Research Bio

Overview:

I am an environmental microbiologist and environmental engineer. I'm interested in understanding how microorganisms today were shaped by environmental stress in Earth's past. Understanding the evolutionary history of a microbe and its biochemical machinery can help give us context into how microbes function in nature today and apply them for novel purposes. This can help us to design and manage systems that improve, for example, soil fertility, wastewater treatment, biofuels, and pest management. During my Ph.D. I studied microbial community diversity and function in full scale wastewater treatment systems. I was investigating how disturbances affect diversity and thus bioreactor function (i.e., nitrogen, phosphorus, carbon, and contaminants of emerging concern). 

Postdoctoral Research:

During my postdocs, I studied the nitrogen cost minimization (an evolutionary strategy of oligotrophs to change their genome architecture),  physiology, biochemistry,  and regulatory mechanisms of nitrate dissimilation (i.e., denitrification and respiratory ammonification) in a dual-pathway nitrate reducer, Intrasporangium calvum. This organism is in the bacterial phyla Actinobacteria and is found in many habitats, particularly soils and wastewater treatment systems. This research helps inform our understanding of how reactive nitrogen (i.e., nitrate, nitrite, & ammonia) is either retained in ecosystems through respiratory ammonification or lost via denitrification, with potential release of the greenhouse gas nitrous oxide. I also worked on several other projects related to nutrient and UV stress in a globally important cyanobacterium Prochlorococcus and a diatom Corethron hystrix, respectively. In Prochlorococcus, our lab studied how under nitrogen deprivation, Prochlorococcus cells shortened their transcripts to reduce N content. For the diatom, we subjected Corethron hystrix to UV stress with a tunable UV light engine and measured photosystem II health and activity using Fast Repetition Rate Fluorometry and transcriptomics to determine its metabolic, protective, and repair mechanisms. This research found that C. hystrix downregulated transcription of its photosynthetic apparatus likely as a protective mechanism. Lastly, I worked with an industry partner (Tu Biomics, Inc.) to develop biocontrol agents for fungal pathogens infecting food crops in California and Nevada. I lead the team with regard to experimental design for molecular microbial ecology, metabolomics, culturing, and pilot system design and construction.

Current Research:

I currently work as a Research Assistant Professor in the Colorado School of Mines in Golden, CO, where I research nitrogen dissimilation, nitrification, and anammox for applied water treatment applications and direct potable reuse. I am the Co-PI of a remediation/reuse of mining impacted water from the gold mining industry in Arequipa, Peru, where we apply advanced water treatment processes, such as Advanced Oxidation Processes (AOP) and  membrane contactors for the destruction or recovery of cyanide in the gold mining industry. We are also investigating biological cyanide destruction/transformation and the mechanisms of microbial cyanide biotransformations.  I am a PI of a collaborative NSF project investigating microbial life in wildland fire smoke; a new scientific field called pyroaerobiology. I am applying many molecular tools to traditional microbiology experiments, including DNA/RNA high-throughput sequencing, DNA-SIP, genomics, metagenomics, and functional genomics (transcriptomics, proteomics, and metabolomics).

Since my postdoc, I have been working on technology development with three of my colleagues on a highly sensitive OD spectrophotometer named MAGI, or Microbial Growth Intervalometer. This instrument uses a multiplexed design (12 channels) with software-driven automation to help investigators detect and measure growth curves of microorganisms in standard Balch-type tubes. The MAGI is highly sensitive and with low-background noise to detect very small and translucent microorganisms, such as ammonium oxidizing bacteria (AOB), ammonium oxidizing archaea (AOA), nitrite oxidizing bacteria (NOB), and Complete Ammonium Oxidizer (CoAmmOx) Nitrospira inopinata. The instrument has added capabilities for remote visualization and data acquisition. See our published open-access manuscript below to learn more about MAGI.

Outreach:

Lastly, I am a professional photographer/cinematographer and have produced multiple science outreach films related to geomicrobiology, water reclamation and reuse, and pyroaerobiology. Blending science and film is a passion of mine because I feel the stories that we, as scientists, create for peer-reviewed publication become more tangible and relatable through film.

Educational and Professional Experiences:

• 2019-Present, Research Assistant Professor, Colorado School of Mines, Civil and Environmental Engineering, Golden, CO

• 2019-2021, Hourly Assistant Research Professor, Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV

• 2016-2019, Postdoctoral Fellow, Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV (Grzymski Lab)

• 2015, Postdoctoral Fellow with ENIGMA at the Dept. of Civil and Environmental Engineering, University of Washington, Seattle, WA (Stahl Lab)

• 2014, Research Associate, Dept. of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO (Cath Lab)

• 2011-2014, Ph.D. Environmental Science and Engineering, Colorado School of Mines, Golden, CO (Drewes/Munakata Marr and Spear Labs)

• 2009-2011, M.S. Environmental Science and Engineering, Colorado School of Mines, Golden, CO (Cath Lab)

• 2005, B.S. Biological Sciences, University of Vermont, Burlington, VT

Selected Manuscripts (Google Scholar Profile)

1. Vuono D.C., Lipp B., Staub C., Loney L., Grzymski J. (2019) A real-time multiplexed microbial growth intervalometer for capturing high resolution growth curves. Frontiers in Microbiology. 10(1135) 1-9.

2. Kobziar L.N., Vuono D.C., Moore R., Christner B.C., Dean T., Betancourt D., Watts A.C., Aurell J., Gullett B. (2022) Wildland fire smoke alters the composition, diversity, and potential atmospheric function of microbial life in the aerobiome. ISME Communications . 2(1) 1-9.

3. Honeyman A.S., Fegel T.S,  Peel H.F., Masters N.A., Vuono D.C., Kleiber W., Rhoades C.C.,   Spear J.R.. (2022) Statistical Learning and Uncommon Soil Microbiota Explain Biogeochemical Responses after Wildfire. Applied and Environemental Microbiology.

4. Vuono D.C., Vanneste J., Figueroa L.A., Hammer V., Aguilar-Huaylla F.N., Malone A., Smith N.M., Garcia-Chevesich P.A., Bolaños-Sosa H.G., Alejo-Zapata F.D., Polanco-Cornejo H.G., Bellona C. (2021) Photocatalytic Advanced Oxidation Processes for Neutralizing Free Cyanide in Gold Processing Effluents in Arequipa, Southern Peru. Sustainability. 13(17) 9873.

5. Vuono D.C., Read R.W., Hemp J., Sullivan B., Arnone J., Neveux I., Blank R., Loney L., Miceli D., Winkler M., Chakraborty R., Stahl D., Grzymski J. (2019) Resource concentration modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium. Frontiers in Microbiology. 10(3) 1-13.

6. Read R.W., Vuono D.C., Neveux I., Staub C., Grzymski J.J. (2019) Coordinated downregulation of the photosynthetic apparatus as a protective mechanism against UV exposure in the diatom Corethron hystrix. Applied Microbiology and Biotechnology, Jan 7.

7. Vuono D.C., Regnery J., Li D., Jones Z.L., Holloway R., Drewes J.E. (2016). rRNA gene expression of abundant and rare activated sludge microorganisms and growth-rate induced micropollutant removal. Environmental Science & Technology. 50(12). 6299-6309.

8. Vuono D.C., Munakata-Marr J., Spear J., Drewes J.E. (2016). Disturbance opens recruitment sites for bacterial colonization in activated sludge. Environmental Microbiology. 18(1), 87-99. 

9. Vuono D.C., C., Benecke J., Henkel J., Navidi W., Holloway R. Cath Y., Munakata-Marr J., Spear J., Drewes J.E. (2015). Disturbance and temporal partitioning of the activated sludge metacommunity. International Society of Microbial Ecology (ISME) Journal. 9. 425-435

10. Vuono D.C., Henkel J., Benecke J., Cath T.Y., Reid T., Johnson L., J.E. Drewes (2013). Flexible hybrid membrane treatment systems for tailored nutrient management: A new paradigm in urban wastewater treatment. Journal of Membrane Science. 446. 34-41 

11. Bräuer S., Vuono D.C., Carmichael M.J., Pepe-Ranney C., Strom A., Rabinowitz E., Buckley D., Zinder S. (2014). Microbial sequencing analysis suggest the presence of a fecal veneer on indoor climbing wall holds. Current Microbiology. 69. 681-689 

12. Prieto A.L., Vuono D.C., Holloway R., Benecke J., Henkel J., Cath T.Y., Reid T., Johnson L., Drewes J.E. (2013). Decentralized Wastewater Treatment for Distributed Water Reclamation and Reuse: The Good, The Bad and The Ugly – Experience from a Case Study. Book Series “Novel Solutions to Water Pollution”, Vol. 1123. Chapter 15, pp 251–266. American Chemical Society.