is declining (4) Changing ocean chemistry (ocean acidification) is having a direct effect on aqua farms on the Pacific Northwest Coast (5) Whales and fisheries interact, from humpbacks to false killer whales (6) Acoustic soundscapes - from deep ocean ecosystems to shallow reef environments and how sound may be affecting biodiversity (7) Human use of oil-based products is causing increasingly less subtle planetary shifts, adding toxicity to the ecosystem and fueling climate change.

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Conference Reports (4)

Conference Report: Marine Biodiversity in the Present:The Known, Unknown and Unknowable

Funded by the Alfred P. Sloan Foundation's, Known, Unknown and Unknowable project. This is the first in a series of three conferences held at Scripps Institution of Oceanography to explore the structure and knowledge of marine systems. The report describes how the conference was organized and the results of the conference.

Marine Biodiversity: Using the Past to Inform the Future

This report covers the second conference supported by the Alfred P. Sloan Foundation's Known, Unknown and Unknowable Program. The conference goal is to explore the structure and limits to knowledge of marine ecosystems and implications of the state of our knowledge to research, policy and society at large.

This conference highlighted the importance of understanding past ecosystems and how they have changed, and asked how we can make use of this historical perspective to better understand the present and to safeguard and manage to future.

The future of marine biodiversity: The Known Unknown and Unknowable

The reports on the third in a series of conferences funded by the Alfred P. Sloan Foundation's, Known, Unknown and Unknowable program. The purpose of the conference was to explore two main aspects of marine biodiversity in the near (2020) future: (a) projections on anthropogenic drivers and (b)projections on impacts on marine biodiversity.

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Information Series (4)

Snapshot Assessment Protocol (SnAP): Guidelines, Tools, and Tips for RapidlyCharacterizing Small-Scale Fisheries.

Recognizing the need for improved coordination, the Small-scale and Artisanal Fisheries Research Network (SAFRN), at the Scripps Institution of Oceanography’s Center for Marine Biodiversity and Conservation (CMBC), was established in 2010 by graduate students as an interdisciplinary hub of students, researchers, and faculty studying small-scale fisheries (SSF). Our goals are to: enhance communication and collaboration across disciplines, projects, and sectors; share research guidelines and methodologies; and connect research to meaningful management actions.SAFRN has developed the Snapshot Assessment Protocol (SnAP), an interdisciplinary, standardized toolkit for describing SSF holistically, including ecological, social, cultural, economic, and governance-related aspects of these fisheries and the related communities. SnAP is a key part of our 2011-2012 project, “Coordinating Research for Sustaining Artisanal Fisheries”, funded by the Waitt Foundation.

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Other Recent Work (198)

Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges.

Naturally produced polybrominated diphenyl ethers (PBDEs) pervade the marine environment and structurally resemble toxic man-made brominated flame retardants. PBDEs bioaccumulate in marine animals and are likely transferred to the human food chain. However, the biogenic basis for PBDE production in one of their most prolific sources, marine sponges of the order Dysideidae, remains unidentified. Here, we report the discovery of PBDE biosynthetic gene clusters within sponge-microbiome-associated cyanobacterial endosymbionts through the use of an unbiased metagenome-mining approach. Using expression of PBDE biosynthetic genes in heterologous cyanobacterial hosts, we correlate the structural diversity of naturally produced PBDEs to modifications within PBDE biosynthetic gene clusters in multiple sponge holobionts. Our results establish the genetic and molecular foundation for the production of PBDEs in one of the most abundant natural sources of these molecules, further setting the stage for a metagenomic-based inventory of other PBDE sources in the marine environment.

Ten questions concerning the microbiomes of buildings

Buildings represent habitats for microorganisms that can have direct or indirect effects on the quality of our living spaces, health, and well-being. Over the last ten years, new research has employed sophisticated tools, including DNA sequencing-based approaches, to study microbes found in buildings and the overall built environment. These investigations have catalyzed new insights into and questions about the microbes that surround us in our daily lives. The emergence of the “microbiology of the built environment” field has required bridging disciplines, including microbiology, ecology, building science, architecture, and engineering. Early insights have included a fuller characterization of sources of microbes within buildings, important processes that structure the distributions and abundances of microbes, and a greater appreciation of the role that occupants can have on indoor microbiology. This ongoing work has also demonstrated that traditional culture- and microscopy-based approaches for studying microbiology vastly underestimate the types and quantity of microbes present in environmental samples. We offer ten questions that highlight important lessons learned regarding the microbiology of buildings and suggest future areas of investigation.

Diversity, structure and convergent evolution of the global sponge microbiome.

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.

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