Chemical Competition between Microscopic Stages of Macrocystis pyrifera and Five Native Kelp Species: Does Giant Kelp Always Lose?

The giant kelp Macrocystis pyrifera is often considered competitively dominant to other kelp species due to its high productivity. However, on the microscopic level, previous studies found that Macrocystis can be inferior to other kelp species through microscopic interspecies chemical competition. Recruitment failure can be caused by neighboring kelps because there is no species specificity in the stereochemistry of the signaling chemical used during reproduction to initiate spermatozoid release; therefore, Macrocystis spermatozoid release is pre-empted by that of its competitors. To date, this interaction has been tested between Macrocystis and only one other kelp taxon, Pterygophora. To test whether Macrocystis is always chemically outcompeted microscopically, I investigated the competitive outcome, by tracking sporophyte production, between Macrocystis and five native kelps using laboratory studies. Tests with Pterygophora californica and Ecklonia arborea showed asymmetric results indicating that Macrocystis was the inferior kelp. Studies using Alaria marginata and Egregia menziesii found symmetric results where both competing species did poorly in the presence of Macrocystis. Lastly, when Macrocystis was settled with Postelsia palmaeformis, there was no significant difference in sporophyte production between polycultures and monocultures for either species. These results indicate that the competitively superior species will vary depending on the specific species interaction

Ecological and Engineering Approaches to Optimizing Algal Biofuels

Algae are ubiquitous in natural ecosystems and have been studied extensively due to their versatility for biofuel production. Most of these studies have been conducted on the grounds of synthetic biology and process engineering with few industrial scale projects considering algal community interactions. Such interactions have often indicated the propensity of increasing overall productivity and reducing community invasability, both important characteristics for scalable projects. However, over 30,000 species of algae have currently been identified with another 20,000 estimated to exist. Within this context, elucidation of these relationships remains extremely resource and time intensive. This thesis outlines a strategy for rapid, high-throughput screening of algal community combinations using a microfluidic platform to synthesize millions of parallel, nanoliter-scale algal communities for analysis of biomass accumulation. Model communities were first studied in a bench scale flask experiment and then examined using microfluidic droplets. These experiments showed consistent results on both positively and negatively interacting algal bicultures. Specifically, these include better performance within bicultures of Ankistrodesmus falcatus and Chlorella sorokiniana as well as Chlorella sorokiniana and Selenastrum minutum with lower performance within the biculture of Selenastrum capricornutum and Scenedesmus ecornis. Biofuels provide a unique opportunity for market penetration in one dominated by petroleum based fossil fuels. They serve as renewable and significantly less carbon intensive alternatives. While the holistic success of algal biofuels will hinge on an amalgamation of these scientific fields, rapid screening of algal communities could prove imperative for discovering community interactions and ideally facilitating a mechanistic analysis of how such interactions arise in natural communities.Master of ScienceNatural Resources and EnvironmentUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/117666/1/DNCarruthers_Thesis_Final.pd

A Recommendation for Polyculture Agriculture to Reduce Nitrogen Loading That Leads to Hypoxia

The natural cycle of nitrogen is an essential part of both plant growth and crop production, but in recent years there has been an increase in nitrogen through the use of synthetic fertilizers. Agricultural surface runoff can carry away the converted, mobile nitrate nitrogen into downstream systems leading to an unnatural influx of nitrogen. This increased nutrient load can stimulate algal growth in the marine ecosystem which can cause an oxygen depletion. When the dissolved oxygen levels fall, the area is deemed ‘hypoxic’ and can no longer support most aquatic life. In recent decades, industrial agriculture has used monoculture practices, which are heavily governed by the use of synthetic fertilizers, to meet crop demand but employing the practices year after year strip away nutrients from the soil. In response, best management practices (BMPs) have been established to reduce the use of synthetic fertilizers and their adverse effects on the environment but a lesser used agricultural practice is polyculture, although utilizing these practices also reduces nitrogen demand. This study looked into both BMPs and polyculture in a comparative light to showcase the benefits of utilizing polyculture practices to reduce both nitrogen demand and hypoxic conditions in downstream systems. A focus was also made to provide recommendations as to when and where polyculture agriculture should be employed to maximize the benefits

METHANOGEN METABOLIC FLEXIBILITY

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are terpene compounds, as methanogen membranes are composed of isoprenoid lipids resulting in a higher flux through isoprenoid biosynthetic pathways compared to Eukarya and Bacteria. To assess the metabolic plasticity of methanogens, our laboratory has engineered the methanogen Methanosarcina acetivorans to produce the hemiterpene isoprene. We hypothesized that isoprene producing strains would result in a decreased growth phenotype corresponding to a depletion of metabolic precursors needed for isoprenoid membrane production. We found that the engineered methanogens responded well to the modification, directing up to 4% of total towards isoprene production and increasing overall biomass despite the additional metabolic burden. Using flux balance analysis and RNA sequencing we investigated how the engineered strains respond to isoprene production and how production can be enhanced. Advisor: Nicole R. Bua

A Comparative Plague Study of Cacao Fungal Disease in Cacao Pods Within Monocultures and Indigenous Agroforests in Ecuador’s Napo Province

This study analyzes the composition of three major fungal diseases in Theobroma cacao fruits compared between monocultures and chakra agroforests in the Napo province of Ecuador with the goal of noting similarities and differences in the disease composition between the two systems, as well as investigate possible variation within this poorly understood category of agroforest to better structure future studies. Cacao pods on sampled trees were counted and fungal infections identified visually and by touch. Chakra systems were selected in the communities of Cinco de Enero and Seis de Marzo to the Southwest of Tena, Ecuador. Monoculture data was collected from Chonta Punta, Ecuador, East of Tena. Black pod rot (Phytophthera spp.) was the most prevalent disease affecting cacao pods in chakra systems, followed closely by frosty pod rot (Moniliopthera roreri). Monocultures exhibited significantly lower proportions of black pod rot and instead were dominated by infections of frosty pod rot. Witches’ broom (Moniliopthera perniciosa) was the least present in both. Overall, monocultures had a much lower rate of infection than chakra systems, likely explained by differences in management intensity, lower rainfall, and differences in cacao. More than half of young pods in both systems were lost due to cherelle wilt, a poorly understood physiological condition with tenuous ties to fungal disease. Subvarieties of cacao nacional exhibited little difference in disease composition, with similar slight differences being observed along an age gradient of cacao trees. Overall, these findings suggest that chakra cacao systems in Tena’s climate suffer greater losses to disease than neighboring monocultures to the East under and would benefit from continued research on responsible factors and the increased application of cultural management practices

Prioritizing food security and livelihoods in climate change mitigation mechanisms: Experiences and opportunities for smallholder coffee agroforestry, forest communities and REDD+

Growing attention to climate change around the world has led to a wide array of policy measures to mitigate its effects. In the tropics, this has led to the proposal of mechanisms to change land use patterns in order to reduce carbon emissions, or promote carbon capture and storage. The rural communities that depend on these resources have increasingly been included in discussions around these mechanisms, in the hopes that rural development could be promoted simultaneously with climate change mitigation. Success in achieving these dual goals has been elusive however, driving continued debates around which territories, actors and mechanisms are best suited to support these efforts. This policy brief examines these issues in the light of new research on smallholder coffee agroforestry, recent evidence on sustainable forest management, and experiences with reduced emissions from deforestation and degradation, forest conservation, sustainable management of forests, and the enhancement of carbon stocks (REDD+). In Mesoamerica, it is becoming increasingly clear that smallholder coffee farmers and forest communities can contribute significantly to mitigate climate change, yet existing mechanisms have offered few avenues for benefitting these actors, and in some cases even threaten to undermine their livelihoods. This work examines these challenges and proposes alternative approaches to climate change mechanisms that could generate opportunities to more meaningfully incorporate and benefit local actors

What goes in and what comes out: A scoping review of regenerative agricultural practices

This scoping review examined peer-reviewed and gray literature to explore what a “no-to-low external input” statement means for regenerative agriculture. Five organic amendment inputs (compost extract, manure, mulch, biochar, food systems waste) and four land management processes (livestock management and integration, crop diversity, tillage reduction, comprehensive approach) were identified. Findings include “no-to-low external input” models arising from processes which function to displace external inputs (e.g., synthetic fertilizer). Organic amendment inputs and regenerative land management processes promote biology and improve nutrient cycling at soil, farm, and landscape scales. Regenerative agriculture overlaps with other farming practices including those associated with agroecology and conservation agriculture

From uniformity to diversity: a paradigm shift from industrial agriculture to diversified agroecological systems

Today’s food and farming systems have succeeded in supplying large volumes of foods to global markets, but are generating negative outcomes on multiple fronts: widespread degradation of land, water and ecosystems; high GHG emissions; biodiversity losses; persistent hunger and micro-nutrient deficiencies alongside the rapid rise of obesity and diet-related diseases; and livelihood stresses for farmers around the world. Many of these problems are linked specifically to ‘industrial agriculture’: the input-intensive crop monocultures and industrial-scale feedlots that now dominate farming landscapes. The uniformity at the heart of these systems, and their reliance on chemical fertilizers, pesticides and preventive use of antibiotics, leads systematically to negative outcomes and vulnerabilities. What is required is a fundamentally different model of agriculture based on diversifying farms and farming landscapes, replacing chemical inputs, optimizing biodiversity and stimulating interactions between different species, as part of holistic strategies to build long-term fertility, healthy agro-ecosystems and secure livelihoods, i.e. ‘diversified agroecological systems’