Biology ETDs

Publication Date

Winter 12-13-2017


Arid-land caves are thought to be extremely nitrogen-limited, but almost nothing is known about how microbes in subsurface arid-land environments obtain this essential element to meet cellular demand. The depth of caves beneath the surface may represent a critical factor affecting microbial nitrogen cycling in these environments. Percolation of water and nutrients from a precipitation pulse event would affect deep arid-land carbonate caves at a much slower rate. To obtain nitrogen in deep, carbonate caves, microorganisms could use fixed N in the host rock for assimilatory biochemical pathways or for a respiratory electron acceptor. However, the latter process leads to losses of bioavailable N through production of N2O and N2, which can only be replaced by N2 fixation or weathering. Fort Stanton Cave (FSC), found near the northern end of the Sacramento Mountains, is the third longest cave in New Mexico. Multicolored secondary mineral deposits of soil-like material, known as ferromanganese deposits (FMD) exist on the ceilings and walls of FSC. I hypothesized that within the FMD I would find the presence of microbial nitrogen cycling genes. Overburden and connectivity with the surface would influence archaeal and bacterial groups found in caves. As FSC is a moderately deep carbonate cave, I hypothesized that the archaeal and bacterial communities residing in the subsurface would differ from their surface counterparts, as extreme oligotrophic conditions in the cave would select for organisms with metabolisms favoring chemolithotrophy and low-nutrient adaptability. To investigate these hypotheses, Illumina shotgun metagenomics and 16S rRNA gene sequencing were used. Sequences were processed and annotated using several bioinformatic methods. Results indicate that there were genes present in the FMD related to nitrification, dissimilatory nitrate reduction to ammonium, denitrification, and assimilatory nitrate reduction pathways. Potential key players include the ammonia oxidizing archaea phylum Thaumarchaeota and the ammonia and/or nitrite oxidizing bacterial phylum Nitrospirae. Core microbiome and taxonomic results show that the archaeal and bacterial communities in surface soils are dissimilar to their cave counterparts. There were also bacterial phyla identified in the cave that were mostly absent in surface soils, suggesting low-nutrient adaptation. Comparing the archaeal FSC dataset to Cueva Villa Luz, Tabasco, Mexico and several caves in Parashant National Monument (PARA), AZ, there were no OTUs shared across all samples. Our results show that cave types, host-rock geochemistry, and depth influence archaeal communities present in these subsurface environments. These results shed light on: a) how microbes in caves acquire and cycle nitrogen, b) the archaeal and bacterial diversity in these environments, and c) drivers that influence their presence of diverse archaea in these subsurface biomes.


Caves, Thaumarchaeota, Thermoplasmata, Fort Stanton, Nitrogen Cycle, Ferromanganese

Document Type


Degree Name

Microbial Ecology

Level of Degree


Department Name

UNM Biology Department

First Committee Member (Chair)

Robert L. Sinsabaugh

Second Committee Member

Diana E. Northup

Third Committee Member

Clifford N. Dahm

Fourth Committee Member

Rebecca J. Bixby

Fifth Committee Member

Lisa Y. Stein

FOAM_N_Cycle_HMMs.xlsx (167 kB)
Supplementary FOAM_N_Cycle_HMMs

Functional_Pipeline.rtf (5 kB)
Supplementary Functional_Pipeline

Qiime_Pipeline.rtf (3 kB)
Supplementary Qiime_Pipeline