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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 761 publications in this collection, published between 2001 and 2023.
Capstone Projects (285)

On Climate Variability and Reproductive Success of a Central Pacific Albatross

Breeding colonies of Mōlī (Phoebastria immutabilis) have shown reproductive declines in association with oceanographic and environmental variables such as the El Niño Southern Oscillation and North Pacific Gyre Oscillation. Reproductive responses to environmental extremes such as those associated with short-term climate events may provide clues to how the species will respond to long-term changes in global climate. This study examines reproductive success of Mōlī on Sand Island, Pihemanu, the largest breeding colony in the world, and finds that different colonies may respond differently to oceanographic variables such as the North Pacific Gyre Oscillation. Further study of the North Pacific Gyre Oscillation and its role in the position of the Transition Zone Chlorophyll front are necessary to more fully understand the dynamics of reproductive success throughout breeding colonies on islands in the subtropics.

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.

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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 (464)

An assessment of actinobacterial diversity in the marine environment

The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using culture-independent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.

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.

Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity

Death due to sepsis remains a persistent threat to critically ill patients confined to the intensive care unit and is characterized by colonization with multi-drug-resistant healthcare-associated pathogens. Here we report that sepsis in mice caused by a defined four-member pathogen community isolated from a patient with lethal sepsis is associated with the systemic suppression of key elements of the host transcriptome required for pathogen clearance and decreased butyrate expression. More specifically, these pathogens directly suppress interferon regulatory factor 3. Fecal microbiota transplant (FMT) reverses the course of otherwise lethal sepsis by enhancing pathogen clearance via the restoration of host immunity in an interferon regulatory factor 3-dependent manner. This protective effect is linked to the expansion of butyrate-producing Bacteroidetes. Taken together these results suggest that fecal microbiota transplantation may be a treatment option in sepsis associated with immunosuppression.

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