Progress 07/01/19 to 06/30/24
Outputs
Target Audience:The target audience was primarily the research community investigating phosphorus-related land management strategies, with the associated implications for phosphorus retention, bioavailability, and loss. We also disseminated our results among the environmental chemistry and microbiology research community at Penn State, operators and consultants in the Pennsylvania water and wastewater treatment industries, and the environmental engineering graduate community at Penn State University. Changes/Problems:During this project we encountered two main problems that hindered our progress. The first was the pandemic, which coincided with the beginning of the project and greatly affected our ability to get necessary research supplies (namely RNA extraction kits needed for metatranscriptomics, due to supply chain limitations caused by testing kits for the RNA-genome virus) and conduct laboratory and field experiments. The second was a drought that affected our planned field experiments, that required the capture of hot-moment precipitation events that would trigger the hypothesized microbial responses to anoxic conditions. This led to us getting a late start, and required us to adapt by designing lab-based microcosm experiments and column experiments (ongoing) to demonstrate what was intended for the field. What opportunities for training and professional development has the project provided?This project had several students involved, through the Environmental Engineering program at Penn State and the Biological and Environmental Engineering program at Cornell University. At Penn State, the USDA support was leveraged with a Fulbright Scholar's participation on aspects of the project, and it will lead to one MS degree, one PhD student, and the partial participation of another PhD student. At Cornell, the USDA support was leveraged with an EPA fellowship in support of a PhD student, who graduated this past year. How have the results been disseminated to communities of interest?The dissemination of results is captured in the Other Products of this report. These include presentations in the Environmental Engineering program at Penn State, the environmental chemistry and microbiology research community at Penn State, the water and wastewater treatment community of practice in PA, and the Chesapeake Bay modeling community. The project was also presented at several international venues, including the International Union of Soil Sciences and two invited seminars in New Zealand. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We accomplished the metatranscriptomic analyses of phosphorus-related microbial responses to transient wetting events in microcosm experiments. The field experiments were delayed beyond the end date due to the pandemic, and then a very dry growing season. We adapted to lab-scale based demonstration of the hot-moment response, captured by metatranscriptomic signatures that metagenomics failed to capture. We are currently doing column-based studies to show the connection between metatranscriptomic and redox potential signatures, and we anticipate publishing these results in the coming year. Outside the scope, we also developed enzyme-based analyses to complement the differential metatranscriptomic outcomes and assist in understanding P-transforming microbial activities.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Duggan DiDominic, Katie L.; Shapleigh, James P.; Walter, M. Todd; Wang, Y. Samuel; Reid, Matthew C.; Regan, John M. (2024). Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix. Journal of Environmental Quality. v. 53, no. 5 p.565-576
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Progress 07/01/22 to 06/30/23
Outputs
Target Audience:The main target audience for this project is the soil science and agricultural/environmental engineering research community working on soil health and nutrient retention and loss, particularly related to the fate of phosphorus. Changes/Problems:We have not been able to conduct the field-based demonstration of P-affecting hot moments due to very limited precipitation events during the periods in which we could access the test plots. (We also had a challenge hiring an assistant with our USDA-ARS partner to assist with these activities, had they been executed.) This is prompting us to move these activities to laboratory contexts, in which we will do both microcosm and column tests under more controlled conditions that should allow us to better unravel the metatranscriptomic responses in these complex soil communities. What opportunities for training and professional development has the project provided?This project involves a PhD student at Cornell (also supported by an EPA fellowship), an MS student at Penn State, and a PhD student at Penn State who is supported by a Fulbright Scholarship but working on complementary research activities. How have the results been disseminated to communities of interest?The dissemination of the results is summarized on the Other Products page of this report. They have included posters at Penn State symposia that involved the Water Research community and the environmental chemistry and microbiology communities. They were also presented at the USDA-sponsored ACES: A Community on Ecosystem Services Conference in Washington D.C. What do you plan to do during the next reporting period to accomplish the goals?We anticipate completing the metatranscriptomic analyses during a hot-moment affecting P mobility, but in a laboratory context due to problems with implementing the field-based activities.
Impacts
What was accomplished under these goals?
We are making progress on the metatranscriptomic analyses of hot moments, but needing to shift to a laboratory-based demonstration of the underlying hypotheses of this project. We are also developing enzyme-based assays to complement the metatranscriptomic analyses, as these will demonstrate the activites presumed by the RNA signatures.
Publications
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Progress 07/01/21 to 06/30/22
Outputs
Target Audience:The target audiences this period were the environmental engineering graduate program at Penn State University, the environmental chemistry and microbiology community at Penn State, and the Pennsylvania water and wastewater industries via the PA Water Environmental Federation. Changes/Problems:This project has experienced several setbacks to the anticipated schedule. Some of those setbacks were reported previously, such as delays waiting for RNA extraction kits due to COVID supply chain issues. In addition, or field work has not progressed as planned, in part related to the USDA-ARS not hiring undergraduate summer technicians during the pandemic and an ongoing drought at the New York test site that precludes studying soil moisture dynamics (the central hypothesis of this project). What opportunities for training and professional development has the project provided?This project has involved three students, one at Cornell University and two at Penn State University. The Cornell student is in Agricultural and Biological Engineering - she received an NSF internship and has been funded through that source. The Penn State students are in Environmental Engineering and are also enrolled in the Biogeochemistry Dual-Title degree program, in which they will receive cross-disciplinary training relevant to this project. The students have been encouraged to present their results at local and regional venues. There is also an undergraduate honors student at Penn State who will be joining the team next year to study the isolation of polyphosphate-accumulating organisms, which will complement the efforts of the graduate students and this project scope. How have the results been disseminated to communities of interest?The results have been presented to the Environmental Engineering graduate program at Penn State University, at Penn State's annual Environmental Chemistry and Microbiology Student Symposium, and at the PA Water Environment Federation's annual PennTec conference. What do you plan to do during the next reporting period to accomplish the goals?We will expand on our microcosm experiments to test variable moisture content effects on iron reduction and phosphorus release, with the addition of different soil types having different iron and organic carbon contents. We will also perform event-based sampling and analysis to observe metatranscriptome responses to moisture fluctuations. This project has also been bridged in a supporting way to activities of another project at Cornell involving woodchips as a slow-release electron donor to promote denitrification of nitrate-laden runoff, through the involvement of graduate student Katie Duggan.
Impacts
What was accomplished under these goals?
We continued to make progress on data mining from three other publicly available metagenomic and metatranscriptomic data sets that involved characterizing the gene expression effects of a single-variable perturbation on soil communities. These perturbations included moisture, carbon dioxide enrichment, and organic electron donor addition. Specific emphasis has been on differential expression of genes related to phosphorus transformations and iron reduction. We also conducted microcosm tests under variable soil mostures to evaluate the biotic and abiotic reactions that affect phosphorus release and fractionation in wetted conditions. These experiments allowed the estimation of kinetics of phosphorus dynamics under different field capacity conditions.
Publications
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Progress 07/01/20 to 06/30/21
Outputs
Target Audience:The target audience this period was the environmental engineering graduate program at Penn State, where the project was presented. Changes/Problems:We encountered considerable delays (about 6 months) waiting for RNA extraction kits necessary to perform our metatranscriptomic analyses. This occured because of supply chain issues related to COVID, due to the SARS-CoV-2 virus having an RNA genome and the PCR-based COVID testing method requiring RNA extraction. There were global shortages and delays of RNA extraction kits for an extended period. This has set us back in our project schedule. What opportunities for training and professional development has the project provided?This project has involved three students, one at Cornell University and two at Penn State University. The Cornell student is in Agricultural and Biological Engineering. The Penn State students are in Environmental Engineering and were admitted to the Biogeochemistry Dual-Title degree program, in which they will receive cross-disciplinary training relevant to this project. They will also have opportunities to infuse their research activities and findings into the training of other students in the program. How have the results been disseminated to communities of interest?The results have been presented to the Environmental Engineering graduate program at Penn State University. What do you plan to do during the next reporting period to accomplish the goals?We will conduct microcosm experiments to test variable moisture content effects on iron reduction and phosphorus release, under controlled conditions, with different soil types. We will also perform event-based sampling and analysis to observe metatranscriptome responses to moisture fluctuations. This project has also been bridged in a supporting way to activities of another project at Cornell involving woodchips as a slow-release electron donor to promote denitrification of nitrate-laden runoff.
Impacts
What was accomplished under these goals?
We made progress on data mining from other publicly available transcriptomic data sets that involved characterizing the gene expression effects of a single-variable perturbation on soil communities. These perturbations included moisture, carbon dioxide enrichment, and organic electron donor addition. Specific emphasis was on genes relevant to this project, i.e., those related to phosphorus transformations and iron reduction. This effort allowed us to develop and test our analysis pipeline, and look for P-related responses in additional contexts beyond our specific focus context.
Publications
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Progress 07/01/19 to 06/30/20
Outputs
Target Audience:
Nothing Reported
Changes/Problems:Given the timing of the award, we were late in the prime spring graduate student recruiting period. Two prospective students declined our offers, and the remaining applicant pool did not include other candidates with the necessary prior background for the engineering and bioinformatics scope of this project. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?With the successful recruitment of two students during the spring 2020 semester, we plan to conduct our field metatranscriptomics experiments.
Impacts
What was accomplished under these goals?
We were unsuccessful at recruiting two graduate students who had the unique combination of engineering and bioinformatics. This set the project back, and our activities were limited to the planning of field activities and plot selection based on prior sampling data at our long-term agricultural research station. Students were recruited at both Penn State and Cornell for the subsequent project year.
Publications
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