Student Research
Geomicrobiology of Lehman Caves
Zoë Havlena, Ph.D. Student, Earth and Environmental Science Department at New Mexico Tech
Some of the world’s largest and most spectacular limestone caves, including Carlsbad Cavern and Lechuguilla Cave in New Mexico, were formed by a process known as “sulfuric acid speleogenesis” (cave formation by sulfuric acid). These caves form where groundwaters charged with hydrogen sulfide (H2S) are exposed to oxygen in cave air or in fresh surface waters. Hydrogen sulfide is the gas that gives rotten eggs their “rotten” smell and is an especially reactive form of sulfur that is unstable in the presence of oxygen. As this hydrogen sulfide is exposed to oxygen, it reacts to form sulfuric acid. Sulfuric acid is the same acid that is in car batteries, and this strong acid rapidly dissolves limestone and creates cave chambers.
We only know of a handful of caves around the world that are actively forming by sulfuric acid speleogenesis. However, so-called “fossil” sulfuric acid caves are more common. These caves are not experiencing sulfuric acid corrosion at present, but they did at some point in the past. Evidence for a past “sulfuric” episode can be found in the form of certain morphological features and mineral deposits, such as the mineral gypsum when it forms as a by-product of the sulfuric acid reaction above.
As part of her Ph.D. research, Zoë Havlena is studying Lehman Caves in Great Basin National Park, Nevada. Lehman Caves may have formed by sulfuric acid speleogenesis several million years ago, and some passages preserve features consistent with sulfuric acid speleogenesis. Until recently, little was known about the geological history and evolution of the cave system, or the geomicrobiological processes occurring within the cave. Zoë is using mineralogical and isotopic analysis to help understand Lehman’s past and is using molecular tools to explore how microorganisms may continue to impact the cave today.
Her work on Lehman Caves is only one portion of Zoë’s research. Zoë earned her master’s degree studying harmful photosynthetic microbial communities known as “lampenflora” in Carlsbad Cavern (see below). She is now a Ph.D. student with Dr. Daniel Jones at New Mexico Tech where, in addition to her work on Lehman Cave, she is studying microbial communities associated with gypsum in the Frasassi Caves, and is trying to understand how gypsum could be used as a microbial habitat and might preserve biosignatures of ancient microbial life.
Extreme Acid-adapted Microbes from Sulfuric Acid Caves
Mackenzie Best, MS Student, Earth and Environmental Science Department at New Mexico Tech
Sulfuric acid caves are hotspots for life in Earth’s subsurface. These caves are a rare type of cave that have underground springs and rivers with dissolved hydrogen sulfide running through them. When that hydrogen sulfide reacts with oxygen, it forms sulfuric acid, which rapidly dissolves limestone and creates cave chambers.
The hydrogen sulfide in these caves is an energy source for life. Certain chemosynthetic bacteria and archaea “eat” hydrogen sulfide in the same way we humans eat organic carbon. These organisms thrive in sulfuric acid caves, where they form the base of a food web that supports entire subterranean chemosynthetic ecosystems that often include invertebrate and even vertebrate animals. Furthermore, because they live off hydrogen sulfide oxidation, these microbes produce sulfuric acid and substantially speed up cave formation.
Some of the most remarkable microbial communities in these caves are known as “snottites.” Snottites are rubbery biofilms that hang from cave walls and ceilings and are formed by microorganisms that live off hydrogen sulfide gas in the cave air. These biofilms are also extremely acidic, pH 0-1, which is more acidic than the acid in your stomach.
For her Master’s research at New Mexico Tech, Mackenzie Best is studying the acid-adapted organisms that form snottites. These organisms are known as extreme acidophiles, and some of the organisms from cave snottites are the most acid-tolerant microorganisms known. Not only are these organisms important catalysts for acid production and cave formation, but extreme acidophiles also have important biotechnological applications for bioremediation and biomining.
Mackenzie is studying novel extreme acidophiles from the Frasassi and Villa Luz cave systems, in central Italy and southern Mexico. She has grown several strains of a bacteria known as Acidithiobacillus, and is testing them in the lab, determining how they make their living and exploring the limits of their acid tolerance. She is also sequencing their genomes and also using another technique called metagenomics to explore other extreme acidophiles in the snottite community. Metagenomics is genome sequencing of a whole microbial community directly from an environmental sample, and Mackenzie is using those data to probe the potential metabolisms of the other abundant and rare members of the community. Some recent abstracts from Mackenzie’s presentations can be found at the links below.
After she completes her Masters degree, Mackenzie is planning to stay at New Mexico Tech to continue working with Dr. Daniel Jones for her Ph.D. In addition to her cave research, Mackenzie has worked as both an exploration and an ore-control production geologist at polymetallic base metal mines in the Democratic Republic of the Congo and Peru. She also worked as a geology consultant on a project using remote sensing and machine learning techniques to identify uranium mines and estimate their production.
Identification and Characterization of Cave Viruses
Joseph Ulbrich, MS Student, Biology Department at New Mexico Tech
Viruses are the most common biological entities on Earth, yet they are some of the least understood. Although the viruses that make headlines are those that infect humans, there are viruses that infect all forms of life. The most abundant viruses on Earth infect bacteria and are known as bacteriophages. Bacteriophages are major controls on bacterial populations in different environments, and can also stimulate nutrient recycling by destroying (or “lysing”) their bacterial hosts in releasing their nutrients for uptake by other cells.
However, very little is known about viruses in caves and how viral dynamics might impact cave ecosystems. Joseph Ulbrich is trying to change that. Joe is a Masters student working with Dr. Thomas Kieft at New Mexico Tech, and is exploring bacteriophage diversity in cave pools.
Joe is studying different pools in Carlsbad Cavern in Carlsbad Caverns National Park. Specifically, he will attempt to quantify viral particles in the pools relative to bacterial and other microbial cells and start to generate a database of cave pool viral sequences. He will also evaluate if human impacts on cave pools are reflected in their viral diversity. He expects to find that cave pools harbor novel viral diversity, particularly in undeveloped parts of the cave.
In addition to his Masters research, Joe also has interests in STEM education and outdoor recreation. He has worked as a summer camp naturalist and has previous research experience in computational chemistry. After completing his Masters, Joe is exploring his options in growing in academia, pursuing a professional career, or joining the Peace Corps. He hopes to make a positive impact and help others wherever his passions take him.
Lampenflora in Carlsbad Caverns National Park
Caves used for tourism, called “show caves,” have many features that make them more accessible for the general public. You will find permanently installed lighting in most show caves worldwide. While necessary for the visitor experience, the introduction of light into a naturally dark environment has negative consequences. Microbial growths called “lampenflora” develop from the lighting. Their green color not only detracts from the cave experience for visitors, but the growth itself damages the surfaces of cave walls and minerals.
The National Park Service recently modernized the lighting in Carlsbad Cavern to an LED system that allows adjustment of color temperature and intensity. This change was an opportunity to see if changing the energy source for the lampenflora could be an avenue to reduce their growth.
The park contracted NCKRI to conduct a study to understand how such adjustments may reduce lampenflora. Through our Academic Program, we started a two-phase student research study with the New Mexico Tech Biology Department under the supervision of Dr. Thomas Kieft.
The first phase funded a Master’s thesis study by Zoë Havlena, who graduated with honors in May 2019. Using the easily adjustable new LED system, she designed an experiment to lower the color temperature of some lights to a range that should be less conducive to the photosynthetic growth of lampenflora. She then measured the growth in comparison to higher, more photosynthetically energy-rich levels provided by the historical lighting setup.
The data did not show the expected trend of increasing levels of growth over time or higher values for sites exposed to higher color temperature light. The study’s results suggest that biofilm growths are more complex than previously thought. From a cave management perspective, the changes to the LED lighting do not seem to produce results consistent with a useful reduction in lampenflora growth. Ms. Havlena’s work was recently published in the journal Applied and Environmental Microbiology, and a detailed NCKRI report of her findings will be published soon.
The second phase of the lampenflora study is to find an effective means of removing lampenflora from caves and discouraging its regrowth. For decades, bleach solutions have been used by show caves worldwide to treat lampenflora. All the while, a better method has been desired that is less toxic and smelly. A variety of other potential treatments are currently under study in New Mexico Tech’s labs through the efforts of multiple biology students. While some of the preliminary results are encouraging, more testing is needed and ongoing.
Zoe Havlena measures airflow and temperature at a lampenflora sampling site. NCKRI staff photo: George Veni. 
Sampling lampenflora on a cave floor for DNA analysis. NCKRI staff photo: George Veni.
Learn about other and current student research projects in NCKRI’s Annual Reports.