Microbial Evolution in the Hot Seat

The hot, mineral-rich fluids circulating within hydrothermal vent systems along the seafloor are one of the top contenders for the location of life’s origin. But despite being an enduring host for life, scientists know little about the evolutionary forces that shape the microbes living in these dynamic habitats.

DCO Deep Life Community members Rika Anderson, (Carleton College, USA), Julie Huber (Woods Hole Oceanographic Institute, USA), and Julie Reveillaud (CIRAD, France), and Deep Energy Community members Jill McDermott (University of Toronto, Canada) and Jeffrey Seewald (Woods Hole Oceanographic Institution, USA), investigated how microbes are evolving within these systems. The researchers collected fluids from two adjacent but geochemically distinct hydrothermal vents and sequenced all the DNA in the samples to create a metagenome. Their analysis showed that the two vents were experiencing different evolutionary pressures, due to challenges in their environments that affect how the microbes evolve. They also identified a recent bloom of bacteria, possibly related to acquisition of new genes to avoid viral infections. They report their findings in a new paper in Nature Communications [1].

The researchers compared microbial communities from the Piccard and Von Damm vent systems located on the Mid-Cayman Rise, a deep mid-ocean ridge south of Cuba where two tectonic plates are slowly separating. Piccard is a black smoker with hot, acidic, sulfur-rich water. At 4,950 meters below the ocean, it is one of the deepest vents ever discovered and sits within a magnesium- and iron-rich mantle rock. Von Damm is just 20 kilometers away on a seamount that is 2,350 meters below the ocean’s surface. It releases cooler fluids that carry methane and organic molecules and is located within a different rock type. “The two sites are incredibly different in terms of their carbon chemistry,” said Huber.

Huber and colleagues collected fluids from these vents during research cruises in 2012 and 2013. Later, Anderson, then a fellow with the NASA Astrobiology Institute, extracted DNA from the samples and sequenced their metagenomes. The researchers assembled this “giant jigsaw puzzle of mixed together sequences” into 73 different genomes representing microbial species from both vents. They then examined the variation within the genomes to see how the microbes are changing and evolving.

“By diving into their genomes you can see different evolutionary pressures going on,” said Huber. “It’s really cool to see distinct evolutionary pathways that these organisms have experienced in these two very different environmental habitats.”

Von Damm had a greater diversity of species than Piccard, but there was some overlap between the sites. When researchers looked at the amount of variation within genomes from the same population, they saw that on average, Piccard had more mutations that would result in functional changes, compared to Von Damm. This finding suggests that competition between the microbes at Von Damm is so fierce that microbes that acquire new, less than optimal mutations rapidly die off.

One bacterium from Piccard, which oxidizes sulfur for energy, named Sulfurovum, was experiencing a bloom in its population. These microbes had acquired genes that may be involved in forming their cell wall and membrane. The researchers speculate that these additional genes may help the microbe escape infection from viruses, take up nutrients, or form a sticky, protective mat called a biofilm.

Anderson cautions that, as with any metagenome sequencing project, they can’t be certain that the assembled genomes are accurate re-creations of microbes living inside the vents, or that the cells are actively engaging in the metabolic activities implied by their genes. Only by finding novel ways to culture these microbes, many of which have so far failed to grow in the lab, will scientists be able to study them in greater detail to see how they function.

Undergraduates in Anderson’s lab are currently sequencing the genomes of individual cells collected from these vent fluids. The DCO’s Census of Deep Life funds this work, which Anderson presented at the Third DCO International Science Meeting in St. Andrews, Scotland in March 2017. The researchers also are in the process of analyzing which genes were turned on at the time of sampling, to get a better idea of the biogeochemical processes that are active at the two sites.

“It’s exciting,” said Anderson. “We’re now able to use these new bioinformatics tools to look at microbial communities in a new way. There’s a lot more to be done.”

 

An opening emits hot fluids near the summit of the Von Damm vent spire, in the Mid-Cayman Rise, just south of Cuba. Credit: Image courtesy of NOAA Okeanos Explorer Program, MCR Expedition 2011.
 
A view of the control van, which monitors the movements and data collected by Jason, the remotely operated vehicle (ROV) used to sample the hydrothermal vents. Credit: Jill McDermott

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