Past Research

The Geomicrobiology Lab has explored the geomicrobiology of various aquatic systems. Below are the past environments in which we have worked.

Laurentian Sinkholes
Deep Sea Hydrothermal Vents
Other environments

Geomicrobiology of Laurentian sinkholes

Overview

High-throughput DNA sequencing is being applied to understand novel microbial mats inhabiting sediments of Lake Huron, where saline, sulfur-rich groundwater emerges 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.

Publications

  1. Grim, S. L., Voorhies, A. A., Biddanda, B. A., Jain, S., Nold, S. C., Green, R., & Dick, G. J. (2021). Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O2 Cyanobacterial Mat Community. Msystems, 6(6), e01042-21.
  2. Klatt, J. M., Chennu, A., Arbic, B. K., Biddanda, B. A., & Dick, G. J. (2021). Possible link between Earth’s rotation rate and oxygenation. Nature Geoscience, 14(8), 564-570.
  3. Dick, G. J., Grim, S. L., & Klatt, J. M. (2018). Controls on O 2 production in cyanobacterial mats and implications for Earth’s oxygenation. Annual Review of Earth and Planetary Sciences, 46(1).
  4. Sharrar, A. M., Flood, B. E., Bailey, J. V., Jones, D. S., Biddanda, B. A., Ruberg, S. A., … & Dick, G. J. (2017). Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron basin. Frontiers in microbiology, 8, 791.
  5. Voorhies, A. A., Eisenlord, S. D., Marcus, D. N., Duhaime, M. B., Biddanda, B. A., Cavalcoli, J. D., & Dick, G. J. (2016). Ecological and genetic interactions between cyanobacteria and viruses in a low‐oxygen mat community inferred through metagenomics and metatranscriptomics. Environmental microbiology, 18(2), 358-371.
  6. Voorhies, A. A., Biddanda, B. A., Kendall, S. T., Jain, S., Marcus, D. N., Nold, S. C., … & Dick, G. J. (2012). Cyanobacterial life at low O2: community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat. Geobiology, 10(3), 250-267.

Field Sites

  • Lake Huron near Alpena, MI

Collaborators

  • Allen Burton
  • Wiebke Ziebis
  • Jake Waldbauer
  • David Fike

Funding

  • Collaborative Research: Revealing the interplay between light, sulfur cycling, and oxygen production in cyanobacterial mats.  National Science Foundation Geobiology & Low-Temperature Geochemistry EAR 1637066.
  • Collaborative Research: EAGER: Genomic insights into microbial mat diversity 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.

Diversity and function of microbial communities in deep-sea hydrothermal plumes

Overview

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 develop new methods to sample, analyze, and model plume microbial ecology and geochemistry.

Publications

  1. Dick, G.J. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol 17, 271–283 (2019). https://doi.org/10.1038/s41579-019-0160-2
  2. Anantharaman, K., Breier, J. & Dick, G. Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME J 10, 225–239 (2016). https://doi.org/10.1038/ismej.2015.81
  3. Li, M., Jain, S., & Dick, G. J. (2016). Genomic and transcriptomic resolution of organic matter utilization among deep-sea bacteria in guaymas basin hydrothermal plumes. Frontiers in microbiology, 7, 1125.
  4. Li, M., Baker, B., Anantharaman, K. et al. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea. Nat Commun 6, 8933 (2015). https://doi.org/10.1038/ncomms9933
  5. Sheik, C., Anantharaman, K., Breier, J. et al. Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin. ISME J 9, 1434–1445 (2015). https://doi.org/10.1038/ismej.2014.228
  6. Reed, D. C., Breier, J. A., Jiang, H., Anantharaman, K., Klausmeier, C. A., Toner, B. M., … & Dick, G. J. (2015). Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents. The ISME journal, 9(8), 1857-1869.
  7. Anantharaman, K., Duhaime, M. B., Breier, J. A., Wendt, K. A., Toner, B. M., & Dick, G. J. (2014). Sulfur oxidation genes in diverse deep-sea viruses. Science, 344(6185), 757-760.
  8. Sheik, C. S., Jain, S., & Dick, G. J. (2014). Metabolic flexibility of enigmatic SAR 324 revealed through metagenomics and metatranscriptomics. Environmental microbiology, 16(1), 304-317.
  9. Li, M., Toner, B., Baker, B. et al. Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nat Commun 5, 3192 (2014). https://doi.org/10.1038/ncomms4192
  10. Li, M., Jain, S., Baker, B.J., Taylor, C. and Dick, G.J. (2014), Metatranscriptomics of pHMO in a hydrothermal plume. Environ Microbiol, 16: 60-71. https://doi.org/10.1111/1462-2920.12182
  11. Dick, G. J., Anantharaman, K., Baker, B. J., Li, M., Reed, D. C., & Sheik, C. S. (2013). The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology, 4, 124.
  12. Anantharaman, K., Breier, J. A., Sheik, C. S., & Dick, G. J. (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proceedings of the National Academy of Sciences, 110(1), 330-335.
  13. Baker, B. J., Lesniewski, R. A., & Dick, G. J. (2012). Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. The ISME journal, 6(12), 2269-2279.
  14. Lesniewski, R. A., Jain, S., Anantharaman, K., Schloss, P. D., & Dick, G. J. (2012). The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. The ISME journal, 6(12), 2257-2268.
  15. Dick, G. J., Lee, Y. E., & Tebo, B. M. (2006). Manganese (II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes. Applied and Environmental Microbiology, 72(5), 3184-3190.

Field Sites

  • Lau Basin (southwestern Pacific)
  • Guaymas Basin (Gulf of California)
  • Cayman Rise (Caribbean)

Collaborators

Funding

  • 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 Research: 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.

Other environments

Biofilms

Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., & Banfield, J. F. (2009). Community-wide analysis of microbial genome sequence signatures. Genome biology, 10(8), 1-16.

Corals

Den Uyl, P. A., Richardson, L. L., Jain, S., & Dick, G. J. (2016). Unraveling the physiological roles of the cyanobacterium Geitlerinema sp. BBD and other black band disease community members through genomic analysis of a mixed culture. PLoS One, 11(6), e0157953.

Deep Sea

Baker, B. J., Sheik, C. S., Taylor, C. A., Jain, S., Bhasi, A., Cavalcoli, J. D., & Dick, G. J. (2013). Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. The ISME journal, 7(10), 1962-1973.

Estuaries

Baker, B. J., Lazar, C. S., Teske, A. P., & Dick, G. J. (2015). Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome, 3(1), 1-12.

Glaciers

Sheik, C. S., Stevenson, E. I., Den Uyl, P. A., Arendt, C. A., Aciego, S. M., & Dick, G. J. (2015). Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time. Frontiers in microbiology, 6, 495.

Mangroves

Schofield, M. M., Jain, S., Porat, D., Dick, G. J., & Sherman, D. H. (2015). Identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product ET‐743. Environmental microbiology, 17(10), 3964-3975.

Oxygen Minimum Zones

Reed, D. C., Algar, C. K., Huber, J. A., & Dick, G. J. (2014). Gene-centric approach to integrating environmental genomics and biogeochemical models. Proceedings of the National Academy of Sciences, 111(5), 1879-1884.