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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Thesis
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UC Irvine Electronic Theses and Dissertations (2017)

Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean’s surface layer despite large environmental variation. There are several phylogenetically distinct lineages within Prochlorococcus and considerable gene gain and loss throughout its evolutionary history. However, the extent to which vertical versus horizontal inheritance shapes its genome diversity across the global oceans is unknown. We observed that Prochlorococcus field populations from a global circumnavigation had a significant relationship between phylogenetic and gene content diversity including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Overall we showed that the environment determines the functional capabilities of successful Prochlorococcus.

We know Prochlorococcus has extensive genetic diversity, including the presence of multiple major clades, its sister taxa Synechococcus displays similar levels of genetic diversity. Prochlorococcus has a clear phylogeography relating to environmental selective pressures, while the biogeography and environmental drivers of Synechococcus clades are more difficult to define. To better characterize Prochlorococcus and Synechococcus genetic diversity we used high throughput sequencing of the marker gene rpoC1 from 339 samples across the Pacific Ocean and Atlantic Oceans. At multiple taxonomic scales (lineage, clade, and SNP) we observed clear parallel biogeography between these two lineages. Overall, this parallel biogeography suggests similar evolutionary selective pressures for these important marine Cyanobacteria.

Oceans are warming and will continue to increase over the next 100 years due to global climate change. Adaptation will likely play a role, but it is unclear how it will impact microbial distributions and processes. To address this unknown, we experimentally evolved a member of the prevalent marine Roseobacter clade to high temperature for 500 generations. We found that this evolved Roseobacter shifted from its usual planktonic growth mode to creating more biofilm at the surface of the culture. Furthermore, this altered lifestyle was coupled with a suite of genomic changes linked to biofilm formation and increased growth in low oxygen transfer environments.

    Cover page: Biogeography and the Adaptive Variation of Marine Bacteria in Response to Environmental Change
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2018)
    Ocean temperatures will increase significantly over the next 100 years due to global climate change1. As temperatures increase beyond current ranges, it is unclear how adaptation will impact the distribution and ecological role of marine microorganisms2. To address this major unknown, we imposed a stressful high-temperature regime for 500 generations on a strain from the abundant marine Roseobacter clade. High-temperature-adapted isolates significantly improved their fitness but also increased biofilm formation at the air-liquid interface. Furthermore, this altered lifestyle was coupled with genomic changes linked to biofilm formation in individual isolates, and was also dominant in evolved populations. We hypothesize that the increasing biofilm formation was driven by lower oxygen availability at elevated temperature, and we observe a relative fitness increase at lower oxygen. The response is uniquely different from that of Escherichia coli adapted to high temperature3 (only 3% of mutated genes were shared in both studies). Thus, future increased temperatures could have a direct effect on organismal physiology and an indirect effect via a decrease in ocean oxygen solubility, leading to an alteration in microbial lifestyle.
      Cover page: Increased biofilm formation due to high-temperature adaptation in marine RoseobacterCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2014)
        Cover page: Extracellular enzyme production and cheating in Pseudomonas fluorescens depend on diffusion ratesCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2016)
        Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.
          Cover page: Global biogeography of Prochlorococcus genome diversity in the surface oceanCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2019)
          The globally abundant marine Cyanobacteria Prochlorococcus and Synechococcus share many physiological traits but presumably have different evolutionary histories and associated phylogeography. In Prochlorococcus, there is a clear phylogenetic hierarchy of ecotypes, whereas multiple Synechococcus clades have overlapping physiologies and environmental distributions. However, microbial traits are associated with different phylogenetic depths. Using this principle, we reclassified diversity at different phylogenetic levels and compared the phylogeography. We sequenced the genetic diversity of Prochlorococcus and Synechococcus from 339 samples across the tropical Pacific Ocean and North Atlantic Ocean using a highly variable phylogenetic marker gene (rpoC1). We observed clear parallel niche distributions of ecotypes leading to high Pianka's Index values driven by distinct shifts at two transition points. The first transition point at 6°N distinguished ecotypes adapted to warm waters but separated by macronutrient content. At 39°N, ecotypes adapted to warm, low macronutrient vs. colder, high macronutrient waters shifted. Finally, we detected parallel vertical and regional single-nucleotide polymorphism microdiversity within clades from both Prochlorococcus and Synechococcus, suggesting uniquely adapted populations at very specific depths, as well as between the Atlantic and Pacific Oceans. Overall, this study demonstrates that Prochlorococcus and Synechococcus have shared phylogenetic organization of traits and associated phylogeography.
            Cover page: Parallel phylogeography of Prochlorococcus and Synechococcus
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2023)
            During May 2018‒December 2022, we reviewed transfusion-transmitted sepsis cases in the United States attributable to polymicrobial contaminated apheresis platelet components, including Acinetobacter calcoaceticus‒baumannii complex or Staphylococcus saprophyticus isolated from patients and components. Transfused platelet components underwent bacterial risk control strategies (primary culture, pathogen reduction or primary culture, and secondary rapid test) before transfusion. Environmental samples were collected from a platelet collection set manufacturing facility. Seven sepsis cases from 6 platelet donations from 6 different donors were identified in patients from 6 states; 3 patients died. Cultures identified Acinetobacter calcoaceticus‒baumannii complex in 6 patients and 6 transfused platelets, S. saprophyticus in 4 patients and 4 transfused platelets. Whole-genome sequencing showed environmental isolates from the manufacturer were closely related genetically to patient and platelet isolates, indicating the manufacturer was the most probable source of recurrent polymicrobial contamination. Clinicians should maintain awareness of possible transfusion-transmitted sepsis even when using bacterial risk control strategies.
              Cover page: Posttransfusion Sepsis Attributable to Bacterial Contamination in Platelet Collection Set Manufacturing Facility, United States.
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2015)
              Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ∼17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.
                Cover page: Physiology and evolution of nitrate acquisition in Prochlorococcus
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