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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2020)

Elemental ratios of particulate organic matter (POM) are key to linking biogeochemical cycles. Microbial uptake and allocation of essential biogenic elements (carbon (C), nitrogen (N), and phosphorus (P)) influence the distribution of nutrients throughout the ocean. This dissertation evaluates the role of environmental stress and underlying phytoplankton diversity in driving regional variation in the ratio of particulate C:N:P. Competing hypotheses predict C:N:P equally well due to regional co-variance in environmental conditions and biodiversity. The Indian Ocean offers a unique positive temperature and nutrient supply relationship to test these hypotheses. We collected 248 POC:N:P observations in the eastern Indian Ocean along this environmental gradient. As phytoplankton community composition was constant, biodiversity changes could not explain the elemental variation. Instead, our data supports the nutrient supply hypothesis over the influence of temperature.

Nutrients concentrations are often below detection limits in subtropical ocean regions. We develop two methods to predict nutrient stress to further evaluate its role in particulate C:P regulation. In the first method, we develop a global remote sensing estimate of surface phosphate. Using a mechanistic framework, we develop an artificial neural network to provide a robust basis for developing a remote sensing estimation of surface phosphate. However, C:P predictions using only phosphate did not match observations in either the South Indian or Pacific subtropical gyres. To address this challenge, we develop a second method by applying genomic shifts among microbial communities as ‘biosensors’ for the in situ nutritional environment. We find that our genome-based trait-model significantly improves our prediction of particulate C:P across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen, and phosphorus stress. Ultimately, we find a combination of nutrient stress accounts for global variation in particulate C:P.

    Cover page: Environmental Controls on Marine Particulate C:N:P Ratios
    • Article
    • Peer Reviewed
      Cover page: Just Passing Through
      • 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 (2022)
        Oceanic nutrient cycles are coupled, yet carbon-nitrogen-phosphorus (C:N:P) stoichiometry in marine ecosystems is variable through space and time, with no clear consensus on the controls on variability. Here, we analyze hydrographic, plankton genomic diversity, and particulate organic matter data from 1970 stations sampled during a global ocean observation program (Bio-GO-SHIP) to investigate the biogeography of surface ocean particulate organic matter stoichiometry. We find latitudinal variability in C:N:P stoichiometry, with surface temperature and macronutrient availability as strong predictors of stoichiometry at high latitudes. Genomic observations indicated community nutrient stress and suggested that nutrient supply rate and nitrogen-versus-phosphorus stress are predictive of hemispheric and regional variations in stoichiometry. Our data-derived statistical model suggests that C:P and N:P ratios will increase at high latitudes in the future, however, changes at low latitudes are uncertain. Our findings suggest systematic regulation of elemental stoichiometry among ocean ecosystems, but that future changes remain highly uncertain.
          Cover page: Global patterns and predictors of C:N:P in marine ecosystems
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2018)
          Variation in ocean C:N:P of particulate organic matter (POM) has led to competing hypotheses for the underlying drivers. Each hypothesis predicts C:N:P equally well due to regional co-variance in environmental conditions and biodiversity. The Indian Ocean offers a unique positive temperature and nutrient supply relationship to test these hypotheses. Here we show how elemental concentrations and ratios vary over daily and regional scales. POM concentrations were lowest in the southern gyre, elevated across the equator, and peaked in the Bay of Bengal. Elemental ratios were highest in the gyre, but approached Redfield proportions northwards. As Prochlorococcus dominated the phytoplankton community, biodiversity changes could not explain the elemental variation. Instead, our data supports the nutrient supply hypothesis. Finally, gyre dissolved iron concentrations suggest extensive iron stress, leading to depressed ratios compared to other gyres. We propose a model whereby differences in iron supply and N2-fixation influence C:N:P levels across ocean gyres.
            Cover page: Nutrient supply controls particulate elemental concentrations and ratios in the low latitude eastern Indian OceanCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Irvine Previously Published Works (2020)
            Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
              Cover page: Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2020)
              Climate-driven depletion of ocean oxygen strongly impacts the global cycles of carbon and nutrients as well as the survival of many animal species. One of the main uncertainties in predicting changes to marine oxygen levels is the regulation of the biological respiration demand associated with the biological pump. Derived from the Redfield ratio, the molar ratio of oxygen to organic carbon consumed during respiration (i.e., the respiration quotient, [Formula: see text]) is consistently assumed constant but rarely, if ever, measured. Using a prognostic Earth system model, we show that a 0.1 increase in the respiration quotient from 1.0 leads to a 2.3% decline in global oxygen, a large expansion of low-oxygen zones, additional water column denitrification of 38 Tg N/y, and the loss of fixed nitrogen and carbon production in the ocean. We then present direct chemical measurements of [Formula: see text] using a Pacific Ocean meridional transect crossing all major surface biome types. The observed [Formula: see text] has a positive correlation with temperature, and regional mean values differ significantly from Redfield proportions. Finally, an independent global inverse model analysis constrained with nutrients, oxygen, and carbon concentrations supports a positive temperature dependence of [Formula: see text] in exported organic matter. We provide evidence against the common assumption of a static biological link between the respiration of organic carbon and the consumption of oxygen. Furthermore, the model simulations suggest that a changing respiration quotient will impact multiple biogeochemical cycles and that future warming can lead to more intense deoxygenation than previously anticipated.
                Cover page: Latitudinal gradient in the respiration quotient and the implications for ocean oxygen availability
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2022)
                Concentrations and elemental stoichiometry of suspended particulate organic carbon, nitrogen, phosphorus, and oxygen demand for respiration (C:N:P:-O2) play a vital role in characterizing and quantifying marine elemental cycles. Here, we present Version 2 of the Global Ocean Particulate Organic Phosphorus, Carbon, Oxygen for Respiration, and Nitrogen (GO-POPCORN) dataset. Version 1 is a previously published dataset of particulate organic matter from 70 different studies between 1971 and 2010, while Version 2 is comprised of data collected from recent cruises between 2011 and 2020. The combined GO-POPCORN dataset contains 2673 paired surface POC/N/P measurements from 70°S to 73°N across all major ocean basins at high spatial resolution. Version 2 also includes 965 measurements of oxygen demand for organic carbon respiration. This new dataset can help validate and calibrate the next generation of global ocean biogeochemical models with flexible elemental stoichiometry. We expect that incorporating variable C:N:P:-O2 into models will help improve our estimates of key ocean biogeochemical fluxes such as carbon export, nitrogen fixation, and organic matter remineralization.
                  Cover page: Global Ocean Particulate Organic Phosphorus, Carbon, Oxygen for Respiration, and Nitrogen (GO-POPCORN)
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                  • Peer Reviewed
                  UC Irvine Previously Published Works (2021)
                  Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or "Bio-GO-SHIP." One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.
                    Cover page: High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects
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