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Open Access Publications from the University of California

Scholarly Works (11 results)

  • Article
  • Peer Reviewed
UC San Diego Previously Published Works (2021)
Microbial taxonomic marker gene studies using 16S rRNA gene amplicon sequencing provide an understanding of microbial community structure and diversity; however, it can be difficult to infer the functionality of microbes in the ecosystem from these data. Here, we show how to predict metabolism from phylogeny using the paprica pipeline. This approach allows resolution at the strain and species level for select regions on the prokaryotic phylogenetic tree and provides an estimate of gene and metabolic pathway abundance. For complete details on the use and execution of this protocol, please refer to Erazo and Bowman (2021).
    Cover page: From microbial community structure to metabolic inference using paprica.
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2021)
    Mangrove-dominated estuaries host a diverse microbial assemblage that facilitates nutrient and carbon conversions and could play a vital role in maintaining ecosystem health. In this study, we used 16S rRNA gene analysis, metabolic inference, nutrient concentrations, and δ13C and δ15N isotopes to evaluate the impact of land use change on near-shore biogeochemical cycles and microbial community structures within mangrove-dominated estuaries. Samples in close proximity to active shrimp aquaculture were high in NH4 +, NO3 - NO2 -, and PO4 3-; lower in microbial community and metabolic diversity; and dominated by putative nitrifiers, denitrifies, and sulfur-oxidizing bacteria. Near intact mangrove forests we observed the presence of potential nitrogen fixers of the genus Calothrix and order Rhizobiales. We identified possible indicators of aquaculture effluents such as Pseudomonas balearica, Ponitmonas salivi brio , family Chromatiaceae, and genus Arcobacter. These results highlight the sensitivity of the estuarine-mangrove microbial community, and their ecosystem functions, to land use changes.
      Cover page: Sensitivity of the mangrove-estuarine microbial community to aquaculture effluent
      • Thesis
      • Peer Reviewed
      UC San Diego Electronic Theses and Dissertations (2024)

      Mangrove forests are among the most productive ecosystems globally, offering critical ecosystem services such as coastal protection, carbon sequestration, and support for mangrove-dependent fisheries. These forests host a diverse range of microorganisms that contribute to nutrient acquisition, disease resistance, and adaptation to salinity stress, yet many of these microbes remain uncharacterized. Mangrove forests are increasingly threatened by habitat loss,climate change, and pollution. The impact of these anthropogenic stressors on the microorganisms that sustain these forests, and on the local artisanal fishery communities, remains largely unknown. This research addresses the effects of land use changes, particularly nutrient pollution associated to shrimp aquaculture, on nutrient cycling, water quality, and microbial community function and structure. It also examines the variability and influence of mangrove zones and flow dynamics on microbial community structure and function in less perturbed mangrove forests. Additionally, this work investigates how salinity and pathogenic stress affect mangrove microbial communities and their functions and develops a model to explore plant-microbe interactions to understand how microbes could provide chemical protection to the plant to tolerate stress. Finally, this research focuses on developing methodologies to build just and equitable partnerships with local Afro-Ecuadorian communities to better understand the impact of pollution and threats to mangrove forests and mangrove-dependent fisheries. The findings of this work offer valuable insights for conservation efforts and provide a framework for addressing ecological challenges in vulnerable coastal regions to climate change.

        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2019)
        Marine eelgrasses are influential to their surrounding environments through their many ecosystem services, ranging from the provisioning of food and shelter for marine life to serving as a natural defense against pollution and pathogenic bacteria. In the marine waters of San Diego, CA, USA, eelgrass beds comprised of Zostera spp. are an integral part of the coastal ecosystem. To evaluate the impact of eelgrass on bacterial and archaeal community structure we collected water samples in San Diego Bay and sequenced the 16S rRNA gene from paired eelgrass-present and eelgrass-absent sites. To test the hypothesis that microbial community structure is influenced by the presence of eelgrass we applied mixed effects models to these data and to bacterial abundance data derived by flow cytometry. This approach allowed us to identify specific microbial taxa that were differentially present at eelgrass-present and eelgrass-absent sites. Principal coordinate analysis organized the samples by location (inner vs. outer bay) along the first axis, where the first two axes accounted for a 90.8% of the variance in microbial community structure among the samples. Differentially present bacterial taxa included members of the order Rickettsiales, family Flavobacteriaceae, genus Tenacibaculum and members of the order Pseudomonadales. These findings constitute a unique look into the microbial composition of San Diego Bay and examine how eelgrasses contribute to marine ecosystem health, e.g., by supporting specific microbial communities and by filtering and trapping potentially harmful bacteria to the benefit of marine organisms.
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2023)
          The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.
            Cover page: Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula.
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2024)
            Microbial ecological functions are an emergent property of community composition. For some ecological functions, this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data from two independent long-term ecological research sites-Palmer LTER in Antarctica and Station SPOT in California-we found that community composition was a strong predictor of BP. The top performing model achieved an R2 of 0.84 and RMSE of 20.2 pmol L-1 hr-1 on independent validation data, outperforming a model based solely on environmental data (R2 = 0.32, RMSE = 51.4 pmol L-1 hr-1). We then operationalized our top performing model, estimating BP for 346 Antarctic samples from 2015 to 2020 for which only community composition data were available. Our predictions resolved spatial trends in BP with significance in the Antarctic (P value = 1 × 10-4) and highlighted important taxa for BP across ocean basins. Our results demonstrate a strong link between microbial community composition and microbial ecosystem function and begin to leverage long-term datasets to construct models of BP based on microbial community composition.
              Cover page: Microbial community composition predicts bacterial production across ocean ecosystems.
              • Article
              Other Recent Work (2022)
              Island Conservation (IC) and Scripps Institution of Oceanography (SIO), UC San Diego, co-convened a meeting of practitioners and researchers to assess the Global Links for Island Marine Restoration(GLIMR). These global experts in the diverse fields of island restoration, invasive species management, and wildlife conservation, were assembled and worked for eight months to evaluate the state of the knowledge of land-sea linkages in the context of invasive species management and island restoration. The result is this white paper synthesis of the science and research recommendations and a manuscript that will be submitted to a peer-reviewed journal. The intended audiences for this endeavor include island communities, governments, conservation and sustainable development non-governmental organizations, scientists, and funders. Throughout the report, readers will find that the key takeaways, identified by the authors, are represented in blue italics. This study was made possible by the generous support from the IC Board of Directors, the Center for Marine Biodiversity and Conservation at SIO, the Nature Conservancy California Chapter, the Leo Model Foundation, and the Archie Arnold Trust.
                Cover page: Island Ocean Connections: Exploring Land-Sea Linkages in the Context of Invasive Mammal Management
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2022)
                Islands support unique plants, animals, and human societies found nowhere else on the Earth. Local and global stressors threaten the persistence of island ecosystems, with invasive species being among the most damaging, yet solvable, stressors. While the threat of invasive terrestrial mammals on island flora and fauna is well recognized, recent studies have begun to illustrate their extended and destructive impacts on adjacent marine environments. Eradication of invasive mammals and restoration of native biota are promising tools to address both island and ocean management goals. The magnitude of the marine benefits of island restoration, however, is unlikely to be consistent across the globe. We propose a list of six environmental characteristics most likely to affect the strength of land-sea linkages: precipitation, elevation, vegetation cover, soil hydrology, oceanographic productivity, and wave energy. Global databases allow for the calculation of comparable metrics describing each environmental character across islands. Such metrics can be used today to evaluate relative potential for coupled land-sea conservation efforts and, with sustained investment in monitoring on land and sea, can be used in the future to refine science-based planning tools for integrated land-sea management. As conservation practitioners work to address the effects of climate change, ocean stressors, and biodiversity crises, it is essential that we maximize returns from our management investments. Linking efforts on land, including eradication of island invasive mammals, with marine restoration and protection should offer multiplied benefits to achieve concurrent global conservation goals.
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2023)
                  Understanding the history of how we studied our ocean in the past and how we study it now will help us develop approaches to make future oceanographic knowledge production more diverse, accessible, and inclusive. The motto of the UN Decade of Ocean Science for Sustainable Development (2021–2030) is, “The ocean we need for the future we want” (Singh et al., 2021). The Ocean Decade gives the ocean sciences community an opportunity to change the way it conducts research, to use ocean science to support sustainable development, and to energize the ocean sciences for future generations. With these goals in mind, we developed an introductory level, student-led graduate seminar that builds on the Ocean Decade framework. A research cruise involving seminar participants followed the seminar sessions. Here, we discuss how we conducted the seminar and highlight directions that are needed to energize future generations of ocean leaders and make ocean science more equitable, inclusive, and accessible.
                    Cover page: The Ocean as a Classroom: Considering the Roles of Equity, Diversity, and Justice in Oceanographic Knowledge Production to Promote Accessibility for Future GenerationsCreative Commons 'BY-NC-ND' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2020)
                    Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.
                      Cover page: Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems
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