Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

Marine chromophoric dissolved organic matter (CDOM) and its related fluorescent components (FDOM), which are widely distributed but highly photobleached in the surface ocean, are critical in regulating light attenuation in the ocean. However, the origins of marine FDOM are still under investigation. Here we show that cultured picocyanobacteria, Synechococcus and Prochlorococcus, release FDOM that closely match the typical fluorescent signals found in oceanic environments. Picocyanobacterial FDOM also shows comparable apparent fluorescent quantum yields and undergoes similar photo-degradation behaviour when compared with deep-ocean FDOM, further strengthening the similarity between them. Ultrahigh-resolution mass spectrometry (MS) and nuclear magnetic resonance spectroscopy reveal abundant nitrogen-containing compounds in Synechococcus DOM, which may originate from degradation products of the fluorescent phycobilin pigments. Given the importance of picocyanobacteria in the global carbon cycle, our results indicate that picocyanobacteria are likely to be important sources of marine autochthonous FDOM, which may accumulate in the deep ocean

Novel analytical approaches to investigate structure, source, and cycling of marine dissolved organic nitrogen

Throughout most of the world’s oceans, the bioavailability of marine dissolved organic nitrogen (DON) acts to limit marine primary production and thus is a key control on marine biogeochemical cycles and carbon sequestration. Understanding the processes that control marine DON cycling and availability, and by extension long-term carbon storage in the ocean, are thus of vital importance. Nevertheless, despite significant research, the mechanisms that lead to the accumulation of refractory DON (RDON) largely remain an enigma. In this thesis, I address this knowledge gap by investigating the source and degradation processes of traditionally studied younger, high molecular weight (HMW) DON and, for the first time, directly isolated older, low molecular weight (LMW) solid phase extracted (SPE) DON. I used a range of novel proxies and analytical approaches, including a new suite of D-amino acids and the first compound-specific specific amino acid measurements across the DON age/size spectrum. These powerful molecular level proxies for proteinaceous marine DON source and cycling allowed me to posit a new theory for bacterial control of RDON production. Finally, I pair these analyses with broader advanced solid state NMR techniques to present new information regarding overall marine DON chemical composition. Together, I use these data to propose a novel theory regarding production of the most refractory nitrogen containing molecules in the ocean, suggesting a fundamental paradigm shift in our understanding of the marine DON pool

ClimateWEST: A Climate Science Activity

Data literacy and the ability to synthesize and communicate complex concepts are core components of modern scientific practice. Here we present the design and implementation of an inquiry activity about climate variability that was taught as a part of the University of California, Santa Cruz (UCSC) Workshops for Engineering & Science Transfers (ClimateWEST) in 2019. The two-day activity introduced interdisciplinary undergraduate and community college transfer students pursuing graduate school to the field of climate science through a series of inquiry activities. Climate science is a complex topic, and research shows that there are certain concepts that are particularly difficult to grasp. Our climate activity focused on disentangling some of those misconceptions, by emphasizing the following themes or core dimensions of climate variability: (1) Climate varies on both shorter timescales (e.g. seasonal or annual cycle) and on longer timescales (e.g. climate change); (2) Both climate and climate trends vary spatially/geographically and are different from global climate; and (3) Climate is complex and includes not only temperature but also other key variables such as precipitation, ice, wind, ocean circulation, etc. We discuss the inquiry components, assessment-driven tools, facilitation and equity and inclusion design, as well as summarize students' progress toward our goals in the activity

Stable carbon isotope amino acids fingerprints of estuarine and freshwater macrophyte and terrestrial primary producers

Plant material was collected from aquatic and terrestrial environments from the Sacramento-San Joaquin River Delta. Carbon isotope values of bulk plant tissue and individual amino acids were measured. Fifty-five specimens were collected, including trees, shrubs, forbs, and grasses as well as floating, submerged, and emergent aquatic plants. Bulk tissues were processed and the carbon isotope values were measured following Tipple and Ehleringer, 2018 (Oecologia, 187, 1053-1075). Amino acids were hydrolyzed, derivatized, and isolated following Vokhshoori et al., 2013 (Marine Ecology Progress Series, 504, 59-72). Carbon isotope values of individual amino acids were measured following Vokhshoori et al., 2013. The purpose of this study was to assess if amino acid fingerprints of macrophyte primary producers were distinct from those of marine primary producers and terrestrial vascular plant species. The goal of this study was to provide a benchmark dataset for the next generation of food web monitoring programs within estuarine and mixed source environments

A new molecular isotopic toolkit to examine estuarine food webs and biogeochemistry: Compound specific isotope analyses of amino acids from aquatic and terrestrial plants of the Sacramento-San Joaquin

Aquatic and terrestrial plant materials were collected from the Sacramento-San Joaquin Delta region. Carbon and nitrogen isotope values of individual amino acids and bulk materials were measured. Fifty-six specimens were collected from three locations within the Delta, two flooded islands, Mildred and Liberty Islands, as well as an adjacent terrestrial riparian habitat (Big Break Regional Shoreline). Specimens included terrestrial trees, shrubs, forbs, and grasses as well as floating, submerged, and emergent aquatic plants. Bulk leaf tissues were processed and the carbon and nitrogen isotope values of bulk tissues were measured following Tipple and Ehleringer, 2018 (Oecologia, 187, 1053-1075). Amino acids were hydrolyzed, derivatized, and isolated following Vokhshoori et al., 2013 (Marine Ecology Progress Series, 504, 59-72). Carbon and nitrogen isotope values of individual amino acids were measured following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (PLoS ONE, 9, 6, e98087), respectively. The purpose of this research was to create a novel molecular isotope toolset to increase the understanding of biogeochemistry and food web structure of the Sacramento-San Joaquin Delta's tidal wetlands and estuarine marshes

Amino acid nitrogen isotopic analysis of aquatic and terrestrial plants from an estuarine delta

Aquatic and terrestrial plants were collected from the Sacramento-San Joaquin River Delta. Nitrogen isotope values of bulk plant tissue and individual amino acids were measured. Fifty-six specimens from thirty-nine native, introduced and invasive species were collected. Growth forms and habits include trees, shrubs, forbs, and grasses as well as floating, submerged, and emergent aquatic plants. Bulk tissues were processed and the nitrogen isotope values were measured following Tipple and Ehleringer, 2018 (Oecologia, 187, 1053-1075). Amino acids were hydrolyzed, derivatized, and the carbon isotope values of individual amino acids were measured following Vokhshoori and McCarthy, 2013 (PLoS ONE, 9, 6, e98087). The purpose of this study was to assess trophic discriminate factors at the base of estuarine systems with multiple primary producers. This study provides an authentic dataset of primary producers for trophic position assessments in estuarine and mixed terrestrial-marine source environments

δ13C analyses of amino acids from co-occurring clams in the San Francisco Bay-Sacramento/San Joaquin Delta

Carbon isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 2.1 and processed following Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from clam muscle tissue, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). The measurement of the carbon isotope values of individual amino acids were conducted following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087), respectively

Seasonal variations in the compound specific isotope analyses of amino acids from co-occurring clams in the San Francisco Bay-Sacramento/San Joaquin Delta

Amino acids were isolated from the muscle tissue of Corbicula fluminea and Potamocorbula amurensis; two co-occurring invasive clams within the San Francisco Bay-Delta system. Clam specimens were collected near Montezuma Slough (Contra Costa County, California) at the confluence of the Sacramento and San Joaquin Rivers twice during the hydrological extremes of 2010 water year (November, 2009 and May, 2010). Carbon and nitrogen isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 2.1 and processed following Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from clam muscle tissue, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). The measurement of the carbon and nitrogen isotope values of individual amino acids were conducted following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087), respectively. The purpose of this study was to monitor biogeochemistry during 2010 water year and assess dietary difference between two co-occurring invasive species. This study focused on two species, C. fluminea and P. amurensis, benthic sessile primary consumers that can inhabit the same environment. USGS Site 2.1 was specifically selected as it exhibited the environmental conditions where both clam species co-existed during 2010 water year. This design allowed for interspecies variation to be explored. Nitrogen isotopes of amino acids were used to isolate variations in nutrient baseline from dietary changes across the season between the two species. Carbon isotopes of amino acid were utilized to understand the diet of the two species at two points in the season

A twenty-year record of carbon isotope values of amino acids from Potamocorbula amurensis

Amino acids were isolated from the muscle tissue of Potamocorbula amurensis, an invasive clam species, collected from two locations in the northern portion of the San Francisco Bay. Clam specimens were collected biannually in 1997, 2002, and from 2009-2017 at both locations. The carbon isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 4.1 (Suisun Bay) and 8.1 (Carquinez Strait) in the San Francisco Bay and processed as described in Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from P. amurensis, derivatized, isolated and the carbon isotope values were measured following Vokhshoori et al. (2013; doi:10.3354/meps10746). The purpose of this study was to assess long-term changes in dietary sources and/or changes in the baseline carbon isotope value of the estuary's food-web following the invasion of P. amurensis

δ15N analyses of amino acids from co-occurring clams in the San Francisco Bay-Sacramento/San Joaquin Delta

Nitrogen isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 2.1 and processed following Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from clam muscle tissue, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). The measurement of the nitrogen isotope values of individual amino acids were conducted following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087), respectively