Atmospheric aerosols (suspension of solid or liquid particles in the present in the atmosphere) can harbor a diverse array of airborne microorganisms and upon deposition into terrestrial or marine systems, airborne microbes can alter function and biogeochemical cycles of the receiving ecosystems. My work focuses on aerosols and their impact on marine environments. The three chapters in this thesis examine 1) the abundance and diversity of airborne microorganisms over the Mediterranean Sea, 2) the impacts of airborne microorganisms on the northern Red Sea surface water microbial diversity and function, and 3) the efficiency of three types of aerosol sampling instrumentation. In the first study, I described the abundance and genetic diversity of airborne bacteria in air samples collected over an East-West transect of the entire Mediterranean Sea and investigated 1) the controls on the diversity of airborne microbes, and 2) the source of the microbes comprising the aerosol microbiome over the Mediterranean Sea. The results show that airborne bacteria represent diverse groups with the most abundant bacteria from the Firmicutes (Bacilli and Clostridia) and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) phyla. Most of the bacteria in the samples have previously been observed in the air at other open ocean locations, in the air over the Mediterranean Sea during dust storms, and in surface water of the Mediterranean Sea. The results demonstrate that airborne bacterial diversity is positively correlated with the mineral dust content in the aerosols and the taxonomic composition differed between major basins of the Mediterranean Sea. In the second study, a mesocosm experiment was conducted to elucidate 1) how bioaerosols collected during dust-events impact prokaryotic and eukaryotic relative abundance in the northern Red Sea (NRS) surface water, and 2) how the changes in community structure affect biogeochemical cycles of the NRS. Results show that the airborne microorganisms and viruses suppressed primary production (as much as 50%), increased bacterial production (as much as 55%), and decreased the diversity of eukaryotes. These results suggest that airborne microorganisms have implications for the carbon cycle in low nutrient low chlorophyll marine ecosystems. The final chapter tests the efficiency of samples collected with three instruments (a membrane filtration device, a liquid impinger, and a portable electrostatic precipitator bioaerosol collector) for culture-dependent (colony-forming units) and culture-independent (DNA yield) studies. The results show that the electrostatic precipitator collected microorganisms significantly more efficiently than the membrane filtration and liquid impingement in both types of studies over the same time interval, primarily due to its higher flowrate.

Earth’s biogeochemical evolution is inferred from the elemental compositions of past seawater and the rock record. These reconstructions generally assume: 1) a known and relatively constant flux of continent-derived solutes through time, 2) that the isotopic composition of these input fluxes is constant over geologic timescales, and 3) that the sensitivity of isotope proxies is constant over geologic timescales. However, it is prudent to test these assumptions in the modern amidst a well-understood natural environment before applying them to reconstructions of the past, where far more unknowns exist. In Chapter 2, I quantified a previously unaccounted for input of continent-derived solutes: groundwater discharge. My results indicate that the global groundwater flux is responsible for 12 – 23% of the riverine flux for Li, Mg, Ca, Sr, and Ba. Moreover, only the isotopic compositions of δ7Li and δ138Ba were indistinguishable from riverine values. The δ26Mg, δ44Ca, 87Sr/86Sr and δ88/86Sr composition were all distinguishable from global riverine values. This difference was interpreted as an indication of the disproportionate role that coastal geology plays on the chemical composition of groundwater discharge. In chapter 3, I constructed the most comprehensive chemical mixing model of the Fraser River to-date, where the [Li], [Mg], [SO4], [K], [Ca], [Sr], δ7Li, δ26Mg, δ34S, δ41K, δ44Ca, 87Sr/86Sr, and δ88/86Sr composition of the dissolved load of the Fraser River was modeled and compared to observational data. The variations observed were consistent with (and able to be successfully modeled as) mixing between the hydrologic outputs of two end-member sources: young igneous rocks of the Coast Range and ancient (Paleozoic/Precambrian) metamorphosed sedimentary/carbonate bedrock of the Rocky Mountains. This result of Chapter 3 provides a first-order approximation of how these isotope systems may co-vary globally if surficial processes were to shift from a regime dominated by young, volcanic bedrock (e.g. trap volcanism) to a regime dominated by the erosion and weathering of collisional orogens dominated by ancient metasedimentary sequences (e.g. Himalayas). Furthermore, I found δ7Li to be the isotope system that correlated most significantly with silicate-derived cation fluxes (R2 = 0.2 – 0.4), which contributes to the growing body of work suggesting it be a more direct silicate weathering proxy than 87Sr/86Sr (Misra and Froelich, 2012). In Chapter 4, I focused on constraining the cycling and export of one of these non-traditional isotopes, δ138Ba, in Gulf of Aqaba seawater. Hot and devoid of riverine inputs, the Gulf of Aqaba has the lowest saturation state for barite of any marine basin in the world (Monnin et al., 1999), which I utilized as a modern analog for arid conditions of Earth’s past. My results indicate that the δ138Ba composition of the exported particulate flux does not vary with respect to regional parameters, such as barite saturation state and primary productivity. Furthermore, the results of this chapter bolster the argument that Δ138Ba, the isotopic offset between barite and seawater from which it precipitated (δ138Baparticulate - δ138Baseawater), is consistently -0.47‰. Overall, in this thesis, I have improved constraints on the magnitude and isotopic composition of groundwater, riverine, and exported particulate fluxes for modern seawater.

Submarine groundwater discharge (SGD) is a mechanism for bringing nonpoint source pollution to the coast. This is particularly true in areas where urban or agricultural practices pollute groundwater. This project sought to understand some of the effects of SGD on coastal water quality at Stinson Beach in Marin County, a community in which residents’ wastewater is treated on-site via septic systems.

Coastal wetlands are highly productive ecosystems and can store large amounts of carbon (C). However, decomposition processes in coastal wetlands also produce and emit greenhouse gasses (GHG), such as methane (CH4) - a potent greenhouse gas that could offset C storage in the wetland soil. Often a patchwork of vegetation and open water, coastal wetlands exhibit strong biogeochemical heterogeneity, resulting in elevated CH4 flux (FCH4) at certain times and locations. These points of elevated FCH4, termed “hot spots and hot moments" (HSHM), experience biogeochemical rates so high they can disproportionally contribute to annual flux rates. Despite the broad utilization of the term HSHM, there is no standardized, statistically rigorous method for identifying HSHM and quantifying their impact on ecosystem processes. Furthermore, the conditions that trigger HSHM of FCH4 are poorly understood, and hot moments are often excluded from wetland FCH4 upscaling and predictive modeling. This study presents a comparative analysis of standard HM identification techniques to find the best HM detection method for coastal wetlands and formalize HM identification best practices. We found that using a rolling Z-score threshold to identify hot moments from eddy covariance (EC) flux data was most suitable for coastal wetlands. Using this approach, we flagged hot moments at nine wetlands in the San Francisco Bay-San Joaquin River Delta (Bay-Delta). We then used the identified HMs to train several data-driven Random Forest (RF) models that leverage EC data to predict the occurrence of HMs. The best performing RF accurately (79%) captured HM absence/presence in the Bay-Delta region, and the relative importance of predictive environment parameters in the model shed light on the best predictors for HM. The method comparison in this study provides a best practices workflow for researchers when defining HSHM, and the RF HM model provides an upscaling methodology that could be used to predict the occurrence of HM FCH4 at sites without EC towers. Thus, the HM identification methodology and the predictive model present a valuable tool for wetland managers and restoration planners who can use the information to prioritize time and resources for mitigating and preventing these rare but high-impact emission events.

Late Holocene climate variability and coastal change

of the Yucatan Peninsula, Mexico

Kyle Houston Broach

The following dissertation contains three studies that use sediment cores to reconstruct past changes in the climate and environment of a tropical lagoon system. These studies provide insight into past droughts and coastal change during geologically recent climate variability and sea-level rise by investigating relationships between geochemical and biological parameters sensitive to different processes occurring on the coast of the Yucatan Peninsula, Mexico.

Chapter one is a foraminiferal fossil record reconstruction of the Celestun Lagoon environment, assessing ecologic response to a change in lagoon salinity and vegetation over the Late Holocene (5,300 years to present). The record and modern environment suggests foraminiferal community composition changes predictably with salinity, but lagoon salinity decreased primarily from restriction of seawater input to the lagoon, and hence reduced mixing between groundwater and seawater, rather than climate-induced increase of groundwater discharge, though climate is a secondary control. The cause of reduced mixing appears to be accumulation of barrier islands and sand spits that progressively isolated the northern lagoon, reducing mixing between groundwater discharge and seawater and shifting the environment from an open marine coast to estuarine lagoon. The transition was accompanied by expansion of the mangrove forest fringing the coastline. Superimposed on this trend, excursions of foraminifera taxa signify higher salinity coinciding with regionally dry periods and indicate that climate is a second-order control on lagoon mean salinity.

Chapter two is a more detailed paleosalinity reconstruction where relations between modern lagoon salinity and both trace metals and isotopes in foraminiferal tests are applied to samples from cores collected along a transect from the northern to southern lagoon. The benthic species Ammonia parkinsoniana is used due to its abundance throughout the lagoon, and paleosalinity tracers recorded in A. parkinsoniana calcite tests are the elemental ratios Sr/Ca, and Ba/Ca and isotopes δ18O and 87Sr/86Sr. Ba/Ca ratios exhibit the highest correlation with salinity while δ18O and 87Sr/86Sr indicate two types of groundwater discharge to the lagoon—a fresh and a brackish source. A mixing model constructed from δ18O and 87Sr/86Sr show that long-term decrease in salinity was due to increased proportions of the brackish groundwater endmember—consistent with the Chapter 1—and decreases in the freshwater endmember coincide with major dry periods in the Yucatan recorded in other paleoclimate archives of the region. Furthermore, sedimentation rates increase briefly at 3,400 and 2,000 years ago, time periods characterized by large-scale reorganization of atmospheric and oceanic currents in the North Atlantic with atmospheric teleconnections to tropical climate. These increases in accumulation rate are interpreted as periods of rapid barrier island accumulation as trade winds and the Loop Current weaken in the Gulf of Mexico and deposit sediments during longshore drift. Chapter two suggests that atmospheric patterns resulting in drought in the Yucatan Peninsula also result in rapid sedimentation and apparent decrease in salinity in coastal lagoons, thus demonstrating the value of a multi-proxy approach in reconstructing paleoenvironmental history in dynamic coastal environments.

Chapter three contributes data and a new hypothesis to the growing body of literature on the boron isotope system. The boron isotope ratio 11B/10B records pH of ambient water in the carbonate shells, proving to be a powerful tool in reconstructing past ocean acidification and atmospheric carbon dioxide concentrations. However, δ11B has not previously been used as a proxy for low-pH spring water discharge. In Celestun Lagoon, boron measurements in A. parkinsoniana are characterized by high variability both in surface sediments along the lagoon and in downcore samples and exhibit weak but significant relationships with the paleosalinity proxies 87Sr/86Sr and Ba/Ca and with the vegetation proxy δ13C. Lower pH caused by respiration of organic matter, recorded in δ13C of calcite, appears to contribute to δ11B variability, yet mean δ11B values of calcite reflect calculated δ11B values of borate based on present understanding of boron systematics, thus indicating that spring discharge exerts a first-order control on lagoon pH and δ11B recorded in foraminifera. This finding is of particular interest to the deep-time paleocommunity because prior to the evolution of foraminifera, and because deep sea sediments older than 180 million years are rare, many calcareous fossils available for δ11B analysis thrived in shallow marine habitats. As efforts continue to find deep-time analogs to modern ocean acidification, low-pH groundwater discharge in coastal zones may complicate interpretations of δ11B results but may be addressed by a rigorous multi-proxy approach.

This dissertation provides a record of coastal and climate change during recent periods of climate variability and sea-level rise over the last 5,000 years to provide context for current climate change in the tropics and an understanding of drivers of variability in the past and the future at low latitude sites.

In California, local stressors on water quantity and quality are pervasive. This dissertation explores questions that can improve our understanding of water quality and quantity issues in two central California systems. Chapter 1 leverages the unique dry period of California’s Mediterranean climate to better understand what water sources sustain critical low flow periods in a geologically complex watershed in central coastal California (San Lorenzo Watershed). Results from Chapter 1 show that both deep groundwater and shallow subsurface flow paths can contribute to baseflow during the summer dry down period, and that geology, specifically bedrock permeability, controls their relative contributions. This research adds to existing studies that are shifting traditional views on baseflow generation processes by showing low flow periods of hydrographs can be sustained by multiple water sources.

Chapter 2 and Chapter 3 investigate spatial and temporal variability of hydrological and biogeochemical processes in a highly altered estuary (the Sacramento-San Joaquin Delta). The Delta is comprised of over fifty peat islands that are drained for commercial agriculture. Herein we refer to this outflow from Delta islands as peat drainage (Chapter 2) and island drainage (Chapter 3). Chapter 2 examines the magnitude of lateral carbon exports from peat drainage and possible controls on carbon release. Results from Chapter 2 can be used to account for a missing term in local carbon budgets. Chapter 3 explores nutrient and trace metal inputs from island drainage and the significance of island drainage mass fluxes relative to major inflows in the system. Results from Chapter 3 suggest that island drainage is an understudied source of nutrients and trace metals, with total nitrogen loads accounting for almost 1/6 of regional inputs during dry water years. Both Chapter 2 and Chapter 3 show that exports from Delta islands are water year and season dependent, highlighting the importance of accounting for multiple time scales in future assessments of mass fluxes in this system.

As the surface ocean equilibrates with rising atmospheric pCO2, the pH of surface seawater is decreasing with potentially negative impacts to coral calcification and coral reef ecosystems. This dissertation is composed of 4 individual studies that explore the impacts of ocean acidification on community reef development, coral calcification rates, and the acclimatization potential of corals to decreasing seawater pH. This is accomplished through in-situ field investigations on a tropical coral reef and laboratory experiments on temperate solitary corals.

In Chapters II-IV, I present findings from field investigations at Puerto Morelos, Mexico concerning the impact of in-situ declines in saturation state (Ωarag) on a reef community. Chapter II is a survey of the impact of saturation state on coral species richness, abundance, and colony size. I observe that while corals are often found in under-saturated waters, species richness, number of individuals, and colony size all decrease with decreasing saturation state. The study concludes that impacts of ocean acidification vary widely by species and geographic distribution, but that overall coral coverage will decline significantly in the 21st century.

Chapter III explores the calcification rates of Porites astreoides corals in low and under-saturated waters and compares them to rates of colonies growing in control zones approximately 10m away. I conclude that decreases in saturation state are associated with significant declines in coral calcification, driven mainly by decreasing density of the skeletal material. Additionally, decreasing saturation state was associated with significant increases in the rate of bioerosion by boring organisms.

In Chapter IV, I address how ocean acidification may impact a reef ecosystem through a year-long recruitment experiment. I deploy limestone tiles in both low saturation and control zones and recover them at 3, 6, and 14 month intervals. Tiles in low saturation zones have up to 70% less coverage of calcifying organisms, coincident with an increase in fleshy algal coverage. Crustose and upright coralline algae are up to 90% less abundant on low saturation tiles after 14 months, despite their ability to establish on the tiles. These findings indicate that calcifying organisms, while physiologically tolerant of low saturation, are outcompeted by fleshy algae under ocean acidification conditions.

In Chapter V, I explore laboratory experiments on a temperate scleractinian coral, Balanophyllia elegans, to address how decreasing pH and level of nutrition impact coral calcification. In these experiments, I manipulate pCO2 (410, 770, and 1220 μatm) and feeding frequency (3 days vs. 21 days) in a closed seawater system to address the energetic requirements of calcification in corals without the aid of the symbiotic dinoflagellate, zooxanthellae. Planulation rates were affected by food level but not pCO2, while juvenile mortality was highest under high pCO2 (1220 µatm) and low food (21 day intervals). While net calcification was positive even at 1220 µatm (~3 times current atmospheric pCO2), overall calcification declined by ~25-45%, and skeletal density declined by ~35-45% as pCO2 increased from 410 to 1220 µatm. Aragonite crystal morphology changed at high pCO2, becoming significantly shorter but not wider at 1220 µatm.

Combined, these chapters suggest that the response of organisms to ocean acidification will be highly species-specific, complex, and will depend on multiple factors, such as community interactions and feeding amount. There is, however, overwhelming evidence suggesting that coral calcification and reef accretion will decline significantly over the 21st century.

We proposed directed field and modeling research to address the following hypotheses: (H1) Submarine groundwater discharge (SGD), its quality, and the percentage that is fresh versus saline, is modulated by season, tides, and wave conditions; (H2) the chemical (nutrient, carbon, trace metal) and biological (human health indicators) composition of SGD is affected by land use and geology; (H3) human health indicators and nutrients can be freely transported through the beach aquifer and are not removed via interactions with the sediments, and (H4) SGD impacts the water quality of the nearshore environment at a level comparable to surficial runoff.

Terrestrial water resources are scarce in arid and semi-arid regions of the world and increasing demands for water worldwide are adding additional pressures on limited water resources. Seawater desalination provides a reliable source of potable water. The process of desalination creates a high-salinity byproduct that is discharged back into the coastal environment by various methods (pipes, diffusers, channels). The brine effluent is often mixed with chemicals used at the desalination facilities and can, without dilution; reach salinities twice of the ambient feed-water. Despite a growing desalination capacity worldwide, the effects of that brine discharge on local coastal environments are not fully understood or constrained.

This thesis investigates the impacts of desalination brine discharge on coastal biology and chemistry, and is comprised of three chapters: Chapter 1 investigates the in-situ impacts of desalination discharge measured before and after the Carlsbad Desalination Plant (California) became operational on both water chemical parameters and benthic macro fauna; Chapter 2 investigates the impacts of desalination brine on corals from The Gulf of Aqaba in a 4-week incubation experiment with salinities 10% above ambient and addition of phosphonate-based antiscalants; and Chapter 3 reviews current knowledge of the impacts of brine discharge on a wide range of coastal organisms.

The Carlsbad Desalination Plant became operational in December 2015, and water, sediment and biological samples were collected prior to operations (December 2014 and September 2015) and after operations began (May and November 2016). A distinct brine plume of salinity 34-37 (ambient salinity 33.3) extending 600m offshore from the discharge point was observed after the plant started discharging. This is despite the coastal area being “high-energy” and previous computer models predicting mixing of the brine to be better. The salinity plume does not have an immediate effect on the benthic environment: Macro fauna abundance (tube-forming Polychaetes) significantly increases compared to post-operation surveys, however the in-faunal organisms show no change. The benthic area around the outfall has same level of disturbance pre and post operations, possibly because of the continuous discharge from the local power plant. A 5-week bioassay of brittle stars in brine treatments indicated a trend towards decreased growth and impaired agility in increased salinities but no significant change was observed. Finally, using mean wave height along the California coast as a proxy for coastal mixing, locations of proposed desalination facilities are compared to the location of Carlsbad Desalination Plant to evaluate the expected mixing properties of those areas.

In the brine incubation experiment of hard corals (Stylophora pistillata, Acropora tenuis, and Pocillopora verrucosa) there were an overall decrease in coral performance and changes in the corals’ physiology. Symbiodinium abundance, protein content and heterotrophic abundances were significantly reduced at the end of the incubation in all three species. In particular, the addition of phosphonate-based antiscalant to a 10% salinity increase reduced the amount of corals tissue symbionts, calcification rates and oxygen production rates. These results suggest that coral reefs may be susceptible to exposure to SWRO discharge and calls for careful selection of locations of SWRO facilities around coral reefs.

Various marine species have various response and resilience to increased salinity and brine discharge. To increase SWRO facilities sustainability and minimize their footprint in the coastal environment, sufficient mixing of the brine effluent is important. Diffusor systems generally provide the best mixing, but co-location of SWRO facilities with power plants, already discharging cooling water, minimizes additional impacts of the brine. Local monitoring of the marine benthic environment is encouraged in locations of proposed desalination facilities.