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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2016)

Polyfluoroalkyl and perfluoroalkyl substances (PFASs) are a group of highly stable organic compounds that provide products with several useful properties, including water, oil, and stain resistance. However, many PFASs are reproductive and developmental toxicants, endocrine disrupters, and potential human carcinogens. They are found globally, such as in contaminated groundwater and surface water and in pristine environments. Since PFAS-containing industrial and consumer products will be disposed into the environment, it is necessary to understand the microbial transformation of these compounds and to develop pollution remediation strategies.

Phanerochaete chrysosporium, a wood-decaying fungus, transformed 6:2 fluorotelomer alcohol (6:2 FTOH), towards less fluorinated polyfluorocarboxylic acids. The most abundant transformation product after 14 days was 5:3 acid (43 mol% of initially applied 6:2 FTOH) when lignocellulosic powder, yeast extract, cellulose, and glucose were added. In addition, four unique 5:3 acid conjugates were identified as products of fungal degradation of 6:2 FTOH. Nutrient supplements, including cellulose, yeast extract, malt extract, glucose, and EDTA, which increase the sulfate and carbon content and trace mineral availability, are necessary for transformation of 6:2 FTOH towards 5:3 acid by P. chrysosporium. These may promote the suite of cytochrome P450 oxygenases and other extracellular enzymes responsible for transforming 6:2 FTOH.

Gloeophyllum trabeum, Trametes versicolor, and several fungal isolates, were also able to transform 6:2 FTOH towards 5:3 acid. While most fungal pure cultures were limited in their ability to transform 6:2 FTOH under the nutrient conditions tested, the resulting metabolites will likely be further transformed in the environment via other biotic or abiotic processes. These studies demonstrate that fungi possess unique biochemical pathways for degrading polyfluoroalkyl substances towards less fluorinated and more biodegradable products. Since manufacturers are increasingly using FTOH-based products, it is necessary to understand the role of various microorganisms on the fate, transport, and transformations of PFASs in the environment.

    Cover page: Fungal Biotransformation of Polyfluoroalkyl Substances: Identification of Growth Substrates for Favorable Biotransformation Pathways
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2018)
    Metallic nanoparticles (NPs), the most abundant nanomaterials in consumer and industrial products, are the most probable class to enter the environment. In this study, wetland-derived microcosms were incubated with copper nanoparticles (Cu-NP) and ionic CuCl2 to investigate acute (10 days) and chronic (100 days) exposure towards nitrogen cycling microorganisms. The microbial ecology of wetlands play a crucial role in balancing nitrogen in pristine environments as well as in areas impacted by high nutrient loads (e.g., at wastewater effluent discharges). Gene abundance and expression changes were monitored using the GeoChip 5.0 high throughput functional gene microarray and metatranscriptomic shotgun sequencing (RNA-seq), respectively. After 10 days, the Cu-NP impacted microbial communities experienced structural shifts within microorganisms associated with dissimilatory nitrogen reduction accompanied by lower nitrate removal as compared to the unexposed controls. By day 100, these differences were largely resolved and nitrate removal was similar to the unexposed control. Furthermore, the Cu-NP exposed microcosms tolerated copper and were more resilient and adaptive than the unexposed controls based on the abundance and expression of other functions, including electron transfer, metal homeostasis, and stress response. These findings suggest sudden influxes of Cu-NPs into wetland systems may impair nitrogen removal initially, but long-term microbial shifts and functional redundancy would promote the net flux of total nitrogen out of the wetlands.
      Cover page: Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles
      • Article
      • Peer Reviewed
      Joint Genome Institute (2023)
      Abstract: Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus–host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
        Creative Commons 'BY-NC' version 4.0 license
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2021)
        Physical samples are foundational entities for research across biological, Earth, and environmental sciences. Data generated from sample-based analyses are not only the basis of individual studies, but can also be integrated with other data to answer new and broader-scale questions. Ecosystem studies increasingly rely on multidisciplinary team-science to study climate and environmental changes. While there are widely adopted conventions within certain domains to describe sample data, these have gaps when applied in a multidisciplinary context. In this study, we reviewed existing practices for identifying, characterizing, and linking related environmental samples. We then tested practicalities of assigning persistent identifiers to samples, with standardized metadata, in a pilot field test involving eight United States Department of Energy projects. Participants collected a variety of sample types, with analyses conducted across multiple facilities. We address terminology gaps for multidisciplinary research and make recommendations for assigning identifiers and metadata that supports sample tracking, integration, and reuse. Our goal is to provide a practical approach to sample management, geared towards ecosystem scientists who contribute and reuse sample data. (IGSN); physical samples; soil; water; plant; leaf; microbial communities; related identifiers; persistent identifiers.
          Cover page: Sample Identifiers and Metadata to Support Data Management and Reuse in Multidisciplinary Ecosystem Sciences
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2021)
          We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
            Cover page: A global metagenomic map of urban microbiomes and antimicrobial resistance
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