Skip main navigation

NOAA logo


  GLERL logo
Skip Research subnavigation

Research Programs

By Subject

By Researcher





This project is no longer current

Exploration of Submerged Sinkhole Ecosystems in Thunder Bay National Marine Sanctuary, Lake Huron

Primary Investigator:

Steve Ruberg - NOAA GLERL

2008 Field Work Ocean Exploration Website


  • Nathan Hawley - NOAA GLERL
  • Tyrone Black - Michigan Department of Environmental Quality
  • Mark Baskaran - Wayne State University
  • Bopi Biddanda, Scott Kendal - Grand Valley State University
  • Steve Nold - University of Wisconsin - Stout
  • Tom Johengen - CILER, University of Michigan
  • Guy Meadows - University of Michigan - Naval Architecture and Marine Engineering
  • Jeff Gray - Thunder Bay National Marine Sanctuary
  • Val Klump, Rob Paddock - University of Wisconsin - Madison
  • Ivar Babb - NOAA Undersea Research Program - University of Connecticut


Recently discovered submerged sinkholes in the Thunder Bay National Marine Sanctuary region (Figure 1) represent unique physical, chemical, and biological systems. Because there has been no systematic search for and study of submerged groundwater vents, little is known regarding the hydrology, biology and geochemistry of submerged sinkholes. We plan to conduct a detailed interdisciplinary investigation of the unique benthic habitats fueled by venting groundwater in the Laurentian Great Lakes using a hydrographic instrument array and ROV/Diver-led exploratory field study.

map of North American Laurentian Great Lakes Basin regions of onshore karst formations

Figure 1: Map of the North American Laurentian Great Lakes Basin showing regions of Devonian-Silurian aquifers potentially having karst formations (left), and regions of above ground karst formations in the Alpena County, MI and submerged sinkholes (including the study sites - Misery Bay containing the El Cajon Bay sinkhole, Middle Island Sinkhole and Isolated Sinkhole) in the Thunder Bay National Marine Sanctuary, Lake Huron (right).


As part of an earlier NOAA-OE funded project with the primary focus on archeology, we located, mapped and explored the Isolated Sinkhole from on board NOAA’s research vessel “R/V Laurentian”, and were able to obtain samples (pumped up to the surface) from the immediate vicinity of the sinkhole (at 93 m depth) using the University of Michigan’s remotely operated submersible “M-Rover” during September 2003. Conductivity in the proximity of the sinkhole was an order of magnitude higher than ambient lake water. The seeping fluid also was characterized by warmer water (by up to 4oC) relative to ambient lake water at depth (Figure 2). Conspicuous white benthic mats interspersed with the brownish mats characterized the lake floor in the vicinity of the sinkhole, and a dark cloudy nepheloid-like plume layer prevailed just over the site of submarine groundwater seepage (Figure 3). The images of benthic mats recorded at the Isolated Sinkhole in western Lake Huron are remarkably similar in appearance to those commonly characterizing cold seep and thermal vent habitats in the ocean. Preliminary results suggested that the Isolated Sinkhole environment was a hot spot of nutrient efflux and microbial activity. In comparison to surrounding deep water, the nepheloid-like layer prevailing just over the site of venting was clearly characterized by higher conductivity and temperatures, higher concentrations of chloride, sulfate, phosphorus, DOC, POC, PON and bacteria . Although the ROV was able to sample the nepheloid layer occurring about 1 m above the lake floor, it was unable to sample the groundwater from beneath the nepheloid layer and directly emerging from the lake floor without disturbing the sediments - hence the composition of this source water at the Isolated Sinkhole remains unknown. Complex linkages existing between surface water and groundwater that are driven by changing hydrologic and climatic conditions may influence both the composition and discharge of groundwater venting in karst sinkholes. These fluctuations may fuel unique life forms and biogeochemical processes in these ecosystems.

conductivity and temperature maps over lake floor and submerged sinkhole

Figure 2: CTD mapping by ROV just over the Isolated sinkhole (at 91 m over a ~35m x 55m area) showing enhanced conductivity and temperature at sites of venting in 9/2003.

sinkhole: benthic white and dark matsmicrobial hot spot

Figure 3: Isolated Sinkhole: ROV-video still images of conspicuous benthic white and dark mats (left, composition unknown) and 1-2 m thick nepheloid-like plume layer (microbial hot spot) prevailing just over the lake floor (right) at the Isolated Sinkhole in 9/2003.

Further pilot studies (July and August 2005, 2006) initiated by the proposal collaborators focused on the habitat and biota at the shallower sinkholes. These studies also yielded exciting new information: at the Middle Island sinkhole (~18m depth), diver observations revealed the presence of massive purple (Figure 4), green and whitish mats. The extensive purple mats occurring along the ridges and on the lake floor were composed of filamentous cyanobacteria (Oscillatoria spp.) (Figure 4). Underlying the lake floor mats was a thick layer (›1 m) of black, sulfidic, organic-rich sediment of unknown origin.

purple benthic mats cyanobacterial filaments

Figure 4: Middle Island Sinkhole: Diver photograph of purple benthic mats (left, photo by Steve Nelson, Noble Odyssey Foundation), and microscopic image of cyanobacterial filaments (right, 200x) from the mid-depth (~18m) Middle Island Sinkhole (Summer 2005).

Field observations and samples from the shallow springs of El Cajon Bay (0.2-1m) in the Misery Bay Sinkholes area also showed extensive green and purple mats (Figure 5). Although the green mats appear to be composed of the green alga Odegonium (not found in the Middle Island Sinkhole), the composition of the purple mats was identical to those found in the Middle Island Sinkhole (viz. Oscillatoria spp.). Furthermore, the white benthic mats found abundantly in the deeper Isolated Sinkhole were quite rare in the shallower Middle Island and were not at all observed at the shallowest El Cajon Sinkhole.

green mats microscopic diatoms and green algae

El Cajon Springs site Oedogonium spp.

Figure 5: Misery Bay Area (El Cajon) Sinkhole: Field photograph showing smaller patches of green mats and larger patches of purple benthic mats (upper left, photo by Elliott Smith, Noble Odyssey Foundation), and microscopic image of cyanobacterial filaments, some diatoms and green algae (upper right, 100x) from the shallow (~0.5-3m) El Cajon Sinkhole (Summer 2005). In 2006, the El Cajon Springs site (lower left) was dominated by filamentous green algae, Oedogonium spp.(close up photo on lower right). The twin springs of ground water resurgence (each, approximately 0.5 m in diameter and visible as circular ripples on the surface) were surrounded by growing (submerged) and decomposing (floating) filamentous green algae.

The inhabitants of submerged sinkhole ecosystems are largely unknown. The presence of benthic mats in these habitats suggests that gradients of sulfur, temperature, and dissolved salts are sufficiently stable to allow accumulation of microbial biomass. Light penetration to the sediment surface may influence microbial community composition, since the shallow sinkholes contain a majority of green algae (Figure 5), whereas the sinkholes at mid-depth are dominated by Oscillatoria-like organisms that have optimal growth rates under low-light conditions (Figure 4). The origin of the organic-rich sediments is also unclear; the carbon may accumulate through planktonic deposition or may be fixed by the Oscillatorian mat. Light does not reach the sediment surface at the deepest sinkhole (Isolated Sinkhole at 93 m). Rather than photosynthetic microorganisms, this sulfide-rich habitat may host chemosynthetic organisms such as sulfate reducing bacteria and methanogenic Archaea. Where oxygen reaches the sediment surface, methane- and sulfur-oxidizing bacteria may be the dominant community members. While these mats were a conspicuous feature of the lake floor habitat (Figure 3), nothing is yet known of their composition. Similarly unknown is the composition of invertebrate and fish communities inhabiting these submerged sinkhole ecosystems.

2008 Field Season
Aerial view of Middle Island Sinkhole

Figure 6: Aerial view of Middle Island Sinkhole

2008 Field Season Research field work and data collection is planned for June 16-20 and July 30-August 7 at the El Cajon, Blue Hole, and Middle Island Sinkholes. Field work will be conducted at the Isolated Sinkhole from September 2-12, 2008.

Field work will include the collection of groundwater samples to determine nutrient content and age and flow volume using radioisotope analysis. Benthic mat samples will be collected for use in pharmaceutical analysis. An ROV will be used to map physical and chemical parameters. Moored instrumentation will be deployed to obtain time series observations of physical, biological, and chemical parameters. In addition, experiments will be undertaken to provide a better understanding of microbial life processes in these unique groundwater vent ecosystems.

YouTube Videos


S. Ruberg, S. Kendall, B. Biddanda, T. Black, W. Lusardi, Russ Green, T. Casserley, E. Smith, S. Nold, University of Wisconsin, G. Lang, S. Constant (accepted), Observations of the Middle Island Sinkhole in Lake Huron - A Unique Hydrogeologic and Glacial Creation of 400 Million Years, Mar. Technol. Soc. J., Winter 2008/2009.

Biddanda, B. A., D. F. Coleman, T. H. Johengen, S. A. Ruberg, G. A. Meadows, H. W. VanSumeren, R. R. Rediske, and S. T. Kendall. Exploration of a submerged sinkhole ecosystem in Lake Michigan. Ecosystems 9:828-842 (2006).

Ruberg, S., D. Coleman, T. Johengen, G. Meadows, H, VanSumeren, G. Lang, and B. Biddanda (2005), Groundwater plume mapping in a submerged sinkhole in Lake Huron, Mar. Technol. Soc. J., 39: 65–69.