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Yucatán Peninsula’s hidden underground life tracks changes at the surface

  • Scientists from Northwestern University in the U.S. led a series of underwater expeditions collecting water samples from the deep web of caves and sinkholes in the Yucatán Peninsula.
  • The southeastern region of Mexico is crisscrossed by numerous flooded and interconnected tunnels, functioning as subterranean rivers — crucial arteries that maintain ecosystems and support millions of people, and connecting directly to the sea.
  • Any disruptions to the microbial communities in these waters could have significant consequences for both humans and marine ecosystems.
  • This research is crucial for assessing the potential environmental impacts of large-scale agriculture or major projects like the building of the Tren Maya railway line.

Beneath the Yucatán Peninsula, in southeastern region of Mexico, lies a vast network of flooded tunnels and caves. These intricate and shadowy labyrinths serve as subterranean rivers, constituting the sole source of drinking water for millions of people. In August 2019, a team of scientists and divers ventured into these passages, driven by the question of what kind of microscopic life thrives under these complex conditions.

Armed with diving suits, specialized tools, and an innovative invention comprising a tube filled with glass containers, the team, led by scientists from Northwestern University in the U.S., successfully obtained water samples to analyze in a lab. The results proved to be astonishing: The research uncovered a vast diversity of microorganisms, enabling the scientists to develop the most comprehensive map to date of the microbial communities inhabiting these waters.

In a 2023 study published in Applied and Environmental Microbiology, led by Northwestern University geobiologist Magdalena R. Osburn, experts emphasized the delicate and indispensable nature of this aquifer system to the region. Any adverse impacts on the microbial communities within these waters, the noted, have the potential to affect the people living at the surface significantly.

The study area, located in the eastern region of the Yucatán Peninsula, is intersected by a multitude of flooded and interconnected tunnels, functioning as underground rivers. These waterways are the sole source of drinking water available throughout the entire region. The diver in the picture is Vicent Rouquette Cathala. Image courtesy of Natalie Gibb.

Patricia Beddows, a hydrogeologist and planetary science researcher at Northwestern, who spearheaded the cave-diving expeditions and co-authored the study, emphasized the importance of conducting this type of research to gauge the impact of amid environmental changes such as the construction of large-scale projects or the effects of climate change.

“Understanding the microbial biogeography, which entails studying the distribution of microorganisms in space and time within the aquifer, holds significant relevance not only for scientific understanding but also for conservation,” Beddows said. “We need these studies to say that there was a change, that the microbial population did suffer losses or that it did change.”

The findings of this research shed light on the vulnerability of microbial communities at a critical time. Environmental organizations such as Sélvame del Tren and SOS Cenotes have been vocal on social media since late 2023 about the environmental impact of construction of the Tren Maya railway line. This tourism project, crossing the Maya Jungle and promoted by the government of Mexico, is already having repercussions on the underground aquifer of the Yucatán Peninsula.

Specialists from these organizations have rigorously documented the environmental impact through videos and photographs, including underwater footage. Their findings reveal that massive steel pilings have penetrated into the underground caves and are now rusting underwater, leading to muddying and contamination of the water. Cement spills are also visible on the rock formations. These interventions in the karst ecosystem, a direct result of the foundation work for the rail megaproject, are predicted to have detrimental effects on groundwater quality, which could lead to severe impacts on the associated ecosystems, according to the scientists.

Image of an underwater immersion where divers from the Sélvame del Tren collective show one of the steel pilings that have pierced the aquifer and are corroding. Image by Sélvame del Tren via Instagram.

The findings

The Yucatán Peninsula sits on a limestone foundation that emerged from the seabed millions of years ago and today spans about 165,000 square kilometers (63,700 square miles). As the bedrock has dissolved over time, it forms what geologists refer to as a karst system. This system is distinguished by its high degree of water impermeability and the abundance of caves and sinkholes, known as cenotes. The infiltration of water into the subsoil gives rise to the aquifer system of the Yucatán Peninsula, renowned as one of the largest and most remarkable karst aquifers on the planet.

The research conducted by the Northwestern University scientists describes the vast aquifer as comprising freshwater, seawater, and a blend of both. This complex system encompasses various regions, ranging from deep and obscure wells without openings to the surface, to shallower cenotes where the sunlight reaches.

The Holaktun cenote, or sinkhole, in Chichén Itzá, Yucatán, Mexico. Image courtesy of ILCP/Amigos de Sian Ka’an.

Despite the existence of a diverse microbiome within this ecosystem, there’s been limited research in this field. While previous studies have taken water and microbial samples from caves and cenote entrances that were more accessible, the Northwestern team succeeded in reaching deeper and darker water passages devoid of light. Their aim was to understand the survival mechanisms of organisms within this distinctive underwater realm.

“Despite the existence of previous research focused on various areas, what was lacking was a comprehensive understanding of microbial life within the aquifer on a regional scale,” Beddows said. She added the research team aimed to fill this gap by providing fundamental insights into the microbial ecosystem of the Riviera Maya region, running from the southern region of Playa del Carmen to Tulum.

For their the study, the divers gathered 78 water samples from 12 distinct locations within the cave system near the Caribbean coast of Quintana Roo state. It was a challenging process that included collecting water from a well 60 meters (200 feet) deep. The researchers also meticulously considered the environmental context of each microbial community at every site. This included factors such as the type of cave, well or passage; the cave system’s characteristics; the distance from the Caribbean shore; the geochemical properties present; and the position within the water cycle.

The scientists and divers collaborated to devise equipment suitable for transporting sterile glass bottles safely into and out of the flooded caves for their research. Divers Nick Tkachenko and Alex Fraser. Image courtesy of Natalie Gibb.

The intricate nature of working in spaces like these required the development of specialized equipment by the divers and researchers. This equipment was designed to transport and use glass bottles safely, ensuring they remained free from contamination until reaching the sampling zones. A single dive could collect up to six samples.

Initially, the divers partially filled the sampling bottles with cenote water to minimize their buoyancy. Upon reaching the desired sampling depth, they opened the bottles, inverted them, and emptied them using compressed air. They then filled the bottles with the underground water for collection.

“We had to build pipes for transporting the six bottles. We installed lids both over and under so that we could retrieve the newest bottle from below and, once filled, position it above, similar to the mechanism of mechanical pencils where you extract the lead from below and insert it from above,” Beddows said.

After exiting the caves, the researchers worked at a local dive workshop, known as Under the Jungle. Typically used to teach diving techniques and promoting diving for scientific purposes, it was repurposed by the researchers as a temporary laboratory. Here, they conducted the initial water filtering to analyze its chemical composition. The research then continued at the labs at Northwestern University to identify the microbial communities through DNA sequencing.

Formations on the inside of the underground caves system in the Yucatán Peninsula. Image courtesy of ILCP/Amigos de Sian Ka’an.

“The data obtained from this analysis, such as genetic material, are highly complex, requiring two or three years of continuous analysis,” said Matthew Selensky, a geobiologist at Northwestern and co-author of the study. Selensky and his colleagues examined the genetic material of the microbial communities meticulously and devised a new computer program to analyze the networks in the data set. These networks revealed the species likely to coexist within the ecosystem.

“The type of cave and its entrance play a crucial role in shaping the composition of microbial communities,” Selensky said. “For instance, cenotes have the capacity to trap surface materials such as leaves or plant debris, which serve as food for microbial communities. These communities exhibit metabolic capabilities focused on sulfur and organic carbon. In contrast, in areas of the aquifer located in dark caves with water but no entrance, there isn’t much material that can get in and the microbial communities are very different.”

Through the analysis of samples and genetic sequencing of the microbial populations, scientists identified diverse microorganism systems organized into distinct patterns, likened to “the typical high school canteen.” Within the cave system, microbial communities tend to aggregate into well-defined groups.

In the makeshift lab established within Under the Jungle, a dive workshop, the research team processed the samples. Matthew Selensky employed a vacuum system powered by a bicycle pump to draw water through sterile filters. This process collected microorganisms on the filters, which were then preserved for subsequent genetic sequencing. Image courtesy of Natalie Gibb.

The Comamonadaceae family of bacteria identified in the analysis exhibited highly social behavior, appearing in nearly two-thirds of these “high school canteen tables.” The researchers’ findings indicate that Comamonadaceae bacteria serve as the ecological cornerstone of the largest community in underground waters.

Understanding all this information, Selensky said, is the basis for understanding issues like human disturbances in these ecosystems as a result of activities such as agribusiness, urbanization, wastewater discharge, tourism and megaprojects.

“Agriculture, for example, introduces significant quantities of nitrogen and other elements into the water that is an important source for millions of people,” Selensky said. “The concern is that these development projects may disrupt the ecology of these caves. We hope that future scientists will be able to analyze our data and compare it with the various impacts once agriculture expands in the region.”

Advanced buoyancy skills are essential for extracting water samples. The diving team used an air hose to empty the sterile bottle, which was then inverted and filled with sample water, while recording the specific depth using wrist-mounted depth gauges. Pictured is diver Vlada Dekina. Image courtesy of Natalie Gibb.

What risks does the aquifer face?

Amigos de Sian Ka’an, an organization that participated in the study, agreed on the importance of the findings for future research into and conservation of the aquifer. Gonzalo Merediz-Alonso, director of the organization and a co-author of the study, said threats of contamination to the groundwater in the Yucatán abound, with cumulative impacts that were previously unknown.

“We will probably need to continue studying this in the future, but we have the hypothesis that certain microbial communities are vulnerable under specific conditions. When exposed to changes in water quality due to human activity, they may be impacted,” said Merediz-Alonso, who is also the president of the Yucatán Peninsula Basin Council. “We do not yet understand the potential implications this could have on the entire trophic network of underground systems.”

He noted that the coastal area of Quintana Roo state boasts an immense number of caves. “Studies conducted by Amigos de Sian Ka’an in collaboration with the Geological Survey of Austria have revealed that there are more than twice the number of caves previously mapped by divers. Importantly, all of these caves, directly or indirectly, lead to the sea.

“These caves and underground rivers offer a more direct pathway for pollution sources to reach the sea,” Merediz-Alonso added. “For instance, in the event of a wastewater discharge, the water reaches the cave more rapidly and flows unhindered to the sea, facilitating contamination of the reef, seagrass beds, and other marine ecosystems.”

This contaminated water could then impact crustaceans, fish and other sea life, he said. And since pollution in Quintana Roo is mainly due to wastewater and agricultural runoff, much of it is laden with organic matter, which means more nutrients for oxygen-hogging algae.

“The nutrient-rich water reaching the reef promotes the growth of algae, which compete with coral and its health,” Merediz-Alonso said. “These algae can also compete with seagrass beds, gradually altering the ecosystem while the cave and cenote waters, when they receive nutrients, see their once crystal-clear water become greenish, filled with sludge, opaque and turbid.”

The halocline is a distinct layer within the water column where salinity undergoes rapid changes with depth. In this region, freshwater from rainfall overlays saltwater. The halocline is visually striking, characterized by undulations that reveal water flow. It also serves as a prominent boundary between distinguishable microbiomes present above and below. Diver Alex Fraser. Image courtesy of Natalie Gibb.

Beddows echoed this observation, saying that megaprojects like the massive pig farms in Yucatán state and the construction of the Tren Maya in Quintana Roo have impacts that extend beyond their immediate vicinity, propagated by the vast network of underground rivers.

“The Mayan Jungle is incredibly fragile and exists within a very delicate ecological balance. As a hydrogeologist and environmental scientist, the changes that concern me the most are not necessarily confined to specific locations,” Beddows said. “When I use fluorescent ink to observe how quickly contaminated water travels from one point to another, we observe that the water flows through underground rivers at speeds of 1 or 2 kilometers [0.6-1.2 miles] per day. This implies that if an incident occurs 5 kilometers [3 mi] from the coast, it could reach the reef within two or three days.”

Merediz-Alonso said humans have a duty of care to the planet’s other living organisms for the impacts that our activities have on them.

“We need to care about the microbiota because it reflects our concern for water, the environment and biodiversity as a whole,” he said. “This scientific article serves as an initial exploration into microbial biogeography, providing insights to further our work on water quality. It serves as a wake-up call to direct our focus toward this invisible world and begin addressing its impacts.”

Banner image: Advanced buoyancy skills are necessary for extracting water samples. The divers’ team utilized an air hose to fully evacuate the sterile bottle, which was then inverted and filled with the sample water, while the specific depth was recorded using wrist-mounted depth gauges. Pictured is diver Vlada Dekina. Image courtesy of Natalie Gibb.

This story was reported by Mongabay’s Latam team and first published here on our Latam site on March 7, 2024.

Related audio from Mongabay’s podcast: A discussion of the ecological and human impacts of the Maya Train with staff writer Max Radwin, listen here:

All aboard Tren Maya: Here’s what we found riding Mexico’s controversial railway

In Mexico, Xalapa’s chronic water scarcity reflects a deepening national crisis

Osburn, M. R., Selensky, M. J., Beddows, P. A., Jacobson, A., DeFranco, K., & Merediz-Alonso, G. (2023). Microbial biogeography of the eastern Yucatán carbonate aquifer. Applied and Environmental Microbiology, 89(11), e01682-23. doi:10.1128/aem.01682-23

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