A Biology Thesis Explores the Mysterious Microbiome of Crystalline Phytoplankton
“More people should know that diatoms exist and are responsible for a large amount of the photosynthesis that goes on, globally,” says Eli Spiliotopoulos, a biology senior thesising on diatoms and the microbes they host. Diatoms are a kind of phytoplankton, single-celled photosynthetic organisms known for their unique ability to create shells made of biological glass in a mesmerizing variety of crystal patterns. They are also one of the most diverse eukaryotic lineages on earth, with over two hundred thousand species, each sporting a distinct, intricate silica shell. Marine diatoms are incredibly efficient at reaping energy from sunlight. Diatom photosynthesis is responsible for as much as a fifth of the Earth’s biologically available energy, while producing oxygen for one of every five human breaths.
For his thesis, Eli is studying the genetics of bacteria that may form symbiotic relationships with a particular species of diatom, Psammoneis japonica. Diatoms excrete mucus and proteins to create a goopy layer on the outside of their silica shells known as a ficosphere, Eli explained, a nutrient-rich area of minimized turbulence that creates a microhabitat around the diatom where bacteria love to settle, making it a likely site for symbiosis.
While Eli had always wanted to research marine life, it seemed unlikely that he would be able to thesis on it due to Reed’s lack of marine biology resources. “As far as diatoms go, I’ve always been interested in them, because they’re these little glass things that live in the sea,” he said. This interest was unexpectedly fulfilled by avoiding live diatoms or bacteria and seawater all together with the help of collaborators.
Sarah Shaack, a geneticist and Eli’s thesis advisor, received sequence data from collaborators at the Alverson Lab at the University of Arkansas, whose researchers are currently working to sequence the diatom genome. Extracting DNA from diatoms is quite challenging due to their glass shells, called frustrules, which can shatter and destroy the biological material within during the extraction process. During their many attempts, the Alverson Lab researchers observed that there were a few species of bacteria that could always be found in the ficosphere of their diatoms, and when they tried growing the bacteria separately they grew 30% less. Intrigued but focused on sequencing the diatom itself, the researchers sent the genetic data from these potential symbionts to Shaack’s lab. As a result, Eli was able to study a marine system using purely genetic techniques. “It was a great deal,” said Eli. “I’m kind of skipping a lot of messy lab work.”
Eli is using this sequence data to analyze the genetics of the diatom-associated bacteria found by the Alverson Lab. Eli’s project involves assembling fragmented genetic data into whole genes and then comparing these genes to the DNA sequences of related bacteria that have been sequenced and studied before. By analyzing how these sequences match, he can make guesses about which evolutionary groups the diatom-associated bacteria belong to, their metabolisms, and how they might benefit or benefit from the diatoms providing their microhabitat.
Eli is looking for indications that the bacteria found in the Psammoneis japonica diatom’s ficosphere are metabolizing organic substances excreted by the diatom, which would be one piece of evidence supporting the hypothesis that they are in fact participating in a symbiotic relationship. Another potential symbiotic function could be iron sourcing, since diatoms are severely limited by the availability of iron in the ocean and some species of marine bacteria are able to concentrate iron.
These kind of nutritional exchanges are a common basis for symbiotic relationships. Beyond reciprocal nutrition, microbiome symbioses can be identified genetically by the lack of certain bacterial genes known to be necessary for survival. Missing crucial genes implies that the bacteria rely on their host to perform certain functions on their behalf.
The field of microbiome research has exploded in the last decade, primarily due to major advances in genetic sequencing and analysis technologies. Increasingly sophisticated techniques make it possible for researchers to glean information about the physiology, metabolism, and evolutionary relationships of bacteria from genetic sequences alone. This technological leap has allowed researchers to investigate an entire world of previously inaccessible microbial relationships that affect everything from the development of autoimmune disease in humans to the ability of certain squid species to glow in the dark depths of the ocean. Diatoms, poorly understood themselves, can now be studied as hosts with their own set of microbial interactions.
While the initial genetic data was provided at the beginning of Eli’s thesis project, analyzing and making sense of sequence fragments can be a time-intensive and daunting task, especially for organisms that have barely been studied. There is little information out there for Eli to work with or use to validate any findings. “I can’t verify anything I do identify...or to see if I have what I think I have,” he said. Because none of the genes Eli is assembling have names or known functions, their possible roles can only be narrowed down by comparing them to similar sequences in other bacteria that have been studied thoroughly by being grown in labs and investigated with other techniques. “I had like three things to go off of, as far as possible things [diatoms and bacteria] share in the symbiosis,” said Eli. “But it also means I might find something no one has found or described before.”
Cover photo: A bucketful of saltwater could contain up to millions of microscopic diatoms, photosynthetic organisms with intricate glass-like shells called frustules. Photo courtesy of DNA Art.