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Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2024)

Particulate organic carbon (POC) is a fundamental component in aquatic ecosystems, acting as a primary energy source for both pelagic and benthic food webs and playing a key role in biogeochemical cycles through nutrient cycling, microbial activity promotion, and carbon sequestration in sediments. This dissertation investigates the distribution, forms, and quality of POC within organic matter pools in the Sacramento-San Joaquin Delta, a highly modified ecosystem. Over recent decades, urban and agricultural runoff, habitat modification, and invasive species have profoundly impacted the ecological integrity and biogeochemical processes within the Delta. The research objectives were: (1) to establish a baseline understanding of POC quantities and develop a comprehensive POC mass balance across the Delta, (2) to identify and quantify contributions from terrestrial sources, aquatic macrophyte vegetation, and phytoplankton to POC, and (3) to use metagenomics to trace POC sources to specific biological species, identify unrecognized contributors, and assess the quality of these particles as a food source.Extensive field campaigns were conducted across three seasons (spring, summer, and fall) to map POC across the Delta, sampling 28 sites in 2021-2022. These surveys revealed critically low POC quantities, indicating Delta-wide particle scarcity. These low levels are likely due to decades-long declines in total suspended sediment inputs, compounded by drought conditions and reduced primary production. Consequently, the POC mass balance showed diminished transport to the San Francisco Bay, with a significant portion (8-37%) diverted to southern water exports, thereby depriving coastal zones of essential particulate inputs and their associated ecological benefits. This issue is not unique to the Sacramento-San Joaquin Delta; similarly modified aquatic ecosystems worldwide may face comparable challenges, necessitating broader consideration of POC dynamics in the management of such environments. By employing an endmember mixing model to apportion key sources of POC (vascular plants, terrestrial inputs, and aquatic macrophytes) using lignin endmembers, I determined that terrestrial inputs (5-75%) and aquatic macrophyte vegetation (<1-71%) contributed larger portions to POC pools on average compared to phytoplankton (16-29%). Across the network of 28 sites in the Delta, increased abundance of macrophyte vegetation did not correlate with higher particulate lignin concentrations. This likely reflects the limitations imposed by particle scarcity suggesting that macrophytes cannot compensate for the reduced sediment inputs in the Delta. Aquatic systems similarly impacted by prolific aquatic macrophyte vegetation should not readily assume that increased biomass directly equates to higher standing water column contributions. Limiting factors, such as the tendency of some species to trap sediments and act as a net sink rather than a source, may govern these dynamics. Building on these findings, amplicon DNA metagenomics was used to investigate the spatial and temporal variations of phytoplankton and vascular plant communities within POC pools across the Delta. Taxonomic profiling identified a combined total of over 468 species, demonstrating the diversity of Delta POC pools. More nutritious phytoplankton food resources like cryptophytes were found to be significantly abundant across the Delta, suggesting that food quantity, rather than quality, may be a limiting factor in Delta food web dynamics. Additionally, this research identified agricultural detritus as a widespread contributor to POC across the Delta, providing direct evidence of the impact of human activities on POC sources and abundance. Understanding these contributions is central for effective management and conservation of similarly impacted aquatic ecosystems worldwide.

    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2019)
    Particulate material comprising the detrital remains of terrestrial plants and macrophytes is a substantial source of organic matter to estuaries and therefore has the potential to support the energy demands of the pelagic aquatic food web. Despite the prevalence of macrophytic or terrestrial particulate organic carbon (tPOC), phytoplankton are nutritionally superior and are thought to be the primary food resource for zooplankton. However, estuarine phytoplankton primary productivity abundances can wax and wane, and often production cannot meet heterotrophic energy needs. In this study, we examined how tPOC (detritus of macrophytes and grasses) may affect survival of a calanoid copepod (Eurytemora affinis) common in the San Francisco Estuary (SFE), an estuary with relatively low phytoplankton primary productivity. Using chemical biomarkers and a targeted DNA metagenomic methodology, we show that E. affinis consumed tPOC (dominated by Schoenoplectus sp., or tule) even when phytoplankton were abundant and tPOC was scarce. Furthermore, we found that a mixed diet of phytoplankton and terrestrial material (1:3 carbon ratio) enhanced the survival of E. affinis over a diet of phytoplankton alone. These data show that tPOC can be a vital supplementary food source for zooplankton, perhaps extending survival during low phytoplankton periods, and may help explain elevated zooplankton abundances in tidal wetlands and other detrital-dominated regions.
      Cover page: Plant detritus is selectively consumed by estuarine copepods and can augment their survival.Creative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2017)
      Evaluating the collective impact of small source inputs to larger rivers is a constant challenge in riverine biogeochemistry. In this study, we investigated the generation of dissolved organic matter (DOM) in a small oak woodland catchment in the foothills of northern California, the subsequent transformation in lignin biomarkers and chromophoric DOM (CDOM) parameters during transport through the landscape to an exporting stream, and finally the overall compositional impact on the larger receiving stream and river. Our study included a natural leaching experiment in which precipitation passing through oak, pine, and grass litter and duff samples was collected after each of a series of storms. Also included were soil trench samples to capture subsurface lateral flow, stream samples along with point-source reservoir inputs, and samples of canopy throughfall, stemflow, and gopher hole (bypass) flow. The litter/duff leaching study demonstrated changing DOM fractionation patterns throughout the season, as evidenced by changing lignin compositions in the leachates with each successive storm. This adds a necessary seasonal component to interpreting lignin compositions in streams, as the source signatures are constantly changing. Released DOM from leaching was modified extensively during transit through the subsurface to the stream, with preferential increases in aromaticity as evidenced by increases in carbon-normalized absorbance at 254 nm, yet preferential decreases in lignin phenols, as evidence by carbon-normalized lignin yields in the headwater stream that was less than half that of the litter/duff leachates. Our extensive number of lignin measurements for source materials reveals a much more complex perspective on using lignin as a source indicator, as many riverine values for syringyl:vanillyl and cinnamyl:vanillyl ratios that have previously been interpreted as degraded lignin signatures are also possible as unmodified source signatures. Finally, this study demonstrated that the impact of numerous small headwater streams can significantly overprint the DOM signatures of much larger rivers over relatively short distances spanning several to tens of kilometers. This finding in particular challenges the assumption that river studies can be adequately conducted by focusing only on the main tributaries.
        Cover page: The Genesis and Exodus of Vascular Plant DOM from an Oak Woodland Landscape
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2021)
        The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure can be quite limited and residence time within river networks is low. Here, we collected DOM samples along a salinity gradient in the Yukon River delta, plume and coastal ocean during peak river discharge immediately after spring freshet and explored the role of UV exposure, microbial transformations and interactive effects on DOM quantity and composition. Our results show: (1) photochemical alteration of DOM significantly shifts processing pathways of terrestrial DOM, including increasing relative humification of DOM by microbes by > 10%; (2) microbes produce humic-like material that is not optically distinguishable from terrestrial humics; and (3) size-fractionation of the microbial community indicates a size-dependent role for DOM remineralization and humification of DOM observed through modeled PARAFAC components of fluorescent DOM, either through direct or community effects. Field observations indicate apparent conservative mixing along the salinity gradient; however, changing photochemical and microbial alteration of DOM with increasing salinity indicate changing DOM composition likely due to microbial activity. Finally, our findings show potential for rapid transformation of DOM in the coastal ocean from photochemical and microbial alteration, with microbes responsible for the majority of dissolved organic matter remineralization.
          Cover page: DOM degradation by light and microbes along the Yukon River-coastal ocean continuumCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)
          The Arctic Ocean is surrounded by land that feeds highly seasonal rivers with water enriched in high concentrations of dissolved and particulate organic carbon (DOC and POC). Explicit estimates of the flux of organic carbon across the land-ocean interface are difficult to quantify and many interdependent processes makes source attribution difficult. A high-resolution 3-D biogeochemical model was built for the lower Yukon River and coastal ocean to estimate biogeochemical cycling across the land-ocean continuum. The model solves for complex reactions related to organic carbon transformation, including mechanistic photodegradation and multi-reactivity microbial processing, DOC-POC flocculation, and phytoplankton dynamics. The baseline DOC and POC flux out of the delta from April to September 2019, was 977 and 536 Gg C (∼80% of the annual total), but only 50% of the DOC and 25% of the POC exited the plume across the 10 m isobath. Microbial breakdown of DOC accounted for a net loss of 168 Gg C (17% of delta export) within the plume and photodegradation accounted for a net loss of 46.6 Gg C DOC (5% of delta export) in 2019. Flocculation decreased the total organic carbon flux by only 6.4 Gg C (∼1%), while POC sinking accounted for 63.3 Gg C (10%) settling in the plume. The loss of chromophoric dissolved organic matter due to photodegradation increased the light available for phytoplankton growth throughout the coastal ocean, demonstrating the secondary effects that organic carbon reactions can have on biological processes and the net coastal carbon flux.
            Cover page: The Transformation and Export of Organic Carbon Across an Arctic River‐Delta‐Ocean ContinuumCreative Commons 'BY' version 4.0 license
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