Bacalar Microbialites Struggle to Survive the Degradation of their Habitat

aerial view of the habitat of microbialites in Mexico
Pie de Página
Quintana Roo, Mexico

Bacalar Microbialites Struggle to Survive the Degradation of their Habitat

In mining, a cruel but efficient warning method was invented: when the workers of the mines descended underground, they carried a caged canary with them. The little bird would sing until it suffocated when the toxic gases, imperceptible to the human sense of smell, flooded the space. That last song was the signal for evacuation. This method was called the "sentinel model" and consists of using a living organism to assess the health of the environment.

More recently, a Mexican scientist has proposed microbialites — one of the oldest forms of life on the planet — as one of the indicators of the health of its habitat, Laguna Bacalar, and the surrounding ecosystem in the southern Mexican Caribbean. The premise is simple, explains Alfredo Yañez Montalvo, a researcher at the Department of Biodiversity Conservation of El Colegio de la Frontera Sur (Ecosur) and the author of the proposal. If this bacterial community called microbialites could emit sounds it would be howling, he says. Microbialites are degrading, being suffocated by the contamination of the water in which they live, and because the surrounding environment is deteriorating due to massive tourism, deforestation, industrial agriculture, unregulated garbage dumps, and irregular sewage discharges. "They are telling us that something bad is happening," warns Montalvo.

What are microbialites?

Popularly known as stromatolites, microbialites are millenary organisms that have existed for 3,500 years. At first glance, they look like simple stones, but when observed through a microscope they appear to be a complex community of unicellular organisms — bacteria — that interact with each other. Over time, they form solid, vertical cylindrical structures that grow just one centimeter per year until they become a reef barrier of no more than 20 meters high, explains Alfredo in his recently published doctoral thesis entitled "Bioinspection of microbialites in two karst systems in the south of Quintana Roo."

The oldest record of these first oxygenators on the planet dates from 3.7 billion years ago; in Bacalar, from 9,500 years ago, according to "Tarjeta de reporte Laguna de Bacalar", a document published in 2021 by scientists from the Yucatan Peninsula.

Microbialites grow on the perimeter of Laguna Bacalar, in the wetland zone / Credit: Juan Pablo Ampudia.

Microbialites are the Earth's greatest survivors and even allies against climate change, as they sequester large volumes of carbon dioxide through photosynthesis, just like plants. They exist only in a few regions in the world such as Australia, Bahamas, the Persian Gulf and Mexico, more specifically, in Bacalar, a tourist destination located in the extreme south of the state of Quintana Roo, increasingly coveted for its location on the shore of the Bacalar Lagoon, known for its scenic beauty and its clear water in multiple shades of blue. It is precisely in this lagoon where the most extensive reef barrier of micriobialites in the world is located, approximately 10 kilometers long... and it is now at risk. “These peculiar giants feel at ease when no one bothers them and when the water where they live is clean and crystalline, but lately, the balance has been broken”, altered by tourist activities and unsustainable urban growth, warns the young microbiology specialist.

This imbalance has caused the microbialites located in the center and south of the lagoon to degrade — losing their structure in ways that can be observed by microscopic analysis — mostly because they are close to the city of Bacalar, which has almost 41,000 inhabitants and receives more than 200,000 tourists per year, according to the National Institute of Statistics and Geography (Inegi, 2020).

To verify this, Montalvo, together with colleagues from Ecosur, took water samples and fragments of these organisms at 15 different points in the lagoon between 2019 and 2020.

"We went in inflatable kayaks to different points. We would leave from resorts, inflate the kayaks, go to the sites, take the samples, return, deflate the kayaks and go to Ecosur to leave the material," he recalls. 

close up shot of microbialite
Microbialites emerge from the sediment and grow just above the surface / Credit: Juan Pablo Ampudia.

Through the analysis of the fragments collected, Alfredo was able to identify each of the bacteria that make up a microbialite and found that those in the northern zone of the lagoon —which is unpopulated— are more diverse than those located in the center and south, where tourist activities are concentrated. While in some there are more than 100 microbes per unit, in others, there are only 20. These are not only degrading but also are filling up with enterobacteria, pseudomonas, aeromonas, and steromonas; bacteria that reach the lagoon due to the irregular discharge of wastewater from the tourist city.

"Microbialites become a kind of sponge: they absorb everything that happens in the water. If we get into the water, the dead cells, those who urinate there, all the waste from the garbage dump, agriculture, drainage, they will absorb them and that is what we are seeing, that they are degrading," says Montalvo.

"And what does degradation mean, that some have fewer microbes? Think of a forest where there are many trees. Each tree belongs to a different species. The more diverse the forest is, the better its ecological functions are. When you lose species of trees in the forest, either by deforestation or disease or whatever, diversity is lost and there is, eventually, ecological degradation. In other words, the functions of the forest are lost; it´s no longer a refuge for animals or a space where they can reproduce; we no longer have shade, birds, all these functions that can be attributed to diversity," he explains.

Thus, the microbialites in the center and south of the lagoon are losing diversity, and with it, their ecological functions. The environmental services they provide, such as oxygen and carbon sequestration, filtration and recycling of nutrients, habitat for other species such as the chivita snail, torito and picudito fish, and mangroves, are diminishing. It´s precisely because of the sensitivity of microbialites to environmental perturbations that the scientist proposes they be considered bioindicators or sentinel models. They offer a picture of the loss of the health of Laguna Bacalar. "And we have to do something about it," Montalvo urges.

tourists in the lagoon
Tourists often climb on the microbial reefs, which harms them / Credit: Juan Pablo Ampudia.

Sewage discharge

One of the main enemies for diversity and survival of the microbialites are the contaminants that are contributed to the Bacalar Lagoon by the irregular discharge of wastewater, reiterates Alfredo Yañez Montalvo. According to data from the Municipal Ecology Department, only 200 of the more than 14,000 homes, hostels and shop stores are connected to the sewage system: less than 1.5 percent use it. The rest have septic tanks or simply holes in the backyard. In these cases, the urine and feces generated gradually infiltrate into the groundwater that feeds the Bacalar Lagoon, the habitat of microbialites. Infiltration of water is a natural process in the region, due to the type of soil, karstic, porous, through which rainwater or leachates, liquids produced as a result of contact with solid waste, easily pass, says Alejandro López Tamayo, hydrogeologist and director of the organization Centinelas del Agua, a non-profit civil association focused on preserving and protecting the aquifer of the Yucatan Peninsula.

This is one of the main sources of nutrients to Laguna Bacalar and the subterranean rivers that cause huge damage to the ecosystem and microbialites, insists Montalvo. The scarce drainage infrastructure is not only a matter of "customs" and lack of political will but mainly because of the budget and technical difficulties, says Tamayo. The Yucatan peninsula is one of the flattest surfaces in the country except for Bacalar, where the terrain is somewhat rugged, with high and low points, with uphill and downhill roads, mostly because it is located on a geological fault originating millions of years ago. That´s why the gravity drainage system, used in the rest of the state and many other places, doesn't work here. What is needed, Tamayo explains, is a vacuum system or a re-pumping system. Romel Pacheco, head of the Ecology Directorate of the municipality from 2018 to 2021, acknowledged that there is not enough budget to pay for a system like that.

Threats to its ecosystem

The water quality of Laguna Bacalar, the site with the highest presence of microbialites in the world, is at its worst. And three recent scientific studies prove it. The first is Montalvo's. The water samples he took for his thesis work showed the presence of ammonium and nitrates: nutrients that change the chemical composition of the water and worsen its quality. In the center and south of the lagoon, where tourist activities are concentrated, he points out, is where the highest levels of these substances were recorded, coming from sewage, but also from the clandestine dumps that proliferate around it.

The second one, still unpublished, but shared for this report, is by Teresa Álvarez Legorreta, also from Ecosur. Teresa is a researcher with decades of experience in the study of water quality in Laguna Bacalar, with more than a decade of experience in the subject.  She confirms what Montalvo said: deterioration of microbialites is a symptom of how bad the water body is. Teresa has been sampling water in the lagoon since 2010, but it was not until 2017 when she began to do it more systematically, at 25 geographic points in the lagoon, in three different climatic seasons, and including sediment samples too.  Nitrogen, phosphorus, organochlorine pesticides, toxic heavy metals such as mercury and cadmium, and others such as lead, copper, zinc, as well as agrochemicals and hydrocarbons, are some of the substances found in the samples collected in the last five years for research, which were used to evaluate the impacts on aquatic organisms, and of which it is possible to affirm: they are a lethal cocktail for microbialites. "It can be seen that water quality has decreased, especially in the center and south of Laguna Bacalar. This is important to point out: where the greatest tourist activities in the area are, the impacts have been seen to be greater," says the environmental microbiology scholar in an interview.

These elements come, Legorreta confirms, from the irregular dumping of wastewater, clandestine dumps, agribusiness, and activities related to mass tourism: from the excessive, unregulated, and unsustainable growth of Bacalar. In the last decade, the hotel infrastructure in the municipality has grown 275% (according to data from the Federal Ministry of Tourism), housing has grown 37% (Inegi) and tourism has increased exponentially, to the extent that in 2019 Bacalar received 213,000 travelers (Ministry of Tourism of Quintana Roo); all without an Urban Development Program that dictates sustainable growth, although that will be discussed later.

tourists at a jetty
Mass tourism is one of the threats to the lagoon ecosystem due to the direct damage it causes to microbialites, also because people stand on these organisms or because boats run aground on them, warn specialists / Credit: Juan Pablo Ampudia.

Legorreta says she is now concerned about the northern part of the lagoon due to the impact of the tropical storm "Cristobal”. In June 2020, the before mentioned storm discharged large volumes of water over the Yucatan Peninsula, especially over Campeche, from where the runoffs, which were not only loaded with rainwater but also with loose soil from deforestation, as well as organic matter, garbage, agrochemicals and other toxic substances accumulated over time, drained until they reached the coast of Quintana Roo and the Bacalar Lagoon, especially in the northern.

On June 5, "Cristobal" left Mexican territory, but left dozens of cities and towns flooded, as well as a Bacalar Lagoon with the worst appearance in decades as the various shades of blue had faded to a dirty and uniform brown. Montalvo compared the water samples from the northern zone that he took in 2020, after the hydrometeorological phenomenon, with those he took 10 years ago at the same site. And the results were “worrisome". "During 2010 to 2020 the organic enrichment with nutrients (dissolved inorganic nitrogen and dissolved inorganic phosphorus) occurred mainly in the northern part of the lagoon, growing by 70%," he explained in an email. The impacts this will have on the northern stromatolites are still unknown.

Given the lack of action by the authorities, a small group of citizens — two businessmen, a tour operator and a photographer — formed an organization they called "Guardians of the Lagoon." In the last two years, David Martínez has dedicated himself to reforesting mangroves and carrying out garbage clean-up days in the lagoon, while Martha Mattiello, another group member, has focused on meetings with the Secretary of the Navy and the Administration Integral Port of Quintana Roo (Apiqroo) to regulate recreational activities such as boat navigation, in addition to urging other businessmen to carry out sustainable tourism.

center and south of the lagoon
The center and south of the lagoon, where tourist activities are concentrated, are the most polluted areas / Credit: Juan Pablo Ampudia.

The third study on the quality of the lagoon water is by the organization "Agua Clara Ciudadanos por Bacalar", which carries out constant monitoring to detect the presence of E. coli, a bacterium that, if ingested, can cause stomach illnesses. Last March 2, says Melina Maravilla, director of the organization, the sampling showed that the lagoon water was "very contaminated". "Not suitable for recreational use. Surface water with strong bacteriological contamination," they noted in the report. Despite this, tourists continue to swim in it.

With these studies, the document "Report Card of Laguna Bacalar" was elaborated at the end of 2021, in which it was concluded that in the central and southern zone the quality of the water has worsened; chemical composition has changed due to the excess of nutrients and microalgae. The increase in nutrients causes a group of bacteria to benefit and displace others. The vacuum left by the displaced microbes is filled by multicellular organisms such as algae and mussels, which are growing rapidly and gradually colonizing the site. If the trend continues,Montalvo predicts, microbialites will continue to degrade, lose structure, fossilize, and become covered with algae and mussels. This is how this ecosystem forged over millennia is changing in the "blink of an eye."

Clandestine dumps

In 2019 the Bacalar municipal landfill was closed by the ejidatarios, communal land owners of Aarón Merino, to exert political pressure on the mayor, Alexander Zetina, from whom they demanded payments for land, according to reports published by local media. During the first days of the disagreement between the municipal authorities and the ejidatarios, none of the trucks in the area collected the garbage. So, residents began to leave bags in the corners, in the middle of the street, among the vegetation, etc. The now ex-mayor had to work with his peer from the neighboring municipality of Othón P. Blanco to obtain temporary permission to deposit the waste at the final disposal site in the town of Mahahual, some 100 kilometers away.

Since then, two clandestine garbage dumps were established and represent another source of contamination for the Bacalar Lagoon and microbialites, as the leachates from the waste infiltrate the subsoil, said Romel Pacheco, head of the Ecology Directorate of the municipality from 2018 to 2021.

bags of trash
Less than two kilometers from the center of Bacalar, in a jungle zone, is one of the largest clandestine dumps in the city / Credit: Juan Pablo Ampudia.

On November 28, 2019, in the framework of the First Cultural Meeting of the Southern Border, held in Bacalar, a group of local residents exposed the garbage collection problem to the attendees and proposed the creation of a Citizen Committee to try to solve it. A week later, says Marco Jericó, activist and one of the main promoters of the initiative, the first ordinary session of the Bacalar Waste Committee was already being held as an inter-sectoral body. The response was overall positive. Civil organizations joined and received advice from two consulting firms, Organi-K and Eukaryota. By January there were already seven thematic subcommittees: separation, composting, special handling, garbage burning, and public health, sanitary landfill, regulations and legislation, and communication.

In short, the group concluded a diagnosis: 40 tons of garbage are generated daily in the city, according to the document. They then developed an Integrated Solid Waste Management Program and selected a neighborhood as a pilot. Mayor Zetina attended the presentation of the program to make a speech and take the official photo, but the plan was never implemented. Neither, then nor now, with the new municipal administration. Meanwhile, the leachates from the open dumps continue to infiltrate the subterranean rivers that flow into the Bacalar Lagoon.


According to the study "Analysis of deforestation processes in Quintana Roo 2003-2018", published in 2021 by the Mexican Civil Council for Sustainable Forestry (CCMSS), Bacalar is the municipality in the state with the most rapid rate of  deforestation in communal lands (ejidos) in the last 15 years. Salamanca, a community founded 20 years ago by Mennonites — a religious group originating in the Netherlands — represents 15.2% of the total number of hectares deforested on communal lands in the state. Currently, the Mennonites extend over an area of 50 square kilometers, which they have deforested without permits from the Secretary of Environment and Natural Resources (Semarnat).

land cleared for agriculture
Deforestation at the hands of the Mennonites extends over 50 square kilometers, where there are now crops / Credit: Juan Pablo Ampudia.

Mennonites in Salamanca grow papaya, watermelon, tomatoes, and beans, that are sold to local businesses. They also harvest soybeans, corn, and sorghum on a large scale. In total, they cultivate four thousand hectares during two or three seasons a year, says Johan Elías Wall, the local governor. That means hundreds of thousands of kilos and liters of agrochemicals poured into the soil. Johan calculates that they use about 300 kilos of DAP 18-46-0 fertilizer per hectare cultivated in each of the three planting cycles, a chemical formula composed of phospho-nitrate, nitro phosphate, stabilized ammonium nitrate, and nitric salt; as well as 100 kilos of Urea fertilizer, and also insecticides to prevent or eliminate pests. To prepare the land and knock down the acahuales — the vegetation covering the fields after mowing or harvesting — they spray glyphosate, an herbicide whose use has been banned in Austria, Colombia, and, as of December 31, 2020, Mexico, due to its harmful effects on health. Spraying chemicals on the porous soil of the Yucatan Peninsula is a problem because of its easy infiltration.

a farmer spraying pesticide
Mennonites spray agrochemicals to prevent pests in the fields, which then infiltrate into the rivers that feed Laguna Bacalar / Credit: Juan Pablo Ampudia.

A recent study by the Amigos de Sian Ka'an, a conservationist civil society organization, indicates that water below Salamanca and also from irrigation runoff from extensive sugar fields in the area, runs into Laguna Bacalar, where thousands of tourists a year bask; home to microbialites.

Colossal structures that are not just stones

Because microbialites are some of the least “sexy” organisms on the planet, no matter how hard Alfredo Yañez Montalvo has tried to publicize their ecological importance, people keep referring to them as "those rocks over there.  Everyone calls them 'rocks,'" he complains. But people are not to blame, because until a couple of years ago, the only sign along the more than 40 kilometers of the lagoon that explained that these are not simple stones, but important organisms for the environment, was made by a local resident concerned about their deterioration.

bacterial formations resemble rocks
The bacterial formations resemble the limestone rock of the region / Credit: Juan Pablo Ampudia.

Although now there are more warning signs, it is not surprising to see tourists riding on them or on stranded boats.

In earlier years, when little was known about their importance, it was common practice to build docks, and fences and place various structures on top of the microbialites.

However, stepping on them or damaging them is serious because it is precisely in the surface layer where the microbes that form them are alive, explains Montalvo.

Microbialites, it is worth noting, are not protected by any legal ordinance, and are not even included in the Mexican Official Norm 059-Semarnat, which lists threatened species or species at risk of extinction. Alfredo has tried to get the authorities to include microbialites on the list, but without success. In fact, he believes that it is one of the ways to protect them and stop their deterioration.

This NOM is mandatory throughout the country and its information helps to develop plans and programs for the conservation of the listed species and for the proper management of natural Resources.

Elvira Carvajal, from the Institute of Biodiversity and Protected Natural Areas of Quintana Roo, has recognized that a legal projection for these organisms is lacking. “It is necessary to update the environmental legislation. First, we must make a good review of what we have at the federal and state levels and, if required, make new adjustments that allow us to keep them healthy for longer," she said.

In the past, there have been various efforts to protect the Laguna de Bacalar, home of the microbialites, and the territory that surrounds it, but without any success. In 2014, the National Autonomous University of Mexico (UNAM) and Ecosur proposed to register it as a RAMSAR, a site of international importance, protected by the Convention on Wetlands, but this caused discontent among the hotel and tourism sectors, so it did not move forward. 

Ricardo Hernández Ruiz produced this story with a grant from EJN’s Biodiversity Media Initiative. It was first published in Spanish on 29 May 2022 in Pie De Página. It has been translated to English and lightly edited for length and clarity. The Biodiversity Media Initiative is supported by Arcadia — a charitable fund of Peter Baldwin and Lisbet Rausing.

Banner image: Bacalar Lagoon is 40 kilometers long, of which 10 kilometers are home to the microbialites / Credit: Juan Pablo Ampudia.

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