Biogeochemical Sulfur Cycling in the Bar-Built Pescadero Estuary: Interdisciplinary Investigations Into Near-Annual Fish Mortality Events

Biogeochemical sulfur cycling in the bar-built Pescadero Estuary: Interdisciplinary investigations into near-annual fish mortality events by Chandra Mercedes Richards A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Environmental Science, Policy, and Management in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Céline E. Pallud, Chair Professor Stephanie M. Carlson Professor Mary K. Firestone Professor David L. Sedlak Fall 2016 Biogeochemical sulfur cycling in the bar-built Pescadero Estuary: Interdisciplinary investigations into near-annual fish mortality events © 2016 by Chandra Mercedes Richards Abstract Biogeochemical sulfur cycling in the bar-built Pescadero Estuary: Interdisciplinary investigations into near-annual fish mortality events by Chandra Mercedes Richards Doctor of Philosophy in Environmental Science, Policy, and Management University of California, Berkeley Professor Céline Pallud, Chair Natural and human impacts on geochemical redox cycling and biodiversity in estuaries have long been a global concern. In estuarine systems, sulfur (S) is a macroelement of great environmental importance. The production and oxidation of hydrogen sulfide (H2S) are highly impacted by biogeochemical and physical conditions, including redox conditions and pH. For decades, hydrogen sulfide (H2S) has been recognized as a major contaminant in estuarine systems due to its direct (toxicity) and indirect (oxidative) effects on aquatic and sediment life. Mass mortality events of fish and migratory birds have occurred in various coastal ecosystems, including bar-built estuaries, which serve as major ecological habitats and as water-purifying marshlands. In this dissertation, I develop an integrated and comprehensive understanding of the geochemical and biological transformations involved in the sulfur redox cycling at the interface of the hydrosphere and pedosphere in a northern California bar-built estuary (Pescadero Estuary, CA) and their consequences on water quality. Fish kills have been more regular and severe at Pescadero than at other nearby California bar-built systems. Across scientific disciplines and spatial and temporal scales, I begin by illustrating the temporal evolution in geochemical conditions in water and sediment from closed to open state to accentuate the decline in water conditions as the estuary opens. I then examine the major anaerobic respiration pathways controlling the biogeochemical cycling of sulfur and its effects on iron (Fe) cycling and pH. Finally, using flow-through reactor experiments and slurry incubations, I investigate the biogeochemical mechanisms that control the production, precipitation, and re-oxidation of hydrogen sulfide in water and sediment. 1 Common in Mediterranean climates (e.g. United States, South Africa, Australia, Europe), intermittent estuaries have received little research attention, which lacks in information on the geochemistry of the systems. In California, bar-built estuaries represent about 75% of over 400 estuaries along the Pacific coastline and function as critical refuges to migratory and endangered fish communities, including federally-threatened steelhead trout (Oncorhynchus mykiss). An established watershed spanning centuries of human use, the bar-built Pescadero Estuary has, however, been afflicted by near-annual fish mortality events of steelhead trout since 1995, occurring with the natural or anthropogenic opening of the sandbar barrier. In Chapter 1, I tracked the temporal and spatial evolution of water and sediment geochemical conditions from closed to open state to highlight the decline in water conditions between states, specifically acidification. This extensive sampling campaign was feasible for this relatively small system and illustrated that the northern tributary, Pescadero Creek, showed a significant departure in geochemical conditions from the rest of the Estuary; this implied that it may be considerably less susceptible to fish die- offs than the rest of the Pescadero Estuary. Using this large-scale interpretation of the Pescadero Estuary, I chose four contrasting study to investigate in more details biogeochemical redox cycling of sulfur and iron in sediment during the closed and open states. The speciation and cycling of sulfur are largely driven by microbial activity and redox conditions. The analysis of Pescadero Estuary pore water profiles confirmed that microbial sulfate reduction to hydrogen sulfide is the dominant anaerobic respiration pathway in both the closed and open states. Moreover, the absence of nitrate and presence of reduced ferrous iron confirmed suboxic, reducing conditions in water and the steady production of acid-volatile sulfides (AVS) and iron sulfides in sediment. Additionally, I observed that iron reduction and sulfate reduction occur concomitantly. In Chapter 3, I corroborated that sulfate reductive processes predominate in the Pescadero Estuary, with greater rates in the closed state than in the open state and also in fine-grained sediments than in coarse-grained sediments. Despite higher values than the EPA-defined criterion for aquatic life, the low concentrations of aqueous hydrogen sulfide imply that it cannot solely cause fish deaths. The majority of aqueous sulfide precipitates as metal sulfides in sediment, who could indirectly be implicated in fish die- offs in the transition from closed to open state upon re-oxidation. The coupled interactions between physical state, sediment conditions, water quality, and overall estuarine health are complex. Linked to climatic conditions and water inflows from ocean and freshwater, the transitional period from closed to open state is characterized by sediment resuspension and mobilization of sediment metal sulfides into the water column where they can be oxidized. In Chapter 4, I demonstrated the oxidative effects of Pescadero Estuary sediments on water conditions using slurry incubation resuspension experiments. I confirmed that aqueous hydrogen sulfide concentrations were low and oxidized quickly (<1 day) and therefore cannot be responsible for fish kills, consistent with the results from Chapter 3. In contrast, the oxidation of sediment AVS was slower, and resulted in their complete removal in six days, with large contents of sulfur released from sediment to water. The oxidation of AVS leads to severe acidification and release of metals (iron, manganese, and zinc) to water. The aqueous metal concentrations reached were greater than the EPA-defined maximum criteria for aquatic life, indicating a potential link to poor fish health. 2 The integration of scientific knowledge across spatial, environmental, and ecological scales is rarely attempted, thus limiting our mechanistic understanding of sulfur cycling and the causal reasons for mortality events in bar-built estuaries globally. The role of sediment and its impacts on ecosystem health, water quality, and aquatic life due to natural and anthropogenic causes is particularly important. This work is the first to examine the natural, direct and indirect effects of hydrogen sulfide at the interface of water and sediment and across spatial and temporal scales in a bar-built estuary. It is also the first to undertake an extensive sampling campaign to pinpoint the temporal evolution of geochemical conditions. As a comprehensive examination of a complex, environmental problem, this study represents an important advancement in the fields of water, soil, and estuarine science. The management and remediation of intermittent systems depends on our ability to predict estuarine conditions, which will be also be used for similar estuaries along the California coast and to meet policy criteria for water quality. Further development of sulfur cycling across scientific disciplines, landscape types, and coastal environments will be achievable to minimize the likelihood of fish mortality events. 3 Dedication This dissertation is dedicated to my mother, Mercedes Tharam Richards. You inspire me every day. “It is not important what you do, but what is important is that you love what you do.” i Curriculum Vitae Name: Chandra Mercedes Richards Degree and date to be conferred: Ph.D., 2016 Collegiate institutions attended: B.S., 2005-2009, Pennsylvania State University, State College, PA, USA Majors: Chemistry (Cum Laude) and Mathematics Ph.D., 2011-2016, University of California, Berkeley, Berkeley, CA, USA Major: Environmental Science, Policy, and Management Professional Publications: Richards, C. M. and Pallud C., 2016. Kinetics of sulfate reduction and sulfide precipitation rates in sediments of a bar-built estuary (Pescadero, California). Water Research, 94, 86-102. doi: 10.1016/j.watres.2016.01.044. Richards, C. M. and Pallud C., 2015. Spatio-temporal physical and geochemical characterization of a California bar-built estuary. 2015 Goldschmidt Conference, Prague, Czech Republic, Talk, Abstract 2724. Huber, E., Jankovitz, J., Richards, C. M., Largier, J., Carlson, S.M., and Sloan, R., 2015. California drought causes apparent loss of steelhead estuarine nursery habitat,” Annual Meeting of the American Fisheries Society California-Nevada Chapter, Santa Cruz, CA, USA, Talk. Richards, C. M. and Pallud C., 2014. Microbial sulfate reduction and sulfide oxidation in littoral sediments of the intermittent Pescadero Estuary. Restore America’s Estuaries 7th National Summit on Coastal and Estuarine Restoration, Washington, DC, USA, Talk, MD-4. Richards,

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