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These supplementary teaching resources align to the open textbook, Fish, Fishing, and Conservation which is a 389-page, peer-reviewed publicly-available, openly-licensed textbook intended for undergraduate students who are exploring majors in Fish & Wildlife. It is also relevant to a general audience or for use in courses which explore social and ethical aspects of fish, fishing and conservation. The open textbook, Fish, Fishing, and Conservation, is freely available at https://doi.org/10.21061/fishandconservation Supplementary teaching resources include a sample course syllabus, schedule, and a variety of assignments. Individuals who wish to share their materials relevant to teaching in this subject area are encouraged to join and share their openly-licensed resources via the Fish, Fishing, and Conservation Instructor Group in OERCommons Are you reviewing or adopting Fish, Fishing, and Conservation for a course? Please help us understand your use by completing this form https://bit.ly/fishandconservation_interest VIVA (Virtual Library of Virginia)

The creation, movement, and consumption of distinct biomolecules by marine organisms has far reaching implications regarding ecosystem material and energy flow and how we manage the marine environment. Lipids are ubiquitous, energy rich biomolecules that are essential for all life and are used for cell membrane structure, energy storage and serve as useful indicators for ecosystem and food web dynamics. In this dissertation, the flow of specific lipid biomolecules through multiple marine environments is measured, explored, and clarified to better understand biogeochemical cycles, marine food webs and ecosystem connectivity. In the first chapter of my dissertation, I measure, quantify, and close the loop of the open ocean microbial hydrocarbon cycle, with implications for priming effects of the ocean microbiome to oil spills. It is estimated that seeps, spills, and other oil pollution introduce ~ 1.3 million tons (1.3 Tg) of hydrocarbons into the ocean each year. Additionally, it is known that globally abundant marine cyanobacteria Prochlorococcus and Synechococcus which account for ~25% of ocean net primary production also produce hydrocarbons from fatty acids. But little is known about the size, turnover and fate of these cyanobacterial hydrocarbons and the implications for the ocean’s microbiome response to future oil spills. From a research expedition in the North Atlantic, I report that cyanobacteria in an oligotrophic gyre mainly produce n-pentadecane which correlates tightly with fluorescence and Prochlorococcus abundance in oligotrophic waters. Using chemical and isotopic tracing I find that pentadecane production and diel dynamics mainly occurs in the lower euphotic zone at the deep chlorophyll maximum. I estimate the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100 to 500-fold, with cyanobacteria producing ~ 130-650 million tons of pentadecane per year. Analysis of sinking particles at the base of the euphotic zone show that nearly all pentadecane (< 0.001 % remaining) is consumed within the euphotic zone, suggesting near complete consumption of these hydrocarbons by hydrocarbon degrading microbes. These findings characterize a wide-spread microbial hydrocarbon cycle that selectively primes the ocean’s microbiome with long-chain alkanes. In the second chapter of my dissertation, I conduct a large-scale feeding experiment on a symbiotic reef-building coral (Stylophora pistillata) in the Red Sea to clarify fatty acid and isotopic biomarker patterns of coral heterotrophy for use in the field. Coral heterotrophy is an often-overlooked facet of coral nutrition that provides essential nutrients that help corals resist and recover from thermally induced bleaching that is degrading reef ecosystems around the world due to rising global ocean temperatures. Yet, methods for measuring coral mixotrophy, the balance between organic matter contributions to the coral host from autotrophic photo endosymbionts and heterotrophy on particles and plankton have typically been too coarse to elucidate source contributions. Through my experiment I show that fatty acids and isotopic biomarkers reliably separate experimental and reef nutritional source groups (heterotrophic or autotrophic). I show that heterotrophic fatty acid biomarkers are reliably recorded into coral host and symbiont tissues, with a divergent metabolic pattern of autotrophic biomarkers as feeding increases due to positive feedback of heterotrophy on the in hospite photo symbiont population. Additionally, I show that nitrogen and essential fatty acids are preferentially recorded into coral tissue while most heterotrophic carbon is respired or exuded as mucous; this shows that the use of bulk carbon isotopes as a feeding proxy for the last ~ 40 years is largely underestimating the contribution of heterotrophy to the trophic ecology of reef building corals. Overall, this finding underscores a connectivity between oceanic phyto- and zooplankton and reef-building coral. In the third chapter of my dissertation, I explore the mixotrophic differences of divergent bleaching responses of Acropora hyacinthus colonies on the forereef of Mo’orea during the 2019 mass bleaching event. During this bleaching event, all colonies of A. hyacinthus on the deep forereef (14 m) bleached and recovered, while colonies on the shallow forereef (5 m) near the reef crest resisted bleaching entirely, despite the same temperature stress. Using fatty acid and isotopic biomarkers I show through several lines of evidence that bleaching resistant colonies near the reef crest were likely consuming more particulate organic matter than deep forereef colonies. This conclusion is supported by isotopic feeding proxies, less isotopic niche overlap of the host and symbiont of resistant colonies, and larger proportions of putative POM fatty acid biomarkers in the host of resistant colonies relative to recovered colonies. This interpretation is in line with observations that benthic communities on the reef crest are a net sink of oceanic POM and that increased reliance on heterotrophy is associated with bleaching resistance. These data show the vital importance of reef environment, coral heterotrophy, and planktonic subsidies in structuring bleaching response of corals in a warming ocean and ultimately show that the reef crest may serve as a potent zone for reseeding coral populations after marine heat waves.

Understanding what factors shape the magnitude of divergence under rapid evolution is critical. Phenotypic divergence, specifically, can be influenced by selective forces such as the environment (climate, geographic distance) as well as non-selective forces (genetic composition of the founding population). Threespine sticklebacks provide a unique opportunity to study the magnitude of divergence under rapid evolution. Marine sticklebacks independently colonized freshwater habitats at the end of the last ice age (~12,000 years ago) generating multiple replicate pairs that represent a natural experiment. However, studies rely on untested assumptions that marine sticklebacks are not phenotypically varied and are unchanged from their ancestors. Here, we test how differential environmental conditions impact the estimated magnitude of phenotypic divergence and parallelism of independent freshwater stickleback populations. We find that marine variation is comparable to freshwater variation. Importantly, the inferred magnitude of phenotypic divergence of each freshwater population is dependent on marine sampling location. The geographic distance and environmental similarity between the marine and freshwater pairs explain a significant degree of variance. When estimating the degree of parallelism among freshwater pairs, marine reference also affects the inferred magnitude. The observed pattern suggests the choice of reference population and its geographic distance are important aspects to consider when estimating freshwater divergence and parallelism. Results also implicate a signature of local adaptation and/or isolation by distance. We provide recommendations for choosing ecologically relevant marine references in future studies on this important evolutionary model system.

Widespread overuse and large-scale production of antibiotics create antibiotic pollution, disrupting environmental microbiota and creating a public health risk. Highly urbanized coastal environments can be under high impact from antibiotic pollution from many trails of polluted effluents and runoff. The city of Long Beach is one such coastal area under high impact, since it is highly urban, industrialized, and experiences frequent sewage spills. We collected water samples from the LA River in a transect running southwest into the San Pedro Channel in order to investigate (1) how does strength of antibiotic resistance change as distance from shore increases, and (2) does antibiotic resistance correlate with composition of the bacterial community. There was no consistent relationship between strength of antibiotic resistance and distance from shore. Instead, we found that bacteria from the Pacific Ocean showed higher antibiotic resistance than bacteria from the LA River in five out of eleven antibiotic treatments. We also found that the alpha diversity of bacterial communities was lower in the LA River samples compared, and alpha diversity positively correlated with strength of antibiotic resistance in four antibiotic treatments. Our findings highlight how prevalence of antibiotic pollution does not always follow a distance dilution, as well as the need for understanding the strength behind antibiotic resistance in marine bacteria.

Marine Protected Areas (MPAs) have been implemented worldwide as a tool for improving the overall health and function of fisheries and marine ecosystems impacted by fishing activity. Monitoring the performance of MPAs in a comprehensive way is crucial for the effective management and thoughtful implementation of new MPAs. In California, mesophotic (30-100m) rocky reef fish communities are a valuable commercial/recreational resource, though the effects of MPAs on this community remain relatively understudied. This is at least partially a result of depth restricted sampling tools that do not typically overlap; SCUBA surveys are generally limited to shallow depths (<30 m) and Remotely Operated Vehicle/Autonomous Underwater Vehicle surveys are often used for deep water (>100m). Additionally, traditional extractive techniques like trawl surveys are limited by their inability to effectively sample high relief rocky habitats, and are not commonly used in MPAs due to their destructive nature. With this study we tested the effects of two MPAs on demersal fish communities living on mesophotic rocky reefs utilizing Baited Remove Underwater Video (BRUV) surveys. We deployed BRUV landers annually from 2019 to 2021 at Anacapa State Marine Reserve/State Marine Conservation Area (SMR/SMCA) and Carrington Pt. SMR. We observed significant positive reserve effects on the total biomass of targeted (i.e., fished) species and on the size structure of individual focal species at both study sites. Relative abundance (MaxN) proved to be a less sensitive metric than biomass for detecting MPA effects, underscoring the utility of a stereo-video camera system that is capable of capturing highly accurate fish measurements. Dissimilar rocky habitat abundance for the deepest depth zones at Anacapa Island, where rockfish (Sebastes spp.) represent the largest proportion of the fish community, is likely one explanation for the negative reserve effect we observed for targeted rockfish abundance at this site. The results of this study provide useful information on how two California MPAs affect valuable fish communities that have historically been understudied and emphasize the importance of accurate fish measurement to detect these effects. This work also highlights the significance of habitat availability on the distribution of species with high habitat affinity. The continued monitoring of demersal fish communities on mesophotic rocky reefs would provide resource managers a more comprehensive understanding of MPA performance in California.

The surface temperature in the Arctic has warmed at twice the rate of the global mean temperature during recent decades. This Arctic amplification of global warming has been a striking feature of climate change, and many studies have investigated what processes contribute to this phenomenon. Many of these processes are often described in the context of climate feedbacks using analyses focused on top-of-the-atmosphere radiative changes. In this context, regional surface warming can then be partitioned into contributions from each feedback process. However, this partitioning can be complicated by interactions between feedbacks themselves and atmospheric heat transport. In the second chapter, we instead apply a feedback-locking approach and evaluate the resulting changes in surface temperature. These results are strikingly different from previous feedback analyses, highlighting the important role of interactions within the climate system. This chapter and many other previous studies focus only on the role of atmospheric and surface processes in Arctic amplification. However, substantial questions remain regarding the role of ocean heat transport. In the third chapter, we investigate changes in oceanic heat fluxes under global warming. We find a mechanism associated with the presence of sea ice that drives enhanced horizontal ocean heat transport into the Arctic region and can contribute substantially to Arctic amplification if this heat is allowed to reach the surface. Currently, only a small amount of the heat stored at depth in the Arctic Ocean can reach the surface, but recent observational studies have argued that sea ice retreat could result in enhanced vertical mixing. In the fourth chapter, we investigate the impacts of a positive feedback whereby increased vertical mixing due to sea ice retreat causes the previously isolated subsurface Arctic Ocean heat to melt more sea ice. We find that an abrupt “tipping point” can occur under global warming, with an associated hysteresis window, for a limited range of parameters. Throughout the thesis, we use idealized models to show how ocean and climate processes can impact Arctic warming, providing insights into possible physical mechanisms that could be at play now or in the future.

We combine consistently dated benthic carbon isotopic records distributed over the entire Atlantic Ocean with numerical simulations performed by a glacial configuration of the Norwegian Earth System Model with active ocean biogeochemistry, in order to interpret the observed Cibicides δ13C changes at the stadial-interstadial transition corresponding to the end of Heinrich Stadial 4 (HS4) in terms of ocean circulation and remineralization changes. We show that the marked increase in Cibicides δ13C observed at the end of HS4 between ~2000 and 4200 m in the Atlantic can be explained by changes in nutrient concentrations as simulated by the model in response to the halting of freshwater input in the high latitude glacial North Atlantic. Our model results show that this Cibicides δ13C signal is associated with changes in the ratio of southern-sourced (SSW) versus northern-sourced (NSW) water masses at the core sites, whereby SSW is replaced by NSW as a consequence of the resumption of deep water formation in the northern North Atlantic and Nordic Seas after the freshwater input is halted. Our results further suggest that the contribution of ocean circulation changes to this signal increases from ~40 % at 2000 m to ~80 % at 4000 m. Below ~4200 m, the model shows little ocean circulation change but an increase in remineralization across the transition marking the end of HS4. The simulated lower remineralization during stadials than interstadials is particularly pronounced in deep subantarctic sites, in agreement with the decrease in the export production of carbon to the deep Southern Ocean during stadials found in previous studies.

Knowledge gaps pertaining to the remediation of freshwater lakes impacted by oil spills have persisted despite recent record highs for oil production and transportation across vulnerable regions in North America. The multiyear Freshwater Oil Spill Remediation Study (FOReSt), conducted at the IISD-Experimental Lakes Area in Canada, is focusing on the efficacy of minimally invasive methods for remediating oil spills in freshwater boreal lakes. In this thesis, the impacts and remediation of diluted bitumen (dilbit) and conventional heavy crude oil (CHV) spills were investigated (year 1), as were a variety of different remediation methods for spills of dilbit on different shoreline substrates (year 2). Two common small-bodied fish, fathead minnows (Promephales promelas) and finescale dace (Chrosomus neogaeus), were used to assess exposure to petrogenic polycyclic aromatic compounds (PACs) in model enclosed shoreline ecosystems impacted by spills and remediated using minimally invasive techniques. Short-term exposure to PACs, the most toxicologically relevant compounds in oil, was assessed in fish using biliary metabolite concentrations. In year one, finescale dace and fathead minnows residing in oil treated enclosures each had biliary pyrene metabolite concentrations that were positively correlated with pyrene concentrations in the water of the enclosures. Three months after the initial spills, fish in the enclosure receiving dilbit were significantly more exposed to PACs than fish in reference enclosures that did not receive oil. In year two, both finescale dace and fathead minnows residing in oil-treated exposures, regardless of shoreline substrate, showed increased exposure to PACs compared to fish in reference enclosures and the pristine lake environment two and a half months after the spills. No significant differences in exposure were observed among the remediation treatments. Biliary PAC metabolite concentrations were positively predicted by parent PAC concentrations in periphyton. PACs in periphyton two and a half months after oil introduction were positively correlated with PACs in the enclosures one week after spills, suggesting fish also had increased exposure to periphyton-bound alkyl-PACs. This thesis validates the use of small-bodied fish in assessing PAC exposure following freshwater oil spills and demonstrates the difficulties in estimating exposure using environmental concentrations in natural systems.

The environment during early life history strongly impacts phenotypic development in all organisms, which further influences developmental trajectory and ecological fitness later in life. Depending on the developmental stage and magnitude of change in the environment, phenotypes may become irreversible and thus have a long-lasting effect later in life. This thesis was designed to better understand how changes in the environment may influence plasticity and variation of metabolic phenotypes of Lake Sturgeon (Acipenser fulvescens) within the first year of life. Broadly speaking, the thesis tested two hypotheses that 1) all measured phenotypes would be plastic; and 2) durations of environmental effects on phenotypic development would be correlated with distinct developmental windows. Studies were developed to examine 1) short-term effects of temperature or diet on metabolic phenotypes such as metabolic rate, energy density, fatty acid profiles, and growth (Chapters 2 and 3) and 2) longer-term effects of temperature or diet during early life on these metabolic phenotypes (Chapters 4, 5 and 6). The first experimental chapter (Chapter 2) examined ontogenetic development of metabolic rate and demonstrated that dietary shifts between Artemia to bloodworm resulted in cessation of growth with elevated routine metabolic rate. Chapter 3 examined how fatty acid profiles and plasma cortisol concentration were influenced by environmental temperature and showed that decreasing temperature led to increases in mono- and polyunsaturated fatty acids in both phospholipids and triglycerides, and food deprivation resulted in lack of difference between baseline and peak cortisol concentrations. Chapter 4 examined how temperature during early life influenced plasticity of growth and showed that temperature post-dietary transition resulted in a transient effect on growth and energy metabolism without long-term effects post-winter. Chapter 5 examined how temperature during early life could influence growth and fatty acid metabolism when fish were exposed to colder temperatures later in life and demonstrated that elevated temperatures resulted in a longer-term effect on growth but lack of transcriptional responses of desaturating fatty acids when exposed to a cold temperature (3.5°C) later in life. The final experimental chapter, Chapter 6 examined longer-term effects of diet at the onset of exogenous feeding on metabolism and growth and demonstrated that an enriched diet resulted in prolonged effects on growth, digestive enzyme activity and survival prior to a simulated overwintering. This doctoral thesis research revealed that all measured metabolic phenotypes were plastic, but subtle changes in temperature and diet during early life history resulted in transient or prolonged effects on growth and metabolism in age-0 lake sturgeon. Results will aid our understanding of cohort and population dynamics as well as contribute to the development of conservation strategies for lake sturgeon, a species at risk or endangered across its natural range.

Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.