Living in an anoxic world: Arsenic cycling supports life for billion of years

Elaina Hancock – UConn Communications

Much of life on planet Earth today relies on oxygen to exist, but before oxygen was present on our blue planet, lifeforms likely used arsenic instead. These findings are detailed in research published today in Communications Earth and Environment.

A key component of the oxygen cycle is where plants and some types of bacteria essentially take sunlight, water, and CO2, and convert them to carbohydrates and oxygen, which are then cycled and used by other organisms that breathe oxygen. This oxygen serves as a vehicle for electrons, gaining and donating electrons as it powers through the metabolic processes. However, for half of the time life has existed on Earth, there was no oxygen present, and for the first 1.5 billion years, we really don’t how these systems worked, says lead author of the study and UConn Professor of Marine Sciences and Geosciences Pieter Visscher.

Light-driven, photosynthetic organisms appear in the fossil record as layered carbonate rocks called stromatolites dating to around 3.7 billion years ago, says Visscher. Stromatolite mats are deposited over the eons by microbial ecosystems, with each layer holding clues about life at that time. There are contemporary examples of microbes that photosynthesize in the absence of oxygen using a variety of elements to complete the process, however it’s unclear how this happened in the earliest life forms.

Theories as to how life’s processes functioned in the absence of oxygen have mostly relied on hydrogen, sulfur, or iron as the elements that ferried electrons around to fulfill the metabolic needs of organisms.

As Visscher explains, these theories are contested; for example, photosynthesis is possible with iron, but researchers do not find evidence of that in the fossil record before oxygen appeared some 2.4 billion years ago. Hydrogen is mentioned, yet the energetics and competition for hydrogen between different microbes shows it is highly unfeasible.

Arsenic is another theoretical possibility, and evidence for that was found in 2008. Visscher says the link with arsenic was strengthened in 2014 when he and colleagues found evidence of arsenic-based photosynthesis in deep time. To further support their theory, the researchers needed to find a modern analog to study the biogeochemistry and element cycling.

Finding an analog to the conditions on early Earth is a challenge for a number of reasons, besides the fact that oxygen is now abundant. For instance, the evidence shows early microbes captured atmospheric carbon and produced organic matter at a time when volcanic eruptions were frequent, UV light was intense in the absence of the ozone layer, and oceans were essentially a toxic soup.

Another challenging aspect of working within the fossil record, especially those as ancient as some stromatolites, is that there are few left due to the cycling of rock as continents move. However, a breakthrough happened when the team discovered an active microbial mat, currently existing in the harsh conditions in Laguna La Brava in the Atacama Desert in Chile.

The mats have not been studied previously but present an otherworldly set of conditions, like those of early Earth. The mats are in a unique environment which leaves them in a permanent oxygen-free state at high altitude where they are exposed to wild, daily temperature swings, and high UV conditions. The mats serve as powerful and informative tools for truly understanding life in the conditions of early Earth.

Visscher explains, “We started working in Chile, where I found a blood red river. The red sediments are made up by anoxogenic photosynthetic bacteria. The water is very high in arsenic as well. The water that flows over the mats contains hydrogen sulfide that is volcanic in origin and it flows very rapidly over these mats. There is absolutely no oxygen.”

The team also showed that the mats were making carbonate deposits and creating a new generation of stromatolites. The carbonate materials also showed evidence for arsenic cycling – that arsenic is serving as a vehicle for electrons — proving that the microbes are actively metabolizing arsenic, much like oxygen in modern systems. Visscher says these findings, along with the fossil evidence, gives a strong sense of the early conditions of Earth.

“Arsenic-based life has been a question in terms of, does it have biological role or is it just a toxic compound?” says Visscher.

That question appears to be answered: “I have been working with microbial mats for about 35 years or so. This is the only system on Earth where I could find a microbial mat that worked absolutely in the absence of oxygen.”

Visscher points out that an important tool they used to perform this research is similar to one onboard the Mars Perseverance rover, currently en route to Mars.

“In looking for evidence of life on Mars, they will be looking at iron and probably they should be looking at arsenic also.”

This work was supported by grants from NSF grant OCE 1561173, ISITE project UB18016-BGS-IS and the São Paulo Research Foundation FAPESP, grant 2015/16235-2. You can also find out more about this work in The Conversation.

DMS researchers show fish to grow slower under future oceanic CO2 conditions

By Elaina Hancock.

As humans continue to send large quantities of carbon into the atmosphere, much of that carbon is absorbed by the ocean, and UConn researchers have found high CO2 concentrations in water can make fish grow smaller.

Researchers Christopher Murray PhD ’19, now at the University of Washington, and UConn Associate Professor of Marine Sciences Hannes Baumann have published their findings in the Public Library of Science (PLoS One).

“The ocean takes up quite a bit of CO2. Estimates are that it takes up about one-third to one-half of all CO2 emissions to date,” says Murray. “It does a fantastic job of buffering the atmosphere but the consequence is ocean acidification.”

Life relies on chemical reactions and even a slight change in pH can impede the normal physiological functions of some marine organisms; therefore, the ocean’s buffering effect may be good for land-dwellers, but not so good for ocean inhabitants.

Baumann explains that in the study of ocean acidification (or OA), researchers have tended to assume fish are too mobile and tolerant of heightened CO2 levels to be adversely impacted.

“Fish are really active, robust animals with fantastic acid/base regulatory capacity,” says Murray. “So when OA was emerging as a major ocean stressor, the assumption was that fish are going to be OK, [since] they are not like bivalves or sea urchins or some of the other animals showing early sensitivities.”

The research needed for drawing such conclusions requires long-term studies that measure potential differences between test conditions. With fish, this is no easy task, says Baumann, largely due to logistical difficulties in rearing fish in laboratory settings.

“For instance, many previous experiments may not have seen the adverse effects on fish growth, because they incidentally have given fish larvae too much food. This is often done to keep these fragile little larvae alive, but the problem is that fish may eat their way out of trouble — they overcompensate – so you come away from your experiment thinking that fish growth is no different under future ocean conditions,” says Baumann.

In other words, if fish are consuming more calories because their bodies are working harder to cope with stressors like high CO2 levels, a large food ration would mask any growth deficits.

Additionally, previous studies that concluded fish are not impacted by high CO2 levels involved long-lived species of commercial interest. Baumann and Murray overcame this hurdle by using a small, shorter-lived fish called the Atlantic silverside so they could study the fish across its life cycle. They conducted several independent experiments over the course of three years. The fish were reared under controlled conditions from the moment the eggs were fertilized until they were about 4 months old to see if there were cumulative effects of living in higher CO2 conditions.

Murray explains, “We tested two CO2 levels, present-day levels and the maximum level of CO2 we would see in the ocean in 300 years under a worst-case emissions scenario. The caveat to that is that silversides spawn and develop as larvae and early juveniles in coastal systems that are prone to biochemical swings in CO2 and therefore the fish are well-adapted to these swings.”

The maximum CO2 level applied in the experiments is one aspect that makes this research novel, says Murray,

“That is another important difference between our study and other studies that focus on long-term effects; almost all studies to date have used a lower CO2 level that corresponds with predictions for the global ocean at the end of this century, while we applied this maximum level. So it is not surprising that other studies that used longer-lived animals during relatively short durations have not really found any effects. We used levels that are relevant for the environment where our experimental species actually occurs.”

Baumann and Murray hypothesized that there would be small, yet cumulative, effects to measure. They also expected fish living in sub-ideal temperatures would experience more stress related to the high CO2 concentrations and that female fish would experience the greatest growth deficits.

The researchers also used the opportunity to study if there were sex-determination impacts on the population in the varying CO2 conditions. Sex-determination in Atlantic silversides depends on temperature, but the influence of seawater pH is unknown. In some freshwater fish, low pH conditions produce more males in the population. However, they did not find any evidence of the high CO2 levels impacting sex differentiation in the population. And the growth males and females appeared to be equally affected by high CO2.

“What we found is a pretty consistent response in that if you rear these fish under ideal conditions and feed them pretty controlled amounts of food, not over-feeding them, high CO2 conditions do reduce their growth in measurable amounts,” says Murray.

They found a growth deficit of between five and ten percent, which Murray says amounts to only a few millimeters overall, but the results are consistent. The fish living at less ideal temperatures and more CO2 experienced greater reductions in growth.

Murray concludes that by addressing potential shortcomings of previous studies, the data are clear: “Previous studies have probably underestimated the effects on fish growth. What our paper is demonstrating is that indeed if you expose these fish to high CO2 for a significant part of their life cycle, there is a measurable reduction in their growth. This is the most important finding of the paper.”

This work was funded by the National Science Foundation grant number OCE #1536165. You can follow the researchers on Twitter @baumannlab1 and @CMurray187.


Prof. Ann Bucklin presented a Webinar hosted by the Marine Biodiversity Observation Network (MBON)

UConn Marine Sciences Professor Ann Bucklin presented a Webinar on July 22, 2020 hosted by the Marine Biodiversity Observation Network (MBON), as well as other international programs focused on marine biodiversity, including GOOS, OBPS, OBIS, and OceanObs RCN, as well as SCOR. The webinar focused on ongoing activities of the SCOR Working Group, MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases. The presentation was followed by a Question & Answer session with three MetaZooGene-member Panelists: Katja Peijnenburg, Todd O’Brien, and Leocadio Blanco-Bercial. The Webinar was recorded and the video (and presentation PDF) can be viewed at this link: www.metazoogene.org/mbon-webinar-2020. Please feel free to share the link with interested colleagues and students.

Ann Bucklin chosen to receive UConn Faculty Excellence in Research and Creativity-Sciences Award

Ann Bucklin (Professor of Marine Sciences) has been chosen to receive the Faculty Excellence in Research and Creativity-Sciences Award. This award is given by the UConn Foundation Alumni Relations Office in recognition of research excellence and highest level of creativity to enhance the University’s academic and creative reputation. The award acknowledges significant and/or creative contributions to a field of knowledge or area of inquiry.

New Faculty Member: Dr. César Rocha

Later this year, Dr. César Rocha will be starting as a new assistant professor in the Department of Marine Sciences (DMS). DMS has been searching for new physical oceanographers to join the ranks of the faculty. It is with great enthusiasm that we welcome César to the University of Connecticut and to the scenic Avery Point campus.

Professor Rocha is currently a postdoctoral fellow at the Woods Hole Oceanographic Institution. In 2018, he received his Ph.D. in Physical Oceanography from the Scripps Institution of Oceanography at University of California, San Diego. Before then, he studied at University of São Paulo in Brazil, where he completed his B.S. in Oceanography and M.Sc. in Physical Oceanography.

Rocha, who hails from Brazil, reflected that his childhood played a large role in his decision to study the ocean. “Even though I grew up in a landlocked city, I used to spend every summer in my family’s house on Brazil’s Green Coast.” He continued, “in those lengthy vacations, I developed an awe for the ocean and this led me to pursue oceanography in college.”

He started oceanographic research as an undergraduate and “never stopped.” Along the way, he is glad to have had “wonderful mentors” to help shape his academic and professional career. Currently, Rocha’s research interests lie in mesoscale and sub-mesoscale flows in the ocean. This scale ranges from 1 to 100 kilometers and includes features such as eddies, fronts, and filament flows of the mixed layer and pycnocline, the layer of the ocean characterized by large density differences. Flows may originate at large scales and cascade to smaller ones, which mix the ocean and cause turbulence. Rocha explains, “Turbulent oceanic flows are responsible for both horizontal and vertical transport of properties such as heat, freshwater, nutrients, and biogeochemical tracers.”

While in graduate school, Rocha was a NASA Earth and Planetary Sciences Graduate Fellow. At UConn, he will continue his relationship with NASA through two NASA-related projects. The first will investigate sub-mesoscale eddies that are generated near topographic features on the ocean floor, which is a part of the Surface Water and Ocean Topography (SWOT) Mission. The second will be with the Submesoscale Ocean Dynamics Experiment (S-MODE), in which he and collaborators will deploy a flotilla of Saildrones, wind and solar-powered uncrewed surface vehicles, to study vertical transport in kilometer-sized fronts of the California Current.

Beyond research, Rocha is enthusiastic about teaching and mentoring. “I enjoy breaking down and distilling complicated concepts and explaining them to others,” he said. “I am committed to continuing to develop myself as an effective instructor.” He plans to create a new hands-on course called Research Computing in Marine Sciences, in order to teach data science and analytical tools in Python.

Rocha is looking forward to the personal and interdisciplinary community at DMS. “I like the idea of being in a department that is big enough to have a robust graduate and research programs, yet small enough so we get to know everybody,” he said. “I am eager to interact with colleagues from all areas of marine sciences.”

In his spare time, Rocha is working on his culinary skills. He also voraciously reads in both English and his native Portuguese. One of his favorite American publications is The New Yorker, for its fascinating and well-produced content.

Meet Kay Howard-Strobel, Research Associate

On the first floor of the Marine Sciences Building, it’s hard to miss the office door belonging to Kay Howard-Strobel because of its humorous sticker, “SAVE THE CRABS, THEN EAT ‘EM.” If you haven’t met Kay, you’ll probably be familiar with some the activities she’s been involved with at Avery Point.

Kay received her bachelors from the University of Mary Washington, where she majored in biology and geology. Then she completed her masters from the Virginia Institute of Marine Sciences (VIMS) in marine geology. Her thesis looked at Chesapeake Bay mud by using spatial autocorrelation to characterize dredge disposal sites in the Chesapeake Bay. “I found sand and mud was even way more fun than rocks and minerals,” she commented.

How Kay got to UConn is an interesting coincidence: “While at VIMS – one of my advisors hosted a visiting professor named Frank Bohlen,” she said. “After graduate school, I moved to Rhode Island with my husband and sent Frank a letter – and here I still am.” For 30 years, Kay has been a researcher in DMS, the first half working with Frank and second with Jim O’Donnell.

Currently, Kay manages, maintains, and configures various oceanographic instruments for field observations, including portable and mooring Acoustic Doppler Current Profilers (ADCPs), profiling and stationary Conductivity-Temperature-Depth (CTDs) sensors, suspended sediment sensors, Autonomous Underwater Vehicles (AUVs) and gliders, nutrient sensors, buoys, and more.

Kay deploys and recovers these sensors on all types of field campaigns too. Work in the field is very weather dependent and preparation constant, so she is ready to go on a moment’s notice. The variety of field work Kay has done is staggering. She said, “Every project is memorable in some way, shape or form…  whether traipsing through marshes and walking amongst reef balls with graduate students, deploying buoys in western LIS off the R/V Connecticut at the crack o’ dawn, squeezing under bridges on the Maritime Skiff, riding flood-gate currents in a johnboat, or running CTD profiles down the Sound on a flat, calm summer day on the Osprey… they’re all good.”

Throughout her three decades at UConn, Kay has been a part of many significant observational projects. One in particular is the Long Island Sound Coastal Observatory, now know as the Long Island Sound Integrated Coastal Observing System (LISICOS). Initially, it started as a buoy in the Thames River that transmitted data in real-time back to Avery Point, which she and David Cohen developed. Now, LISICOS is an interdisciplinary network of buoys, radar, weather stations, and water quality measurements. Public, private, and state users have to come to rely on that data for recreation, policy, and monitoring

Kay also enjoys CrossFit and playing soccer. She is one of the longest standing, most valuable members of the Department’s Friday afternoon pick-up soccer games.

DMS is enriched by and fortunate to have Kay Howard-Strobel as an expert observationalist in our midst.

Marine Sciences History: Growing Towards Gender Equality

It has been over 50 years since the University of Connecticut established Avery Point as a regional campus and nearly 40 years since the formalization of the Department of Marine Sciences (DMS). At that time, national feminist and civil rights movements were in full swing as well. In the decades that followed, especially the past 20 years, a primary focus of these movements has been increasing and retaining diversity in science, technology, engineering, and mathematics (STEM), which includes oceanography. Since the early 2000s, DMS has successfully narrowed the gender-gap among faculty members.

Barbara Welsh was the first female faculty member in DMS. She was hired in the 1980s and helped establish hypoxia monitoring and nitrogen management programs in Long Island Sound. Her research revealed phytoplankton blooms and the resulting alarmingly low oxygen concentrations in Western Long Island Sound in the summer.

The next female professor to join was Annelie Skoog, who studies marine organic matter cycling. Another early female leader was Associate Professor in Residence Patricia Kremer, who studied gelatinous plankton. After Barbara retired, Annelie remained the only tenured female faculty member. All other women faculty were research scientists and not professors. The most common title being Research Professor, with levels assistant, associate and full.

A few members of the department recalled a faculty meeting in 2002, in which half the members present were women. However, as the only female tenure-track professor present, Annelie was the only woman allowed a vote.

As a part of larger UConn initiatives to promote diversity and opportunities for underrepresented groups, DMS sought to grow as a department and recruit talented new faculty for hire. In 2005, Ann Bucklin became the first female department head and lead many efforts to formalize department proceedings.

Since then, Heidi Dierssen, Penny Vlahos, Julie Granger, Kelly Lombardo (who moved to Penn State University in 2019), Melanie Fewings (who moved to Oregon State University in 2018), Samantha Siedlecki, and Catherine Matassa have joined the tenure-track faculty ranks.

Additionally, Sandy Shumway, Jamie Vaudrey, and Jennifer O’Donnell have been members of the research faculty and key contributors to the Department. Claudia Koerting has been an integral part of developing the undergraduate program and maintaining instrumentation. A partnership with Mystic Aquarium added four women – all active and successful marine researchers – as affiliate faculty-in-residence: Tracy Romano, Maureen Driscoll, Laura Thompson, and Ebru Unal.

After conversations with many of these stellar scientists, it became clear that the culture in science overall has shifted greatly. Both Claudia and Penny commented that neither of them had any female professors throughout their entire academic careers. Whereas current graduate and undergraduate students can attest that female professors in the sciences are now entirely usual. However, disparities among different scientific disciplines remain. Today, the percent of people in physics and engineering identifying as female at the doctorate level is approximately 20% (Women in Physics and Astronomy 2019 Report, American Institute of Physics).

The culture that has been cultivated and continues to grow in DMS strives for diversity, inclusion, and equity on all academic levels including students, staff, and faculty.

On a final note, here are some statistics based on current departmental records. As of April 2020, all four research staff, six of eight postdoctoral research associates, 7 of 18 tenured or tenure track faculty, and four of five research faculty are women.

Ocean Bacteria Make Nutrients Out of Air

Image courtesy of the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), https://www.jamstec.go.jp/e/about/press_release/20180523/

It’s finally springtime in the Northeast USA, so gardeners are looking to fertilize their plants and flowers. Have you ever stopped to wonder what is actually in the big bags of soil you spread on your lawn?

In most cases, it is a mixture of nitrogen and phosphorus. Both are limiting nutrients for the base of the food chain, aka plants. Phosphorus makes its way into soil and the ocean through weathering of rocks. Nitrogen, on the other hand, is trickier, because although it makes up over 70% of the atmosphere, this gaseous form (N2) is unusable by plants and animals.

So how does nitrogen get from the atmosphere into a usable form? The process is called “nitrogen fixation.” On land, bacteria in soil do the heavy lifting by converting N2 into organic nutrients like ammonium (NH4+) and nitrate (NO3) that are usable by plants. In the ocean, blue-green cyanobacteria are the most abundant type of bacteria to fix nitrogen. Collectively, these organisms are called diazotrophs, and account for close to 90% of natural nitrogen fixation.

In a recent collaborative publication, Associate Professor Julie Granger and Professor Craig Tobias contributed their expertise on the nitrogen cycle in the ocean. The study included scientists from various institutions and focused on standardizing procedures for measuring diazotrophic activity in field sample incubations.

Oceanographers are interested in understanding the magnitude and rate of nitrogen fixation by diazotrophs. These rates vary significantly depending on the location, whether coastal or open ocean, poles or equator, shallow or deep. Ultimately, scientists aim to evaluate what controls the reservoir of nitrogen in the ocean from measurements and its influence on ocean fertility. Unfortunately, researchers currently employ differing techniques, causing uncertainty in whether estimates of nitrogen fixation rates are inter-comparable among research groups and among ecosystems.

Granger, Tobias and colleagues focus on the 15N2 tracer method for this study. Therein, water samples from a particular depth and region of the ocean are incubated and supplemented with isotopically-labeled nitrogen gas (15N2 gas).

Isotopes refer to the different masses an element can have depending on its atomic structure. Nitrogen can have atomic mass of 14 or 15, which are referred to as 14N or 15N. Naturally occurring nitrogen is predominantly 14N, such that adding a dollop of 15N can facilitate the tracking of nitrogen transformations.

During incubation, living diazotrophs in the water samples convert nitrogen gas (including the labeled 15N-gas) into nitrogen nutrients. At the end of the incubation, the isotopic composition (whether 14N or 15N) of the newly “fixed” nitrogen is measured. This method allows scientists to track the amount and rate of atmospheric nitrogen gas that was converted into nitrogen nutrients at a particular ocean location.

Over the years, renditions of the 15N2 tracer method have been conceived, including some with questionable practices. As not all are created equal, Granger, Tobias and co-authors ultimately recommend the so-called “dissolution” and the “bubble release” methods over others.

Additionally, Granger and Tobias stress the importance of adhering to proven mass spectrometric procedures to quantify 15N, which is crucial for obtaining representative estimates.

The paper thus states, “While the research community may remain divided as to which variant of the method to follow, the standardization of some key practices will enable intercomparability among estimates, to better discern temporal and biogeographical trends, as well as environmental controls on ocean N2 fixation.”

While both Granger and Tobias are proud of the resulting document, they agree that they will never again engage in the Herculean effort that is achieving consensus: “Herding cats is harder than science.”

Trichodesmium, a common diazotroph, blooming in the ocean. Image courtesy of NASA’s Earth Observatory image archive.


White, A.E., Granger, J., Selden, C., Gradoville, M.R., Potts, L., Bourbonnais, A., Fulweiler, R.W., Knapp, A.N., Mohr, W., Moisander, P.H., Tobias, C.R., Caffin, M., Wilson, S.T., Benavides, M., Bonnet, S., Mulholland, M.R. and Chang, B.X. (2020), A critical review of the 15N2 tracer method to measure diazotrophic production in pelagic ecosystems. Limnol Oceanogr Methods. doi:10.1002/lom3.10353