Hauling field gear up Gothic Mountain…
Bridges viral metagenomics of yellow-bellied marmot fecal samples with InSAR-based landslide detection and fungal pathogen immunity research, reflecting a methodologically diverse cluster united by mountain ecosystem contexts and molecular or remote sensing protocols.
The research gathered here spans an unusually broad set of topics — the viruses that live inside yellow-bellied marmots, the slow movement of unstable mountain hillslopes, fungal recognition by the immune system, and the human history of mountain landscapes. What ties these threads together is a shared interest in how living things and physical landscapes interact in mountain environments like the Gunnison Basin around the Rocky Mountain Biological Laboratory (RMBL). Each line of work asks, in its own way, what is hidden in plain sight: viruses we cannot see without sequencing, landslides moving too slowly for the eye to detect, immune responses operating at the molecular scale, and meanings embedded in landscape that only emerge through careful study.
A few key concepts help orient a reader. Viral metagenomics is the practice of sequencing all of the viral genetic material in a biological sample — for example, marmot feces — without first growing the viruses in a lab. A common preparatory step is rolling circle amplification, a technique that uses an enzyme called phi29 DNA polymerase to copy circular DNA templates many times over so that even rare viral genomes can be detected. This approach has revealed enormous viral diversity in wildlife, including phage-host interactions, the ecological relationships between bacteriophages (viruses that infect bacteria) and the bacteria living in an animal's gut. On the immunity side, the body defends against fungal invaders through processes like complement activation (a cascade of blood proteins that tags pathogens) and phagocytosis (the engulfing of pathogens by immune cells such as neutrophils).
The landscape side of the neighborhood centers on mass wasting — the downslope movement of soil and rock through landslides, slumps, and creep — which shapes mountain valleys, threatens infrastructure, and contributes to long-term denudation of ranges like those around Gunnison County. Modern remote sensing can detect ground movement at millimeter-to-centimeter scales across entire watersheds, vastly expanding what was previously mappable by foot. Finally, the concept of power of place reminds us that mountain landscapes are not only physical but also cultural: training grounds, battlefields, and research sites accumulate meaning through human use. These concepts together frame a neighborhood about detecting, measuring, and interpreting things that mountain environments quietly contain.
The oldest study represented here long predates RMBL's modern molecular and remote-sensing era. Sims (Sims, 1956) characterized pitchblende-bearing veins in the Central City district of Colorado, documenting that uranium mineralization occurred in three stages — a uranium stage, a pyritic stage, and a base-metal stage — with pitchblende concentrated in structurally controlled openings along four of six principal fracture sets . While focused on economic geology rather than ecology, this work established a tradition of detailed Colorado mountain geoscience that later landslide and geomorphology studies build upon.
Mass displacement and sediment transport processes involving landslide material movement
DNA amplification technique that amplifies circular DNA templates using phi29 DNA polymerase
Ecological relationships between bacteriophages and their bacterial hosts involving infection, replication, and lysis or lysogeny
Landscapes encountered in daily life through interaction with material and people that are invested with power, where people develop special meanings ...
A comprehensive protocol for extracting, amplifying, sequencing and analyzing viral DNA from fecal samples to identify microviral genomes. Uses rollin...
Microscopic analysis of MASP binding to fungal pathogens using fluorescence techniques.
Measurement of neutrophilic phagocytosis of fungal conidia using recombinant components.
Systematic mapping of WWII defensive positions using Global Navigation Satellite System technology to create detailed plans of military features inclu...
Standardised experimental burns on three types of leaf material (fresh, dried and senesced) to measure flammability parameters.
Activation of the complement system is mediated by the interaction between pathogens and pattern recognition molecules (PRMs); mannose-binding lectin ...
1. Tropical grasses fuel the majority of fires on Earth. In fire-prone landscapes, enhanced flammability may be adaptive for grasses via the maintenan...
Activation of the complement system is mediated by the interaction between pathogens and pattern recognition molecules (PRMs); mannose-binding lectin ...
Outbreaks of emerging coronaviruses in the past two decades and the current pandemic of a novel coronavirus (SARS-CoV-2) that emerged in China highl...
Archeological survey in the Grizzly Ridge new-lands acquisition in the Black Canyon of the Gunnison National Monument recorded eight prehistoric arche...
Work on marmot viromes has revealed that yellow-bellied marmots harbor a remarkable diversity of small DNA viruses. Khalifeh and colleagues identified 26 cressdnaviruses and several additional circular DNA molecules in just 13 fecal samples, with 19 of the cressdnaviruses falling outside any established viral family (Khalifeh et al., 2021). That same study identified seven genomoviruses and a novel anellovirus, MarFaTTV1, which appears to belong to a newly proposed genus called Aleptorquevirus (Khalifeh et al., 2021). A follow-up study by Tijerino and colleagues recovered 63 unique microvirus genomes — bacteriophages in the family Microviridae — from only three marmots, with genome sizes from roughly 4,265 to 7,225 nucleotides (Tijerino et al., 2022). Strikingly, only two of those 63 microviruses were shared across all three animals, showing that gut viral communities vary substantially between individuals (Tijerino et al., 2022). Together these results suggest that marmots, an iconic RMBL study species, host viral communities far richer than previously appreciated.
On the landscape side, Lowry and colleagues used satellite radar interferometry from the ALOS-1 mission to map ground motion across the East Muddy Creek Landslide Complex in Gunnison County — the same hillslope system that destroyed Colorado State Highway 133 in 1986–1987 (Lowry et al., 2020). Their analysis detected previously unrecognized ground displacement at very slow to extremely slow velocities, expanding the known footprint of active sliding well beyond areas identified by traditional field mapping (Lowry et al., 2020). Line-of-sight velocity mapping revealed displacements ranging from about 1 to 5.5 centimeters per year, with mass displacement rates on the order of 8 to 9 × 10⁵ cubic meters per year for individual landslide elements between 2007 and 2011 (Lowry et al., 2020).
A third strand draws attention to the cultural dimensions of Colorado mountain landscapes. Scott documented how the U.S. Army's 10th Mountain Division trained at Camp Hale at roughly 2,750 meters elevation — terrain more demanding than the 700–1,500 meter Italian Apennine battle zones the division later fought in — and showed how this preparation produced a specialized mountain infantry without prior U.S. Army precedent (Scott, 2021). Using GNSS-based battlefield archaeology, Scott mapped roughly 100 defensive features on Hill 913, including bunkers, trenches, and bomb craters (Scott, 2021).
The temporal distribution of these publications shows a clear shift. After Sims's mid-twentieth-century geology, the neighborhood is dominated by work published since 2020. Recent studies have leveraged two technological revolutions: high-throughput sequencing combined with rolling circle amplification for viral discovery in wildlife (Khalifeh et al., 2021; Tijerino et al., 2022) (Tijerino et al., 2022), and satellite-based remote sensing for landscape monitoring (Lowry et al., 2020). Cultural-landscape scholarship using GNSS mapping (Scott, 2021) represents a parallel methodological frontier in which precise spatial tools are applied to historical questions. The trajectory points toward routine, high-resolution surveillance of mountain systems — viral, geomorphic, and historical — at scales and sensitivities that earlier generations of researchers could not achieve.
Many basic questions remain. For marmot viromes, it is unknown whether the cressdnaviruses, anelloviruses, and microviruses detected in feces actively infect marmot tissues, infect their gut bacteria, or simply pass through with diet, and whether viral community composition relates to marmot health, social behavior, or hibernation physiology. For Gunnison Basin landslides, the long-term controls on accelerating or decelerating creep — climate, snowmelt timing, groundwater, and bedrock structure — are not yet resolved, and integrating radar-based motion records with field geology remains a frontier. More broadly, the neighborhood points toward a need for cross-disciplinary syntheses that link the hidden biological diversity of RMBL's animals to the moving, weathering landscapes they inhabit and to the human histories layered upon them.
Khalifeh, A., Blumstein, D.T., Fontenele, R.S., Schmidlin, K., Richet, C., Kraberger, S., Varsani, A. (2021). Diverse cressdnaviruses and an anellovirus identified in the fecal samples of yellow-bellied marmots. Virology. →
Lowry, B.W., Baker, S., Zhou, W. (2020). A Case Study of Novel Landslide Activity Recognition Using ALOS-1 InSAR within the Ragged Mountain Western Hillslope in Gunnison County, Colorado, USA. Remote Sensing. →
Scott, J.M. (2021). Power of place and landscape. →
Sims, P.K. (1956). Paragenesis and structure of pitchblende-bearing veins, Central City District, Gilpin County, Colorado. Economic Geology. →
Tijerino, C.L., Blumstein, D.T., Kraberger, S., Varsani, A. (2022). Microvirus Genomes Identified in Fecal Samples from Yellow-Bellied Marmots. Microbiology Resource Announcements. →