By Jennifer Tsang
A Microbial Diversity course student sampling at Trunk River Lagoon, Falmouth. The yellow patch at left is a natural bloom of sulfide-oxidizing phototrophs. Credit: Elise Cowley
A scientific discovery often starts with a chance observation made by open minds who realize its potential. This happens over and over again in the MBL’s Advanced Research Training courses.
In 2014, students and faculty in the MBL’s Microbial Diversity course made such a serendipitous observation. A team followed up on it in the coming years and last week, published their insights in the journal Environmental Microbiome.
The story started at Trunk River lagoon, near the Shining Sea Bike Path in Falmouth, Mass., which for decades has been a “natural laboratory” for the Microbial Diversity course along with other local field sites, such as Sippewissett Marsh. (The course, established at MBL in 1971 by Holger Jannasch, will celebrate its 50th anniversary this year).
"A few days after we had waded through the shallow section of Trunk River lagoon, our footprints turned yellow,” says senior author Emil Ruff, a course teaching assistant in 2014-15 and now a scientist at the MBL.
Ruff hypothesized that the yellow suspension (which the course participants called microbial “lemonade”) was a sulfur bloom generated by microorganisms that couple photosynthesis to the oxidation of sulfur. The students’ footsteps likely stirred up decaying sea grass and other organic material, releasing sulfide into the water and creating a habitat suitable for rare microbes to bloom.
Lead authors (l-r) Srijak Bhatnagar, Elise S. Cowley and Emil Ruff after sampling at Trunk River Lagoon. All three were Microbial Diversity teaching assistants and led the research team (self-dubbed "Lemonheads") that completed the study. Credit: Emil Ruff
Blooms of microorganisms are not uncommon in water bodies. Some are so huge that they are visible from satellites. Some are harmful, because they can be toxic for animals, or lead to oxygen depletion in certain areas of the ocean. Blooms generated by high sulfide concentrations are generally a concern, as they can become toxic for fish, mussels and birds. There are many open questions about what triggers bloom formation and collapse.
The next year, Ruff and a team from the Microbial Diversity course returned to Trunk River with the goal of intentionally creating and tracking blooms to study how microbial communities form and change over time. They dug holes in the lagoon and added poles that allowed them to sample daily from several depths without disturbing the water column.
“Often in microbial ecology, we try to understand an ecosystem in its steady state. But it remains unclear how long it takes for an ecosystem to recover after a disturbance and what it takes to establish a diverse [microbial] community,” says Ruff. The experimental design allowed the research team to follow the microbial community as it began to assemble, matured and stratified over time, and collapsed at the end of the bloom.
Understanding these dynamics is particularly important in estuarine ecosystems, such as Trunk River lagoon, that are exposed to natural and human disturbances. Estuaries not only provide important protection from coastal erosion, they also capture carbon from the atmosphere and sequester it. They also serve as a food source and breeding ground for much of the coastal biodiversity.
“The ecology and biogeochemistry causing the sulfur-driven blooms showed us how quickly things can turn, and how ecosystems and microbiomes can rapidly change upon disturbances,” says Ruff.
The Microbial Diversity course team sampling at Trunk River. Credit: Drone photo by Rhys Probyn
One surprising finding was where the bloom’s microbes -- called anoxygenic phototrophs -- found optimal living conditions. Prior to the study, it was generally thought that many of the bloom microbes could not grow in the presence of oxygen. Finding them in mildly oxic waters led the researchers to examine their genomes. They found that certain species of Chlorobiales - the bacterial lineage responsible for most of the bloom biomass and the yellow color -- encode enzymes that combat oxygen stress, which could explain the microbes’ oxygen tolerance. This and other insights have already initiated new course research projects.
Like the different functions of the microbes in the Trunk River estuarine community, the Microbial Diversity course brings together teaching fellows, faculty and students with diverse backgrounds and research foci.
“What I found remarkable is the range of expertise in the course,” says Ruff. “You can assemble a group of researchers that can look at all aspects of an ecosystem, including microbiology, physics, chemistry and everything in between. This holistic approach is what the course stands for and passes on to its students each year, for the past 49 years.”
Citation: Srijak Bhatnagar et al (2019) Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental Microbiome, DOI: 10.1186/s40793-019-0348-0
Homepage photo: Setting up sampling poles at Trunk River. Credit: Sebastian Kopf
This work was carried out at the Microbial Diversity course at the Marine Biological Laboratory in Woods Hole, Mass. The course was supported by grants from National Aeronautics and Space Administration, the US Department of Energy, the Simons Foundation, the Beckman Foundation, and the Agouron Institute.
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.
Contact: dkenney@mbl.edu; 508-685-33525
WOODS HOLE, Mass. -- How did the monstrous giant squid – reaching school-bus size, with eyes as big as dinner plates and tentacles that can snatch prey 10 yards away -- get so scarily big?
The giant squid has long been a subject of horror lore. In this original illustration from Jules Verne’s “20,000 Leagues Under the Sea,” a giant squid grasps a helpless sailor. Credit: Alphonse de Neuville
Today, important clues about the anatomy and evolution of the mysterious giant squid (Architeuthis dux) are revealed through publication of its full genome sequence by a University of Copenhagen-led team that includes scientist Caroline Albertin of the Marine Biological Laboratory (MBL), Woods Hole.
Giant squid are rarely sighted and have never been caught and kept alive, meaning their biology (even how they reproduce) is still largely a mystery. The genome sequence can provide important insight.
“In terms of their genes, we found the giant squid look a lot like other animals. This means we can study these truly bizarre animals to learn more about ourselves,” says Albertin, who in 2015 led the team that sequenced the first genome of a cephalopod (the group that includes squid, octopus, cuttlefish, and nautilus).
Led by Rute da Fonseca at University of Copenhagen, the team discovered that the giant squid genome is big: with an estimated 2.7 billion DNA base pairs, it’s about 90 percent the size of the human genome.
Albertin analyzed several ancient, well-known gene families in the giant squid, drawing comparisons with the four other cephalopod species that have been sequenced and with the human genome.
She found that important developmental genes in almost all animals (Hox and Wnt) were present in single copies only in the giant squid genome. That means this gigantic, invertebrate creature – long a source of sea-monster lore – did NOT get so big through whole-genome duplication, a strategy that evolution took long ago to increase the size of vertebrates.
So, knowing how this squid species got so giant awaits further probing of its genome.
“A genome is a first step for answering a lot of questions about the biology of these very weird animals,” Albertin said, such as how they acquired the largest brain among the invertebrates, their sophisticated behaviors and agility, and their incredible skill at instantaneous camouflage.
“While cephalopods have many complex and elaborate features, they are thought to have evolved independently of the vertebrates. By comparing their genomes we can ask, ‘Are cephalopods and vertebrates built the same way or are they built differently?’” Albertin says.
Albertin also identified more than 100 genes in the protocadherin family -- typically not found in abundance in invertebrates -- in the giant squid genome.
“Protocadherins are thought to be important in wiring up a complicated brain correctly,” she says. “They were thought to be a vertebrate innovation, so we were really surprised when we found more than 100 of them in the octopus genome (in 2015). That seemed like a smoking gun to how you make a complicated brain. And we have found a similar expansion of protocadherins in the giant squid, as well.”
Lastly, she analyzed a gene family that (so far) is unique to cephalopods, called reflectins. “Reflectins encode a protein that is involved in making iridescence. Color is an important part of camouflage, so we are trying to understand what this gene family is doing and how it works," Albertin says.
In a rare event, a live giant squid (Architeuthis dux) is hauled to the surface on a baited hook in Japan. The giant squid can be 40 feet long tip-to-tail and weigh nearly a ton. Credit: Tsunemi Kubodera
“Having this giant squid genome is an important node in helping us understand what makes a cephalopod a cephalopod. And it also can help us understand how new and novel genes arise in evolution and development,” she says.
Citation: Rute R. da Fonseca, et al (2020) A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience, DOI: 10.1093/gigascience/giz152
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago
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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.