Progress 04/01/19 to 03/28/24
Outputs
Target Audience:Navajo Technical University (NTU) students were able to present their research at Navajo Technical University Research Days. Kirby Morris, an NTU student presented key results of the project at the Mycological Society of America Annual meeting in July 2023. She won the best undergraduate student presentation award for her efforts. Northern Arizona University(NAU) PI Gehring included some of the NTU/NAU research in presentations she gave at regional meetings and departmental seminars in the School of Forestry and Department of Biological Sciences at NAU. The project was also discussed informally at a Climate Change workshop led by Navajo Technical University that included educators and land managers from the Navajo Nation and several other tribes. Changes/Problems:There were no major changes as this final year was focused on completion of data collection, analysis of the data and presentation. What opportunities for training and professional development has the project provided?Training was continued on how to identify drought tolerant and drought intolerant pinyons in the field based on their architecture, to make measurements of those trees that are associated with drought tolerance (architecture, shoot growth, stem- and cone- boring moth herbivory), and to identify and collect ectomycorrhizal root tips. An NTU student who learned the details of morphotyping ectomycorrhizal fungi also learned how to analyze root tips using DNA based methods (DNA extraction, PCR, Sanger sequencing) to obtain a species level identification. The sequence analysis used was shared with a group of NTU students during the regular weekly zoom meetings between NTU and NAU. NTU student Kirby Morris completed the collection of a strong data set on ectomycorrhizal associations and associated spectra, learned how to analyze those data and presented them at national conference in 2023. She graduated with a degree in Environmental Sciences from NTU and transitioned to the MS program in Biology at NAU as a member of a Sloan Foundation supported program to promote diversity in STEM. PI Chischilly arranged for Dr. Perry James to present a Navajo blessing prior to field sampling and also included Dr. James in some of our zoom meetings where he shared Navajo perspectives on pinyon-juniper woodlands and broader topics in environmental science and ecology. How have the results been disseminated to communities of interest?The results have been disseminated by students at local venues such as the NTU research day and also at a national conference bu NTU student Kirby Morris. NAU PI Gehring also shared some of the results with land managers in Arizona, New Mexico, and Colorado through invited presentations. There is growing interest in the conservation of pinyon-juniper woodlands across the southwest so the data we had collected was of great interest to some managers and also students at both NTU and NAU. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Our goals this year were to integrate the hyperspectral images and mycorrhizal fungal data that were collected the previous year and to begin disseminating those results. These results include: 1. Hyperspectral data from194 Pinus edulis trees were analyzed - 155 for calibration and 39 for validation. Of the 194 tree spectra, 106 were from trees that were known or presumed to be drought tolerant and 88 were from trees known or presumed to be drought intolerant based on canopy architecture (presumed drought tolerant) or measurements of physiology, growth or mortality during drought (known drought tolerant). The spectral range analyzed was from 450-2200nm which includes important plant properties such as water absorption and nutrient availability. Pinyons designated as drought intolerant had higher reflectance across much of the spectra than pinyons designated as drought tolerant. The model trained on the calibration dataset with one component from a principal components analysis accurately identified 71.8% of the trees.The important wavelengths of the spectra distinbuising the tree types were mostly within the ~700nm - 1800nm -- the Near Infrared (NIR) and Shortwave infrared regions (SWIR). NIR is associated with leaf structure, thickness, etc and SWIR is associated with water content and foliar biochemistry like Nitrogen and cellulose. 2. Hyperspectral data collected from the same trees before the monsoon season and after the monsoon season, corresponding to the driest and wettest times of the year also showed significant differences in the expected directions for the water contenct portion of the spectra. The differences between drought tolerant and drought intolerant trees were similar in both wet and dry sampling periods. 3. Measurements of ectomycorrhizal fungal abundance and community composition were obtained from drought tolerant and drought intolerant trees in Arizona and New Mexico. The Arizona sampling extended a long-term study that showed consistent differences between drought tolerant and drought intolerant pinyons before the onset of drought in the southwest. As drought intensified the community differences between the two tree types decreased in magnitude. During the most recent sampling, the drought tolerant and drought intolerant trees had similar fungal communities dominated by a single genus of fungus, Geopora. Geopora was formerly common on only the drought tolerant trees but it dominates all of the trees indicating a significant decline in fungal diversity with drought. Samples from New Mexico near the NTU campus also had abundant Geopora, but some of the samples were difficult to score because of dry conditions during the collection period. New samples have been collected and will be analyzed as part of the MS thesis of former NTU and current NAU student, Kirby Morris. 4. We had hoped to detect a signal of Geopora abundance with the hyperspectral imaging but this was not possible because Geopora ranged from 88-100% of the fungal community of both drought tolerant and drought intolerant trees, insufficient variation to detect any patterns.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
MORRIS, K. , C. Gehring , G. Trimber , A. Whipple , P. Heinrich , S. Chischilly, and C. Doughty. Drought tolerant and drought intolerant pinyons converge in fungal communities during drought but differ in leaf spectra.
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Progress 04/01/22 to 03/31/23
Outputs
Target Audience:Navajo Technical University (NTU) students were able to present their research at more venues this year due th easing of the COVID-19 pandemic. The venues included Navajo Technical University Research Days, a regional meeting that brought together scientists and land managers and a regional meeting focused on student research. Northern Arizona University (NAU) PI Gehring included some of the NTU/NAU research in presentations she gave at international and regional meetings. Changes/Problems:This year presented fewer challenges as the Covid-19 pandemic eased and we were able to have research exchanges rather than relying entierly on zoom meetings with limited visits between NTU and NAU. However, the ectomycorrhizal work was challenging remotely and the NTU student who spent the summer at NAU made the most progress. NTU students will be visiting NAU in April 2023 to get additional training in person. What opportunities for training and professional development has the project provided?Training was more extensive this year as several NTU students learned how to identify drought tolerant and drought intolerant pinyons in the field based on their architecture, to make measurements of those trees that are associated with drought tolerance (architecture, shoot growth, stem- and cone- boring moth herbivory), and to identify and collect ectomycorrhizal root tips. Students also learned how to make hyperspectral measurements and what those measurements mean re. tree physiology and chemistry. One student learned the details of morphotyping ectomycorrhizal fungi and is now sharing that knowledge with other NTU students (once additonal microscopes were acquired by NTU from NAU). In addition to in person training, team members continued their weekly zoom meetings to discuss project goals and accomplishments and to participate in on-lline training and data sharing sessions. Kirby Morris completed the collection of a strong data set on ectomycorrhizal associations and associated spectra, learned how to analyze those data and presented them at several conferences. She applied and received several scholarships and has been admitted as an MS student in Biological Sciences at NAU, competing successfully for a fellowship that starts in August 2022. PI Chischilly arranged from Dr. Perry James to present a Navajo blessing prior to field sampling that was valuable to all participants. How have the results been disseminated to communities of interest?The results have been disseminated at several conferences as described previously at NTU, regional and international meetings.There was interest from land managers in both the hyperspectral and ectomycorrhizal results as concern about the fate of pinyon juniper woodlands grows with increased warming and drying conditions in the southwestern USA. What do you plan to do during the next reporting period to accomplish the goals?1. We plan to complete analysis of the hyperspectral data of the New Mexico trees and compare the results to those of the Arizona drought tolerant and drought intolerant trees to see if similar patterns emerge. We will then use the ASD instrument to measure an additional set of trees to determine at random to see if the spectral signatures are different enough to detect drought tolerance without using some of the other phenotypic markers we have used in the initial NM and AZ studies. 2. We will finish processing the ectomycorrhizal root tips collected from the New Mexico trees to determine if drought tolerant and drought intolerant trees differ in their ectomycorrhizal fungal communities as expected from the results from Arizona trees. We can also test to see how different the communities of Arizona and New Mexico trees in fungal community composition. 3. We will write up the results that we have with Kirby Morris as lead author on the first manuscript focusing on the ectomycorrhizal results with some integration of the hyperspectral results. We expect to write a second paper that goes into the hyperspectral results in more depth with Co-PI Heinrich likely to lead that manuscript with NTU students and PI Chischilly as co-authors.
Impacts
What was accomplished under these goals?
This year we were able to make signficant progress in several areas: 1. The NTU team marked and mapped 50+ trees on the mesa near the NTU campus that had the architecture of drought tolerant and drought intolerant trees based on studies in Arizona. Trees were photographed, tagged and geolocated with GPS and the data entered into a spreadsheet and used to generate a map of the study site using GIS. PI Chischilly worked with students in person until they felt comfortable working independently. 2. The NAU team was able to visit NTU in April of 2022 with the ASD hyperspectral imaging system. A team of six NTU students (Kirby Morris, Chase Bebo, Randy Henry, Cassandra Tabaha, Jared Pino, and Davina Spencer), project lead Steve Chischilly, and NAU's PI Gehring, Co-PI Heinrich and graduate student Gillian Trimber collected hyperspectral data on the trees selected by the NTU team along with seedlings of known maternal seed source from the NTU common garden. The team collected needles, put them in individually labeled bags and brought them back to the laboratory where the ASD imaging system was set up. All students learned how to use the ASD machine along with learning important factors to consider in making measurements. 3. The NAU team visited NTU a second time in the summer of 2022 to work with NTU students to collect additional data on the study trees including shoot length, basal trunk diameter, and moth herbivory. The students also learned how to collect ectomycorrhizal roots from the study trees and began those collections. Collection work continued during the late summer and early fall of 2022. All data were entered into a spreadsheet shared with all students/collaborators 4. NTU student Kirby Morris worked on processing the Arizona and New Mexico collections of ectomycorrhizal root tips while participating in an NSF funded Research Experience for Undergraduate program at NTU during the summer of 2022. The program provided the Gehring lab with some supply funding which allowed Kirby to analyze the roots morphotypically as part of the USDA NIFA funding but also to analyze them using DNA based methods. The morphological analysis is complete for the Arizona samples and almost complete for the New Mexico samples. Kirby gave several presentations based on her work with the Arizona samples (see above) as the data she collected was combined with data from several previous collections to provide a record of change with drought. Kirby learned how to extract DNA from the ectomycorrhizal root tips, amplify it using PCR and to sequence the DNA using the Sanger method. Other NTU students learned how to analyze the resulting DNA sequences using the STADEN package (free ware) and to blast them to get an identity using GenBank through a zoom session. They will have additional in person training on these techniques this April. 5. NAU collaborator, Dr. Chris Doughty, showed the NAU group and NTU's Kirby Morris a new way to analyze the hyperspectral data that was simpler and more definitive than the techniques described last year. The results showed that drought tolerant and drought intolerant trees from Arizona differed in their spectral signatures, principally in the area of the spectrum associated with water absorption. The New Mexico data will be analyzed this way during the spring of 2023 after we are sure that the drought tolerant and drought intolerant designations based on canopy architecture are correct.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
MORRIS, K. , C. Gehring , G. Trimber , A. Whipple , P. Heinrich , S. Chischilly, and C. Doughty. Drought tolerant and drought intolerant pinyons converge in fungal communities during drought but differ in leaf spectra.
Environmental Science and Natural Resources Undergraduate Student Research Showcase Event, October 21, 2022, and Environmental Science and Data Virtual Showcase on December 20, 2022.
Also, on March 2-7, 2023, at the American Indian Higher Consortium Conference in Albuquerque.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
MORRIS, K. , C. Gehring , G. Trimber , A. Whipple , P. Heinrich , S. Chischilly, and C. Doughty. Drought tolerant and drought intolerant pinyons converge in fungal communities during drought but differ in leaf spectra.
American Indian Higher Consortium Conference, Albuquerque, NM, March 2023.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
MORRIS, K. , C. Gehring , G. Trimber , A. Whipple , P. Heinrich , S. Chischilly, and C. Doughty. Drought tolerant and drought intolerant pinyons converge in fungal communities during drought but differ in leaf spectra.
16th Biennial Conference of Science and Management for the Colorado Plateau and Southwest Region. Flagstaff, AZ, September 2022.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Gehring, CA. et al. Drought, invasive species and fire: Can understanding mycorrhizal fungi help address key challenges in a warming world?
Keynote address, 11th International Conference on Mycorrhizas, Beijing, China, July 2022 (delivered remotely due to Covid-19 travel restrictions).
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Progress 04/01/21 to 03/31/22
Outputs
Target Audience:Due to the Covid-19 pandemic, our target audience has been generally limited to the students involved in the project and in classes taught at NTU and NAU. Several students were able to make poster presentations at a research conferences at NAU and NTU. At these presentations, the students reached a broader audience of other students, faculty members and invited members of the general public. Changes/Problems:Although the pandemic has significantly limited our travel and required a no-cost extension, if we are able to travel as planned, we will be able to meet most of the project objectives. As described previously, we are using instruments from NAU rather than from the Army Research Lab because our collaborator there was too ill to continue work on the project. The NAU instruments are not state of the art like the Army instruments were expected to be, so our data quality may not be as high. However, students will still learn about the techniques and how to use an instrument that is widely used in research today. What opportunities for training and professional development has the project provided?Training was still limited this year due to the Covid-19 pandemic, but we met weekly by Zoom with six NTU students, one-two NTU faculty and the NAU team (two faculty, one staff member and three interested graduate students). We discussed project goals, background and methods. NTU students worked with the NTU PI to select trees for measurement when the NAU team could bring the spectrophotometer to NTU. One student was able to travel to NAU during the summer of 2021 to join the REU program there. While his project was focused on junipers, the student, Chase Bebo, was able to go to the NAU field site and participate in some of the measurements. How have the results been disseminated to communities of interest?Some project goals and results were communicated beyond our research group during research symposia presented at NAU and NTU. We hope that broader dissemination will occur during 2022 and early 2023. summary of major poster presentations: Chase Bebo, Steven Chischilly, Abhishek RoyChowdhury1, Catherine A. Gehring, and Amy V. Whipple. Juniper Germination with Hormones and Mechanical Treatment. Poster presentation at Northern Arizona University Research day and at Navajo Technical University Research Day. Chase Bebo, Phazion Osborne, Randy Largo, Steve Chischilly, Amy Whipple, Catherine Gehring. Research-Based Climate Change Impact Assessment on Pinyon Pine for Black Mesa. poster presentation at Navajo Technical University Research Day, students won third place prize What do you plan to do during the next reporting period to accomplish the goals?the NAU group will travel to NTU with the ASD instrument during the spring (April 22-24) and during the summer (dates to be determined) to train students to make the spectral measurements and also to measure associated phenotypic traits, including ectomycorrhizal fungal abundance and community composition. Weekly zoom meetings will take place before and after those trips to process data, discuss findings and work on data products. Two NTU students will have the opportunity to spend the summer at NAU as part of an REU program. One of these students will be in the Gehring lab and the other in the Whipple lab. Some of the research they conduct will further the goals of this project,including measuring spectra and ectomycorrhizal fungal traits on seedlings grown in the NAU greenhouse.
Impacts
What was accomplished under these goals?
Most of the work this year was focused on the spectral measurements needed to address objectives 1 and 2. Due to the Covid-19 pandemic, travel between NAU and NTU was not possible, so initial work happened at the NAU field site and common garden. Weekly Zoom meetings helped NTU students stay connected as we discussed project goals, the utility of spectral measurements, the biology of drought tolerant and drought intolerant trees. NTU students selected and GPSed trees for future measurements when NAU researchers could visit . Preliminary analyses and results were shared with students as well. Please see the details below. Purpose We collected pinyon needle reflectance spectra hoping to be able to relate pinyon ecological characteristics to reflectance. We used trees from two locations. The first is a long-term research site (Sunset Crater) where NAU has demographic, ecological and genetic information for adult trees. The second is a common garden (Pinyon Garden) where we have planted seedlings that come from known maternal families with quantified drought tolerance which is also negatively associated with resistance to damage by a moth, Dioryctria albovitella.. Seedlings in the common garden are also subjected to differential watering treatments. We replicated spectra measurements before (May) and after (July) the Arizona monsoon to see if we could detect differences in water stress. Late May is the hottest and driest time of the year at the Arizona study site when water stress is expected to be the highest, while monsoon moistures arrives in July and trees are expected to have far lower water stress. Data Preparation Needle reflectance spectra were recorded using an ASD FieldSpec 4 spectroradiometer. Illumination was provided with a ThorLabs SLS201L stabilized light source and an Art Photonics custom fiber optic splitter. The fiber-optic splitter routes light to the target and returns reflected light to the ASD spectroradiometer. After set-up, the ASD unit and ThorLabs light source were allowed to warm up for a minimum of 30 minutes to stabilize the lamp and sensors. So far, we have collected spectra for needles on 103 small garden trees and 37 adult trees from the main Sunset Crater Area. The garden trees represent 20 maternal trees with known drought tolerance/moth susceptibility and four watering treatments, no water, low water, medium water, and high water. Both sets of trees were sampled before and after monsoon season. For each tree, we collected three needles. Garden needles were scanned three times and main area needles five times. Data cleaning was as follows. Spectra were examined visually and obviously bad spectra were discarded. Data were imported into R using the module "spectrolab" with the spectra file name becoming the individual spectraID in a R Data Frame. and splice corrected (to align spectra between the three sensors in the spectrophotometer) using the R module "Prospectr". Once the data were aligned noisy sections below 450nm and above 2300nm were clipped off using R "data.frame" tools. Finally, spectraID was parsed into a tree identifier names "PCG" and numeric needle identifier "needleId" and a scan identifier "measureId". Using PCG the scan data was merged with categorical survey data for each tree. For the garden tress this included PCG - the tree identifier MT - Pre or Post Monsoon time of measurement (coded PRE or POST) Mom - the Tree code of the scanned tree's maternal parent TREATMENT - watering treatment (coded 0, 1, 2 or 3) Moth - moth susceptibility of the maternal tree (coded S - susceptible or R- resistant); susceptibility to the moth is inversely related to drought tolerance For Adult trees only the tree identifier ("PCG") and seasonality of scanning ("MT") were available. Next, we created versions of the data where the means of each spectra were calculated for each tree grouped by MT to retain the difference between pre- and post-monsoon scans named "gardenTreeMeans" and "mainTreeMeans". Next we created versions with categorical variables were excluded from the data frames called "mainTreesMeansNoCats" and "gardenTreesMeansNoCats" to allow principle component analysis (which can only be run on numeric variables). Finally, we subset the averaged spectra data frames by retaining bands of interest. As a first attempt, we retained the spectra for the 650nm chlorophyll band +/- 20nm and the 970, 1200, 1450, and 1930nm water absorption bands +/- 20nm. These datasets were named "gardenTreesMeansNoCatsSubset" and mianTreesMeansNoCatsSubset". Analysis We conducted Principal Component Analysis on the raw data, means, and subset bands datasets using the R module "prcomp". In each case PCA showed a large amount of the variation in the data was explained by the first and second principal components. To see whether our categorical variables were related to any clustering we used the R "ggfortify" module and "autoplot" feature to plot the first two components with coloring determined by various categorical variables. Results Thus Far We were interested in whether we could discriminate between drought intolerant (moth resistant) and drought tolerant (moth susceptible) trees and whether we could detect water stress in the trees via reflectance spectra. To do this we calculated principal components for the means of spectra by tree and a subset of spectra representing the chlorophyll and several water absorption bands. When we calculated principal components for the three datasets (raw, tree means, and subsetted bands) we obtained similar results. In each case, while the first couple of principal components captured 70-80% of the variability in the datasets, none of our catagorical variables were strongly clustered. Using a subset of spectra representing the chlorophyll and water bands did not substantially improve the ability to discriminate among trees. Next Steps We plan to explore the PCA data in more detail examining eigenvalues to identify individuals and components that have large effects. We are planning to further refine subsets of the spectra data or combining spectra into band means to reduce noise in the dataset. We are also looking into other analytical techniques to continue our analysis. We also will be collecting data on April 23, 2022 near NTU. NTU students have selected trees that display the architecture of moth susceptible (drought tolerant) and moth resistant (drought intolerant) trees on sites adjacent to the NTU campus. The NAU team will be able to visit the NTU campus for the first time since the onset of the Covid-19 pandemic. Measurements will be made on 80 trees selected by NTU students and also a subset of the NTU common garden seedlings. We will be able to address the questions describe about for drought tolerance using NTU trees, and also make additional comparisons of pinyons growing in New Mexico and Arizona. NTU students will be trained to make spectral measurements during this trip, with future weekly zoom meetings used for training on data analysis and interpretation. In addition to the spectral data, we will measure tree growth, moth herbivory and ectomycorrhizal fungal community composition as described in our proposal. Sample processing for ectomycorrhizal fungal communities is already underway using collections made last summer in Arizona. Additional sampling and analysis will take place this summer at NTU using the same trees measured in April 2022.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Chase Bebo, Steven Chischilly, Abhishek RoyChowdhury1, Catherine A. Gehring, and Amy V. Whipple. Juniper Germination with Hormones and Mechanical Treatment. Poster presentation at Northern Arizona University Research day and at Navajo Technical University Research Day.
Chase Bebo, Phazion Osborne, Randy Largo, Steve Chischilly, Amy Whipple, Catherine Gehring. Research-Based Climate Change Impact Assessment on Pinyon Pine for Black Mesa. poster presentation at Navajo Technical University Research Day, students won third place prize
|
Progress 04/01/20 to 03/31/21
Outputs
Target Audience:Due to the Covid-19 pandemic, our target audience has been generally limited to the students involved in the project and in classes taught at NTU and NAU. Two students were able to make virtual presentations at a regional meeting. Changes/Problems:Some of the challenges that began last year have continued. We are still not able to work with Dr. Ligon as stated above, but we have developed alternatives, though this has taken some time as described. The ASD instrument used by our new collaborators was not well suited to imaging needle-leaved trees so we had to have a new cable made to solve the problem. This new cable seems to be working and we are hoping to initiate field tests in the coming weeks. The pandemic has been a challenge to most aspects of the project, but most of the team members are now fully vaccinated and hopeful that travel will be allowed to enable us to complete the project. Enthusiasm for the work remains high, fortunately. What opportunities for training and professional development has the project provided?Training of students was intially limited to Zoom meetings during the reporting period, but students were able to learn about pinyon cone collection, seed extraction, seed viability testing and seed storage. As described above, students were able to collect cones at a variety of field sites and to assemble a data base for future use. More experienced faculty shared techniques with students over zoom and via a google drive with protocols and images. More detailed training will commence again for the 2021 reporting period as soon as travel restrictions due to the Covid-19 pandemic are lifted. We expect that NTU students will be able to learn how to use the instruments that NAU researchers have been trouble shooting to conduct field work in New Mexico during the summer and fall of 2021. Students will then be able to learn how to use the instruments and analyze the resulting data. They will also measure tree phenotypes and learn how to conduct the mycorrhizal assessments. How have the results been disseminated to communities of interest?Some of the research on pinyon ecology was presented by NTU student, Dalyna Hannah at the New Mexico Research Symposium, and at the Navajo Technical University 8th Annual Research Day. The work presented was a collaborative effort between Dalynah and other NTU and NAU students and faculty. Title: Testing restoration methods for pinyon pine on the Navajo Nation Soil clay/stoniness likelihood on successful Restoration of pinyon pine on the Navajo Nation Authors: Dalyna Hannah, Chase Bebo, Ryan Data, Ehren Moler, Maria Hernandez, Amy Whipple, Paul Heinrich, Catherine Gehring, Steven Chischilly What do you plan to do during the next reporting period to accomplish the goals? As mentioned above, we plan to start measuring all of our NAU Pinyon Common Garden and Sunset Site trees where drought tolerance is known starting in April 2021 using the hyperspectral imaging system that is now finally working well. We hope to be able to make measurements on the NTU common garden and surrounding pinyons this summer as long as travel is permitted.We will then also be able to make the plant trait and fungal measurements we proposed and to establish the greenhouse experiment this fall.
Impacts
What was accomplished under these goals?
The Covid-19 pandemic has significantly limited our work because Navajo Technical University and Northern Arizona University faculty, staff and students have had very limited opportunities to travel and have not been able to do any of the personnel research exchanges that were planned for the summer of 2020. We still met to discuss the project on a weekly basis via zoom and did some work separately to further project goals. A key goal of this project and a related USDA NIFA project was to collect pinyon seeds for the greenhouse experiment necessary to meet objective 3. Fortunately, it was a very good year for pinyon seed production in many parts of New Mexico and Arizona. The student research teams were able to collect cones from 172 trees in New Mexico and 223 in Arizona, most of which yielded viable seeds. GPS locations were recorded for all trees so that we can return to them for drought tolerance assessments. We had planned to assess drought tolerance first and then collect seeds, but the pandemic meant we had to be opportunistic and conduct the activities that we could. Students were able to collect cones by traveling individually or in pairs while following Covid protocols. In addition to collecting cones, the NAU group was able to make progress on objectives 1 and 2 by forming new collaborations as described in last year's report. However, the pandemic limited our activities significantly because of travel and lab access restrictions. We have three accomplishments to report. First, we were able to use an NAU drone and sensor to test some methods to replace the instrumentation to be supplied by our Army Research Lab collaborator, Dr. David Ligon, who continues to have medical problems. Also, travel to the Army Research lab to work with Dr. Ligon and others has not been possible. In the summer of 2020, we collected 4-band high resolution data using a DJI Mavic II drone and Micasense RedEdge-MX sensor at the NAU Sunset Crater Long-term Pinyon Research site. We flew drones at the site twice to collect data in the visible and near-IR spectra at sub-meter resolution. This site includes trees whose demographics have been studied for 30+ years and many know drought-resistant and drought-non-resistant trees. We will use these data and known drought resistant of trees to classify trees. We will also use this data to build models to detect dead and dying pinyon for a related project. Second, we acquired 3-meter resolution 4-band satellite data from the Planet.com PS Scene product for the Sunset Crater and Crown Point sites from 2017-2020/1 using April and Feburary dates. We are working to add 0.5-meter resolution data as well. We hope to use these data to scale up from our higher-resolution drone data in order to classify trees by drought resistance category and detect pinyon mortality over large areas economically. NTU students will be trained to work with these data once we add the 0.5m resolution data. Third, we are developing protocols to use a ASD Fieldspec 3 to measure reflectance spectra for individual needles on pinyon from the NAU Pinyon Common Garden, the Crown Point Common Garden and associated field sites with known drought tolerant and drought intolerant pinyons. To do this we are using a needle clip and fiberoptic splitter cable to illuminate individual needles using a ThorLabs lamp. We found that the existing cable that came with the instrument was only able to transmit 400-1800nm In order to acquire complete 300-2500nm spectra, we had a special fiberoptic cable built by ArtPhotonics. We are now able to get clean spectra for the full range that the spectrophotometer can measure. We plan to start measuring all of our NAU Pinyon Common Garden and Sunset Site trees where drought tolerance is known starting in April 2021. We hope to be able to make measurements on the NTU common garden and surrounding pinyons this summer as long as travel is permitted.We will then also be able to make the plant trait and fungal measurements we proposed and to establish the greenhouse experiment this fall. While we have been able to make some progress, we expect to request a no-cost extension to allow us to complete all project objectives. The pandemic has really limited our activities.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
New Mexico Research Symposium.
Title: Testing restoration methods for pinyon pine on the Navajo Nation Soil clay/stoniness likelihood on successful Restoration of pinyon pine on the Navajo Nation
Authors: Dalyna Hannah, Chase Bebo, Ryan Data, Ehren Moler, Maria Hernandez, Amy Whipple, Paul Heinrich, Catherine Gehring, Steven Chischilly
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Progress 04/01/19 to 03/31/20
Outputs
Target Audience:Due to Covid-19, our target audience has been limited to the students involved in the project and in classes taught at NTU and NAU. Changes/Problems:Plans for travel to the Army Research Lab this summer to 1) complete construction of the imaging instruments and 2) learn how to use them and analyze the resulting data had to be cancelled due to the Covid-19 pandemic and also the medical leave of our key collaborator, Dr. David Ligon. It had been difficult to get feedback from Dr. Ligon beginning in fall of 2019 causing the team to look for other options beginning in early 2020. To solve the problems presented by this situation, we have initiated new collaborations and will borrow instruments from individuals at NAU. However, some troubleshooting is necessary as the instruments were not used directly for needle-leaved plants previously. That process is underway but has led to some delays. NTU students have unfortunately not been able to participate in direct measurements as hoped, but the NTU and NAU teams meet regularly and communicate about the project. As soon the troubleshooting is complete, there will be images, etc to share and more active participation by NTU students. What opportunities for training and professional development has the project provided?As mentioned above, most of the training on the project happened during summer of 2019 at the Army Research Lab when the initial instruments were constructed. Training of students is now limited to Zoom meetings where we discuss the new options available to us and the troubleshooting necessary to get the instruments working. The experience is still valuable to students who are learning about the different kinds of technologies and also about how researchers overcome roadblocks in science. More detailed training will commence again for the 2020 reporting period as soon as travel restrictions due to the Covid-19 pandemic are lifted. NTU students will then be able to learn how to use the instruments and analyze the resulting data. They will also measure tree phenotypes and learn how to conduct the mycorrhizal assessments. 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?As mentioned briefly above, we plan to image and phenotype the trees and seedlings with known drought tolerance status using both LIDAR and hyperspectral techniques this coming year providing that the instrument troubleshooting continues to go well. We hope to establish LIDAR and hyperspectral signatures associated with drought tolerance by early spring of 2021. We will then conduct the same measurements on trees of unknown drought tolerance status near the NTU campus and surrounding areas in later spring and summer of 2021. One additional project goal we have is to collect seeds from putatively drought tolerant trees that are found near NTU and surrounding areas of New Mexico. This summer appears to be a good year for collecting cones, so we are planning significant collections and will GPS locate all of the trees used. We will then include these trees in our sampling using the hyperspectral imaging system and other traits next summer. The students have been able to travel to local areas to assess cone production with PI Chischilly and have identified appropriate sites and established protocols for cone collections and seed extraction.
Impacts
What was accomplished under these goals?
During the summer of 2019, PI Chischilly, Co-PI Heinrich and one NTU student worked with collaborator Dr. David Ligon at the Army Research Lab to begin construction of instruments that could be used to image the drought tolerant and intolerant trees both using LIDAR and hyperspectral techniques. One of these instruments was brought back by PI Chischilly to the NTU campus to be used with further instruction from Dr. Ligon. NAU Co-PI also traveled to the Army Research lab to work with Dr. Ligon and NTU faculty and students. The second instrument was to be completed during the summer of 2020 upon PI Chischilly and an NTU student's return to the Army Research Lab this summer. Unfortunately, all plans for travel during the summer of 2020 were cancelled due to the Covid-19 pandemic. Work with Dr. Ligon was further suspended because of medical issues for Dr. Ligon.. The NTU and NAU teams quickly moved to develop a plan B, which involved utilizing imaging equipment available at NAU, including a different hyperspectral machine and a drone-based system to estimate tree shape. These instruments are being provided by new collaborators, Dr. Chris Doughty and Dr. Andrew Richardson who agreed to allow us to use them. The NAU hyperspectral imager has been used chiefly for broad leaved trees, not pines, so troubleshooting has been necessary to get the system to work on pinyon needles. Although NTU has been involved in discussions about the instrument during weekly Zoom meetings, NTU PIs and students have not been involved in the troubleshooting due to Covid-19 travel restrictions. NAU Co-PI Heinrich has taken the lead on the troubleshooting and it is hoped that measurements will commence by mid-August of 2020,followed by tree phenotyping including assessment of mycorrhizal fungal communities. Imaging will take place in 2021 at areas around NTU as proposed. Because of the pandemic, it may be necessary to request a no-cost extension in order to accomplish all project goals.
Publications
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