Though they may be small, microorganisms are the most abundant form of life in the ocean. Marine microbes are responsible for making of the organic carbon that鈥檚 usable by life. Many marine microbes live near the surface, depending on energy from the sun for photosynthesis.

Yet between the low supply of and high competition for some key nutrients, like nitrogen, in the open ocean, scientists have puzzled over the vast diversity of microbial species found there. Researchers from the 91探花, in collaboration with researchers from 12 other institutions, show that time of day is key, according to a published Jan. 20 in Nature Ecology & Evolution.

The effort began in 2015, when scientists in the , a program now co-led by 91探花oceanography professor , looked at microbes in the surface of the North Pacific Subtropical Gyre, the Earth鈥檚 largest stretch of contiguous ocean.

鈥淸We were interested in] understanding how that fluctuation of photosynthesis during the day and the absence thereof at night propagates through the microbial community [in the ocean],鈥� explained co-first author , who did the work as a doctoral student at the 91探花and is now a postdoctoral researcher at the University of Chicago. 鈥淭hat influences how the ecosystem overall functions, how much carbon is stored, where the carbon moves around, and how organisms might interact with each other.鈥�

By integrating data on the timing of metabolic processes of different microbes in the surface ocean throughout the 24-hour light cycle 鈥� from the transcription of genes for proteins used in metabolism to the synthesis of molecules, like lipids, into the microbes鈥� cells 鈥� the researchers discovered that the coexistence of such diverse microbes may not be dictated by competition, but by the timing of their nitrogen uptake.

With staggered uptake of the essential nutrient nitrogen, 鈥渋nstead of having to compete with the whole field, [microbes] only have to compete with the organisms that share that specific shift with [them]. Perhaps that’s one way that the competition is slightly alleviated and can facilitate all of these diverse microbes being able to live off of the same nutrient source,鈥� said co-first author , a doctoral student at Georgia Tech.

Because of the interdisciplinary team present on the 2015 research cruise, data on almost the entire metabolic process was collected simultaneously from the same water every four hours, giving researchers an unprecedented look at how metabolic activity differs among these microbes throughout the 24-hour cycle.

鈥淐ollecting all these different sample types 鈥� at the same time is really a first way to look at the whole ecosystem all at once from all these different perspectives,鈥� , a co-first author and research scientist at the Gloucester Marine Genomics Institute.

The data revealed that most of the activity occurred at four time points: dusk (6 p.m.), night (2 a.m.), morning (6 a.m.) and afternoon (between 10 a.m. and 2 p.m.). While these times were important for many types of microbes, different groups鈥� activities at each time weren鈥檛 uniform.

鈥淩ealizing that various types of microbes acquire nitrogen at different times of day helps to answer a long-standing question in oceanography: How can there be such an incredible diversity of life, all essentially in the same place at the same time?鈥� said co-author , a 91探花professor of oceanography. 鈥淏eing able to explain the underlying reasons for this diversity will help oceanographers better predict how these communities may shift as the ocean changes.鈥�

, a 91探花research scientist in oceanography, is also a co-author. The research was supported by grants from the Simons Foundation, the National Science Foundation, Woods Hole Oceanographic Institution and the U.S. Geological Survey.

A full list of authors is available with the .

For more information, contact Boysen at aboysen@uchicago.edu or Ingalls at aingalls@uw.edu.

This post was adapted from a by Georgia Tech.

A by 91探花 oceanographers, published this summer in Nature Microbiology, looks at how photosynthetic microbes and ocean bacteria use sulfur, a plentiful marine nutrient.

Sulfur is the odorous element that gives beaches their distinctive smell. The new study focused on sulfonates, in which a sulfur atom is connected to three oxygen atoms and a carbon-based molecule. In the ocean, phytoplankton use energy from the sun to create sulfonate molecules. Bacteria then consume the sulfonates to gain nutrients and energy.

, then a 91探花postdoctoral researcher in oceanography and now an assistant professor at the University of Florida, drew on recent genetic studies of soils to learn which microbial pathways are used to process sulfonates in the ocean. The study first focused on 36 marine microbes that the team cultured in the lab, using a UW-developed method to test which organisms produce sulfonates on their own in a lab environment.

The study discovered “some striking similarities between sulfonate pathways in terrestrial and ocean systems,” Durham wrote in a in Nature Microbiology that discusses the project. In soils, plants typically produce sulfonates. In the oceans most sulfonates are also produced by photosynthetic organisms, in this case by unicellular phytoplankton.

The study then considered microbes in the open ocean that cannot yet be bred in the lab. During a 2015 north of Hawaii co-led by a team of researchers including and , both professors of oceanography and senior authors on the new study, microbial samples were collected at different times of day and night. The researchers then froze the samples in order to analyze their genetic and chemical contents back in Seattle.

“We returned from sea with a freezer’s worth of samples that generated over six terabytes of data for us to explore,” Durham wrote, “a major computational hurdle.”

The team eventually succeeded in extracting the relevant data and found patterns that backed up the findings from the lab samples. They also detected a day鈥搉ight rhythm in sulfonate metabolism that reflects the activity of photosynthetic organisms.

“Sulfonates are produced and consumed by certain groups of microbes, so we can use them to track specific relationships in seawater communities,” Durham said. “And because sulfonates contain a carbon鈥搒ulfur bond, they are part of the global carbon cycle which controls the flux of carbon dioxide into and out of the ocean. This is increasingly important to understand as the climate changes.”

Other co-authors are Angela Boysen, Laura Carlson, Ryan Groussman, Katherine Heal, Kelsy Cain, Rhonda Morales, Sacha Coesel and Robert Morris, all at the UW. This research was funded by the National Science Foundation, the Simons Foundation and the Gordon and Betty Moore Foundation.

For more information, contact Durham at b.durham@ufl.edu, Armbrust at armbrust@uw.edu, or Ingalls at aingalls@uw.edu.

91探花 oceanographers have now found that vitamin B-12 exists in two distinct versions in the oceans. A microbe thought to be a main supplier of B-12 in the open oceans, cyanobacteria, is actually making a “pseudo” version that only its kin can use.

The has implications for where algae and other organisms can get a vitamin that is essential to fueling marine life. The paper is in the Jan. 10 issue of the Proceedings of the National Academy of Sciences.

“I think the world is getting used to the idea that all lifeforms are in some ways dependent on microorganisms,” said corresponding author , a 91探花associate professor of oceanography. “This is another case where microorganisms are playing a really big role in the survival of others, but not quite in the way that we had expected.”

All animals, from humans to whales to sea cucumbers, need vitamin B-12. But only certain microbes can make the complex, cobalt-containing molecule. For land dwellers a main source is the microbes that thrive in animals’ guts, which is why beef is such a good source of B-12. Shellfish also accumulate a lot of B-12. In the surface waters of the open oceans, a main supplier of B-12 was believed to have been .

But the new paper uses various techniques 鈥� including sampling in the Pacific Ocean, genetic analyses and growing bacterial cultures in the lab 鈥� to prove that cyanobacteria make a different form, known as “pseudo” B-12.

That means that all the other light-absorbing phytoplankton in the oceans are getting their B-12 from somewhere else.

“Phytoplankton are incredibly important as the base of the marine food web, for oxygen generation on Earth and carbon uptake in the ocean,” said first author , a 91探花doctoral student in oceanography. “Somebody’s making B-12 for them, and it’s not who we thought it was.”

The first hint of a knockoff form of B-12 came from the marine algae , a popular health supplement. Analyses of its contents in Japan showed an unusual form of the B-12 molecule.

In previous research, Heal developed a in seawater that can distinguish between similar molecules. The new study applied that technique to see where different forms of vitamin B-12 exist in the open ocean.

“When I started looking, I saw that in some parts of the ocean the pseudo B-12 is even more common than the regular B-12,” Heal said.

The research confirms that virtually all cyanobacteria, the dominant form of light-harvesting organisms in oceanic gyres and other parts of the open ocean, only make and use pseudo B-12. The two forms of B-12 are incompatible, so cyanobacteria also have a different form of the protein that requires that vitamin to function.

“Nobody has shown that this molecule, pseudo B-12, exists in the environment,” Heal said. “Now we know where it comes from, why it’s there, and we have some hints that it can be rearranged.”

The marine environment might contain a specialized subset of microbes that can convert pseudo B-12 into regular B-12, creating a sort of black market for the converted vitamins.

“That would require several specific microbes to coexist in the same place, and suggests a complex interdependency,” Ingalls said.

The authors also show that for many parts of the ocean it now appears that regular B-12 is directly supplied by marine archaea. Experiments in the study show that archaea may be the dominant source of B-12 in parts of the ocean where they live, furthering from the 91探花research group.

“To understand the marine ecosystem, you have to understand what supports growth,” Ingalls said. “We know where nitrogen and phosphorus come from. But for vitamin B-12, a molecule we’ve known about for more than half a century, we’re only now realizing who’s making it in the marine ecosystem.”

The research was funded by the National Science Foundation and the Simons Foundation. Other 91探花co-authors are Wei Qin, Francois Ribalet, Anthony Bertagnolli, Willow Coyote-Maestas, Laura Hmelo, Allan Devol, Virginia Armbrust and David Stahl; and James Moffett at the University of Southern California.

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For more information, contact Heal at kheal@uw.edu and Ingalls at aingalls@uw.edu or 206-221-6748.

NSF Grants: OCE1228770, OCE1046017

An increasingly popular method to deduce historic sea surface temperatures uses sediment-entombed bodies of marine archaea, one of Earth’s most ancient and resilient creatures, as a 150-million-year record of ocean temperatures. While other measures have gaps, this one is increasingly popular because it promises to fill in gaps to provide a near-global record of ocean temperatures going back to the age of the dinosaurs.

But 91探花 research shows this measure has a major hitch: The single-celled organism’s growth varies based on changes in ocean oxygen levels. Results published in August in the show that oxygen deprivation can alter the temperature calculations by as much as 21 degrees Celsius.

“It turned out that oxygen has a huge, dramatic effect,” said corresponding author , a 91探花associate professor of oceanography. “It’s a big problem.”

Recent research shows these archaea, which draw energy from mere whiffs of ammonia, make up about 20 percent of microbial life in the oceans. Their bodies are plentiful in the ocean floor.

A method uses fats in the archaea’s cell membrane to measure past ocean temperatures, including during a about 56 million years ago that is one of the best historical analogs for present-day climate change, and a of up to 11 degrees Celsius during a period of low ocean oxygen about 100 million years ago, when other records are scarce.

Climate scientists found they could measure ocean temperature by looking at the change in the index, a temperature proxy named for the 86-carbon lipids in the cell membrane, which often tracks the surrounding water temperature.

The method seemed to work better in some samples than others, prompting Ingalls and her co-authors to wonder about its physiological basis. The newly published experiments tested that relationship and found an unexpectedly strong response to low oxygen.

“Changing the oxygen gives us as much as 21 degree Celsius shift in the reading,” said first author , a 91探花doctoral student in civil and environmental engineering. “That’s solid evidence that it’s not just a temperature index.”

This means the TEX-86 measurements are inaccurate in parts of the ocean that may have experienced oxygen changes at the same time 鈥� for example, in low-oxygen zones or during major extinction events. This is exactly when the archaea are a popular index since other life forms, whose shells can provide a chemical signature for their growth temperatures, are absent.

It’s not known exactly why the archaea shift their lipid membranes. They may adapt to a temperature change by making their membrane tighter or less brittle in the new environment, Ingalls said. Low oxygen is another big environmental stressor.

“The envelope that encloses the cell is sort of the gatekeeper, and when stress is encountered of any kind, that membrane needs to adjust,” Ingalls said.

The new study is the first to actually look at how these archaea grow in different temperatures. These archaea are famously hardy 鈥� it’s the same group that lives in Yellowstone hot springs 鈥� but they have stymied attempts to grow them in captivity.

Qin was first author of a that was the first to grow and compare individual strains of the marine Thaumarchaeota archaea under different conditions. He used samples from Puget Sound, a Seattle beach and a tropical-water tank at the Seattle Aquarium to show that related strains occupy a wide range of ecological niches.

In the new paper, he shows that the membrane lipids of different strains can have different temperature dependences. Some of them are a straight line, meaning they would be a good indication of past temperature, but others are not.

He also did experiments in which he changed the oxygen concentration of the air above the culture flasks. Results show that as the oxygen level drops, the TEX-86 measures rise dramatically, with reading spanning 15 to 36 degrees C even though all samples were grown at 26 C.

“This index provides an amazing historical record, but it’s very important how you understand it,” Qin said. “Otherwise it could be misleading.”

Knowing that oxygen affects the membrane structure can help improve interpretation of the TEX-86 record. Researchers can disregard samples from low-oxygen water to improve the accuracy of the technique, which as it is used now has error bars of about 2 degrees C.

“Plus or minus 2 degrees is not very good when you think about the sensitivity of the climate system,” Ingalls said. “This gives us a new way of thinking about the data.”

Next, the 91探花team hopes to do more experiments to learn how other factors, like nutrient levels and pH, affect these archaea’s metabolisms.

“We think there’s reason to believe that there’s all kinds of things that could affect the membrane lipid composition, not just temperature,” Ingalls said.

The research was funded by the National Science Foundation. Other co-authors are , , and at the 91探花and at the University of Southern California.

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For more information, contact Ingalls at aingalls@uw.edu or 206-221-6748, Qin at ericqin@uw.edu or 206-543-5454 and Stahl at dastahl@uw.edu or 206-685-8502.

NSF grants: MCB-0604448, MCB-0920741, OCE-1046017, OCE-1029281, OCE-1205232.

91探花 researchers used new tools to measure and track B-12 vitamins in the ocean. Once believed to be manufactured only by marine bacteria, the new results show that a whole different class of organism, archaea, can supply this essential vitamin. The results were presented Feb. 24 at the meeting in Honolulu.

“The dominant paradigm has been bacteria are out there, making B-12, but it turns out that one of the most common marine bacteria doesn’t make it,” said , a 91探花associate professor of oceanography.

All marine animals, some marine bacteria and some tiny marine algae, or phytoplankton, need B-12, but only some microbes can produce the large, complex molecule. So like human vegetarians on land, marine organisms may be scouring for food that can help stave off vitamin deficiency.

“If only certain bacteria can make B vitamins, that can make B-12 a controlling factor in the environment. Is it present or not?” said , a 91探花oceanography graduate student. “Studying the marine microbiome can help us understand what microbial communities could be supported where, and how that affects things like the ocean’s capacity to absorb atmospheric CO2.”

The 91探花team is the first to show that marine , a single-celled organism that evolved totally separate from bacteria and all other living things, are making B-12. Relatives of these tiny critters are known for unusual behavior like living inside hot springs and underwater volcanoes.

The Seattle team managed to grow a common type of open-ocean archaea in the lab, no mean feat, and show that it not only makes enough B-12 to support its own growth but can supply some to the environment.

“It’s hard to quantify their contribution,” Ingalls said. “This is a first glimpse at their potential to contribute to this pool of vitamins.”

The analysis was done at a new that does detailed analysis of proteins and other carbon-based chemicals in the ocean. The researchers used high-tech tools, including liquid chromatography and mass spectrometry, to identify the tiny amount of vitamins among all the dissolved matter and salt in the seawater. The 91探花method is unique in that it is the only one that can distinguish among the four forms of B-12 vitamins.

Field experiments involved sampling seawater in Hood Canal, near Seattle, and in the Pacific Ocean hundreds of miles offshore. The results showed that B-12 was present in small amounts in all water samples. Concentrations were low enough in some places that vitamin deficiency among tiny marine algae, or phytoplankton, is likely.

“Having a very small amount doesn’t mean there’s a very small supply,” Ingalls said. “Low concentrations can indicate something that’s highly desirable to marine organisms.”

The next step, researchers said, is to connect different microbes’ activity with the production of B vitamins, to see which organisms are responsible where, and to look at how ocean vitamins affect the type and amount of phytoplankton growing in the water.

Recent sequencing of the genomes of marine microbes has revealed genetic pathways in bacteria and archaea for creating B vitamins, but just because the gene is there doesn’t mean it’s being used. Marine microbes often adapt their behavior depending on the environment. In the case of vitamins, some bacteria make more B-12 if a phytoplankton is nearby, supporting their eventual food source.

Making a B-12 vitamin, which has a metal core and complex surrounding structure, involves 30-some steps.

“People think that’s why many organisms have lost it from their genomes,” Heal said. “It’s just too expensive to make it, and it’s easier to get it from food.”

The 91探花team hopes to learn which microbes are producing B-12 vitamins where, to better understand how the base of the marine food web works, how it might alter in a changing environment, how oceans might help regulate atmospheric carbon dioxide, and where marine animals could go to get a well-balanced diet.

“The public really has a very strange relationship to microorganisms,” Ingalls said. “People know they cause disease, so they want to kill them. But they’re also the only reason that we 鈥� or whales, fish or coral reefs 鈥� are alive.”

Collaborators are David Stahl, E. Virginia Armbrust, Allan Devol, Wei Qin and Laura Carlson at the UW, James Moffett at the University of Southern California and Willow Coyote, an undergraduate from Evergreen State College who will also present a poster at the meeting. The work was funded by the National Science Foundation.

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For more information, contact Ingalls at 206-221-6748 or aingalls@uw.edu and Heal at 206-543-7521 or kheal@uw.edu.

Heal will present poster #552 Monday, Feb. 24 from 4 – 6 p.m. at the Ocean Sciences meeting in Honolulu.