Julia W Neilson

Interests

Teaching

Classroom teaching is not included in my position description. I serve on graduate student committees and advise undergraduates for Honors Thesis research. I also teach guest lectures on soil health and the mine reclamation for the Dept. of Mining Engineering

Research

My research focus is soil health. A primary environmental goal is to gain a mechanistic understanding of associations between soil microbial taxonomic and functional diversity and the sustainability of vegetation in arid ecosystems and in lands degraded by anthropogenic disturbance.

Courses

Scholarly Contributions

Chapters

• Neilson, J. W., & Ortiz, M. (2015). Bacterial and archaeal diversity on cave speleothem and rock surfaces: a carbonate cave case study from Kartchner Caverns. In Microbial Life of Cave Systems(pp 105-120). De Gruyter, Berlin Germany.

Journals/Publications

• Ossanna, L. Q., Serrano, K., Jennings, L. L., Dillon, J., Maier, R. M., & Neilson, J. W. (2022). Progressive belowground soil development associated with sustainable plant establishment during copper mine waste revegetation. Applied Soil Ecology.
• Kushwaha, P., Neilson, J. W., Barberan, A., Chen, Y., Fontana, C. G., Butterfield, B. J., & Maier, R. M. (2021). Arid ecosystem vegetation canopy-gap dichotomy: influence on soil microbial composition and nutrient cycling functional potential. Applied and Environmental Microbiology. doi:10.1128/AEM.02780-20
• Meredith, L., Troch, P. A., Chorover, J. D., Maier, R. M., Neilson, J. W., Barberan, A., Meira-Neto, A. A., Matos, K. A., Volk, M. J., Bugaj, A. S., Abramson, N., Dontsova, K. M., Stegen, J. C., Danczak, R. E., Volkmann, T. H., & Sengupta, A. (2021). Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System.. Frontiers in Microbiology, 12(3414).
• Neilson, J. W. (2021). Contrasting community assembly forces drive microbial structural and potential functional responses to precipitation in an incipient soil system. Frontiers in Microbiology, 12, 754698.
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  Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre-and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.
• Neilson, J. W. (2021). Soil microbial community and abiotic soil properties influence Zn and Cd hyperaccumulation differently in Arabidopsis helleri.. Science of the Total Environment, 803, 150006. doi:doi.org/10.1016/j.scitotenv.2021.150006.
• Chen, Y., Neilson, J. W., Kushwaha, P., Maier, R. M., & Barberan, A. (2020). Life history strategies of soil microbial communities is an arid ecosystem. ISME Journal, online journal, doi.org/10.1038/s41396-020-00803-y. doi:doi.org/10.1038/s41396-020-00803-y
• Kushwaha, P., Neilson, J. W., Barberán, A., Chen, Y., Fontana, C. G., Butterfield, B. J., & Maier, R. M. (2020). Arid Ecosystem Vegetation Canopy-Gap Dichotomy: Influence on Soil Microbial Composition and Nutrient Cycling Functional Potential. Applied and environmental microbiology.
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  Increasing temperatures and drought in desert ecosystems are predicted to cause decreased vegetation density combined with barren ground expansion. It remains unclear how nutrient availability, microbial diversity, and the associated functional capacity vary between vegetated-canopy and gap soils. The specific aim of this study was to characterize canopy vs gap microsite effect on soil microbial diversity, the capacity of gap soils to serve as a canopy-soil microbial reservoir, nitrogen (N)-mineralization genetic potential ( gene abundance) and urease enzyme activity, and microbial-nutrient pool associations in four arid-hyperarid geolocations of the western Sonoran Desert, Arizona (USA). Microsite combined with geolocation explained 57% and 45.8% of the observed variation in bacterial/archaeal and fungal community composition, respectively. A core microbiome of amplicon sequence variants was shared between the canopy and gap soil communities; however, canopy-soils included abundant taxa that were not present in associated gap communities, thereby suggesting that these taxa cannot be sourced from the associated gap soils. Linear mixed-effects models showed that canopy-soils have significantly higher microbial richness, nutrient content, and organic N-mineralization genetic and functional capacity. Furthermore, gene abundance was detected in all samples suggesting that is a relevant indicator of N-mineralization in deserts. Additionally, novel phylogenetic associations were observed for with the majority belonging to and uncharacterized bacteria. Thus, key N-mineralization functional capacity is associated with a dominant desert phylum. Overall, these results suggest that lower microbial diversity and functional capacity in gap soils may impact ecosystem sustainability as aridity drives open-space expansion in deserts.
• Honeker, L. K., Gullo, C. F., Neilson, J. W., Chorover, J., & Maier, R. M. (2019). Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings. FRONTIERS IN MICROBIOLOGY, 10.
• Neilson, J. W. (2019). Assessing microbial community patterns during incipient soil formation from basalt. Journal of Geophysical Research Biogeosciences, 124, 941-958. doi:doi.org/10.1029/2017JG004315
• Neilson, J. W., & Hottenstein, J. D. (2019). Soil microbiome dynamics during pyritic mine tailing phytostabilization: understanding microbial bioindicators of soil acidification. Frontiers in Microbiology, 10, 1211. doi:doi:10.3389/fmicb.2019.01211
• Valentin-Vargas, A., Neilson, J. W., Root, R. A., Chorover, J., & Maier, R. M. (2018). Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions. SCIENCE OF THE TOTAL ENVIRONMENT, 618, 357-368.
• Honeker, L. K., Neilson, J. W., Root, R. A., Gil-Loaiza, J., Chorover, J., & Maier, R. M. (2017). Bacterial Rhizoplane Colonization Patterns of Buchloe dactyloides Growing in Metalliferous Mine Tailings Reflect Plant Status and Biogeochemical Conditions. MICROBIAL ECOLOGY, 74(4), 853-867.
• Neilson, J. W., Califf, K., Cardona, C., Copeland, A., van, T. W., Josephson, K. L., Knight, R., Gilbert, J. A., Quade, J., Caporaso, J. G., & Maier, R. M. (2017). Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. MSYSTEMS, 2(3).
• Santos, A. E., Cruz-Ortega, R., Meza-Figueroa, D., Romero, F. M., Jesus, S. J., Maier, R. M., Neilson, J. W., David, A. L., & Molina, F. (2017). Plants from the abandoned Nacozari mine tailings: evaluation of their phytostabilization potential. PEERJ, 5.
• Neilson, J. W., Sengupta, A., Maier, R. M., Chorover, J., & Troch, P. (2016). Soil lysimeter excavation for coupled hydrological, geochemical, amd microbiological investigations. J. Vis. Exp., 115, e54536. doi:doi:10.3791/54536
• Stein, M. M., Hrusch, C. L., Gozdz, J., Igartua, C., Pivniouk, V., Murray, S. E., Ledford, J. G., dos, S., Anderson, R. L., Metwali, N., Neilson, J. W., Maier, R. M., Gilbert, J. A., Holbreich, M., Thorne, P. S., Martinez, F. D., von, M. E., Vercelli, D., Ober, C., & Sperling, A. I. (2016). Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. NEW ENGLAND JOURNAL OF MEDICINE, 375(5), 411-421.
• Neilson, J. W., Quade, J., & Matmon, A. (2015). Seismic origin of the Atacama Desert boulder fields. Geomorphology, 231, 28-39.
• Nelson, K. N., Neilson, J. W., Root, R. A., Chorover, J., & Maier, R. M. (2015). Abundance and Activity of 16S rRNA, AmoA and NifH Bacterial Genes During Assisted Phytostabilization of Mine Tailings. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION, 17(5), 493-502.
• Ortiz, M., Legatzki, A., Neilson, J. W., Fryslie, B., Nelson, W. M., Wing, R. A., Soderlund, C. A., Pryor, B. M., & Maier, R. M. (2014). Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. ISME JOURNAL, 8(2), 478-491.
• Valentin-Vargas, A., Root, R. A., Neilson, J. W., Chorover, J., & Maier, R. M. (2014). Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: A mesocosm experiment. SCIENCE OF THE TOTAL ENVIRONMENT, 500, 314-324.
• Neilson, J. W., Jordan, F. L., & Maier, R. M. (2013). Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis. JOURNAL OF MICROBIOLOGICAL METHODS, 92(3), 256-263.
• Ortiz, M., Neilson, J. W., Nelson, W. M., Legatzki, A., Byrne, A., Yu, Y., Wing, R. A., Soderlund, C. A., Pryor, B. M., Pierson, L., & Maier, R. M. (2013). Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ. MICROBIAL ECOLOGY, 65(2), 371-383.
• Neilson, J. W., & Legatzki, A. (2012). Factors influencing observed variations in the structure of bacterial communities on calcite formations in Kartchner Caverns, AZ, USA. Geomicrobiology Journal, 29, 422-434.
• Neilson, J. W., Quade, J., Ortiz, M., Nelson, W. M., Legatzki, A., Tian, F., LaComb, M., Betancourt, J. L., Wing, R. A., Soderlund, C. A., & Maier, R. M. (2012). Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. EXTREMOPHILES, 16(3), 553-566.
• Maier, R. M., Palmer, M. W., Andersen, G. L., Halonen, M. J., Josephson, K. C., Maier, R. S., Martinez, F. D., Neilson, J. W., Stern, D. A., Vercelli, D., & Wright, A. L. (2010). Environmental Determinants of and Impact on Childhood Asthma by the Bacterial Community in Household Dust. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 76(8), 2663-2667.
• Neilson, J. W., & Legatzki, A. (2011). Bacterial and archaeal community structure of two adjacent calcite speleothems in Kartchner Caverns, Arizona, USA. Geomicrobiology Journal, 28, 99-117.
• Neilson, J. W., Zhang, L., Veres-Schalnat, T. A., Chandler, K. B., Neilson, C. H., Crispin, J. D., Pemberton, J. E., & Maier, R. M. (2010). Cadmium effects on transcriptional expression of rhlB/rhlC genes and congener distribution of monorhamnolipid and dirhamnolipid in Pseudomonas aeruginosa IGB83. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 88(4), 953-963.
• Mendez, M. O., Neilson, J. W., & Maier, R. M. (2008). Characterization of a bacterial community in an abandoned semiarid lead-zinc mine tailing site. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 74(12), 3899-3907.
• Ikner, L. A., Toomey, R. S., Nolan, G., Neilson, J. W., Pryor, B. M., & Maier, R. M. (2007). Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona. MICROBIAL ECOLOGY, 53(1), 30-42.
• Drees, K. P., Neilson, J. W., Betancourt, J. L., Quade, J., Henderson, D. A., Pryor, B. M., & Maier, R. M. (2006). Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(12), 7902-7908.

Presentations

• Ledesma, J., Babst-Kostecka, A., Maier, R. M., Neilson, J. W., & Rasmussen, C. (2022, November). Effects of Long-Term Stockpiling on Soil Quality and Potential for Mine Site Reclamation in Semi-Arid Regions. University of Arizona ENViSion Research Symposium. Tucson.
• Murawska-Wlodarczyk, K., Wlodarczyk, T., Babst-Kostecka, A., Neilson, J. W., & Maier, R. M. (2021, December). The effect of capping material on successful seed germination and seedling growth for quantification of root development in the underlying contaminated tailings. Society for Mining, Metallurgy, & Exploration (SME) 2021 conference. Tucson, AZ.
• Murawska-Wlodarczyk, K., Wlodarczyk, T., Neilson, J. W., Rasmussen, C., Maier, R. M., & Babst-Kostecka, A. (2022, March). Effects of long-term stockpiling on soil quality and potential for mine site reclamation in semi-arid regions. University of Arizona ENViSion Research Symposium. Tucson, AZ.
• Chen, Y., Neilson, J. W., Kushwaha, P., Maier, R. M., & Barberan, A. (2020, August). Microbial life history strategies in arid soils. Ecology Society of America Annual Meeting. Virtual: Ecology Society of America.
• Neilson, J. W. (2020, December). Are the Microbes Important: Indicators of soil development during mine waste reclamation. Chilean Society for Microbiology Annual Meeting. Virtual: Chilean Society for Microbiology.
• Neilson, J. W., Maier, R. M., Gornish, E., Kline, A., Farrell, H., Fontana, C., Ossana, L., & Jennings, L. (2020, November). Understanding plant-soil associations during revegetation of reclaimed mine tailings in southern Arizona. Soil Science Society of America Annual Meeting. Zoom.
• Ossanna, L. L., Serrano, K., Jennings, L. L., Maier, R. M., & Neilson, J. W. (2020, November). Vegetation-driven soil development during waste rock reclamation at a copper mine. Soil Science Society of America Annual Meeting. Virtual: SSSA, ASA, CSA TriSocieiteis.
• Maier, R. M., Chorover, J. D., Root, R. A., Gil-Loaiza, J., Neilson, J. W., & Hottenstein, J. D. (2019, Jan). Soil Microbiome Dynamics during Revegetation of Pyritic Mine Tailings: Understanding Microbial Bioindicators of Soil Acidification. SSSA International Soils Meeting. San Diego, CA: SSSA.
• Neilson, J. W. (2019, June). Soil Microbiome Resilience to Stress: How much is too much?. USDA Agricultural Research Station Western Regional Research Center Invited Talk. Albany, CA: USDA.
• Neilson, J. W., Kushwaha, P., Barberan, A., Maier, R. M., & Butterfield, B. J. (2019, June). Linking Microbial Phylogenetics and Genetics of N-cycling Potential in Arid Soils. ASM Microbe. San Francisco, CA: American Society of Microbiology.

Poster Presentations

• Lauman, S., Gornish, E., Fontana, C., Kline, A., & Neilson, J. W. (2023). Seeding techniques and plant species selection to enhance copper mine revegetation success. ALVACE Poster Presentation.
• Neilson, J. W., Gornish, E., Babst-Kostecka, A., & Lauman, S. (2023). Seed mixes: what to look for and how to customize them. Society for Mining, Metallurgy & Exploration Annual Conference.
• Lauman, S., Fontana, C., Kline, A., Gornish, E., & Neilson, J. W. (2021). Improving copper mine revegetation success in arid climates. SME Arizona annual meeting. Tucson, AZ.
• Maier, R. M., Neilson, J. W., Babst-Kostecka, A., Wlodarczyk, T., & Murawska-Wlodarczyk, K. (2021, December). The effect of capping material on successful seed germination and seedling growth for quantification of root development in the underlying contaminated tailings. Society for Mining, Metallurgy, & Exploration (SME) 2021 conference. Tucson, AZ.
• Neilson, J. W., Fontana, C. G., Lauman, S., Ledesma, J., Kline, A., Maier, R. M., & Gornish, E. S. (2021, November 7-10). Impact of hydroseeding season and AMF inoculation on belowground fertility indicators during copper mine revegetation. ASA-CSSA-SSSA Annual Meeting. Salt Lake City, UT: Soil Science Society of America.
• Neilson, J. W., Ledesma, J., Babst-Kostecka, A., Maier, R. M., & Rasmussen, C. (2021, November). Effects of long-term stockpiling on soil quality and potential for mine site reclamation in semi-arid regions. ASA-CSSA-SSSA International Annual Meeting. Salt Lake City, UT: ASA-CSSA-SSSA Tri-Societies.
• Neilson, J. W., Maier, R. M., Gornish, E., Kline, A., Ledesma, J., Lauman, S., & Fontana, C. (2021). Impact of hydroseeding season and AMF inoculation on belowground fertility indicators at an Arizona copper mine. Soil Science Society of America annual meeting.
• Rasmussen, C., Neilson, J. W., Maier, R. M., Babst-Kostecka, A., & Ledesma, J. (2021, December). Effects of long-term stockpiling on soil quality and potential for mine site reclamation in semi-arid regions. Society for Mining, Metallurgy, & Exploration (SME) 2021 conference. Tucson, AZ.
• Rasmussen, C., Neilson, J. W., Maier, R. M., Babst-Kostecka, A., & Ledesma, J. (2021, November). Effects of Long-Term Stockpiling on Soil Quality and Potential for Mine Site Reclamation in Semi-Arid Regions. 2021 ASA, CSSA, SSSA INTERNATIONAL ANNUAL MEETING. Salt Lake City, UT.
• Rasmussen, C., Neilson, J. W., Maier, R. M., Babst-Kostecka, A., & Ledesma, J. (2021, November). Effects of Long-Term Stockpiling on Soil Quality and Potential for Mine Site Reclamation in Semi-Arid Regions. 2021 ASA, CSSA, SSSA International Annual Meeting. Salt Lake City, UT.
• Kushwaha, P., Maier, R. M., Neilson, J. W., Babst-Kostecka, A., Kushwaha, P., Maier, R. M., Neilson, J. W., & Babst-Kostecka, A. (2020, November). Linking the rhizosphere microbial community with variability in Zn and Cd hyperaccumulation in the model species Arabidopsis halleri. 2020 ASA-CSSA-SSSA International Annual Meeting. Virtual.
• Ledesma, J., Ossanna, L., Placido, D., El Shikha, D. E., Dong, C., Ponciano, G., McMahan, C., Neilson, J. W., & Maier, R. M. (2020, November). Associations between soil rhizosphere bioavailable phosphorus solubilizing microorganisms, and guayule growth stage and rubber production.. ASA-CSSA-SSSA Annual Meeting. Virtual: ASA-CSSA-SSSA Tri Societies.
• Maier, R. M., Gornish, E., Neilson, J. W., Ossana, L., & Jennings, L. (2019, December). Biotic potential of degraded soil development on reclaimed mine tailings in Southern Arizona. American Geophysical Union Annual Meeting.
• Neilson, J. W., McMahan, C., Placido, D., Ponciano, G., El Shikha, D. E., Dong, C., & Ossanna, L. (2019, September). Dormancy and the guayule (Parthenium argentatum G) soil microbiome. Association for the Advancement of Industrial Crops Annual Meeting. Tucson,AZ: AAIC.
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  Poster presentation at the annual meeting for the Association for the Advancement of Industrial Crops
• Neilson, J. W., Ossanna, L., Jennings, L. L., Serrano, K., & Maier, R. M. (2019, January). Nitrogen dynamics as a biogeochemical indicator of revegetation progress for mine waste rock. Soils Across Latitudes International Soil Science Meeting. San Diego, CA: Soil Science Society of America.
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  Poster presentation at the SSSA Annual meeting
• Neilson, J. W., Ossanna, L., Jennings, L. L., Serrano, K., & Maier, R. M. (2019, June). Nitrogen dynamics as an indicator of mine waste revegetation progress. ASM Microbe. San Francisco, CA: American Society for Microbiology.
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  Poster presentation at the American Society for Microbiology annual meeting.
• Meredith, L., Troch, P. A., Maier, R. M., Chorover, J. D., Neilson, J. W., Dontsova, K. M., Volkmann, T., Stegen, J., Barberan, A., & Sengupta, A. (2018, August). Structural and functional response of incipient basaltic microbial community to shifts in soil moisture regime. Goldschmidt. Boston, MA.
• Meredith, L., Troch, P. A., Maier, R. M., Chorover, J. D., Neilson, J. W., Dontsova, K. M., Volkmann, T., Stegen, J., Barberan, A., & Sengupta, A. (2019, January). Structural and Functional Response of Microbial Community in an Oligotrophic Basalt Soil System to Shifts in Rainfall Regimes. Soil Science Society of America (SSSA) International Soils Meeting “Soils Across Latitudes”. San Diego, CA: Soil Science Society of America.