Michigan Geomicrobiology Lab

Microorganisms have dominated the history of Earth, playing an intimate role in shaping its chemical and physical properties.  Microbes continue their role as agents of biogeochemistry today as they drive a wide range of processes, including the cycling of carbon, oxygen, nitrogen, sulfur, and metals.  Our research interests are focused on this interplay between the biosphere and the geosphere, examining how microbes drive geochemistry and how geochemistry in turn shapes microbial diversity, metabolism, and evolution.  Many biogeochemical cycles are actively driven by genetically encoded molecules that are often carefully regulated to be produced only under certain environmental or physiological conditions.  Thus an understanding of biogeochemical cycles that take place on global scales demands knowledge of dynamics that take place on molecular scales.  As such, our research relies heavily on molecular-biological approaches that are closely coupled with geochemical approaches to achieve an integrated view of geomicrobiology.  

Cyanobacterial harmful algal blooms. Harmful algal blooms (HABs) are a global threat to freshwater ecosystems, water resources, and human health. The interplay of microbial, ecological, and chemical processes causes toxin production and formation of lake “dead zones”. This project will better understand this problem by integrating new approaches, including community 'omics, to a local natural laboratory, Lake Erie, which experienced the largest HAB in recorded history in 2011.

photo by Tom Archer

field sites: Lake Erie

collaborators: Vincent Denef, Tom Johengen, Rose Cory, Steve Ruberg, Tim Davis, Melissa Duhaime, David Sherman, Tim James


Building capacity for freshwater science: Integrating microbial genomics, environmental chemistry, and ecosystem processes to understand harmful algal blooms. University of Michigan Water Center.
Diversity and function of microbial communities in deep-sea hydrothermal plumes.  This project addresses questions of how deep-sea microbial communities respond to and transform potential energy sources emanating from deep-sea hydrothermal vents, such as methane, ammonium, sulfur, iron, and manganese. We work with a large team of collaborators to devleop new methods to sample, analyze, and model plume microbial ecology and geochemistry.

field sites: Lau Basin (southwestern Pacific), Guaymas Basin (Gulf of California), Cayman Rise (Caribbean)

collaborators: Brandy Toner, Chip Breier, Houshuo Jiang, Christopher Klausmeier, Patrick Schloss, Jason Sylvan & Katrina Edwards


Unveiling the microbiology that underpins deep-sea biogeochemistry. Gordon and Better Moore Foundation Marine Microbiology Initiative #2609.

Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes. National Science Foundation Biological Oceanography OCE 1029242.

Collaborative Reserach: Integrating geochemistry, microbiology, and hydrodynamics: A model for trace element transport and fate in hydrothermal plumes. National Science Foundation Ridge2000 (Marine Geology and Geophysics) OCE 1038006.


Geomicrobiology of Laurentian sinkholes. High-throughput DNA sequencing is being applied to understand novel microbial mats inhabiting sediments of Lake Huron, where saline, sulfur-rich groundwater emereges from submerged sinkholes. This system is a fantastic analog of ancient microbial mats, and a model system for understanding the role of cyanobacteria in Earth's oxygenation.

field sites: Lake Huron near Alpena, MI

collaborators: Steve Ruberg, Bopi Biddanda, Scott Kendall, Steve Nold, Nathan Sheldon, Allen Burton



Collaborative Research: EAGER: Genomic insights into microbial mat diveristy and Proterozoic geobiology. National Science Foundation Geobiology & Low-Temperature Geochemistry EAR 1035955

Will Climate, Invasives and Toxicants Imperil Unique Biodiversity in the Great Lakes? University of Michigan Mcubed.




Genetics, biochemistry, physiology, and genomics of Mn(II)-oxidizing bacteria that catalyze the formation of biogenic Mn oxides.

Microbe-metal interactions in Lake Erie sediments. Every summer metals are mobilized from sediments as bottom waters go anoxic due to eutrophication. We are identifying microorganisms that influence their mobility and fate.

field sites: Lake Erie near Cleveland, OH

collaborators: Steve Ruberg, Edwin Guasp

Signatures of nucleotide composition in microbial genomes. Microbial genomes display charatcteristic features of nucleotide composition, such as %GC content and oligonucleotide (e.g. tetranucleotide) frequency. We are exploiting these genome signatures for binning metagenomic DNA sequence fragments and tracing the evolutionary history of microbial genomes.

acid mine drainage

Geomicrobiology of acid mine drainage (AMD).  This project investigates how microbes drive the dissolution of pyrite and the formation of acid mine drainage.  Community genomics and proteomics are used to understand molecular mechanisms and evolutionary processes in this extremely acidic, chemolithoautotrophic ecosystem.  Our work has focused on sulfur cycling, assembly of metagenomic DNA sequences, and bioinformatic methods to analyze low-abundance community members.

Approaches and technical interests:
• metagenomics and metatranscriptomics of microbial communities in natural environments; functional approaches for identifying genes and enzymes. 
• bioinformatics.
• biochemistry: protein purification and enzyme function.
• microbial physiology: isolation and physiological studies of microbes in pure culture.