Deccan Traps Microbes Get By with a Little Help from Their Friends

For the first time, scientists have drilled deep into the Deccan Traps, a giant, 65-million-year-old lava flow in Western India, and the 2.5 billion-year-old rock beneath. DCO scientists from Indian Institute of Technology Kharagpur, India have sequenced and analyzed the DNA in these layers to understand how communities of microbes have evolved to survive in this isolated environment.

In 1964, the Indian government completed a dam on the Koyna River to create a reservoir for a hydroelectric power plant in Maharashtra in western India. This dam lies within the Deccan Traps, an area covered with layers and layers of lava from massive volcanic eruptions nearly 65 million years ago, which now consists of an area of around 500,000 square kilometers. Three years after completion of the dam, a magnitude 6.3 earthquake rocked the area, followed by several hundred smaller quakes. To investigate the reservoir-triggered seismicity, the Indian government began a scientific deep drilling project at the site. 

DCO Deep Life Community members Avishek Dutta, Pinaki Sar (both at Indian Institute of Technology Kharagpur, India), and colleagues were on hand during the exploratory drilling to collect fresh cores samples from down to 1500 meters. Now, for the first time, they have sequenced the DNA of microbes living in the basalt layers of the Deccan Traps and the underlying 2.5-billion-year-old Archean basement rock. The researchers discovered that the microbes form interconnected networks to survive in this extreme and nutrient-limited environment, creating communities that are specifically adapted to the geochemistry of the host rock. The researchers report their findings in a new paper in Scientific Reports [1].

“This is the first investigation of continental crusts in this region, which has experienced massive volcanism and other geologic disturbance,” said Sar. “We were fortunate that geomicrobiologists like us were given the opportunity to explore the rocks directly as they were coming out from the interior of Earth’s crust.” 

Dutta and Sar
Avishek Dutta and Pinaki Sar stand at the drilling site, with the Deccan Traps in the background. Credit: Pinaki Sar

The researchers placed the fresh rocks directly into an oxygen-free chamber and then froze the samples. Back in the lab, they removed any outside parts contaminated by drilling fluids. They extracted DNA from the powdered rock, and sequenced a subset of the samples through the DCO Census of Deep Life. Sar’s group even developed their own sequencing facilities and bioinformatics pipeline to process and analyze the resulting data. The bioinformatics pipeline may soon be publicly available for use by other scientists.

The researchers compared the communities of microbes living in the basalt from the Deccan Traps, the underlying basement rock, and the thin transition zone between them. “We have some interesting observations,” said Sar. “The nature of microorganisms are not that much different between the basalt and the granite. But what is varying is the microbial networks – how different species interact with each other.” 

Based on the genes that the researchers detected, microbes use the limited amounts of nitrite, sulfur, and hydrogen available, coupled with some fermentation of organic compounds and methane production. The microbes likely are picking up and recycling each other’s metabolites to survive in these isolated environments, with slightly different communities having evolved in basalt and basement rock.

These ancient rocks are low in carbon, but researchers were surprised to see that bicarbonate (HCO3-) likely is a major carbon source for microbes in the Deccan basalts. “In most of the other subsurface systems, carbon dioxide is the prevalent carbon input for microbes, which tailors the subsurface community structure in a different fashion,” said Dutta. The analyses showed a higher abundance of genes related to metabolic pathways for using bicarbonate. 

Deccan drilling
India’s Ministry of Earth Sciences drilled 3000-meter boreholes into the Koyna-Warna region to investigate earthquakes associated with the building of a dam on the Koyna river in the 1960s. Credit: Pinaki Sar

It is not yet clear how these different communities have evolved. The basalt rock from the traps is very dense and has few fractures and pores, but it is possible that at some point during its 65-million-year history, fractures in the rock allowed fluids to travel through the area, introducing new microbes, distributing nutrients, and impacting the current community makeup. The intense pressure of being buried under so many layers of rocks, as well temperatures that range from around 26 degrees Celsius at the surface to 53 degrees Celsius at 1500 meters deep, also impacts the types of organisms that can survive in this extreme environment. 

“In spite of the severe scarcity of nutrients and environmental extremes, how these microorganisms managed to survive and populate the entire underworld of the Deccan traps and continental crust remains an open question,” said Sar.

The researchers also are growing enrichment cultures of the deep microbes under high pressure with DCO Deep Life Scientific Steering Committee member Douglas Bartlett at Scripps Institution of Oceanography. The researchers plan to study the physiology of these organisms in more detail, to see if their behavior matches the predictions based on the DNA analyses.

“Evolution and adaptation of life in these dark, nutrient-poor provinces of the Deccan subsurface may be an important clue to studying life in extraterrestrial bodies, like Mars, which have a similar basaltic surface,” said Dutta.  

In 2016, Dutta attended the DCO Summer School in Yellowstone National Park, USA, where he enjoyed meeting fellow graduate students and postdocs and leaders in the field of deep carbon research. “The exposure and opportunities that DCO provides to early career scientists are unmatched,” said Dutta.

Currently, the group is expanding their geomicrobiological investigations by sequencing microbial DNA and growing enrichments of cells from basement granitic rocks obtained through a recent 3000-meter-deep pilot well drilled in the Koyna region; a project of the Ministry of Earth Sciences, Government of India in collaboration with the International Continental Scientific Drilling Program
 

Deccan core
Avishek Dutta holds a piece of core from the Deccan Traps basalt. Credit: Pinaki Sar

 

Main image: Avishek Dutta takes physical and chemical measurements of the drilling fluids during the drilling process. Credit: Pinaki Sar

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