A. Bruce

Cahoon

Courses Taught

• BIO1010, Principles of Biology
• BIO1011, Principles of Biology Laboratory
• BIO 3130, Plant Physiology and Cell Function
• BIO3600, Molecular Genetics

Research Interests & Recent Publications

My research focuses on two broad areas – Appalachian algal & microbial biodiversity and cell organelle gene expression. 

Appalachian Algal & Microbial Biodiversity:

Our region of Appalachia is considered a biodiversity hotspot both colloquially and by professional biologists.  Interestingly, a review of the primary scientific literature provides very few published studies on this phenomenon, which begs the question, how do we know this?  The best-known example of this diversity is the numerous endemic freshwater mussels found in the Clinch River system but little is documented about other groups of organisms, especially microscopic primary producers such as beneficial algae and bacteria.  To address the paucity of published accounts, UVA Wise students and I have been surveying microscopic freshwater dwelling prokaryotes (bacteria) and eukaryotes (collectively known as “protists”) using genomics techniques such as organellar genome sequencing and environmental DNA meta-barcoding.  Genome sequencing allows us to archive the DNA sequences of whole organellar chromosomes from local organisms while meta-barcoding gives us the ability to identify many (up to thousands) of microbes from a single sample by using modern DNA sequencing methods. To date we have produced millions of DNA sequences and identified thousands of microbes from surface waters and caves in the Appalachian region of far Southwest Virginia. 

Organelle RNA Processing:

Organelles (mitochondria and chloroplasts) are semi-autonomous entities within the cytoplasm of eukaryotic cells.  They were once free-living proteobacteria (mitochondria) and cyanobacteria (chloroplasts) that were incorporated into pre-eukaryotic cells by a process known as endosymbiosis.  As a result, these organelles have their own genomes that are mostly circular chromosomes but in some cases are linear or composed of numerous fragments.  My students and I use molecular genetic tools to explore how the hybrid gene expression systems in endosymbiotic organelles (mitochondria and chloroplasts) have resulted in a unique set of post-transcriptional processes.  Recent discoveries made by UVA Wise students include mRNA circularization in human and algal mitochondria and the presence of polyU additions on the mRNAs of green algal chloroplasts.

Recent Publications 
* UVA Wise Student

Isabella J. Maggard*, Kayla B. Deel*, Tina W. Etoll*, Rachael C. Sproles*, Tim W. Lane & A. Bruce Cahoon (2024) Freshwater mussels prefer a diet of stramenopiles and fungi over bacteria. Scientific Reports volume 14, Article number: 11958 

Isabella J. Maggard*, Kayla B. Deel*, Ying Gao, A. Bruce Cahoon (2024) The Soil Microbiomes of American Ginseng (Panax quinquefolius) Cultivated in North America Differ by Location But Not Always by Disease Status. Phytofrontiers

A Bruce Cahoon, Katherine M. Johnson, Sydney M. Brown, Kalina M. Manoylov, James A. Nienow.  (2024) The chloroplast and mitochondrial genomes of two Gomphonema parvulum(Bacillariophyta) environmental isolates from South Carolina (USA) and Virginia (USA). Journal of Phycology

Kendall Davids*, Margie Tucker, Walter Smith, Bruce Cahoon (2023). The mitochondrial genome of Aneides aeneus (Green Salamander). eBio Notes 1:1-21

Lucie O Hornberger*, Isabella J. Maggard*, Robin A. Matthews & A. Bruce Cahoon. (2023) Cryptomonas pyrenoidifera organellar genomes and estimation of its ITS2 sequence diversity using lineage directed barcode primers.  Phycologia

A. Bruce Cahoon and Robert VanGundy (2022). Alveolates (Dinoflagellates, Ciliates, and Apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves. Environmental Microbiology Reports.

Marvin W. Fawley, Karen P. Fawley, A. Bruce Cahoon (2021) Finding needles in a haystack – extensive diversity in the Eustigmatophyceae revealed by community metabarcode analysis targeting the RbcL gene using lineage-directed primers. Journal of Phycology

Grayson C.R. Proulex*, Marcus J. Meade*, Kalina M. Manoylov, A. Bruce Cahoon (2021). Mitochondrial mRNA processing in the chlorophyte alga Pediastrum duplex and streptophyte alga Chara vulgaris reveal an evolutionary branch in mitochondrial mRNA processing. Plants, 10:576

Kendall V. Morse*, Dylan R. Richardson*, Teresa L. Brown, Robert D. VanGundy, A. Bruce Cahoon (2021) Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession. PeerJ: e10757

Blia Lor, Merry Zohn, Marcus J. Meade*, A. Bruce Cahoon and Kalina M. Manoylov (2021) A morphological and molecular analysis of a bloom of the filamentous green alga Pithophora. Water. 13:760

Marcus Jerryd Meade*, Grayson C. R. Proulex*, Kalina M. Manoylov, A. Bruce Cahoon. (2020) Chloroplast mRNAs are 3’ polyuridylylated in the green alga Pithophora roettleri (Cladophorales). Journal of Phycology.

Landon G. Mance*, Ishaat Mawla*, Steven M. Shell, A. Bruce Cahoon (2020) Mitochondrial mRNA fragments are circularized in a human HEK cell line. Mitochondrion. 51:1-6 (2019) 

Brandon Thompson*, Dylan Richardson*, Robert D. Vangundy, A. Bruce Cahoon Metabarcoding comparison of prokaryotic microbiomes from Appalachian karst caves to surface soils in Southwest Virginia, USA.  Journal of Cave and Karst Studies 81:244-253

Grayson C. R. Proulex*, Blia Lor, Kalina M. Manoylov, A. Bruce Cahoon (2019) The chloroplast and mitochondrial genomes of the green alga Pediastrum duplex isolated from Central Georgia (USA). Mitochondrial DNA Part B 4:2

Katy Mullins*, Robert D. VanGundy, A. Bruce Cahoon (2019) Unexpected amounts of human DNA discovered in Appalachian karst cave systems. Lux: Undergraduate Scholarship at the University of Virginia’s College at Wise. 2:74-94

Roseanna M. Crowell*, James A. Nienow, and Aubrey Bruce Cahoon (2019)  The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica.  Journal of Phycology. 55:352-264

A. Bruce Cahoon, Ashley G. Huffman*, Megan M. Krager, Roseanna M. Crowell* (2018) A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA. Metabarcoding and Metagenomics 2:e26939

A. Bruce Cahoon and Ali A. Qureshi(2018)Leaderless mRNAs are Circularized in Chlamydomonas reinhardtii Mitochondria. Current Genetics. 64:1321-1333

Christen M. Klinger, Lucas Paoli, Robert Newby, Matthew Yu-Wei Wang, Hyrum D.Carroll, Jeffrey D. Leblond, Christopher J. Howe, Joel B. Dacks, Bruce Cahoon, Richard G. Dorrell, and Elisabeth Richardson  (2018) Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends.  Genome Biology and Evolution. 10:1019-1038

Cahoon, A. B., Nauss, J.N.*, Stanley, C.D.*, Qureshi, A. (2017) Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides no Evidence of Organellar RNA Editing.  Genes 8(2)