As increasing human demand and decreasing in global reserve, fossil fuel will no longer be able to sustain human energy usage in the near future. Algae based biofuel is an alternative energy source that has the potential to replace the demand of fossil fuel due to the high productivity and minimum land usage. However, considering the high cost, algae biofuel is not ready for practice in large industrial scale. Scientist put a lot of efforts on modifying algae genome to improve their productivity. But the ecological approach on create algae productive communities has been rarely practiced. In this study we tested how algae biomass productivity and resistance by grazers affected by algal species diversity. 11 different species of single celled algae were assigned into different combinations, and the changing in chlorophyll-α concentration and cell number for each treatment group has been recorded as the reference of cell productivity. Daphnia was introduced into the culture to test the ability to resist consumer grazing for each combination. There is no liner relationship among algae diversity, biomass productivity and resistance to Daphnia grazing. The biomass productivity and the ability to resist Daphnia grazing varies widely between combinations. Overyielding only been observed in some specific algae combinations. It is possible to reduce the cost of algae-based biofuel by creating a productive algae community. Extra effort is required to find the desired combination.

In 2014 North American River Otters expanded up the North Fork of the Merced River into previously and historically unoccupied Yosemite Valley. Their range expansion posed the questions: 1) What are river otters preying upon in Yosemite Valley? 2) Could invasive Signal Crayfish provide a prey subsidy that promotes the upward elevational expansion of river otter populations into Yosemite Valley? To answer these questions, otter scats were collected and prey DNA present in the scats was amplified using a metabarcoding approach. The diet data revealed that invasive Signal Crayfish were present in 100% of scats collected and native Sacramento Sucker was present in only 16% of the scats. These results indicate that invasive Signal Crayfish are the most important diet species in the river otter diet, and the invasion of the Yosemite Valley by Signal Crayfish may have provided essential nutritional resources that facilitated upward elevational range expansion by river otters from Central Valley drainages. This study adds to the body of literature supporting the use of next-generation sequencing technologies and environmental DNA for addressing the ecology of species and ecosystem dynamics in the natural world.

Multiple aspects of the global environment are changing rapidly, including rising temperatures, altered biogeochemical cycles and a redistribution of biodiversity. Different aspects of environmental change may interact through synergistic processes or interference; however, how these processes magnify or dampen one another’s effects on lakes is largely unknown. My dissertation research explores the independent and interactive effects of warming and resource supply on lake food webs from multiple perspectives. Chapter 1 investigates the independent and interactive effects of temperature, supply and origin of dissolved organic material, and atmospheric nitrogen deposition on prokaryotic and eukaryotic microbial community composition and diversity in Sierra Nevada lakes. Chapter 2 focuses on stoichiometry and growth of phytoplankton communities in response to warming, nutrient addition and grazing in three Dutch lakes across a productivity gradient. Chapter 3 explores whether the competition-defense tradeoff regulates coexistence within or among members of phytoplankton communities across a productivity gradient, and how warming may alter this tradeoff. These studies collectively show that resource supply is more important than temperature in regulating microbial community composition and stoichiometry across a variety of lake ecosystems. Additionally, interactive effects of temperature, nutrient supply, and grazing on phytoplankton community stoichiometry, growth rates, biomass buildup and functional group composition depend on the trophic state and size structure of communities. Finally, turnover in communities along productivity gradients resulted in a positive correlation between nutrient and grazer limitation across taxa among lakes, but no relationship between top-down and bottom-up limitation within lakes. This result suggests that traits like small cell size that make phytoplankton more susceptible to grazing also confer strong responses to nutrient pulses in low-nutrient environments. Thus, my results provide no support for the hypothesis that costly defenses against grazing increase nutrient limitation, resulting in a tradeoff between nutrient and consumer limitation. In fact, the opposite pattern was found whereby the taxa that are most sensitive to grazing and nutrients are segregated in the least productive system, and the responses to both factors decline in more productive lakes due to increasing dominance by inedible forms. My thesis demonstrates functional associations among the traits of microbes that shape their responses to climate, resources and consumers, promote diversity at the local and regional scales, and determine how aquatic ecosystem productivity is controlled by multiple limiting factors.

Freshwater ecosystems have less surface area than the oceans but play an outsized role in the global carbon cycle. Organic matter produced in situ or entering as terrestrial detritus may accumulate in sediments, be respired and released as CO2 to the atmosphere, or exported to the ocean. Aquatic decomposition of terrestrial detritus, periphyton primary productivity, benthic invertebrates (decomposers and grazers), and invertebrates that emerge from rivers contribute to the transport of carbon both downstream and between the terrestrial and aquatic ecosystems. I asked how decomposition rate, primary productivity, benthic macroinvertebrate biomass, and emergent macroinvertebrate biomass change with stream order in Yosemite Valley and El Portal, California, USA. In Summer 2019, I collected data at 19 sampling sites in the Merced River and its tributaries (Tenaya Creek and Yosemite Creek). Along with my main variables – decomposition rate, periphyton growth rate, benthic invertebrate biomass, and emergent invertebrate biomass – I considered environmental factors – elevation, temperature, and waterflow velocity. I found faster leaf decomposition at lower elevation and higher temperatures. Also, decomposition declined marginally with increasing invertebrate biomass. Other fluxes and stocks showed no relationship to stream order. Low elevation, high order rivers may therefore become more heterotrophic and release more CO2 to the atmosphere as a result of faster mineralization of allochthonous organic material without apparent compensatory increases in photosynthetic uptake. How the balance of photosynthesis and respiration in ecosystems will respond to climate change is one of the major unknown feedbacks in forecasting the future course of carbon accumulation.

San Diego is known for its temperate Mediterranean climate and beaches; however, human activities that compromise water quality degrade environmental conditions and impose economic and social costs. Urban runoff is one of the most serious threats to San Diego's coastal water quality, contributing to harmful algal blooms, low dissolved oxygen concentrations and impacts on economically important marine and estuarine taxa. Nutrients and toxins originate from residential, agricultural and industrial sources, and the land usage within watersheds determines their loadings. Economic development that improves human well being may either benefit water quality or further contamination of coastal ecosystems. The purpose of this study was to identify relationships between chemical and isotopic indicators of water quality and land usage and watershed socioeconomics composition. I found that areas with low socioeconomic status (SES), mostly in the southern watersheds, exhibited lower water quality scores based on composite indices. Interestingly, coverage of open, developed, impermeable or agricultural land uses was not directly correlated with water quality as I expected. Overall, water quality declined in southern watersheds where residents have the poorest socioeconomic status. My thesis suggests that anthropogenic activity and low socioeconomic status contribute to poor water quality and contamination of coastal environments. The role of economic development in transforming land use and affecting water quality needs to be evaluated in relation to other hydrologic factors that determine export of nutrients from watersheds to the ocean.

Gut microbiota influence their host’s health through pathogenic resistance and immunological responses, nutrient uptake, metabolism, and digestion. A fish’s gut microbiome can be affected by its diet, environment, and host genetics and adaptation. The hybrids of the Owens River Tui Chub and the Lahontan Tui Chub live in freshwater stream and lake habitats within the eastern Sierra Nevada mountains. Fish living in flowing versus still water environments often experience divergent selective pressures leading to differences in behavior, morphology, physiology and diet. My thesis compares gut microbiomes of lake and river populations of wild hybrids of the Owens River Tui Chub and the Lahontan Tui Chub. Five lake populations and two stream populations were sampled and their gut microbiomes were characterized by sequencing the 16s gene. Stream sites had a higher abundance of Firmicutes and Cyanobacteria, while lake sites had a higher abundance of Fusobacteriota. The microbial community composition varied between lake and stream habitats, with habitat type explaining 6% of the variation. However, the population of origin explained 25% of the variation, indicating that population is more important than habitat type for gut microbiomes. In addition to sampling wild fish, a reciprocal transplant experiment was performed where fish were placed in lake or stream mesocosms to ask whether the fish’s microbiome is plastic in response to habitat shifts or determined mainly by the fish’s population of origin. The experiment found that transplanting Tui Chub between lakes and streams resulted in a significant change within the composition of the fish’s gut microbiome, suggesting that the microbiome is highly plastic in response to habitat shifts. These data suggest that gut microbiomes vary between lake and stream populations of Tui Chub, but that geographic location is more important than habitat type. In addition, the gut microbiome is a plastic trait that is under stronger control by host habitat than host phenotype or genotype.

Microbes contribute to aquatic ecosystem functioning and fitness of macroscopic organisms such as freshwater zooplankton. Many factors affect the taxonomic compositions of zooplankton-associated and free-living microbial communities in lakes, yet how these communities change seasonally in lakes remains poorly understood. In this study, we investigate how free-living microbial communities and those associated with different zooplankton host species change in response to fluctuations in their natural environment across time and space. We repeatedly sampled zooplankton and water from six lakes in the eastern Sierra Nevada mountains of California, USA across a summer season. Analysis of 16S rRNA gene sequencing found marginal differences in the compositions of the free-living and zooplankton-associated microbial communities; however, they shared the same dominant classes of bacteria suggesting that horizontal transmission is a main mechanism driving the assembly of freshwater zooplankton microbiomes. The free-living and zooplankton-associated microbial communities significantly changed across the five sampling time points. Out of all measured environmental variables, lake temperature and dissolved organic carbon concentrations were the strongest predictors of microbial community composition. We did not find significant differences in the microbial communities across the six lakes, despite geographical separation, as well as differences in elevation, environmental conditions, and zooplankton community composition. Our results suggest that temporal variation plays a stronger role than spatial variation in shaping zooplankton-associated and free-living microbial communities of alpine lakes.

Global environmental changes are rapidly transforming ecosystems. As a result, populations will face changes in environmental conditions over short timescales that can threaten their persistence. When dispersal to more suitable habitats is not possible, the threat of extinction can be ameliorated through distinct, but non-exclusive biological mechanisms, including phenotypic plasticity, which refers to changes in traits mostly common due to shifts in gene expression, and genetic adaptation by rapid evolutionary shifts in gene frequencies. In my dissertation research, I studied the phenotypic and molecular population responses of a freshwater zooplankton (Daphnia) from Sierra Nevada mountain lakes of California to anthropogenic environmental variation caused by climate change and introduced predators. Hence, populations with different environmental histories may diverge in response to changing selective pressures, such as those caused by such as warming and introduced predators, because they might differ on the level of plasticity and adaptation they show to current environmental conditions. In Chapter 1, I show that different Daphnia populations were equally able to evolve plasticity in response to selection by different temperature regimes for two years in field experiment. This results highlights the importance of evolution of plasticity in response to temperature regime, thus in Chapter 2, I explore whether or not a population of Daphnia exhibits genetic variation that confers shifting plasticity in response to temperature throughout the annual cycle, since there is strong seasonal variability in temperature in most lakes located in temperate climates Studying Daphnia population from Blue Lake I found a marked distinction in plastic responses between Daphnia collected in the beginning and end of the growing season, indicating that seasonal temperature variability has distinct effects on plasticity for different traits. In Chapter 3 I studied the possible molecular mechanisms behind phenotypic response to temperature and how it is affected by predation. I studied two Daphnia genotypes collected from Blue and Gardisky Lakes. Overall our results suggest that both genotypes can reach similar fitness through distinct underlying molecular mechanisms, but also that they have distinct environmental sensitivities to stressors. Together these findings illustrate the variation and the importance of plasticity in addition to the potential for its evolution in maintaining Daphnia populations as key species in freshwater ecosystems, helping to mitigate the effects of climate change on food webs and ecosystem processes.

Interactions among members of ecological communities often vary spatially in response to environmental differences. Yet interactions can also vary spatially as a result of biotic factors such as differences in species traits or variation in other species interactions. It is necessary to understand the conditions under which each of these drivers of variation has an effect in order to predict how species interactions will be affected both by changes in the environment and in biotic communities. In this thesis, I explore mechanisms that may cause species interactions to vary across space at local, regional and continental scales in salt marsh plant communities. Chapter 1 investigates the relationship between the environment (means and variability) and community diversity and stability in time-series data from the east and west coasts of North America. Chapter 2 experimentally investigates the effect of sea-level rise on species interactions within a marsh. Chapter 3 seeks to understand geographic variation in plant interactions among six sites spanning the California coast. Chapter 4 uses a common garden experiment to test whether spatial variation in species interactions are driven by differences among plant populations or the environment. Finally, Chapter 5 describes geographic patterns of variation in herbivore pressure to determine whether herbivory drives regional differences in interactions among plants. I found that changes in mean conditions, including sea level, can affect community diversity, stability and strength of species interactions. Environmental variability only affects community stability and diversity when it is relatively large, so increases in variability with climate change may cause plant community dynamics to become affected by both variability and means. Species interactions vary geographically along the west coast, but unlike on the east coast, do not show consistent trends with latitude. Rather, interaction strengths may differ due to trait variation among plant populations and differences in herbivore pressure. My thesis demonstrates that environmental conditions and local factors, including intraspecific phenotypic variation and herbivory, both determine the nature of species interactions in salt marshes, and that the west coast of North America shows geographic patterns in interactions that are distinct from those found on the east coast.

Temporary freshwater ecosystems like vernal pools sustained by precipitation are a hotbed of diversity with unique species that have evolved life-histories to cope with the impermanence of their environments. Climate change is expected to amplify interannual variation in precipitation in many regions; therefore, future vernal pool ecosystems may face greater uncertainty in hydroperiod. The impact of elevated fluctuations in water supply on aquatic communities in temporary environments is unknown. To understand the response of invertebrate communities inhabiting ephemeral freshwater pools to variation in rainfall, we conducted a mesocosm experiment manipulating rainfall to alter the amount and variability of precipitation over 4 years.

We found that precipitation affected invertebrate abundances, but increasing variability had little effect on population densities and that past conditions are weak predictors of current population levels. The first three years of the experiment coincided with a historic drought in San Diego, CA, while the final year was the second wettest on record. Many aquatic invertebrate species that were present initially became extinct across experimental treatments during the drought, suggesting that some native species cannot survive prolonged periods of drying in small pools. Our results indicate that some vernal pool invertebrate populations are highly resilient to interannual variation in precipitation while others were unable to persist through a historic drought even when precipitation was experimentally enhanced.