Cody Sheik

 

- Ph.D. 2011 University of Oklahoma

- B.S. 2004 University of Oklahoma

Website: www.AquaticGeomicro.com

 

Microorganisms are extraordinary catalysts. They arose early in Earth’s geologic history and have since evolved sophisticated cellular machinery, contributing to most of Earth’s low-temperature geochemical cycles. My laboratory takes a multi-disciplinary approach, combining microbial ecology, physiology, genomics and geochemistry, to address fundamental questions that scale from a single microbial cell to an entire ecosystem. To address our questions, many of which are first order due to the state of the field, my lab combines traditional microbiology techniques of isolation, enrichment, and rate measures with molecular based approaches (such as metagenomics and metatranscriptomics) and geochemistry to elucidate the role of microorganisms in aquatic environments.

 

Microbe-water-rock interactions

Our understanding of subsurface and hot spring microbial communities is woefully primitive, especially when compared to other environments such as the human gut. There are primary gaps in knowledge regarding what microbes inhabit these extreme environments, the metabolic roles of these microbes, and what physical factors influence microbial biogeography. As an extension of my work on hydrothermal vent plumes, which derive their chemical signatures from deep water-rock interactions, we have begun several projects focused on understanding how microbial metabolism and communities are shaped by water-rock interactions and vice versa.

 

• Biogeography of subsurface microbial communities. In 2016, I joined an international team of geomicrobiologists and microbial ecologists to explore and synthesize the diversity of subsurface microorganisms using data generated through the Deep Carbon Observatory’s Census of Deep Life sequencing initiative. Here we are using existing datasets to understand the biogeography, diversity and taxonomic identity of subsurface microorganisms on Earth.
• Metabolic foundations of subsurface microbial communities. We are trying to understand how microorganisms and their metabolisms interact with host rock and waters in the Soudan Iron mine in northern Minnesota. My lab has focused on analyzing preliminary molecular data (16S rRNA and shotgun metagenome data). Molecular data as well as isotopic data suggest acetate producing microorganisms are primary producers in the formation. Our group is now moving forward to specifically test this hypothesis.
• Are all terrestrial hot springs created equal? Terrestrial hot springs are one of the oldest environments on Earth and host a unique microbiota. However, we know little about how water-rock interactions shape the elemental stoichiometry of hot springs and how elemental composition shapes the metabolic diversity of microorganisms. I have initiated a collaboration to examine the diversity of microbial metabolisms at hot springs in Yellowstone National Park, Ecuador, and the Azores. 

Freshwater microbial element cycling

As primary mediators of geochemical cycles, microorganisms are an important lynchpin of all ecosystems. However, due to our inability to cultivate the majority of Earth’s microorganisms, large gaps in knowledge exist with regards to the function and physiology of a vast swath of the population. Given the dearth of information regarding most microbes, our knowledge of how microorganisms influence food webs and the carbon cycle in aquatic systems is limited. My lab is interested understanding these processes in both freshwater and marine ecosystems. 

 

• Sediment microbial processes. Past research highlighted freshwater sediments as significant sources of methane and carbon dioxide. Thus, in a changing climate, understanding carbon cycling from a microbial perspective in freshwater ecosystems is imperative. My lab has begun studies of sediments from lakes varying in size and nutrient load, using relic DNA to extrapolate past communities. Emerging results from our studies on Lake Superior suggest microbial communities in the sediments are highly dynamic and structured by lake region, depth, and proximity to land. Additionally, these sediments are veritable treasure troves of novel microbial phyla, suggesting that we have only scratched the surface of understanding sediment biogeochemical cycles. 
• Phytoplankton physiology, microbial interactome, and harmful algae blooms. Phytoplankton are keystone members of aquatic systems and as such have been intensely studied. However, many primary questions still remain especially for harmful algal blooms (HABs). Currently much of this work focuses on the Great Lakes, but will extend to inland lakes and can scale easily to marine systems. Again, taking a molecular approach, my lab is ground-truthing traditional microscopy-based taxonomic surveys of phytoplankton by sequencing highly conserved, phylogenetic marker genes. Additionally, we are using metatranscriptomics (RNA sequencing) to identify the genes expressed at the time of sampling. Using these data, we hope to identify physiological responses of phytoplankton to potential stressors, such as nitrogen or phosphorus limitation.  

 

 

 

Please see my Google Scholar Page

 

• BIOL 3502 - General Microbiology
• BIOL 4201/5201- Bioinformatics for Biologists
• BIOL 3987- Communications in Biology
• GEOL 4095/5095- Geology Special Topics: Geobiology: Slime Through Time

Current Graduate Student Projects

• Emily Hyde, (M.S., Integrated Biosciences)
• Jennifer Knack, (Ph.D., Integrated Biosciences) (co-advisor w/Hicks)
• Kaela Natwora, (M.S., Integrated Biosciences)

Hobbies

In my free time you may find me trail running, baking bread, hiking/backpacking and playing guitar.