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Deep, dark, wet: Revealing the microbiome of caves

A deep, pit-like sinkhole with a surface opening (allowing sunlight to spill in) housed the most microbial communities.

Spanish speleologist and diver Vicente Fito explores the cave system known as Garra de Jaguar (Jaguar's Claw), near the construction site of Section 5 South of the Mayan Train between the resorts of Playa del Carmen and Tulum
Spanish speleologist and diver Vicente Fito explores the cave system known as Garra de Jaguar (Jaguar's Claw), near the construction site of Section 5 South of the Mayan Train between the resorts of Playa del Carmen and Tulum - Copyright AFP MIGUEL RIOPA
Spanish speleologist and diver Vicente Fito explores the cave system known as Garra de Jaguar (Jaguar's Claw), near the construction site of Section 5 South of the Mayan Train between the resorts of Playa del Carmen and Tulum - Copyright AFP MIGUEL RIOPA

The Yucatán Peninsula’s underwater caves play host diverse microbial communities, according to a new study that set out to map the cave system’s microbiome. The cave system’s microbial composition is distinct from the nearby sea. The network of caves are located near the Caribbean coast in Quintana Roo, Mexico.

To gather the samples necessary for the full evaluation to be made, Northwestern University cave divers collected 78 water samples throughout the complex web of underwater caves. This indicated that the microbial communities vary between cave systems forming distinct “neighbourhoods”.

The Yucatán carbonate aquifer is an extensive area of sinkholes and caves, many of which are complex and located underwater caves. The cave network contains areas of freshwater, seawater and mixtures of both. The habitats range from pitch-black, deep pits with no direct openings to the surface to shallower sinkholes sparkling with sunlight. One of the trickiest to access is the Sac Actun system, and area that includes a distinctive, 60-meter-deep pit.

For each site, the researchers considered the environmental context of each microbial community, including cave type (pit or conduit), cave system, distance from the Caribbean coast, geochemistry and position in the water column. This revealed how the microbial communities formed distinct niches (based on variations between distinct water masses such as salinity, conductivity, temperature, pH, redox potential, ionic composition, as well as dissolved oxygen, organic carbon, and inorganic carbon abundances).

Mexican President Andres Manuel Lopez Obrador's flagship tourist train project in the Yucatan peninsula has met opposition from environmentalists and indigenous communities
Mexican President Andres Manuel Lopez Obrador’s flagship tourist train project in the Yucatan peninsula has met opposition from environmentalists and indigenous communities – Copyright AFP Jewel SAMAD

To collect the samples the divers entered inaccessible places, including deep, dark passageways of unlit waters. This provided the evidence that, in general, the microbial communities within the cave system tend to cluster into well-defined habitats.

In the laboratory, scientists filtered cells out of each sample and analysed its chemistry. Then, the researchers developed a new computational program to perform network analysis on the data set. The resulting networks showed which species tend to live together.

There was one family of bacteria (Comamonadaceae) which was more diverse, having been found in two-thirds of the sampled locales.  These Gram-negative, aquatic organisms have heterotrophic denitrification capability while using organic compounds as electron donors.

A deep, pit-like sinkhole with a surface opening (allowing sunlight to spill in) housed the most microbial communities — segregated into layers of distinct niches throughout the water column.

According to lead researcher Magdalena R. Osburn: “These are incredibly special samples of underground rivers that are particularly difficult to obtain. From those samples, we were able to sequence the genes from microbial populations that live in these sites. This underground river system provides drinking water for millions of people. So, whatever happens with the microbial communities there has the potential to be felt by humans.”

The researchers conclude that the core microbiome could modulate different biogeochemical regimes depending on location.

The research appears in the journal Applied and Environmental Microbiology. The research is titled “Microbial biogeography of the eastern Yucatán carbonate aquifer.”

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Written By

Dr. Tim Sandle is Digital Journal's Editor-at-Large for science news. Tim specializes in science, technology, environmental, business, and health journalism. He is additionally a practising microbiologist; and an author. He is also interested in history, politics and current affairs.

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