The genetics of adaptation to human-dominateD environments

Uncovering the genetic architecture of herbicide resistance in Amaranthus tuberculatus
Herbicide resistance in agricultural weeds is an emerging phenomenon that poses a major challenge to crop production worldwide. Understanding the genetic architecture of resistance––how many genes are involved and what their relative contributions are––is important for predicting how this trait evolves in response to agricultural selection. For most herbicides, the current understanding of resistance genetics is limited to a few large-effect target-site resistance (TSR) mutations affecting herbicide target enzymes. Recent work has shown that, for glyphosate, TSR mutations alone do not explain the full extent of resistance variation observed in the field, suggesting a more complex genetic basis that also includes non-target-site resistance (NTSR) mechanisms. My first PhD project follows up on this observation with a multi-trait GWAS study dissecting the genetic basis and polygenicity of NTSR to three common agricultural herbicides in Amaranthus tuberculatus, a major North American agricultural weed exhibiting widespread resistance to multiple herbicides. By clarifying the basic genetic architecture of herbicide resistance, this study sets the groundwork for more accurate tracking of how resistance evolves across space and time in response to selection by herbicide-wielding farmers.

Monitoring biodiversity in a changing world

Mapping the macrofungal diversity of the Peruvian Amazon
According to one recent estimate, the earth is home to approximately 2.5 million species of fungi, but only about 150,000 have been described by science. While just a tiny fraction (<0.4%) of described species have been assessed for extinction risk, 50% of the species assessed to date are considered threatened. This suggests that the world risks losing many of its fungi before their existence is even documented. This is especially true in megabiodiverse ecosystems like the Amazon rainforest, where threats like illegal mining, logging, and agricultural expansion are destroying and fragmenting the forest at an alarming rate. For the past few years I have conducted fieldwork with local researchers in the Peruvian Amazon focused on documenting macrofungal diversity and describing new species of mushrooms as part of a multi-year inventory project in two Peruvian national parks, Parque Nacionál de Tingo Maria and Parque Nacional Yanachaga-Chemillén. I have also contributed to macrofungal inventories in the Madre de Dios and Lima regions as part of a broader effort to describe Peru's fungal diversity led by Revolución Fungi, a fungal research and education nonprofit.

Microbial responses to ecological change

Understanding the microbial ecology of Florida red tides
Karenia brevis is an algal species that forms toxic “red tide” blooms in the Gulf of Mexico, causing massive fish kills and economic damage in coastal Florida. These massive blooms are driven in part by anthropogenic nutrient pollution and habitat degradation cause by development in Central and South Florida. The trajectory of K. brevis blooms is believed to be influenced by microbial interactions, but these are not well characterized, especially in the context of bloom termination, which can occur quite abruptly. We hypothesized that marine viruses contribute to bloom termination by either infecting K. brevis directly or infecting associated beneficial bacteria, and we attempted to isolate them from bloom seawater to cause lysis in vitro. In infection experiments conducted several months apart, viral lysis of K. brevis cultures was observed and produced a growth response in bacterial and phage populations. Through flow cytometry and metagenomics, we identified several viral and bacterial taxa associated with K. brevis cell death. This finding underscores the importance of microbial community dynamics in K. brevis blooms and creates the potential to use community-level eDNA monitoring to inform bloom forecasts.

Details: Anne E Booker, Cong Fei, Shady A Amin, James Custer, Kai Watkins, William Yaeger, So Hyun Ahn, Nayani K Vidyarathna, Alexandra Burns, Sarah Klass, Patricia M Glibert, Cynthia A Heil, Frederik Schulz, Joaquín Martínez Martínez, Complex viral interactions revealed for the harmful bloom-forming dinoflagellate Karenia brevis, ISME Communications, 2026;, ycag051, https://doi.org/10.1093/ismeco/ycag051

Harnessing microbes for sustainable agriculture

Microbial biocontrol for fungal pathogens of cacao
Organic cacao production in South America is severely impacted by the fungal pathogens Moniliophthora roreri and Moniliophthora perniciosa, which attack maturing cacao pods and severely reduce yields. As a result, organic cacao production is increasingly unprofitable and smallholder cacao farmers must turn to expensive and ecologically-damaging fungicides for pathogen control. Native microbial biocontrol agents represent a potential alternative strategy that would allow farmers to continue to maintain their organic certifications, but few studies to date have assessed the diversity or biocontrol potential of native microorganisms in South American cacao-producing countries. During a 9-month research fellowship at the Universidad Nacional Agraria de la Selva in Huánuco, Perú, I evaluated the diversity and biocontrol potential of yeasts isolated from cacao plantations in the province of Leoncio Prado. This work identified several indigenous yeast strains associated with local cacao plantations that control both M. roreri and M. perniciosa effectively in vitro and show potential to be developed into broad-spectrum biocontrol agents for cacao diseases.

Details: DIVERSIDADE E SISTEMÁTICA DE LEVEDURAS EPIFÍTICAS ASSOCIADAS AO CACAUEIRO (Theobroma cacao) NA PROVÍNCIA DE LEONCIO PRADO, PERU

Developing low-tech mushroom farms in Sierra Leone
Food insecurity is a grave issue faced by millions of people across the globe and is growing in severity as a result of climate-related stressors on agricultural systems. Mushroom production, an agricultural approach that is profitable and scalable due to its low input requirements, short turnaround times, year-round viability, and utilization of agricultural byproducts, holds significant potential in contributing to food security. However, commercial mushroom production is difficult to pursue in low-resource settings due to a lack of capital and unreliable electricity access. After four years of research and experimentation in rural Sierra Leone, our team validated a low-cost, low-tech, and reliable approach for commercial mushroom production. In our conference paper, we describe a highly modular process for spawn propagation, substrate pasteurization, inoculation, and harvest, which has promise as a cost-effective and reliable method for contributing to food security in Sierra Leone and similar low-resource settings.​

Details: Yaeger, W., Jawed, M., Tauman, D., Ho, P., Ali, A., Gomanie, N. N., & Mehta, K. (2022, September). Modular methods for oyster mushroom cultivation in low-resource settings. In 2022 IEEE Global Humanitarian Technology Conference (GHTC) (pp. 30-37). IEEE.