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Research Projects


Department of Project: Stockbridge School of Agriculture

Deficiencies of mineral elements in diets of humans are on the rise worldwide, even in the United States. These deficiencies limit the physical, intellectual, and mental health activities of the affected people. Poor or deterioration of soil fertility and the concomitant decline in agricultural productivity are major concerns in the World. Organic production of vegetables and fruits is growing, and it is important to assess if organic fertilization will sustain the quantity and nutritional values of foods grown from plants equally to the current practices of conventional farming. A current project in the Massachusetts Experiment Station studied organic and conventional fertilization of vegetable crops in relation to productivity and elemental nutrient composition for human nutrition. Biochar is charcoal produced from pyrolyzed biomass. Research suggests that biochar is a good amendment to enhance physical, chemical, and other agronomic qualities of soils. Amendments with biochar are reported to increase storage of carbon in soil, to increase fertility of soils, and to increase productivity and elemental nutrient composition of crops. The production of biochar from crop and other vegetative residues may be a strategy for management of organic waste. This project will investigate the benefits that might be obtained by use of biochar in enhancing yields and nutritional quality of vegetable crops. A review of literature has shown that additions of biochar to soils or growth media may improve plant nutrition through enhanced acquisition of nutrients by crops grown in biochar-amended media. Results have been variable and need some verification with further research. Biochar applications may replace some of the needs for regular fertilization of crops. Use of biochar has imparted tolerance of crops to saline and metals-contaminated soils. Research that needs further study was noted to be investigations of the use of biochar with organic fertilizers, especially ones of origins from sparingly soluble minerals, such as rock phosphate and rock dusts. This investigation is needed to determine if use of biochar with organic fertilizers or with difficultly soluble fertilizers will improve their efficacy. The enhancement of production with biochar of high-quality seedlings used as transplants has received limited attention and is worthy of further investigation to establish crops in the field or greenhouse. This proposed project will address use of biochar in the establishment of seedlings and in improving the efficacy of organic and chemical fertilizers.

Department of Project: Stockbridge School of Agriculture

Better knowledge of how to beneficially use residuals and reclaimed water is essential for environmental protection, soil quality, crop yield, food safety and human health. From this project, we will generate new and useful information on beneficial use residuals and reclaimed water. We will examine the fate, processes and bioavailability of various contaminants (including antibiotics, nanoparticles, nanoplastics) in soils. Analytical methods for nanoparticles and microplastics will be developed, and these methods are expected to be used widely by students, scientists and professionals. In addition, we will modify biochars to make functional biochars to be used in soil improvement and remediation. Furthermore, we will provide the fundamental and useful data for developing nano-enabled technology for sustainable agricultural production.


This project investigates new sustainable markets for New England seafood. Climate change challenges the socio-economic and environmental sustainability of New England's seafood industry. A warming Gulf of Maine compounds the complex puzzle of ecosystems, fish population dynamics, and catch limits for specific fisheries. Cascading effects on fishermen, seafood processors, markets, and restaurants provide a network of challenges that are difficult to disentangle. This multifaceted challenge highlights the need for collaborative, cross-disciplinary research to build sustainable new markets for seafood. This proposal brings together a team with diverse expertise in ecology, climate change adaptation, economics, stakeholder engagement and product development. We aim to support the fishing industry by investigating consumers’ seafood choices, sustainable fishing practices, and seafood products that contain lesser known yet abundant species.   

The work will obtain new data to support ongoing pilot-work and support future proposals. Pilot data include:

  1. Fisherman’s perspectives on local and underutilized fish species and preservation methods,
  2. Consumer acceptability of new artisanal preserved fish products. Seed grant funds will be used to execute semi-structured interviews with New England fisherman, an online consumer survey, and a consumer sensory experiment. These funds will support the collaborative relationship between team members, building an interdisciplinary working group to pursue larger research funds.

Department of Project: Veterinary & Animal Sciences Dept.

1-The issue under investigation in this proposal is important because reproductive performance in beef and dairy cattle is often suboptimal resulting in increased intervals to conception and/or rebreeding failures that collectively reduce farm revenues due to decreased milk production or calf production efficiencies. Therefore, approaches that facilitate conception and increase conception rates will benefit the farmer and the economy in general.

2-The Umass research groups in this grant, Drs. Fissore and Visconti will be focused on two of the three Objectives,

Objective 1: Identify Mechanisms that Regulate Ovarian Function and Oocyte Quality during the Estrous Cycle.

Objective 2: Determine Factors Associated with Fertilization, Embryo Development, and Conceptus-Endometrial Interactions that Dictate Pregnancy Success.

3-Colleagues working in fertilization, embryo development, and fertility in mammalian species including humans, post-docs and graduate students, technicians, undergraduate students, embryologists, and producers.  

4-Oocyte quality is of one the parameters affected in high milk-yield cows. Therefore, examining how specific molecules and mechanisms might be downregulated or inactivated in those animals will improve the quality of the oocytes and their developmental potential such that a higher proportion of the fertilized oocytes and early embryos can progress to implantation and term-pregnancy. A second area is to prepare the sperm for fertilization akin to what happens in the female reproductive tracts. We plan to pre-treat bull sperm prior to adding it to oocytes or females. Recent studies from the Visconti lab show that changing the metabolic status of mouse sperm prior to fertilization can enhance post-fertilization outcomes, including embryo development and implantation success. We will extend these to the bovine sperm and embryos.

Department of Project: Biology Dept.

Water is an increasingly scarce resource for agriculture thus engineering plants that use water efficiently is a primary goal for scientists. A recent approach in achieving water-efficient crops is to breed or engineer plants that can rapidly open and close their stomata in changing environments (Lawson and Blatt 2014, Raven 2014). During the day, plants may become shaded or enjoy a sudden but transient increase in sunlight as sun angles change (or are reflected) or as clouds and/or other obstacles block the sun. Plants that are shaded cannot photosynthesize; if the stomata are open in the shade, water is being lost while no carbon assimilation is taking place. Reciprocally, a transient increase in sunlight may warrant rapid stomatal opening, so extra energy can be assimilated into carbon. This is apt to happen many times a day, on different regions of the plant. Therefore, stomata that open quickly during high light or close quickly during low light will assimilate more carbon while losing less water.
Interestingly, nature has already engineered rapid stomata. Within the plant family, grass stomata have a unique morphology. In grasses, guard cells are dumbbell-shaped rather than the more common kidney-shape. The pair of guard cells are laterally flanked by a pair of subsidiary cells, or helper cell, which are also uniquely shaped (Figure 1C; Gray et al., 2020). Grass stomata open and close much faster than stomata from a variety of other species (Johnsson et al. 1976, Grantz and Assmann 1991, Franks and Farquhar 2007). It is thought that both the shape of the guard cells, and the presence of the subsidiary cells contribute to this rapid opening and closing (Franks and Farquhar 2007; Gray et al., 2020; Raissig et al., 2017), however since the mechanism of rapid stomatal opening and closing in grasses is not well understood, this is yet unproven. Maize (corn) plants are members of the grass family. Maize has many features that make it amenable to study include: well-established genetics including characterized "diversity panels" of inbred lines, fully sequenced genomes from multiple inbred lines and reverse genetic collections; ability to make transgenic plants; and large cells amenable to microscopy. Therefore, experiments in maize are well poised to investigate grass stomatal formation and function. While the unique shape of
grass guard cells likely contributes to their function, this proposal will focus on subsidiary cells. Specifically, we will determine the genes required to form subsidiary cells and genes unique in mature functioning subsidiary cells.

Department of Project: Microbiology Dept.

We designed full-size field trials to test the effectiveness of sorghum-maize intercropping at the UMass Crop and Animal Research and Education Farm in South Deerfield, MA. Plots of sorghum monocrop and maize monocrop served as controls with two intercropping systems, alternating row and mixed seeding intercropping. All four planting treatments were coupled with DMPP application to compare the biological inhibition of sorghum to an artificial inhibitor. Nitrogen and potassium fertilizers were applied in a manner similar to local practices, with DMPP application occurring concurrently. Plants were grown throughout the summer and harvested in early October for the 2021 and 2022 growing seasons to represent a typical corn system in Massachusetts.

The methodology of this work relies primarily on the capture and analysis of N2O gas leaving the soil, which represents a loss of nitrogen from the system as well as a problematic source of greenhouse gas emissions. To capture this gas flux, we implemented static chambers placed over the soil for a period of 30 minutes and sampled gas from the chamber every 15 minutes. Gas samples were loaded into pre-evacuated glass vials and analyzed through gas chromatography. To ascertain the temporal variability of N2O flux, these measurements were carried out throughout the New England summer every 2 or 3 days. This sampling scheme is more intensive than those typically employed in the literature, with many studies measuring gas flux on a weekly basis or longer gaps. The high frequency of sampling events allowed us to better account for stochastic variables in the system such as soil moisture and temperature fluctuations as they changed throughout the season.

In addition to gas flux, we collected data on soil temperature and moisture, as well as detailed atmospheric data from a nearby weather station at the research farm. At the end of the growing season, we collected above ground biomass from representative areas of each plot to measure bulk yield for silage production, the intended production outcome for this experiment.

To further understand the underlying mechanisms of the reduction in N2O flux we periodically and destructively took bulk soil and root samples for microbial community analysis. In this analysis we compared the abundance of microbial communities responsible for nitrogen transformations in the soil, mainly ammonia-oxidizing bacteria and archaea as well as denitrifying bacteria. We will also be coupling these comparisons to more broad observations of the microbial community structure at high resolution to get insights into how the wider microbial community responds to N2O reduction treatments and intercropping systems.

The need to feed the ever-growing human population while decreasing greenhouse gas emissions from large-scale agriculture remains a global problem of paramount importance. One major source of these emissions is through nitrous oxide (N2O) production, a greenhouse gas with a warming potential nearly 300 times that of CO2. This potent greenhouse gas is formed through the action of soil microbes when they compete for artificial nitrogen fertilizer. While there are synthetic inhibitors that reduce N2O emissions, there can be many off-target effects. A promising alternative to these inhibitors is leveraging the natural ability of some plants to antagonize the microbial production of N2O, termed Biological Nitrification Inhibition (BNI). This ongoing research utilizes the BNI capacity of Sorghum bicolor, a staple grain crop in Africa and Southern Asia intercropped with corn (Zea mays). Plants were grown as monocrops or intercrops with alternating row and mixed seeding at the UMass Crop and Animal Research and Education Farm in South Deerfield, MA. These cropping treatments were repeated with an artificial nitrification inhibitor, DMPP, for comparison. Throughout the growth season, soil gas flux samples were collected via chambers covering the soil and analyzed through gas chromatography. Measured N2O concentrations over time were then converted to overall flux (production and consumption) to determine the reduction in N2O emissions. In addition to gas measurements, soil and roots were destructively sampled periodically throughout the growth season. Community analysis of the bulk soil and rhizosphere will reveal the microbial community’s response to the different cropping systems or the synthetic inhibitor treatment at high levels of resolution. At the end of the field season, plants were harvested to determine overall yield for all treatment groups. This experimental design has been repeated for a second year to account for seasonal variations in weather patterns. Throughout both years of the field trial, we found nearly 20% fewer N20 emissions in the sorghum monocrop plots as well as with mixed seed intercropping with the addition of DMPP, compared to the corn monocrop control. Total plant biomass production was not influenced by either treatment variation.

        The core hypothesis of this work is that the BNI capacity of sorghum will result in more nitrogen fertilizer available for both corn and sorghum when planted in close proximity, as well as reduced N2O emissions. The inhibitory chemicals secreted from the sorghum roots will affect the root zone of corn when planted in a way that both root systems overlap. This effect will lead to more plant-available nitrogen, lower N2O emissions, and higher silage yields for both corn and sorghum in intercropped systems. We expect this effect to be most pronounced in the mixed seeding plots as those plants are grown in the closest proximity. This work will determine the efficacy of intercropping corn, a plant with heavy nitrogen fertilizer needs with sorghum, a plant which has evolved ways to better compete with soil microbes for the available nitrogen applied as fertilizer, compared to the commercial inhibitor DMPP. To better understand the role of soil biological processes in controlling plant available nitrogen, a subsequent, complimentary experiment will be carried out this year to uncover the mechanism of action of the sorghum inhibition. These experiments together investigate a promising alternative to the current synthetic inhibitors in an effort to reduce greenhouse gas emissions in large-scale agriculture, while simultaneously reducing the amounts of artificial nitrogen fertilizer required to grow corn in today’s agriculture. Both resulting effects, the increased nitrogen fertilizer availability and reduced N2O production, will directly support the chosen objective, and widen our understanding of soil health and resilience. Resilience of this agricultural system is further supported by the documented drought resistance of sorghum, which will be needed with the expected longer drought periods in the currently changing climate. These changes will directly affect farmers who produce crops for silage.

Department of Project: Stockbridge School of Agriculture

Non-point source pollution including excess nutrients, organic particles, fecal coliform bacteria, and additional pathogens is considered high risk at many animal operations, especially equine facilities. A common issue in these animal facilities is overgrazing which is the main cause of mud, resulting in serious threats to the environment as well as to animals and humans.  In addition, most equine facilities are regularly faced with a major challenge related to the large amount of manure produced by animals at the facility. Some of the challenges related to manure include 1) lack of manure storage 2) close proximity of manure pile(s) to nearby water bodies 3) animals' direct access to streams and other bodies of water, 4) undesirable characteristics of horse manure due to exceptionally high C:N ratio which makes the waste unusable for agriculture uses. In Massachusetts, there are estimated to be over 26,000 domesticated horses within the state. There are roughly 50,000 acres of land being used in MA for equine operations, therefore, there are about two horses for every acre of dedicated land- which is one fourth of the current recommended practice. It is estimated on average one 1,000 lb. horse will produce approximately 9 tons of manure. When including bedding, stall waste could be as much as 12 tons per horse per year. Managing this waste properly is a growing challenge for equine facilities, especially at places where land availability is limited, and the horses are kept in small acreage and stalls. Runoff from the stables to high traffic areas, manure piles, and unmanaged and overgrazed pastures are the main contributing factors to environmental degradation. Many horse owners do not have enough resources and background to make significant changes in their current practices including pasture, mud, and nutrient management. This provides opportunity for conducting research on various aspects of pasture management, manure management and provides information to remediate the negative impacts of equines on the environment.

Department of Project: UMass Cranberry Station

Cranberry production has a long history in Massachusetts (MA) that adds important economic and aesthetic value to the region.  About 30% of US acreage and the two largest cranberry handler companies are located in Massachusetts. Threats to the sustainability of cranberry production in MA and elsewhere in the US come from many sources: consumer demands for sustainable but inexpensive products, commodity pricing in an industry that is currently over-supplied with juice concentrate, changes to industry (handler) fruit quality standards, rising costs for energy and pest management products, climate change, and changing standards in pesticide use to accommodate global marketing. 

The majority of cranberry acreage in MA is still under old cultivars with low productivity and poor disease resistance and MA does not have a breeding program for new cultivars. Growers in MA are interested in bringing in new hybrid cultivars from breeding programs in New Jersey and Wisconsin. However, without proper cultivar evaluation under MA growing conditions, growers are hesitant to do so because of the significant financial risk.  This project will evaluate new hybrid cultivars under MA growing conditions and provide growers with reliable data to use in decision making when considering bog renovation.


Department of Project: Microbiology Dept.

The diverticulated crop organ of the common house fly, which is the major insect vector of numerous human food pathogens (e.g., Escherichia coli) is the major reservoir or storage area for this, and other, important food pathogens. It has also been demonstrated that this is where horizontal transmission of antibiotic resistance to E. coli occurs. Thus, the diverticulated crop organ is an essential component in the transmission cycle between pathogens and human foods/food crops. At the same time, the salivary glands of house fly are directly involved in vectoring pathogens and, are intimately involved in pathogen transmission. Almost nothing is known about the physiological factors involved in the regulation of both crop filling and emptying of the adult house fly. Even more concerning is that we know even less about the effect of various pathogens, either food pathogens or pathogens of the house fly vector, on salivary gland regulation. What effect does the salivary gland hypertrophy virus have on normal crop organ function? A better understanding of how these two essential organ systems are regulated, will give researchers a better picture of how to use this information to explore novel, non-chemical control strategies that can be directed at interfering with the normal regulation of these two organ systems. Ultimately, non-traditional control strategies will be developed that rely on interfering with the function of these two organ systems, both of which are essential to the fly. It is the objective of this project to develop non-traditional control strategies, thus reducing fly resistance to insecticides. Thus, by compromised longevity of the vector, pathogen vectoring, and/or reproductive development of the flies can be interfered with resulting in death, abnormal flight ability, and or reduced fecundity.

Department of Project: Biology Dept.

Pollination is critical for yield of many crops, but many pollinator species are in decline due to a variety of stressors including pathogens, pesticides, and insufficient food resources. Our work will ask how flowering plants and land use around farms affects the number of bee individuals and species at farms, and how effective bees are at pollinating sunflower crops. We will also determine how diet and floral resources affect bee health and ability to resist disease. Finally, many crops have seeds that are treated with pesticides to improve growth, but these pesticides can be incorporated into pollen and affect bees. We will ask how the amount of water a plant receives affects the concentration of pesticides in pollen, and the consequences for bees. Taken together, this work represents a comprehensive approach to understand some of the factors involved in pollinator decline.

Department of Project: UMass Cranberry Station

We will collaborate with various companies that are developing OMRI approved products (Coppers, Beneficial Microbes/Biocontrol agents and systemic resistance inducers) and identify compounds with proven efficacy in other cropping systems. Identified compounds will be integrated with registered Group 3 & 11 fungicides and will be evaluated for their efficacy in managing cranberry fruit rot and enhancing fruit quality (fruit color as evaluated by total anthocyanin content, fruit firmness and fruit size as evaluated by fruit weight). The proposed novel treatments will be evaluated in comparison with traditional grower standards (all chemicals) and non-sprayed controls. The study will be conducted on State bog at UMass Cranberry Station, East Wareham. All the treatments will be replicated five times in 4 x 4 ft (1.2 x 1.2 m) plots. All the local recommended fertilization, irrigation and pest management practices will be followed. Fungicides/novel compounds in each treatment will be applied at designated phenological stages using a CO2 powered backpack sprayer. In late September, from each replicated plot, all fruit from within an arbitrarily selected 1 foot-square area will be harvested by hand. Yield data will be obtained by converting the weight of the berries from 1 foot-square area to barrels/acre. Berries will be evaluated for fruit rot incidence (number of rotten berries/total number of berries x 100). An additional 500-gram subsample from each replicated plot will be used for fruit size and fruit color evaluation. Fruit firmness will be evaluated for samples of 50 healthy berries from each plot.

Department of Project: Stockbridge School of Agriculture

In Massachusetts, several invasive insect species are either already affecting or pose a serious threat to the specialty crop industry. Stakeholders have voiced the need to address the most destructive invasive insects threatening their crops. In recent years, there has been interest in reduced-risk materials with insecticidal properties for the invasive pest spotted wing Drosophila (SWD), a vinegar fly that attacks berries and other soft-skinned fruits such as peach and cherry. Of particular interest are low-cost materials that could be used as attractants in traps or as insecticidal food-based baits, as opposed to broad-spectrum insecticides applied to the foliage against some pests. In this project, we will determine whether materials that are commonly available in households can be used to attract adult SWD to traps. Efforts will be made to develop an inexpensive insecticidal bait. The response of female codling moth and Oriental fruit moth, two important pests of apple, pear, and related crops, to lures that are based on plant material will be quantified under laboratory and field conditions. Our ultimate goal is to develop a food bait for SWD that is inexpensive and effective. This project also seeks to improve the effectiveness of monitoring systems for codling moth and Oriental fruit moth. If successful, results may lead to the development of more effective monitoring systems for these two moth pest species.

Department of Project: Biology Dept.

This proposal describes a next-generation sequencing (NGS)-based approach to identify genes that control unisexual flower development in Zea mays (maize). Maize develops separate male flowers in the tassel and female flowers in the ear (Klein etal., 2018). The development of unisexual flowers is important for hybrid crop production - separate tassel and ear flowers allow humans to very easily make controlled crosses (Phillips, 2010).  Many cereal crops related to maize, like rice and wheat, have unisexual flowers, hampering hybrid seed production (Kellogg, 2015). In addition, the same process that leads to the development of maize flowers in the tassel - carpel suppression - also occurs in half of all ear flowers, effectively halving the number of seeds a maize ear could produce (Cheng et al., 1983).  Thus, modifying the genes that control carpel suppression using CRISPR/Cas9 genome engineering could allow crop engineers to generate unisexual flowers in other grass crops, and to improve yield in maize (Gao, 2018).

Department of Project: Biology Dept.

Objective 1: Characterize and quantify PGP microbe effects on belowground plant growth using B. distachyon accession Bd21-3 expressing luciferase and inoculated with B. subtilis strain GB03.

We recently transformed B. distachyon accession Bd21-3 with a constitutive luciferase reporter system consisting of the luciferase-encoding LUC2o gene coupled with the proZmUBI1 promoter, derived from a maize ubiquitin gene. Adding D-luciferin to growing plants within the rhizotron system allows imaging of growing root and shoot tips. Creating Z-projections of daily images permits  visualization of older roots in more developed plants. These efforts have allowed us to quantify how root area changes over time in plants grown with an unidentified microbial community. Further refinement of these scripts, as well as protocols to capture other aspects of belowground growth will enrich the toolkit that we have to understand PGP bacterial effects.

In this aim we will grow 16 replicates of B. distachyon accession Bd21-3 transformed with the luciferase reporter system in standard rhizotron conditions. Following our best-practices results from prior trials, we will inoculate plants at the seed stage upon sowing. All seeds will be surface-sterilized using 15% bleach plus 0.1% Triton-X. The sterilized seeds will be incubated on damp paper towels at 4°C for one week (vernalization), to synchronize germination, and then sown in sterilized rhizotrons filled with model soil with washed ryegrass stems as organic matter. For inoculation, spores of B. subtilis GB30 will be cultured in LB for two days. A subculture will then be established and grown until an OD600 between 0.75 and 1.5 is achieved, corresponding to the bacterial log phase. Bacteria will then be pelleted and resuspended in phosphate buffered saline.

            At planting, 8 replicates of B. distachyon will be inoculated with B. subtilis BG03 and 8 mock-inoculated with saline solution. Plants will be grown in a controlled chamber under 16 hours of light at 24°C and 8 hours of dark at 20°C. To maximize the likelihood of detecting microbial growth-promoting effects, fertilizer will be withheld. Starting upon seedling emergence and on a daily basis 500 µL of luciferin will be added to the water of each plant. Plants will be imaged every three hours in our custom chamber equipped with an Andor iKon-M CCD camera. Plants will be imaged until about two weeks after flowers emerge and the stem has completely elongated. The time series of images will be analyzed to estimate total above and below ground growth over time and to compare these to each other. Using the bioinformatic tools we have developed we will assess BG03 effects on root architecture, root growth patterns, and root area, as well as shoot growth patterns, allowing us to understand how above and belowground growth differ from each other and how they are differentially affected by inoculation.


Objective 2: Assess the differential effect of B. subtilis strain GB03 on growth of B. distachyon accessions that are parents of established mapping populations in controlled rhizotron environments.

Several B. distachyon recombinant inbred line (RILs) populations have been established, are publicly available, and are in use in the Hazen lab. These RILs have the advantage that both parents and all lines are nearly homozygous and have been genotyped across the genome with either whole-genome sequencing (WGS) or genotyping-by-sequencing (GBS). To determine which set of RILs can be used to identify loci governing PGP bacterial response in B. distachyon, we will inoculate 8 selected parents with B. subtilis strain GB03, which we have shown to have an effect at least on B. distachyon accession Bd21-3. Seeds will be prepared as in Objective 1 The length of cold-treatment will be extended to two or four weeks for those accessions previously found to require longer vernalization periods to trigger flowering. Spores of B. subtilis GB30 will be prepared as in Objective 1.

            For each parental accession we will carry out 8 replicates of inoculated plants and 8 replicates of controls mock-inoculated with phosphate buffered saline. Plants will be grown in a controlled chamber under 16 hours of light at 24°C and 8 hours of dark at 20°C. To maximize the likelihood of detecting microbial growth-promoting effects, fertilizer will be withheld.

We will harvest and phenotype plants at flowering and at senescence, which will allow us to assess if observed effects are dependent on developmental stage. We will work with a total of 256 plants (8 accessions x 8 replicates x 2 treatments x 2 developmental time points). Phenotypes to be evaluated will encompass those displaying genotype x microbe interactions in our pilot study (SLA, LAR, stem height, and dry root weight), phenotypes important for bioenergy and forage crops (total biomass), and phenotypes of relevance to cereal crops (flowering time, seed number, and seed weight).

Growth phenotypes will be examined for response to PGP-bacteria application. Trait responses will be compared among B. distachyon genotypes, allowing us to identify what traits have an across-the-board response to PGP microbial inoculations and which are genotype -specific. B. distachyon genotypes displaying different responses to B. subtilis will be identified as ideal parents for mapping populations that can be used to map plant genes influencing PGP microbe x plant genotype interactions.


Objective 3: Upon establishing microbial effects on mapping parents, phenotype growth on a selected set of mapping populations to identify genes controlling response to B. subtilis strain GB03.

We will use our results from Aim 1 to proceed with the set of genotyped RILs with the greatest parental contrast in growth response to PGP microbial application and, secondarily, the most similar flowering times or vernalization requirements. For the chosen mapping population, we will work with 100 RILs chosen randomly and the two parents. We will inoculate 8 replicates of each RIL and parent with B. subtilis GB03 and mock-inoculate 8 further replicates as in Objectives 1 and 2. Planting and growth conditions will be as above. The length of vernalization needed for each RIL is unknown, as each RIL is a novel combination of parental genotypes. Thus all RILs will be subjected to 2 to 4 weeks of vernalization, based on the vernalization requirements of the parents. The same phenotypes as in Objective 2 will be scored at the same developmental stages. This will entail inoculation, growth, and phenotyping of 102 x 2 x 8 = 1632 plants.

To identify the loci underlying PGP bacterial response, mapping will be carried out on the set of mock-inoculated RILs and separately on the set of inoculated RILs. We will use genotypes obtained from whole genome sequencing or genotyping by sequencing, which has been approved for all crosses from Aim 2 by JGI (Joint Genome Institute). QTLs detected in the inoculated set and not the mock-inoculated are likely to represent loci involved in growth response to B. subtilis GB30. We will use the package R/qtl2 which can handle dense genetic markers like those produced by whole-genome sequencing and GBS for mapping. Haley–Knott (HK) regression will be used for genome scans to associate genotype with phenotype. If the degree of missing data in the sequenced RILs is deemed too high, we will carry out SNP imputation prior to regression analysis. Permutation tests will be performed in R/qtl2 to establish QTL significance, with BLUP-based estimates of QTL effects.

As an alternative to separate mapping in inoculated and mock-inoculated RIL sets, a degree of differential response can be calculated for each trait in each RIL by subtracting the mock-inoculated trait values from the inoculated ones. QTL mapping will be carried out as above for each trait differential response, to identify loci underlying growth responses to GB03 applications.

Department of Project: Biology Dept.

Corn (Zea mays) is the most widely cultivated grain crop in the United States and is extensively consumed in the American diet. Because of corn's prominence as a staple grain throughout the world, the nutritional quality of corn has received substantial attention. The metal micronutrient content of corn, especially iron and zinc, is of considerable interest since breeding for improved micronutrient content and availability would have substantial impacts on human health. Unfortunately, maize has naturally low levels of iron in grain, making it impossible to breed maize lines that have adequate iron for human nutrition. In this project, we will leverage knowledge about iron signaling and iron movement to address the possibility of enhancing iron accumulation in maize kernels by manipulating gene expression artificially. Our long-term goal is to produce food crops with improved iron nutrition for human and animal consumption.

Department of Project: Stockbridge School of Agriculture

The project will employ established field and laboratory methods to measure litter decomposition, soil organic matter turnover, and nitrogen transformations. These methods could include isotope labeling and recovery, litter decomposition, quantifying soil organic matter, gross nitrification and nitrogen mineralization, potential net nitrification and net nitrogen mineralization, nitrous oxide production, carbon mineralization, and quantifying microbial biomass. These measurements are often collected from both field equipment and laboratory microcosms. The results are analyzed using a variety of tools. Generally, graphing tools are first used to examine trends in the data. The data will then be statistically analyzed using linear mixed models and, potentially, model selection. The statistical output is combined with graphic trends and site background information to interpret data and produce study outcomes. This study will incorporate formal education programs. The research project will be the basis from which to train a graduate student on methods in soil biogeochemistry and incorporation of applied research into graduate study. The field sites and methods will be incorporated into formal laboratory instruction for undergraduates. Involving undergraduates provides both inclusion in primary research and evidence of how research outcomes can be incorporated by farmers. 

Department of Project: Stockbridge School of Agriculture

We will use a combination of field work, greenhouse experiments, incubations, laboratory methods (including physiochemical, molecular, and spectroscopic analyses), advanced imaging, stable isotope tracing, multi-omics (DNA/RNA sequencing, metabolomics, proteomics), and computational approaches to characterize and measure soil organic matter and its dynamic interactions with the ever-changing soil environment and its inhabitants. In the near future, our work will focus on the fate of organic N inputs and their interactions with soil minerals. This mineral associated organic N pool (often referred to as MAOM-N) is a critical but overlooked component of the soil N cycle. As part of a collaborative, multi-institutional project, we will investigate the following questions:

How does the relative abundance and chemistry of MAOM control N availability?

How do MAOM-N pools and MAOM-N dynamics vary across different cropping systems and management practices?

How do roots mobilize MAOM-N?

How do these processes contribute to plant productivity, resource use efficiency, and soil C storage?

First, we will use spectroscopy (e.g., FTIR, NEXAFS), sequential extractions, elemental and chemical analyses (e.g., IRMS, TOC, TON, FTICRMS), and imaging (e.g., SEM, TEM, IR microscopy, STXM-NEXAFS) to characterize MAOM-N present in paired soil samples maintained under annual wheat (conventional tillage and fertilization) vs perennial grasslands (no tillage or fertilization). Our soil sampling sites represent a gradient of soil texture and climatic conditions. Next, we will conduct incubations and greenhouse experiments to investigate how this MAOM-N is formed, transformed, and mobilized by plants and microbes. We will use stable isotope tracing to distinguish the fate of different organic matter sources within the complex soil matrix.

Department of Project: Stockbridge School of Agriculture

A New England Food Vision is the outcome of a regional collaboration, led by the University of New Hampshire, that began in 2014 in response to climate change, local economics, and food security (Donahue et. al, 2014). The Vision identified the potential to increase local food production and enhance our agricultural sector economics. To increase our local animal production, the Vision identified the need to locally produce 64% of the feed that is concurrently required. The feasibility of this goal heavily depends on the utilization of marginal lands not suitable for row crop production to be managed as pasture and hay land. Fortunately, there is also an increasing movement among both consumers and farmers for grass-fed production in New England, as evidenced by the 2019 formation of the New England Grazing Network.

Regionally appropriate management techniques are necessary to support farmers shifting to increased pasture-based feed production systems. It is well understood that well-managed perennial grass systems have great potential to sequester carbon and protect water quality (Franzluebbers et al., 2012; Eyles et al, 2015; Oliveira et al., 2019). However, poorly managed systems can introduce environmental harm due to over grazing and non-point source pollutants. Moreover, nutrient management and grazing management must be fine-tuned in order to maximize production, long-term sustainability, and economic viability.

Our work seeks to reduce the reliance on synthetic nitrogen fertility in pastures to increase environmental sustainability and reduce the cost of production. We also seek to extend the grazing season so as to reduce the necessity to produce hay to feed animals during winter months, as hay production requires labor and fuel costs as well as fossil fuel emissions. This work hopes to increase the understanding of nitrogen cycling as influenced by the effect of forage composition on manure-N composition, which can in turn support farmers in nutrient planning. Finally, we seek to further investigate the effect of grazing height on the regrowth of common grass species and their physiology. Knowledge of the physiology over time is critical to careful management plans that support maximum production and can help predict responses to environmental stresses that accompany climate change.

Department of Project: Microbiology Dept.

The research outlined here is designed to clarify how microbial diversity influences soil carbon persistence and ecosystem function and how climate change reshapes these relationships. Our focus is on necromass, or new soil organic matter derived from dead microbial bodies as part of the microbial community turnover. 

First, we will use model soils (comprised of sand, clay, microbes and simple substrates) in combination wiht 18O-water to investigate how microbial community diversity impacts soil carbon stabilization and carbon use efficiency of necromass. We expect that the necromass derived from more diverse communities will be more difficult to decompose, resulting in lower carbon use efficiency.

Second, we will leverage an ongoing Harvard Forest Long-Term Soil Warming Experiment to ask how chronic warming affects the relationship between ecosystem multifunctionality and microbial diversity. This project will also explore how that relationship changes over season, the duration of long-term warming, and across soil horizons. We expect that the warmed plots would have higher ecosystem multifunctionality and microbial diversity, producing a stronger positive relationship between the two.

Finally, we will use metatranscriptomic data from the Harvard Forest Long-Term Soil Warming Experiment to examine how long-term warming impacts the relationship between functional diversity and ecosystem multifunctionality. Through this project, we will explore functional diversity as an alternative to taxonomic diversity when examining the relationship between diversity and ecosystem function. We predict that functional diversity will have a positive relationship with ecosystem multifunctionality, and that decomposition related genes will be the primary drivers of this relationship.

Plant diseases cause crop loss, reduce food production and threaten global food security (Savary et al., 2012). Focusing on two distinct pathosystems that cause Fusarium vascular wilts and the Basil downy mildew (BDM), respectively, we propose to establish a pipeline to dissect host-pathogen interactions and provide novel means to develop disease resistant cultivars in order to manage plant diseases that threaten food security.

Department of Project: Stockbridge School of Agriculture

Prior to the turn of the 21st century, most U.S. states produced few to no grapevine, primarily because of limitation in cold hardiness and disease and pest resistance of the Vitis vinifera, the European grapevine species that comprises most commercial cultivars grown in the U.S. in traditional production regions.  The recent introduction of new, interspecific hybrid cultivars that incorporate more of the world natural diversity of grapevine species and thus, more climate resilience and disease and pest resistances, has allowed the development of grape industries in regions previously considered unsuitable.  The major V. vinifera cultivars grown worldwide were selected over decades or even centuries for best suitability in European regions and were then spread to California's and other arid western U.S. states.  Therefore, in comparison to V. vinifera, the evaluation of the new hybrids for non-traditional regions needs more time.  Moreover, in face of climate change, continued evaluation of V. vinifera and hybrid cultivars is critical to maintaining the grapevine industries in both traditional and non-traditional grapevine growing regions.  Economically, grapevine cultivars evaluation is one of the most significant components of grapevine industry: “Planting a poorly-adapted cultivar in the wrong place is a costly mistake.”  As new grapevine regions experience continued growth, the subsequent economic impact that comes with it is dependent on improving quality and quantity of grapes and wines produced. Continued discovery, development, and evaluation of grapevine cultivars is critical for maintaining sustainability and growth within the whole grapevine industry sector.  To respond to the need created by climate change and the growth of the grapevine industry in non-traditional regions, new cultivar selections are produced by breeding programs.  Testing of new cultivars is typically limited to a few areas.  Coordinated, multi-state testing is needed to evaluate adaptation in a variety of environments.  With changing climate and increased weather variability, cultivar adaptation, including physiological hardiness and robustness to changes in insect and disease pressure will be an increasing issue.  This project leverages substantial investments made in breeding programs and helps evaluate genotype x environment interactions.

Department of Project: Veterinary & Animal Sciences Dept.

The relationship between domesticated animals and humans is a close one, and has existed for at least ten thousand years. It is important to understand the immune defenses of many animals, in addition to the immune defenses of humans and mice. The goal of our project is is characterize the genetic diversity of a family of immune receptors in domesticated animals and use this information for selective breeding and the design of better vaccines.

Department of Project: Veterinary & Animal Sciences Dept.

Sheep are valuable livestock species that have been raised for their production of meat, milk, fleece, and other by-products. More importantly, given their anatomic and physiologic similarities to humans, genetically modified sheep have become an important human disease model in pharmaceutical and biomedical research. Compared with somatic cell nuclear transfer and random transgenesis, CRISPR/Cas9-mediated genome editing is highly efficient and precise. However, due to the impaired developmental competence of embryos cultured in vitro, the overall success rate is still low when blastocyst embryos are transferred into the recipients. In this study, we propose to optimize the microenvironment of in vitro cultured sheep embryos by modulating the culture matrix stiffness, fluid flow, and embryo rolling, to improve the developmental competence of blastocysts, which stage allows for a much faster and less-painful non-surgical embryo transfer than the surgical procedure. Our proposed research, if successful, will innovatively streamline the production of genetically modified sheep and other large livestock animals, to increase both human and animal health and welfare.

As an important group of crops, legumes are prized for their high protein content, which is thanks to their remarkable ability to make their own nitrogen nutrient through a symbiotic relationship with a particular group of bacteria. We still do not fully understand the legume genes that allow these plants, but not most others, to enter this nitrogen-fixing symbiosis. Evolution through millions of years has turned this relationship into a very elaborate process, requiring hundreds if not thousands of genes from both partners. To speed up the rate of scientific discovery, we developed a genetic method based on the CRISPR/Cas9 technology to examine genes suspected to be involved in this mutualistic interaction. This approach will allow us not only to study one gene at a time, but multiple genes at once if necessary. We will carry out the research on a small legume species easy to manipulate in the laboratory, but the findings will have important implications for important crops, such as soybeans, peas, and peanuts.

Brucella spp. are Gram-negative bacteria that infect animals and humans. B. abortus, B. melitensis, and B. suis are major pathogens of cattle, goats and sheep, and swine, respectively. Brucella infections in these food animals have significant economic impacts in areas of the world where they are not controlled by effective eradication programs. In their main animal hosts, brucellosis causes spontaneous abortion or birth of weak offspring, reduced milk production and infertility. Transmission occurs by direct contact with infected blood, placentas, fetuses and consumption of raw animal products, especially milk and milk products (Nicoletti 1989). Understanding the physiology of these bacteria and how host infection is modulated is therefore important for control of these pathogens.

Bacteria manage changes to their environment, such as the stress of host infection, by altering the levels of RNA, protein and signaling molecules to cope with these changes. Proteases play central roles in bacterial physiology. They modulate the activity of cellular proteins and remove damaged proteins from cells. Because proteolysis is irreversible the catalytic function of cellular proteases must be tightly regulated. While the extent and capacity of proteolytic control in Brucella is unknown, modern proteomic strategies have now made it possible to capture this important facet of bacterial regulation.

In this proposal we aim to chart the dynamic proteome in Brucella abortus, identify the roles of specific regulators in controlling these dynamics, and share these results with the scientific community by making a searchable open-access databases. We believe that this atlas will provide a starting point for all those studying Brucella to either identify new candidates of interest or to validate regulatory mechanisms for targets under study. Given the economic and agriculture impact of brucellosis on animal hosts, we predict that this insight will spur understanding of how to manage Brucella infections and reduce the economic burden of this disease.

Department of Project: Resource Economics Dept.

We will develop a mathematical model that predicts how farmers (or firms) will make decisions when choosing between two markets. The markets we will study include a wholesale market, where farmer's products are no different from all other farmers, and a farm-to-school market where the farmer's products are differentiated (the farmer is known and the products are known to be locally produced). We will then design economic experiments that could be used to test the model's theoretical results. Plans for the design will focus on determining how farmers will allocate their products among the two markets given different levels of transaction costs and market power. We will also work on the design of a preliminary experiment to determine the social preferences of the "farmers." The choices of these "farmers" will then differ according to their social preferences, the transaction costs they face in marketing their products, and the amount of market power they possess and the school possesses.

Department of Project: Microbiology Dept.

Pathogens including viruses are known to be major contributors in the decline of honeybee colonies, yet we are only now beginning to understand the epizootiology of these agents. A primary reason for this lack of knowledge is the microscopic and submicroscopic nature of these bee pathogens. As part of our research we have developed and are continuing to develop molecular methods that allow us to detect and monitor the prevalence and spread of these infectious agents in bee populations.
In addition, we will be exploring the utility of small bio-reactive molecules for use in controlling viruses and protozoan pathogens without harming bees

Department of Project: Biology Dept.

A scale insect pest has been outbreaking on cranberries in Massachusetts every year since 2012, and in 2022 it is the most damaging pest of Massachusetts cranberries, affecting a majority of commercial bogs. To manage it, we need to understand basic facts about its biology, but right now we don't even know what to call it: we don't know what species it is.  It looks like the species Diaspidiotus ancylus, Putnam scale, and that is what it has been called in the literature and in presentations to growers.  But taxonomists have long suspected that multiple distinct species may have been erroneously lumped together under the name Diaspidiotus ancylus, and we have recently corroborated this hypothesis using DNA evidence.

                The goals of this project are to figure out: how many species are in this group, which plants each species attacks, how each species is distributed geographically, how they can be told apart from each other, and what their scientific names ought to be.  The group has a complex history, originally having been described as 11 different species, before these were lumped together. To help assess which of those 11 species are valid, and whether additional, yet-unnamed species need to be recognized, we will collect members of this species group and their close relatives from many locations in Massachusetts and around the eastern and midwestern US, including 22 so-called "type" localities, in 13 states, from which these species and their closest relatives were originally described.  We will sequence DNA from 3 different genes and use this in conjunction with previously-collected DNA data and other information to assess where the species boundaries lie. 

                The direct target audience for our research results will be our fellow entomologists, especially those dealing with pests identified as Diaspidiotus ancylus that attack cranberries, blueberries, other orchard crops, and ornamentals.  This study will lay the groundwork for a revised classification of the group, and for published guides to the identification, host plant use, and distribution of the consituent species -- not least, we will finally have a valid and correct name for the cranberry pest, and a published means of telling it apart from the lookalike species with which it has long been confused.  This will result in more accurate information about the pest and its biology being conveyed to growers and informing pest management.

Natural products have a long history of providing novel compounds either directly or as lead compounds for human therapeutics, nutrition and agricultural applications. Fungal diversity has evolved over 900 million years and concurrent with this evolution in diversification of the natural product chemistry resulting in an impressive array of compounds known as specialized metabolites. In the organisms, natural products have biological activity to enable adaptation of the organism to its' ecological niche, ranging from profound effects of hormones to sometimes only the subtle effects observed under specific environmental conditions mediated by more specialized metabolites. In agricultural systems fungal metabolites can cause detrimental effects and large losses to agricultural crop yields, at the same time because of their biological activity these specialized metabolites can be translated for use as human therapeutics1-3. A significant renewed interest in mining fungi (and plants) for specialized metabolites is the availability of massive sequencing data and their potential for widespread use in agriculture, industry and as pharmaceutical agents.


Department of Project: Nutrition Dept.

Food insecurity has increased during the COVID-19 pandemic. The COVID-19 pandemic has exposed inequities in food insecurity and food access among diverse populations. Food access has decreased in part because of the additional restrictions on going out and gatherings. For example, purchasing shelf-stable foods to decrease shopping trips or closure of congregate meal sites.

Beyond COVID-19, it is important to better understand the unique challenges and coping strategies among diverse groups that influence food security and food access because adequate nutrition is critical to overall human health and well-being. Consumption of fruit and vegetables is a major contributor to adequate nutrition for all age groups. Older adults are at increased risk for inadequate nutrition due to unique barriers to obtaining fruits and vegetables. For example, inability to travel to grocery stores or other traditional food outlets can be particularly challenging for older adults who may have limited physical mobility and / or few transportation options, especially if they no longer drive. Social isolation is another characteristic that is related to lower fruit and vegetable intake and independently impacts health among this population. In both urban and rural areas, specific buyers including older adults (> 60 years of age) and lower income individuals and families may have limited access to fruits and vegetables. Producers such as small and medium scale farmers may be interested or engaged in viable markets that could help close the gap between fruit and vegetable need and access.

The study aims to gain a better understanding of how influencers of healthy eating (such as transportation constraints and social isolation) impact food insecurity and food access during economic shocks or a public health crisis (e.g., COVID-19 pandemic) and in the following years. Another aim of the study is to better understand and address programmatic implementation challenges that arise from operating during a pandemic compared to normal operating conditions and how changes may improve operations ongoing in the years following the initial economic shock or initiation of the pandemic.

The goals and objectives of this project are to better understand: 1) the barriers and facilitators of specific buyers to purchase fruits and vegetables; 2) proposed solutions by specific buyers for closing the gap between need and supply; 3) the perspective of producers on viable markets for closing the gap between need and supply; and 4) the impact of COVID19 on food security, food access, and food programs that aim to improve access to healthful foods and decrease food security.
The proposed study is in response to community partners in Massachusetts interested in examining Senior Food Box distribution, Farmers Markets Programs, and other distribution systems that assist older adults and diverse populations in obtaining fresh fruit and vegetables and, in turn, improve diet quality and contribute to achieving adequate nutrition. The proposed study examines questions about how to best serve the needs of older adults and diverse populations in terms of fruit and vegetable accessibility, affordability (costs), quality, and variety including meeting the requests of ethnically and racially diverse populations. The study also examines the perspectives of producers to meet needs and demands of buyers.

A better understanding of the perspectives of our target audiences, the producers and buyers, on demand and supply of fruits and vegetables, will benefit both audiences by improving the food system to increase fruit and vegetable availability, purchase, and ultimately consumption in an effort to improve adequate nutritional intake for individuals and families, and potentially increasing the health and well-being among diverse populations of individuals, families, and communities. A better understanding of the inequities in the food system and food access will provide insights on how to address them.

The proposed project will use surveys, focus groups, and key informant interviews to meet the goals and objectives of the project. These methods will facilitate gaining the perspectives of producers and buyers. Dissemination of findings among producers and buyers as well as academic and extension researchers and practitioners will be done through written materials (e.g., project reports, white papers, and academic journal articles) and presentations.

Department of Project: Nutrition Dept.

The proposed study aims to examine the nutritional health, food insecurity, and maternity care experiences of immigrant women in Massachusetts and in communities outside of the state. Through community engagement, interviews, and surveys of 10-15 immigrant women, as well as secondary data analysis of data on immigrant and refugee women in Massachusetts, our study hopes to demonstrate the importance of the migration experience, place of residence, and host communities in facilitating optimal health and nutrition outcomes for immigrant women and their families. We work with community partners and Extension Nutrition Education Program (NEP) staff to examine and interpret study findings. This process will increase engagement of our extension educators and community partners in research on their communities and facilitate an accurate interpretation of research findings. Our work is also important for generating ideas for innovative nutrition programming to meet community needs; developing and implementing training for NEP staff and educators; and for formulating policies that prioritize investments in nutrition, food security, and health infrastructure for communities in transition and immigrants in the U.S.

Department of Project: Nutrition Dept.

Obesity has become a major public health threat with substantial economic losses and medical costs in the U.S. and worldwide due primarily to its strong link with metabolic complications and diseases including inflammation, type 2 diabetes, and cancer. Thus, prevention and/or even delay of such conditions is of critical importance for improving public health. The USDA dietary guidelines for Americans strongly recommend increased consumption of fruits and vegetables that are rich in antioxidants and bioactive components to prevent or attenuate diet-related chronic diseases and to improve overall health. As person's diet is a key contributor to health and disease risk, agriculture has been a core sector of economic viability and food production systems with the increasing recognition of the interface between nutrition and agriculture. Epidemiological and clinical studies have repeatedly demonstrated many health benefits of food-based bioactive components by modifying the risk of disease, suggesting that bioactive molecules in our diet can be effective in preventing or delaying the disease process. Therefore, it is important to identify and characterize the novel bioactive molecules from food-grade plants and crops that may contain the principal components for enhancing human health and preventing diseases. Our long-term goal is to define the protective effects of bioactive food components in agricultural crops and develop effective dietary strategies designed to reduce obesity-linked health complications. The objective of the proposed study is to determine the extent to which cranberry bio-actives affect fat cell metabolism including lipid metabolism and thermogenesis, resulting in the contribution to suppressed adipocyte inflammation and dysfunction. The discovery of novel health effects of bioactive components will not only provide the scientific basis for dietary recommendations to increase public health, but also offer economic viability of crop farming and sustainable production to local farmers and growers. The outcome of this research will help achieve the national goal of agricultural and nutritional research to improve public health and prevent diet-related chronic diseases, thereby benefiting consumers and agricultural industry.

Department of Project: Resource Economics Dept.

The food industry is under transformation due to some important changes in consumer preferences. With a trend towards a healthier lifestyle, food quality, nutrition, and safety are increasingly important to consumers today. There is an increasing demand for more information about the nutritional content of food, for food considered healthy and health-enhancing. However, at the same time, obesity and diabetes rates continue to rise and so do health care costs as a result. There is significant interest in developing and implementing policies to address these problems and promote healthy eating. In this Hatch project, we examine the effects of two public policies aimed at improving consumer health outcomes.  More specifically, we propose estimating the welfare effects of a policy proposal that bans use of partially-hydrogenated oil in food products leading to a ban on trans fat. Partially hydrogenated oil as a source of trans fat, is a primary cause of deaths related to heart attack and obesity in the United States. However, use of partially-hydrogenated oil as an ingredient, even in small amounts, significantly decreases cost of production by providing longer storability and shelf stability. To evaluate welfare effects of this ban, taking into account the demand- and supply-side responses, we use the microwaveable popcorn market as a case study, use Nielsen retail scanner datasets, and estimate a consumer demand model for microwaveable popcorns. We recover consumer preferences as well as marginal cost of production. We propose estimating counterfactuals by allowing firms to endogenously choose prices as well as product portfolios. Using our model, we can simulate the expected product offerings in the market as well as the prices of those products, hence we can compute the total gain in welfare from both before and after the ban is imposed.


Department of Project: Nutrition Dept.

Mounting epidemiological and experimental evidence consistently indicates that obesity is a robust risk factor for colorectal cancer. As obesity has reached an epidemic level and further increases are projected in the future, it is critical to understand the mechanism(s) responsible for the link between obesity and colon cancer risk. Novel observations from our two recent studies indicate that a specific bacterium, Turicibacter, and the bacterial metabolite butyrate may act as mediators linking high fat diet-induced obesity and intestinal cancer, but not for genetically-induced obesity and intestinal cancer. This project aims to define this innovative mechanism, and thereby to inform the development of dietary strategies for preventing dietary obesity related intestinal cancer.

Commercial Horticulture

Department of Project: Stockbridge School of Agriculture

For the development of molecular diagnostic detection tools (by color change) for dollar spot pathogen, turfgrass leaves and thatch will be sampled biweekly from May through September for total DNA extraction. Molecular-based markers specifically targeting dollar spot pathogen will be designed based on sequences of dollar spot genomes which are publicly available and using existing programs. The designed DNA markers will be tested for validation using those DNAs including positive control DNA extracted from dollar spot culture grown on PDA. After validation, the markers will be tested using DNA extracted from leaves and thatch, before and after dollar spot symptoms, on multiple golf courses in MA and CT.

For the development of molecular diagnostic detection tools (by color change) for fungicide resistance in dollar spot pathogen, pure culture of dollar spot fungus will be isolated from infected leaves to be collected from fairways, putting greens, or tee boxes on golf courses only where superintendents are suspicious of resistance development due to the lack of control or shortened application interval. These isolates, along with previously characterized sensitive and insensitive isolates will be tested in vitro for sensitivity to each fungicide class on fungicide-amended PDA media.  After in vitro assays indicate putative resistance or reduced sensitivities, putative resistant isolates will be used for target gene sequencing for detection of mutation.  After mutations are confirmed, molecular-based markers specifically targeting each mutation in each fungicide class will be designed using sequences of dollar spot genomes which are publicly available and using existing programs. The designed DNA markers will be tested for further validation using DNA extracted from infected leaves from golf courses with suspected resistance in MA and CT.

Department of Project: Stockbridge School of Agriculture

The goal of the project is to improve irrigation and fertilization practices in ornamental plant production in order to improve production efficiency and to reduce the environmental impact of ornamental plant production by limiting nutrient laden runoff from nurseries and greenhouses. Improving production practices relies on a better understanding of plant water and fertilizer needs as well as assessment of improved application methods. To further improve practices the influence of different soilless media components will be assessed as these components vary in their ability to hold and retain water and nutrients. The use of water holding capacity improving additives such as hydrogels and surfactants will be assessed for use in production and interactions with fertilizers.  Improving production practices helps growers to produce the best quality plant possible with the least added inputs in a more environmentally friendly manner.

Community & Economic Vitality

Department of Project: Resource Economics Dept.

The food industry is being transformed by two important changes. It has recently been characterized by rising concentration, partly due to a number of large mergers since the beginning of the new millennium.[1]  In addition, the advent of the internet is affecting the source of advertising and the method of purchase for many food products. Firms in the industry must devise strategies to adapt to and capitalize on these changes that have the potential to affect market structure and performance. We propose research on the food industry with two related components that examine the effect of firms' strategies in pricing and advertising on market concentration and market performance.  The first component ("Concentration and Fragmentation in the Age of Digital Advertising") examines the effect of digital advertising on market concentration using beer sales data, which provides the advantage of observing two similar, but distinct markets - light and regular beers. The second component ("Market Reactions to Potential Entry") investigates the role of price variation in defending against market entry. For this component we use data on steak sauce sales. These data are particularly advantageous for this study because of the limited number of brands and the infrequent nature of consumer purchases in this market.

Department of Project: Environmental Conservation Dept.

Widespread, international and local interest in greening municipalities and increasing urban tree canopy cover continues, largely through community-based tree planting initiatives. It is generally estimated that newly-installed (i.e., planted) trees require at least 3 or more years before establishment, when they resume pre-transplant growth rates. Most trees installed in the urban environment are dug from the nursery field with a spade and wrapped in burlap and a metal basket (‘B&B’ or ‘balled and burlap’ or ‘BnB’). There is interest, however, by tree enthusiasts (i.e., shade tree committee members, Master Gardeners, etc.) and professional urban foresters (i.e., tree wardens/municipal foresters), in planting trees grown using other easier-to-plant systems, including a variety of container-grown (CG, IGF) and bare-root (BR) tree production methods. Ideally, trees that are being planted persist longer than the individuals that are installing them, thus trees grown from these production systems, must have the potential to grow long-term and reach maturity to provide optimal value in relation to the social, economic, and environmental services that urban trees are known for. This may be a challenge, since urban environments often present very difficult growing conditions that foster widespread urban tree morbidity and premature mortality. Though advances in understanding have been made, there is a dearth of empirical data describing the survival and growth of these trees, with the preponderance of research considering trees growing in traditionally forested environments or agricultural plots, rather than urban settings. Since budget constraints are routinely identified as a key limiting factor relative to urban forest management practices, there is also a need for further information concerning the longer-term costs associated with maintaining newly-installed urban trees.

Collecting growth and maintenance cost data on established urban oak specimens in Amherst, MA, produced using various nursery systems will 1) add to the overall base of knowledge concerning urban tree growth and survival 2) enable the quantification and further understanding of the relationship of urban tree growth/survival and nursery production system 3) Enable the quantification and further understanding of the long-term costs associated with planting and maintaining urban trees. The long-term goal of this work is to gather local, empirical data that will help urban forest practitioners consider the appropriate (i.e., most cost-effective, best-performing) nursery production system, when selecting trees for urban planting in Massachusetts and other New England communities.

Department of Project: Resource Economics Dept.

The food industry is under transformation due to some important changes in consumer preferences. With a trend towards a healthier lifestyle, food quality, nutrition, and safety are increasingly important to consumers today. There is an increasing demand for more information about the nutritional content of food, for food considered healthy and health-enhancing. However, at the same time, obesity and diabetes rates continue to rise and so do health care costs as a result. There is significant interest in developing and implementing policies to address these problems and promote healthy eating. In this Hatch project, we examine the effects of two public policies aimed at improving consumer health outcomes.  More specifically, we propose estimating the welfare effects of a policy proposal that bans use of partially-hydrogenated oil in food products leading to a ban on trans fat. Partially hydrogenated oil as a source of trans fat, is a primary cause of deaths related to heart attack and obesity in the United States. However, use of partially-hydrogenated oil as an ingredient, even in small amounts, significantly decreases cost of production by providing longer storability and shelf stability. To evaluate welfare effects of this ban, taking into account the demand- and supply-side responses, we use the microwaveable popcorn market as a case study, use Nielsen retail scanner datasets, and estimate a consumer demand model for microwaveable popcorns. We recover consumer preferences as well as marginal cost of production. We propose estimating counterfactuals by allowing firms to endogenously choose prices as well as product portfolios. Using our model, we can simulate the expected product offerings in the market as well as the prices of those products, hence we can compute the total gain in welfare from both before and after the ban is imposed.


This research considers ways that "social infrastructure" and "green infrastructure" can mitigate the impact of climate change and severe climate emergencies on vulnerable populations in Springfield, Massachusetts and similar cities. While there is ample research on ways to protect vulnerable populations (elderly, low-income, and minority populations) from climate change, very little research addresses the role that social infrastructure and green infrastructure can play. Even less research addresses this situation as it pertains to cities like Springfield, the small to mid-sized former manufacturing centers that comprise the country's "legacy cities," commonly known in Massachusetts as "Gateway Cities.". Springfield and other similar cities tend to have particular challenges that larger, richer cities do not experience to the same degree. Mid-sized legacy cities have relatively weak economies and have higher proportions of vulnerable residents (especially poor and elderly). With limited budgets, many of these cities have trouble meeting basic needs and lack the resources to invest in neighborhood parks and community infrastructure. Through community engagement, interviews, and surveys of neighborhood residents, our study may help demonstrate the importance of investing in these types of infrastructure. Our work may also be an important incentive for cities to implement capital projects or policies that give priority to investments in social and green infrastructure.

Environmental Conservation

Department of Project: Environmental Conservation Dept.

As Massachusetts faces increasing pressure from population expansion, along with increasing challenges due to climate change, we seek a solution to the growing demand in housing that supports the local timber industry and rural economies and also creates an opportunity to store more carbon both in our buildings and across our regional forested landscape. Recent advances in timber technology have produced promising new methods for meeting some of the demand for building materials, as well as the need to store carbon.

Department of Project: Geosciences Dept.

Reliable, sustainable sources of clean water are increasingly hard to come by. But did you know that there are a lot of additional benefits from cultivating and protecting freshwater wetlands atthe source of some of these waters? Wetland ecosystem services include, but are not limited to, providing verdant habitat and food supply for a large diversity of plant, animal and insect species, water filtration, slowing and spreading of floodwaters, limiting erosion, storage of carbon and other nutrients, temperature buffering, pollinator habitat and forage lands, and water storage. One of the most basic, defining metrics of a wetland is, as the name implies, its wetness. The relative water content in the soil can be assessed in a variety of ways, and this quantity alone is important for reasons beyond wetland function. Specifically, for a wetland to become established and remain functional independently, sufficient water must be present throughout the year to favor wetland plants and animals, which thrive in wet environments but are unlikely to outcompete invasives or other species in drier regimes. We forsee a continued interest in wetland restoration in Massachusetts and predict that measurable metrics to assess the success of such restoration efforts are desired. Two recent developments support this: first, Massachusetts DER created a new Cranberry Bog Program in 2018 to facilitate exactly these types of restorations, and second, Living Observatory (LO) has begun a learning collaborative of scientists, artists, and wetland restoration practitioners to document the science and best practices of freshwater wetland restoration projects. Building on recent projects and successes, we propose to identify and establish a comprehensive catalog of metrics for measuring the success of freshwater wetlands that have been restored. We will continue our observations of soil moisture and subsurface thermal regimes, and add additional observations of weather and climate variables, phenological change, subsurface water levels, water chemistry, and microclimates and topographic influences of microtopography and other restoration practices.

Department of Project: Environmental Conservation Dept.

Regeneration is the future of Massachusetts forests. It is critical for the conservation of the State's forestlands and for the continued provisioning of the myriad ecosystem services they provide (sustainable timber and wood products, carbon storage,wildlife habitat, clean drinking water, biodiversity, recreational opportunity, and aesthetic/intrinsic value). Global change related factors including novel climatic conditions, invasive plants, deer overpopulation, and habitat fragmentation threaten current and future forest regeneration within Massachusetts. These threats come at a critical time when we are already observing increased mortality of economically and ecologically important tree species across the State at the hands of non-native pests and pathogens. Ensuring successful regeneration of desired tree species and natural communities within these damaged forests is paramount to the continued health, vigor, and viability of the State's forest resources.Adaptive forest management may be used to overcome contemporary regeneration challenges, ensuring the conservation of healthy and valuable forest ecosystems. However, we currently lack sufficient regeneration data and scientific understanding of the various factors impacting regeneration to develop and test meaningful adaptive management strategies.

Department of Project: Environmental Conservation Dept.

The expansive growth of solar photovoltaics (PV) in Massachusetts has helped make the state a leader in renewable energy production, but there have been public concerns regarding the development of agricultural lands for solar PV electricity production.  In response to these concerns, the Massachusetts Department of Energy Resources (DOER) included provisions in the new state solar energy program which limit conventional ground-mounted solar arrays on farmland, while encouraging innovative "dual-use" technology.   Under the new Solar Massachusetts Renewable Target (SMART) program, there is a significant financial incentive for dual-use systems which limit shading and obstructions, and require continued agricultural production on the land below and around solar arrays.

Dual-use systems are still novel, and to a degree experimental.  What agricultural activities are most compatible with dual-use is not well understood, nor is whether the new incentive will be sufficient to spur significant adoption of dual-use cropping systems.  UMass has important roles in the development and adoption of dual-use systems.  First, UMass Extension will serve as a clearinghouse of information and an educational resource for the agricultural and solar energy communities regarding the new technology and new incentive program.  Second, UMass faculty will provide feedback to DOER and the agricultural community regarding the success of the program, and suggest any modifications that could help further the goal of promoting expansion of renewable energy capacity, while preserving farmland and agricultural production capacity within the state.

In keeping with these roles, UMass Clean Energy Extension (CEE) is proposing an investigation that will address gaps in agricultural knowledge about the impact of dual-use systems on agricultural methods and productivity, while also exploring farmer motivations and decision-making around the adoption of this new technology.

Department of Project: Microbiology Dept.

The world fisheries production has levelled off and most of the main fishing areas have reached their maximum potential. In contrast, the global human population is increasing; thus, the demand for aquatic food products also increase. Global aquaculture production attained 90.4 million tons in 2012, generating an incomes US$ 144.4 billion, and the production of food fish was 66.6 million tons. Epitheliocystis is a serious skin and gill disease in fish, believed to be caused by pathogenic intracellular bacteria. The disease has been reported in at least 90 species of marine and freshwater fish in both the southern and northern hemisphere. It affects a number of commercially important aquaculture species, including salmon, kingfish, trout and bream. Infection in these fish species is characterized by the development of cysts, typically in the gill epithelia, promoting the fusion of gill lamellae. This condition is usually benign; however, sometimes it can be associated with a high mortality, particularly in cultured fish. Infections can lead to respiratory distress and death, particularly in cultured and juvenile fish. While fish mortality data attributed to epitheliocystis is sparse, a remarkably broad range of 4%-100% observed mortality rates has been reported. Even with the recent molecular advances in identifying the pathogens, the reservoirs and modes of transmission of the etiologic agent(s) of this disease remain largely unknown. Bacteria belonging to the order Chlamydiales are an extremely important and diverse group of pathogens of vertebrates, which include respiratory diseases of fishes. Chlamydial infections of fish are emerging as an important cause of epitheliocystis in new and established aquaculture industries [6, 8]. However, empirical data and direct evidence relating to the etiology, treatments and epidemiology remain limited, highlighting the need for more work to better characterize this disease across the different hosts and locales affected.  We hypothesize that Chlamydia-like organisms are an important etiologic agent of epitheliocystis. We believe that a better understanding of disease transmission, mechanism of disease process and host range will provide a basis for preventing this emerging disease in aquaculture. Upon successful completion of this project, we will (1) have a better understanding of the etiologic agent(s) of epitheliocystis; (2) have an understanding of how the disease is transmitted and possible reservoirs in the aquaculture setting for common fish species; (3) determine the treatment regimen most effective at preventing and eliminating epitheliocystis in commercial fisheries settings and (4) pilot an effective screening/diagnostic test for early detection and confirmation of epitheliocystis.

Department of Project: Environmental Conservation Dept.

Forest conservation and management is already complex in New England.  Changes in temperature, precipitation, winter conditions and the timing of seasons have already been documented, and further changes are expected well into the future (Horton et al. 2014). Changes in forest conditions and the geographic distribution of forest types are likely to threaten some ecosystems more than others. Areal coverage of boreal forest and Northern hardwood forests are projected to decline based on model projections (Janowiak et al. 2018). This would affect those species of plants, animals, fungi and other organisms that depend on these ecosystems (Janowiak et al. 2018).
Ecosystems within forested environments, such as streams and wetlands, are also likely to undergo changes that will make it difficult to support viable populations of fish and wildlife and maintain forest biodiversity. For example, as air temperatures rise, corresponding increases in water temperature will further stress cold-water streams. As a result, cold-water stream habitats may disappear or become smaller and more fragmented (Preston 2006, Manomet Center 2013).
Landowners, foresters, conservation organizations, and municipal officials (forest decision- makers) need research-based information on potential impacts on forests and spatially explicit information to guide adaptation strategies and actions. Active conservation measures are necessary to: limit stream warming, identify and conserve potential cold-water refugia, strategically target land protection for refugia for threatened forest types, and ensure terrestrial and aquatic connectivity to maintain viable populations of species dependent on these threatened forest ecosystems. To increase resistance and resiliency to climate change, forest management practices will need to change to ensure species and structural diversity, and adjust to emerging threats, such as invasive species, pests and diseases. 

Department of Project: Environmental Conservation Dept.

Forest dynamics and the spatial and temporal modeling of the dynamics of Food-Energy-Water (FEW) systems at a watershed scale are critical for sustainable land and resource management. The assessment of vegetation (Forest and plant biomass) and land use dynamics is vital for scientific innovation and for enhancing local and regional sustainability and resilience. Assessing built, natural, and social components and their interactions as a dynamic system can lead to comprehensive strategies that improve food production, conservation, energy efficiency, and water resources. Dynamic changes in FEW systems are complex processes, especially the state of the complex system and its trajectory over time. As the population increases and new demands on ecosystem services, watersheds face environmental, energy, and food challenges. This could include polluted waterways, floods, droughts, loss of forest and green space, energy inefficiencies, crop loss, yield loss, soil erosion, increasing density of built structures, and a deterioration in watershed services. Increasing population densities increase built components causing higher forest loss, impervious cover, wastewater discharges, stormwater surges, nonpoint source pollution, loss of open space, farmland loss, and habitat fragmentation that substantially impact watershed systems. Agricultural land is also at increasing risk from urbanization with pressure to produce more in a limited area and with limited resources.

The nexus between food, energy, and water (FEW) has strong interaction with land use-based assessment, requiring system-based modeling for policy. The system information on interactions, tradeoffs, trajectories, thresholds, and endpoints in FEW systems is needed to evaluate sustainable patterns and processes that can be used to manage built, natural, socioeconomic, and cyber systems. We propose to study these issues at a regional watershed scale through integrated spatial and temporal modeling of forest dynamics at a watershed scale. 

The goal of this research is to simulate and optimize interactions in patterns and processes in built, natural, and socioeconomic components and forest dynamics on FEW services based on a multiscale system at the watershed scale. Specifically, (i) to evaluate baseline spatial and temporal changes in FEW systems at the watershed scale; (ii) To assess the influence of changing built and natural environment on FEW dynamics and processes; (iii) to evaluate farmland management and its impacts on FEW systems; (iv) to study attitude, values, and behavior towards FEW outcomes under land-use patterns and conservation alternatives; (v) to develop a multiattribute, optimization model for pattern and BMP choice to enhance watershed sustainability for FEW provision; (vi) to develop a web-based decision support system (WDSS) with site-specific information for stakeholders on FEW resilience and conservation choices.

The target audience will include farmers, land owners, municipal officials, private forest owners, government agents, nonprofits, educators, scientists, and professionals. The information generated will cover the watershed-based assessment, strategies to sustain water resources through forest management, handling increasing urban demands through forest BMPs, supply augmentation potential through forest ecosystem functions, and potential effects of LID at the watershed scale. Educators can use the information to develop simple classroom activities demonstrating workshop concepts. 

Research activities in the Connecticut River Watershed with result in outcomes that directly benefit the target audience through capacity building and spatial information that will be helpful for decision-making. The workshops will provide information on the spatial distribution of water supplies and use and trends in distribution. The workshop will recommend strategies to sustain water resources and will involve brainstorming and breakout sessions to develop implementation plans. A website will be developed for the project and will be used to disseminate information to communities within the watershed and watersheds throughout the region and the US

Department of Project: Biology Dept.

Many bee pollinators are in decline, and exposure to diseases has been implicated as one of the potential causes. In my lab, we have already established that pollen from one domesticated sunflower source dramatically reduces Crithidia infection loads in the common eastern bumble bees in the laboratory, and that consumption of this pollen improves performance of healthy and infected bee microcolonies. We will expand this work by growing many sunflower cultivars and related taxa, collecting pollen, and repeating laboratory assays to establish how widespread this medicinal trait is across sunflower-related taxa.

Department of Project: Environmental Conservation Dept.

Forests are the natural vegetative cover for most of New England. In many parts of our region, the forests have been clearedtwice over the last 150 years, yet today they continue to dominate the landscape. Our forests have also faced threats, such asthe introduced chestnut blight, which removed the American chestnut (Castanea dentata), a once dominant tree species, fromthe landscape. Despite this and other losses, we continue to enjoy the many essential benefits forests provide to our daily lives,such as clean water, climate change mitigation, wildlife habitat, scenic landscapes, recreational opportunities, and forest products. In other words, our forests are inherently resilient. However, we are now facing an uncertain future, in which our forests will encounter many, often interacting, stressors, of particular note are forest conversion and parcellization (Stein et al. 2005; Olofson et. al. 2016); invasive insects (Hicke et. al.2012, Lovett et. al. 2016), and climate change (Franklin et. al. 2016, Janowiak et. al. 2018). Though our forests have shown themselves to be resilient, they also have characteristics that make them vulnerable to these stressors to varying degrees (e.g.,aging forest landowner population, simplified forest structure, and uniform composition). While there is uncertainty as to how our forests will react to these stressors, we can be confident that our forests will change. Understanding the ways in which these stressors will change our forests and developing strategies to address them is critical to maintaining the essential forest services on which we rely.


Department of Project: Stockbridge School of Agriculture

Increasing environmental stresses make crops ever more succeptible to the impact of plant viruses. Plant viruses affect plant functioning and, specifically, the root system. For example, virus infected cover crops may hamper root growth and activity. This may influence the effect of cover crops on the cycling of carbon and other nutrients in soils. Consequently, virus infections may undermine the beneficial use of cover crops to improve soil health, with unclear consequences for soil carbon storage, greenhouse gas emissions, and nutrient status. This project therefore tests how plant virus infection influences the impact of cover crops on soil carbon and nutrient cycling.