Progress 10/01/17 to 09/30/19
Outputs
Target Audience:This project provided experiential learning opportunities in microbial population biology for undergraduate and graduate students, with application to agriculture research. At every step of the project methods, students were actively involved in data collection and analysis. The Program Director has mentored six undergraduate students (2 females, 5 males), two of which are underrepresented minorities and additional undergraduates will be recruited throughout the duration of the project. Two graduate students (Cooper Park and Joshua Smith, who are both pursuing a PhD Molecular Evolution and Systems Biology) started in the PD's lab in Fall 2017. Both students worked on this project and were partially funded by the NHAES funding. Research output was made available to the public through active collaboration with the UNH farm managers and extension staff. The PD and her students actively worked with the farm managers, especially during sample collection. Publications that materialized from the project have been generated. One was published in the journal Frontiers of Microbiology. A second manuscript is currently under review in the journal Scientific Reports. These papers are expected to reach diverse audience, including scientists and students from other institutions, agriculture-related researchers, local, state and federal government officials. Conference presentations also allowed us to directly communicate and share data with other researchers. Changes/Problems:A major positive change in this research project was that we were able to expand the sources of ourStreptomycesbacteria. The project originally included only soil, compost and soil-dwelling invertebrates. In addition to the original sources mentioned and in collaboration with many faculty scientists in UNH and University of New Mexico, we were able to obtain samples from: Chihuahuan Desert, New Mexico; permafrost from Alaska; bats and caves from New Mexico and Arizona;sunken forests in New Hampshire. What opportunities for training and professional development has the project provided?Students involved in the project have developed the necessary research skills (wet-lab and bioinformatics) in microbiology that are integral in agricultural sciences. Students will be able to apply the concepts and methods to investigate other agriculturally relevant microorganisms (e.g., nitrogen-fixing bacteria, plant pathogens, food-borne pathogens). Application of genome sequencing methods and analytical tools in agricultural research will be an important step in moving the field of agriculture forward. Hence, scientists and students who have background in agrigenomics will be able to contribute substantially to drivingsustainable productivity and developing solutions to the mounting challenges of feeding the world's growing population. The PD has mentored two PhD students (Cooper Park and Joshua Smith), both of whom are pursuing their PhD in Molecular Evolution and Systems Biology. The PD mentored a total of 16 undergraduate students: Sharlene Amadorα αγ*%Fall 2016 - Spring 2019 John Ball*#α%Spring 2018 to date Kelsey Bourne. Spring 2017 Kevin Marc Dioneda*αFall 2016 - Spring 2018 Thomas FarrarβFall 2018 to date Katherine Loiselle. Fall 2017- Spring 2018 Lindsay MarchβFall 2017- Spring 2018 Krista Mastrogiacomo*%Spring 2018- Spring 2019 Colin McGonagleα α*Spring 2017 - Spring 2019 Jennifer Mydosh%Spring 2019 Michael Pellitteri*βSpring 2019 to date Nicholas Ritzo*α%Spring 2017 - Spring 2018 Griffin Nye*%Fall 2018 to date Taylor Schwartz*αSpring 2017 - Spring 2018 Sean VigeantβFall 2018 - Spring 2019 Dania Zaiterα%Spring 2018- Spring 2019 *Recipient of the UNH Summer Undergraduate Research Fellowship (SURF) αRecipient of the UNH Undergraduate Research Award (URA) βSenior thesis γCollegework study #Weeks fellowship %Hourly paid lab assistant How have the results been disseminated to communities of interest?The PD and her students have disseminated the results of this project through publication in international peer-reviewed journals and presentation in national conferences. Oral and poster presentations by the PD and her two graduate students in the 2017, 2018 and 2019 annual conference of the American Society for Microbiology and the Boston Bacterial Meeting. Graduate students also presented their results in the Departmental Graduate Seminar Series and the Annual Graduate Research Conference organized by the UNH Graduate School. A total of 10 undergraduates that the PD has mentored have also presented their results in the UNH Undergraduate Research Conference in 2018 and 2019. To promote public understanding and interesting in learning and careers in science and technology, specifically in microbiology and genomics, the PD has also collaborated with UNH Photography Professor Julee Holcombe and Microbiology Laboratory Coordinator Amy Michaud to develop a photo collection of the microbial diversity in soils and other environmental sources. These photos will be exhibited at the UNH Dimond Library art gallery for an exhibit that will be open to the UNH community, local elementary and high schools, and the general public. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Cellulose degradation by soil bacteria is a critical component of agricultural ecosystems and composting facilities.Streptomycesbacteria constitute one of the most abundant members of the microbial decomposer community. However, a complete understanding of the genetic diversity and cellulolytic activity ofStreptomycesremain lacking, which can hinder our ability to maximize the contributions of specific microbes to agriculture and biofuel production. This study aims to address this gap in our knowledge by determiningStreptomycesdiversity and cellulose degradation rates in various habitats in NH. Output from this work will have a broad and significant impact in improving crop production under various environmental conditions and in enhancing composting processes for large-scale biofuel production. The overall goal of this application is to determine the genetic and ecological factors that contribute to the heterogeneity in cellulose degradation ofStreptomycesbacteria from soil, soil-dwelling invertebrates and compost. We will address the following objectives: Determine the population structure ofStreptomycesstrains in soil, compost and soil-dwelling invertebrates Determine rates of cellulose degradation of free-living and animal-associated Streptomyces strains Define the genomic properties of representativeStreptomycesstrains with the highest capacity to degrade cellulose in vitro Accomplishments: The PD has completed major activities in this project, which include the collection of hundreds of bacterial isolates from multiple sites and habitats, population-level genomic analysis, integration of research in Microbiology courses taught by the PD. All strains have been archived at -80oC and will be provided free of charge to the research community upon request. Results from this project were: (a) Remarkable levels of species and strain-level diversity ofStreptomycesexists within the same environment and from different environments. (b) Whole genome sequencing of strains reveal variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and other genes. These BGCs encode enzymes and other proteins that help the bacteria degrade cellulose and other compounds in the soil. We also observed variation in recombination, with some strains donating or receiving DNA more often than others. Overall, these results suggest that genome sequences can provide valuable information about the cellulose degradation potential of differentStreptomycesspecies from both soil and animals, which can be leveraged to maximize crop production, composting and biofuel production. Leveragingthe output from the NHAES project as preliminary data, the PD received a five-year $1.17 million CAREER grant from the National Science Foundation (NSF) to study the genomic diversity ofStreptomycesbacteria. This grant will fund a graduate student, at least ten undergraduate research assistants, and one postdoctoral fellow. This grant will also fund outreach activities to educate the broader community and non-scientists about the contributions of microbes in agriculture and environment The PD and co-investigator Dr. Brian Barth received a $15,000 grant from the UNHCollaborative Research Excellence (CoRE) to further expand the goals of the NHAES project.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Park CJ, Andam CP. 2019. Within-species genomic variation and variable patterns of recombination in the tetracycline producer Streptomyces rimosus. Frontiers in Microbiology. 10:552. 12 pages PMCID: PMC6437091 DOI: 10.3389/fmicb.2019.00552
- Type:
Journal Articles
Status:
Under Review
Year Published:
2019
Citation:
Belknap KC, Park CJ, Barth BM, Andam CP. 2019. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria. Scientific Reports. Under Review
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The output of this research has broad and significant impacts, with applications in the fields of agriculture, composting and bioenergy. "Super-degrader" Streptomyces strains can be used to deliver value-added products, such as bioethanol, and sustainable energy from biomass and complex agricultural wastes. This research will also inform studies on identifying how the structure and function of microbial communities in diverse ecosystems respond to human-induced environmental changes (e.g., pollution, land use change, climate change). Moreover,a crucial approach to addressing global health threats and environmental degradation is to maximize our ability to explore the chemical diversity already found in nature and understand how it arose. An importantsource of drugs or drug precursors with broad pharmaceutical and industrial application, including serving as the most effective antibiotics, are natural products produced by Streptomyces. Hence, this project will have broad and tangible impacts in the discovery of novelstrains that can produce enzymes, molecules and other bioactive natural productsfrom previously unrecognized sources in nature for drug development, agriculture and industry.The target audience of this project include the local communities interested in organic matter decomposition (for example, UNH Organic Dairy Farm), scientists interested in discovering novel enzymes and compounds, students who want to obtain additional training in environmental microbiology and bioinformatics. In Spring 2018, I have taught Gen 713/813 Microbial Ecology and Evolution. The course had 16 undergraduates and three graduate students.In this course, I have included topics on the diversity of Streptomyces and other decomposers and their role in ecosystem functioning and interactions with other organisms. I have also incorporated bioinformatics modules using video tutorials and access to UNH's Ron teaching server in this course to provide fundamental command line skills and the different steps in genome data analysis (data quality control, genome assembly, genome annotation, genome comparison). The incorporation of the bioinformatics modules in the course was done in collaboration with the Hubbard Center for Genome Studies. In Summer 2018, I collaborated with Dr. Kelley Thomaswho is the Course Director of theBioinformatics T3: Train The Trainer,The Integration of Bioinformatics into an Undergraduate Biology Curriculumheld at theMount Desert Island (MDI) Biological Laboratory, Harbor, ME. This one-week summer course supports bioinformatics training of undergraduate instructors so that they can effectively integrate bioinformatics into their science curricula. T3 course participants come from around the country. This summer, I developed a protocol for the isolation and enrichment of Streptomyces from environmental sources (soil, invertebrates, decomposing organic material). Course participants in the course were trained to isolate, culture and enrich forStreptomyces, whose genomes they will sequence and analyze. The isolates collected by the course participants will be included in my lab's culture collection. Changes/Problems:We have received 175 Streptomyces isolates from our collaborator Dr. Diana Northup (University of New Mexico), which were collected from bats inhabiting caves in New Mexico and Arizona. We decided to include these in our analyses so we can better compare the genetic diversity of Streptomyces from different animal hosts and geographical sites. What opportunities for training and professional development has the project provided?Two graduate students Joshua Smith (PhD) and Cooper Park (MS, switching to PhD in Fall 2018) started in my lab in Fall 2017. Cooper undertook projects related to Streptomyces and was funded as a GRA.I am also co-adviser to Kaitlyn Belknap (MS; with Dr. Brian Barth) and she is also working on Streptomyces. Several undergraduates have been mentored in Streptomyces biology, in particular, on the isolation, enrichment, culturing and DNA extraction of different Streptomyces. These students include: Sharlene Amador, John Ball, Kevin Dioneda, Krista Mastrogiacomo, Nicholas Ritzo, Taylor Schwartz and Dania Zaiter. In Fall 2017, Sharlene and Nick were paid as hourly lab assistants using the AES funds. In Spring 2018, Nick, Taylor, Sharlene, and Kevin received the Undergraduate Research Award (URA). In summer 2018, Sharlene, Krista and John each received the Summer Undergraduate Research Fellowship (SURF) to work in my lab. Kevin, Nick and Taylor received their degrees in May 2018. How have the results been disseminated to communities of interest?In May 2018, I was aGrand Award Judge at the Intel International Science and Engineering Fair (ISEF) held in Pittsburgh PA. ISEF isa program of the Society for Science & the Public) and is the world's largest international pre-college science competition.Thecategory I judged was Computational Biology & Bioinformatics. In May 2018, I was also a Judge in the Sigma Xi Student Research Showcase, an online science communication competition forundergraduate, graduate, and high school students. I judged two categories:Microbiology & Molecular Biology, Ecology & Evolutionary Biology. While these activities are not directly linked to my Streptomyces project, they allowed me to share my research activities to the competition participants through direct interaction and discussion with them. What do you plan to do during the next reporting period to accomplish the goals?For the second year of this project, we aim to conduct whole genome sequencing of representative isolates using the Illumina platform at the Hubbard Center for Genome Studies. We have been developing a pipeline for the assembly, annotation, pan-genome analyses and phylogenetic analyses of bacterial genomes using the Premise server. We will also conduct preliminary assays and optimize methods to Streptomyces growth in different liquid media. We are also finishing a book chapter on horizontal gene transfer and genome evolution of Actinobacteria to be published by Elsevier in 2019, which will be submitted to the editors on December 1, 2018. Streptomyces are members of the phylum Actinobacteria. We are currently finishing writing the manuscripts on the program Renuc that GRA Cooper Park developed, two manuscripts on within-species genomicvariation in Streptomyces, and another program called HERO (recombination detection in bacterial populations) that Cooper also developed. We aim to submit these to journals in early 2019. NHAES GRA Cooper Park will be presenting his results in the 2019 annual meeting of the American Society for Microbiology in San Francisco CA.
Impacts
What was accomplished under these goals?
The role of decomposer microorganisms in converting raw materials into energy-rich compounds and in maintaining the flow of energy is of paramount importance in maintaining sustainability and stability inside an agricultural or composting system.Streptomycesbacteria constitute one of the most abundant members of the microbial decomposer community. Their ability to break down cellulose, hemicellulose, lignin and chitin make them critical players in biomass decomposition in any habitat. However, a complete understanding of the genetic diversity and cellulolytic activity ofStreptomycesremain lacking, which can hinder our ability to maximize the contributions of specific microbes to agriculture and biofuel production. This study aims to address this gap in our knowledge by determiningStreptomycesdiversity and cellulose degradation rates in various habitats in NH. This project aims to determine the genetic diversity of cellulose-degradingStreptomycesbacteria in soil, compost and soil-dwelling invertebrates. We will pursue the following objectives: Determine the population structure ofStreptomycesstrains in soil, compost and soil-dwelling invertebrates.Our first year funded by NHAES was devoted to sample collection, bacterial isolation, DNA extraction and sequencing for initial bacterial classification, all of which fulfills part of Objective 1. We have collected approximately 1,500 Streptomyces isolates from multiple sources (earthworms, soil, eukaryotes) and of these, DNA has been extracted from approximately 1000 isolates. We are currently in the process of sequencing the 16S rRNA and rpoB genes of these isolates to obtain an overall picture of their population structure and genetic diversity.All cultures are archived in glycerol solution at -80oC and provided free of charge to the research community upon request. Determine rates of cellulose degradation of free-living and animal-associatedStreptomycesstrains. We are optimizing media and growth conditions for Streptomyces using 2 isolates as test organisms. Define the genomic properties of representativeStreptomycesstrains with the highest capacity to degrade cellulose in vitro. We have sequenced the genomes of 100 isolates and are currently in the process of assembling and annotating the genome sequences. Our initial analysis shows that these closely related genomes are highly variable and contain numerous biosynthetic gene clusters and accessory genes, some of which are associated with cellulose degradation.
Publications
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