BIOS-SCOPE Scientists Reflect on the Project’s Success – and Look Ahead to its Future

BIOS-SCOPE group photo

The BIOS-SCOPE team gathers on the program’s eleventh cruise with 18 scientists and two marine science technicians on board. Photo by Emmy Jarris

Now in its eighth year, BIOS-SCOPE is a multi-institutional, multi-disciplinary initiative that annually gathers scientists from Bermuda, Europe, the United Kingdom and the United States to explore fundamental questions about the ocean’s biogeochemical cycles and how diverse communities of marine microbes influence the carbon cycle and other fundamental processes and, ultimately, the planet’s ability to sustain life. An overarching goal of the project is to form and foster collaborations across scientific disciplines, an aspect that enables the team to advance their understanding of the interactions of organisms and compounds at various scales, across both time and ocean depths. Along the way, the principals and collaborators of BIOS-SCOPE (Bermuda Institute of Ocean Sciences – Simons Collaboration on Ocean Processes and Ecology) have formed professional bonds and friendships that add value to the work. On the eve of the program’s eleventh cruise from ASU BIOS – with 18 scientists and two marine science technicians on board, Currents spoke with BIOS-SCOPE Co-Principal Investigators and adjunct faculty Craig Carlson (University of California, Santa Barbara) and Stephen Giovannoni (Oregon State University) and Investigator Rachel Parsons (ASU BIOS Microbial Ecology Laboratory) about the project’s past, present and future.

Currents: What are some of the biggest takeaways from the project so far?

Carlson: One thing that makes the project unique is that we own our own wire time, water budget and ship time, and we can place the study in the context of the much bigger BATS (Bermuda Atlantic Time-series Study) program, which provides a very rich detailed backdrop. The BIOS-SCOPE program is designed to bring in expertise from a whole bunch of different marine science disciples and sub-disciplines where we can attack questions from a whole bunch of different angles that we wouldn’t be able to do by just hopping on a BATS cruise or looking at the BATS data. It’s a unique opportunity to get a mechanistic understanding of how or what is explaining some of the patterns.

Giovannoni: The processes behind this microbial world have been unseen, invisible. And some of those invisible things we’ve been able to see for the first time. For example, we used to think little cells had to swim to find their food and now we know that you don’t have to swim – you can just float and get a big piece of the pie that way. So that was an advance in our understanding. We have a better understanding of how cells use arsenic, because there’s a lot of arsenate in sea water. And we have a better understanding of how cells use gases that are in the water. There’s sort of a big picture thing here. You know, science doesn’t stay the same. It changes over time, it evolves. So, if you go back to the ‘80s, when we started this, the idea that you would take genes out of seawater and clone them was kind of crazy and that’s where we started. But since that time, the entire world of oceanography has been changed by genome sequencing. Everybody’s now sequencing everything and it’s just revolutionary. It’s almost hard to over-emphasize what a big change that has been. And yet, scientists solve one problem and then they just bump into the next one. That’s just the way it always is. And the problem they’ve bumped into is connecting the dots between that DNA and what’s actually happening in the water. So, it would be kind of grand to say we’re going to solve that problem. But if you look at the collection of investigators in the BIOS-SCOPE team, they’re actually pretty well equipped to get to the next level by breaking it down. We’re not trying to break it down too far; we’re just trying to break it down to the next level. Take someone like Alex Warden (GEOMAR Helmholtz Centre for Ocean Research Kiel/Marine Biological Laboratory Woods Hole, MA.). There’s silica in the spring but it runs out. And it turns out what she has discovered – we’re not 100 percent certain but I think it looks like she’s right – that there are cells at BATS in the summer that use silica, but they just use it a lot more carefully because there’s not very much. Those are the silica flagellates that she discovered. So that’s a piece of the story we didn’t know about. Then we’re lucky to have Ferdi Helweger (Technical University of Berlin), who is the kind of modeler that really loves to take those specific pieces of the big story and really build them into a model. Ferdi wants everything he can get his hands on that matters. And he’s going to put that in the model.

Parsons: And members of BIOS-SCOPE have discovered viruses for SAR11, which is the most abundant bacteria in the ocean. So, we are trying to look to see if we have SAR11 phage.

Giovannoni: We’ve got kind of a grand strategy and only time will tell how well that works, but we’re excited about it.

Currents: Why is Bermuda (ASU BIOS, in particular) a great location for this research?

Carlson: Bermuda is in a unique position because BIOS has been studying this system and site for 70 years or more…and that allows us to explore patterns. What got Steve and I together is that we saw patterns from the biogeochemistry as well as the microbiology and…we’re able to drill down and see what’s driving or controlling one or the other. With the BIOS-SCOPE program, we can attack problems on a whole variety of scales, not just decadal or seasonal or annual but we can look at diurnal patterns too. It allows us to look at ocean patterns in a way we hadn’t been able to before at this site. I would say the BIOS-SCOPE project has a variety of levels and scales that we’re trying to unravel in both time and space – through the water column and through time. One of the things that makes work out here in Bermuda unique is we have this annual process where the storms pick up, it gets cold and causes mixing in the water column and that becomes kind of a biogeochemical reset. And then…we see successional patterns. And our job is to try to see if there are linkages on what’s driving what, and how does the chemistry lead to response by microbes and then how do the microbes then transform the chemical patterns we’re observing. There’s lots of different layers and we all have our boutique questions we’re drilling down on and some of them are pretty reduced, but they’re exciting because we’ve looked at these patterns for a long time, but we hadn’t been able to address them…from a field perspective. The BIOS-SCOPE funding has allowed us to take over a ship for small periods of time where we can just focus on the exact questions that we want using the wire and targeting the depths and collecting the water that we need to do that work.

Currents: Can you talk a bit about the BIOS-SCOPE team and collaborators?

Carlson: BIOS-SCOPE is a cool program in that we have a really great energetic, enthusiastic group of PIs. It’s not just a collaboration where you have a bunch of people together and you do your own thing on a project, but our PIs and our investigators really do interact with each other and take advantage of each other’s expertise to move that bar forward. I think that’s been one of the really satisfying, gratifying parts of this project. And we are constantly bringing in new visions, new young people that are…moving in directions we wouldn’t have thought of. So, it’s a real nucleus. It’s kind of a cool launching pad.

Currents: What are the various scientific disciplines represented in the project?

Carlson: BATS is the big mother program that we are embedded into. They provide us the nitty-gritty details at least on the geochemistry and hydrography. But the expertise within our program includes marine chemists (Liz Kujawinski and Mac Saito‘s groups at WHOI); a particle biogeochemist at the University of Miami (Hilary Close’s group); a phytoplankton ecologist (Alex Worden, MBL); and a modeler (Ferdi Helweger). Then, of course, we have the expertise here at BIOS. Leocadio Blanco-Bercial and Amy Maas (protistan and mesozooplankton ecologists) and Ruth Curry’s MAGIC (glider) program. Steve is a molecular microbiologist, has expertise in understanding the fine details of how microbes’ physiology interacts with biochemistry. Then, my group is considered microbial oceanographers, where we look at process scale interactions between microbes, their distribution patterns, how they interact and transform organic matter. And Ben Temperton (University of Exeter), his focus is on looking at how we can better understand viral dynamics through metogeonomic processes and metatranscriptomics processes, and he also helps us with our bioinformatics component. What I always tell my students is (marine science) is very much an interdisciplinary science. You don’t have to be an expert at everything, but you need to know somebody who’s an expert at everything your interested in and that’s what we’ve done with building the BIOS-SCOPE team by bringing in very specific expertise to make those linkages and push science forward.

Currents: Can you describe the significance of BIOS-SCOPE to the broader world of environmental science, conservation, and/or education?

Carlson: If someone said why are you studying ocean microbiology or the ocean itself, one of the things we’re keenly interested in is understanding the carbon cycle and how the ocean mediates the movement of carbon dioxide from the atmosphere into the surface ocean and how that gets moved from the surface ocean into the interior ocean depths. And what we do know is physics plays an important role in that, but biology also plays an important role. So where do microbes fit into this story? They’re driving the show. They’re the ones that are controlling the fixation of carbon dioxide into organic matter and, on the heterotrophic side, they are also the organisms that remineralize it or convert it or recycle it back to its inorganic constituents. So, what we do see is that organic matter in both dissolved and particulate phases is produced in the surface and some of it is resistant and persistent to degradation, but if you move that organic matter into the interior of the ocean into a different suite of microbes, they have the capability of consuming materials that were resistant in one place but become available in another. That has big implications with regard to sequestration of organic matter or sequestration of carbon. So, we would say we are interested in the carbon cycle and, knowing now that microbes and mesozooplankton control and govern these large biogeochemical cycles, our project is looking at the mechanistic linkages between microbes, their community structure and how they’re controlling those distribution patterns.

Giovannoni: In the world we live in today, the carbon cycle is a central issue to everyone. Sometimes I explain our job as, “we’re just accountants.” It’s like money. Where is it going and how fast is it going there? Carbon scientists are kind of like that too. They’re trying to figure out where the carbon is, how much, and how much it’s changing. And, of course, all the transactions are done by microorganisms. BATS is really special because globally the oceans are becoming hotter, the ocean surface especially is getting warmer and warmer. And that increases what we call stratification and decreases the amount of nutrients available. So BATS is just a natural laboratory. We kind of lucked out, actually, working out here at BATS. Every spring, there’s a lot of nutrients in the water column. And people who don’t live here don’t know that it gets cold in the winter and windy. But in the summer it gets hot. So, we get to see every single year this cycle that really mimics what’s happening globally. This really is a phenomenon – the oceans are becoming depleted in nutrients, chlorophyll is dropping. So, this gives us a chance to focus on how organisms adapt to that ultra-low nutrient world. To live in the Sargasso Sea at this time of year takes a very special group of organisms that are adapted to that ultra-low nutrient ecosystem. Understanding that and how that impacts the flow of carbon through the system is really where we have the biggest opportunity to make a contribution.

Steve Giovannoni

Co-PI of the BIOS-SCOPE project, Steve Giovannoni, collects seawater samples from the ship’s CTD. Photo by Jessica Godfrey

Currents:  How significant is BATS to the BIOS-SCOPE project?

Carlson: A perfect description is it’s a test bed. It’s like a laboratory setting that we can go back to and look at every year and hone and refine our questions and hone and refine our techniques and study them. That makes it powerful. We have water collected on every BATS cruise. So, even though we’re not here all the time, we have a lot of samples that are collected so we have a sample stream that comes in and it’s distributed to our PIs. Rachel helps oversee that logistical operation. It’s an onerous task but it gets done and it allows us to study both the chemistry and then our specific questions with regard to our specific samples. Then we get together at a particular time of year at sea for what we call a process cruise where we set up experiments on the boat. We’re really fortunate to be integrated with the BATS program because we get this regular stream of samples that comes to us every month. And then we go in once or twice a year and say “Okay, we’re going to study this particular question and what’s happening in the spring or the summer or the fall or the winter.” The Simons Foundation International provides that opportunity by giving us six days of boat time per year, which includes mobilization and demobilization, so we’re at sea for about four days. We also have cruises of opportunity where if (there are) other cruises that we can hop on in this area, we do and take advantage of those opportunities.

Parsons: What’s really nice about the BATS program is, for instance, when Steve says let’s sample arsenic, I can sample arsenic for a year. Steve can test that the protocol is working and then we can continue sampling for as long as needed. BATS have been very forthcoming and have done extra sampling for us, as needed.

Giovannoni: That’s a really nice example because we had no idea if what we were doing would work. It’s often out of the question for scientists in a laboratory somewhere on the mainland to experiment with water from ocean gyres and trying things out for the first time on a ship to see if they work is not an efficient use of resources. But because of being connected to this oceanographic program, fresh samples were shipped to us and we now have the first complete annual cycle of arsenic speciation in the water column.

Carlson: We also have a lot of gear and samples and equipment that are here. So, when we go to these meetings or our workshops or our monthly BIOS-SCOPE all-scientists calls and we say, “we should really try this,” we’ll say “Rachel, do we have this stuff there?’” And she’ll say, yeah, and we’ll send it out to BATS on the next cruise to see if we can grab a sample for testing. So, we have flexibility because of the infrastructure provided by Bill Curry and BIOS. We have the flexibility to be creative, to try things out that we wouldn’t necessarily be able to do if it was just a dedicated cruise across the Atlantic or something like that.

Parson: We’re very, very thankful to Rod Johnson (ASU BIOS assistant scientist), who rarely says no on the BATS cruise.

Carlson: If it wasn’t for the dedicated personnel like Rod and the BATS team, none of this kind of time-series work would happen. Those guys are incredible and they’re very accommodating.

Currents: What is the relevance of the project beyond Bermuda?

 Carlson: While its major focus is in the Sargasso Sea, it has far-reaching comparative-contrast implications to see how this system compares to others (research in the high North Atlantic and the Pacific, for example).

Currents: Can you recount a favorite story about BIOS?

Carlson: One time Steve was chief on a cruise, and we sailed out of Charleston, South Carolina. You never want to sail a boat out of the yard because they’ve just been fixing the boat for a long period of time. We were taking it straight out, right back to Bermuda, and there were a lot of hiccups along the way.

Giovannoni: All the lights go out on the ship at two in the morning, people are yelling. We’re still at the dock for that, still trying to get going. And then we finally got here and got ashore, and Bill Curry was there, and he said, “Steve, why did you take the ship out of the yard?” And I said, “I’m naïve?”

Carlson: The reason we took it out of the yard is because the timing was perfect. We both teach on the quarter system. It was our spring break. We could get in there early…and then get back for the start of the next quarter. Except that we were delayed in the yard, so I got back a little late.

Giovannoni: Craig missed the first week of classes. We got to know Charleston pretty well.

Carlson: There’s lots of stories from science stories to fun interactions. One of the things that’s always rewarding about coming to BIOS or when I lived here and worked here is you have a lot of really awesome marine scientists who come to this place all the time. It’s a cool melting pot of different ideas. We kind of get carried away with our own ideas in our own institutions but having the freedom just to come and talk about your interests is really a rewarding part about hanging out and being at BIOS.

Currents: You’ve seen the Institute ebb and flow over the years, what are your thoughts on the latest developments in the life cycle – specifically, BIOS joining Arizona State University?

Carlson: This is big. The potential is huge. It provides a unique level of stability for the institution and the program, with a larger potential investment into the infrastructure as well as the ship operations, which is always good.

Giovannoni: The students of today are different. You can’t fly them all to Bermuda, but students really value virtual experiences and I think with the experience of a remote field station through this partnership with ASU you’re making that accessible to this really large group of students. I think that’s a really interesting experiment and I’m optimistic.

Carlson: But it’s also a hybrid. So, it’s not only that you have the remote teaching or interactions remotely with lots and lots of people, but if you capture the interest of folks that want to come and embed themselves in the field experience, they can. So, you’re really talking to an audience that can build the next generation of marine scientists.

Currents: What’s on the agenda for next week’s cruise?

Carlson: Organized chaos! We have a specific set of experiments that we’re going to conduct and a lot of over-the-side operations that meet a very rigorous, round the clock schedule. We’ll be at sea for four and a half days and I don’t expect us to be sleeping too much because this is our opportunity to do that work. We’re going a little farther east than Hydrostation S and that’s about 25 kilometers southeast of the island. We’re going to go into what’s called an anticyclonic eddy and…we’ll stay with that feature for four days to see if we can pick up patterns within that feature.

Parsons: I will say this cruise is crazy. There are so many experiments and so many bottles, I don’t know if there’s actually room for any people! There seem to be a lot of experiments going on in this cruise that are of the “let’s see if it works” type. So, if it does work, I’m pretty sure they will be back doing more experiments. Or maybe that’s something that we, the people here at BIOS, might be able to do for them on subsequent cruises. And, I will say I have a great team of students at the moment. And while it’s great to get them to do their own work and their own experiential learning, they’ve all been told that they have to wash the bottles, make some slides and help BIOS-SCOPE get out to sea. It was a huge bottle washing week before everybody arrived, but they all seemed to enjoy themselves.

Carlson: I think one of the things Rachel just pointed out is one of the strengths of BIOS-SCOPE and the long stretch of funding that we’ve had. We are afforded the opportunity to do the look-and-see type of experiments – this is high risk, could be high payoff type of work. We always go to sea with a set of core operations. Those are locked – we have them all the time, so that just helps build our record and our ability to interpret these trends. But we do have these “let’s just try it” experiments. And if it’s successful, then you drill down on that question further. So, part of these cruises is designed to gather data that we know has been successful and just continue to increase our database, but also, by looking at those patterns, we can come up with hypotheses and say maybe we’re right, maybe we’re not but we have the opportunity to explore it.

Currents: Beyond the 2023 cruise, what’s next on the horizon for BIOS-SCOPE?

Carlson: Once we get back from this cruise, everyone that’s participating will take their own samples back to their own laboratories and start drilling down on those analyses. Then our job is to turn those data into manuscripts and publications to inform the bigger scientific community. We also are gearing up towards an all-scientists meeting that will happen in February. That’s where all of our core group and some invited guests will all come together for a two- to three-day workshop and we’ll focus on what we’re finding, what we plan to do next, how we move forward on the next question. Also, Steve and I have been working at BATS since we met in the ‘80s and, in the ‘90s, we started having organized programs where every month we collected nucleic acids, DNA, at different positions in the water column. So, we have a 30-year record of that DNA collected pretty much uninterrupted monthly. With BIOS-SCOPE funds last year we had two teams descend on UCSB and Oregon State where we extracted all of the samples that were at those institutions so that we have a very complete archive record of DNA that was recently sequenced. We have all the sequence in hand now and we’re going to use that as a springboard to look at how patterns in microbial communities may or may not have changed over both seasonal cycles as well as decadal patterns. It’s a one-of-a-kind data set and we’ve yet to scratch the surface of that.

Giovannoni: It is the oldest DNA metagenomic record on earth.

Currents: Anything else you’d like to add?

Carlson: One of the things that I personally love about marine science is it’s expeditionary. It’s an adventure type of science. So, you can look at data, look at patterns, but then you get the opportunity to go to places and do things that handfuls of people get to do. It’s really appealing in that way.

Parsons: While I can’t read minds, I can pretty much read Steve’s and Craig’s. Prior to BIOS-SCOPE, Craig, Steve and I worked on the Microbial Observatory for ten years, so we know each other, we know how each other works.

Carlson: When (NSF’s Microbial Observatory funding) ended in 2014, it was like well, looks like we’re wrapping up things in BIOS. Then I got a call from Program Officer Marian Carlson of Simons Foundation International asking if we could put together a program and I said I think we can do that. I called Steve and said, “We’re getting the band back together!”.

Parsons: We’re kind of more like a family.

Carlson: We’ve got good chemistry.