Scientists of fifty years ago could not imagine our technologies today, nor could they know how much their samples would have empowered us now.
This realization, combined with our contemporary understanding that microbes are sentinels of planetary health, compels us to think carefully as we too have a responsibility to scientists fifty years ahead of us.
So this October, we gathered twenty-one experts from four continents at the Helmholtz Institute of Functional Marine Biodiversity (HIFMB) to think about some ambitious questions: What would an ocean observing system meant to last decades look like? What can we do now for those decades ahead of us, and enable discoveries we cannot yet imagine?
Over two intensive days, the Marine Microbial Observatories for the Future Workshop (MMOFF) discussed long-term observatories with considerations from sampling to storage to funding. The workshop was endorsed as an official Activity under the UN Ocean Decade, recognizing its alignment with the global vision for transformative ocean science.
The purpose of this blog post is to give you some insights into the discussions, challenges, and opportunities that emerged from two days of wrestling with these tough questions.
The Marine Microbial Observatories for the Future (MMOFF) workshop participants from top left to bottom right: A. Murat Eren (Meren), Jesse McNichol, Teodor Georgiev, Jodie van de Kamp, Enrique Montes, Adam C. Martiny, David Needham, Thomas Stjernegaard-Jeppesen, Michael (Mike) S. Rappé, Alejandra Prieto-Davó, Jed Fuhrman, Sarah J. Tucker, Samantha (Sam) Setta, Elisha Wood-Charlson, Kathleen (Katie) Pitz, Ioulia Santi, Yosmina Tapilatu, Matthias Wietz, Luke Thompson, Raïssa Meyer, Amelia Hine.
What may not be apparent to those who are not neck-deep in the waters of marine microbial ‘omics is the disconnect in the state of the science and the capacity to implement research and monitoring of marine microbiomes. At unprecedented scale, advances in ‘omics (e.g. metagenomics, (epi-)genomics, transcriptomics, metabolomics) have unlocked fundamental insights into microbial evolution and ecology, elucidated microbial roles in climate, food webs, and ecosystem functioning, and identified countless applications for biotechnology and natural resource management. But our ocean observing systems often remain fragmented, underfunded, and struggling to keep pace with the questions we are asking. It is time to fix that.
Developing a vision for a future global marine microbial ‘omics observatory requires input from a diverse set of skills, mindsets, and expertise. Our workshop team included people running time-series, building data infrastructures, setting policy, coordinating global networks, publishing findings, and wrestling with the daily chaos of samples, sequences, and spreadsheets. Not surprisingly, our two days of lively workshop discussions led to very different opinions and sometimes completely orthogonal ways of looking at the same problem. Yet, despite these differences, what emerged was a strong collective feeling that we are in a unique position to build a legacy for the future. Something worth pursuing together.
To build momentum, gain clarity on our vision, and share and shape these ideas with a broader community, one concrete outcome of the workshop is to write a synthesis paper. That is coming. But we’re here now to give you a first glimpse of what happened, what was discussed, and where this might be heading.
Digging in
The workshop discussions were centered around themes: samples, data, standardization, funding, policy, challenges, and opportunities. We approached each theme through the lens of time: What can we envision for the future? What can we enact in the present? What can we learn from the past? Thus, each morning, whether by bike, on foot, or via public transport, our twenty-one participants arrived jet-lagged but energized, ready to wrestle with questions that span decades.
“The bikes are coming!” A wholesome moment was the workshop’s participants arriving on bikes, riding in a pack across the HIFMB grounds, a peloton reaching their finish line.
Some discussions, like the one on samples, were particularly lively. Looking back 50 years, we acknowledged that the technologies we have today to collect, process, and analyze marine microbiome samples were unimaginable back then. This gave us freedom to think wildly about the next 50 years. Autonomous sampling devices may roam the global ocean collecting tandem metagenomes and metatranscriptomes from <1mL of seawater. High-resolution sampling of marine microbial communities may serve as biosensors of ecosystem health, pinpointing the onset of harmful algal blooms, or utilized for rapid management decisions about certain fisheries. Indeed, while individual scientists and programs are implementing some of these ideas, they are yet to reach a scale that is long-term or regional, nevermind global. Yet, we know this is achievable - just think of the rapid deployment of wastewater monitoring systems to track regional, national, and multinational COVID-19 trends through biomolecules.
The MMOFF workshop was structured as a discussion based around the themes of samples, data, standardization, funding, policy, challenges, and opportunities.
We agreed that this exciting future might also consider using the samples we are collecting right now to understand how microbial communities and their impacts on the ocean ecosystem have changed and continue to change over long periods of time. If this is a viable scientific pursuit (which we obviously think it is :)), what are the most “legacy-rich” samples we can be saving right now. Currently, the way we attain the biomolecules of marine microorganisms is on filters that have small holes so small that they allow seawater to pass, but trap the microbial cells. So what is the ideal way to store these samples for the future: is it DNA extracted from a filter, the filter itself, or just frozen seawater with all the microbes preserved inside it? The details of how, where, and when we should be saving samples to ensure that they are usable for future scientists is nuanced. But one consensus was unequivocal: when building a legacy of samples and data, two things cannot be recovered if missed at collection - the material sample and its environmental and methodological metadata. You either capture them in the moment or lose them permanently. Another practical consideration we more or less agreed upon was the inclusion of internal DNA or mRNA standards in future samples when possible so that our analyses of the sequences could lead to absolute rather than relative abundances. The idea of necessitating other standardization in sampling efforts was a path less desired. Wholesale standardization can expose all samples to the unanticipated biases or constraints. Where standardisation truly matters, however, is environmental and methodological metadata - detailed metadata and clear methods characterization are as critical to sample comparison as standardization of the way protocols are reported.
Following the idea of learning from past sample collections, we considered resequencing historical samples with modern day technologies. Currently, we could utilize samples that were collected >10 years ago to look for patterns of climate-mediated evolution on marine microbial populations. In fact, this would be a nice proof of principle for our larger goal and we are coordinating a project to do just this – learn from the resequencing of past samples.
While the discussions focused on individual themes (samples, data, standardization, funding, policy, challenges, and opportunities), it was inevitable that they would intersect. In multiple sessions, we identified the need to establish a collective voice in order to gain support from funding sources, scientific societies, policy, our colleagues, the public, and intergovernmental groups. Yet, we could not escape that the appetite for and urgency to build a global marine microbial ‘omic observatory varies with location and audience. For example, a coastal community that is experiencing potentially life-threatening harmful algae blooms may be particularly excited to start tracking these microbial communities right away, while an inland community may not see this as an equally important priority.
The nuts and bolts of shifting marine microbiome observations from largely a research enterprise to one of research and monitoring also stretched the boundaries of our themes on standardization, policy, samples, and data. Imagine that marine microbial ‘omics were collected, analyzed, and immediately released to the public through a team of autonomous samplers, national and federal employees, and AI (and non-AI) computer programs. Implementing a governmental monitoring system means that access to policy-relevant information (e.g. information pertaining to climate and weather modeling, ecosystem modeling, fisheries management, water quality and safety) is more secure than if these data were collected under grant funding cycling. This would also supplement research initiatives that examine locations or temporalities out of the bounds of the government monitoring initiatives, while continuing to fuel innovation, expansion of scientific knowledge, and the development of industrial and environmental applications.
The road ahead
As we refine and share this vision for the future of marine microbial ‘omic observatories, we hope to gain the input of many. The road to building this vision is long and perilous – changes in scientific funding and priorities, inequitable access to scientific and management resources, gaps in understanding between science and policy are only a few of the potential obstacles.
We took walking breaks during both workshop days to get the brain and body going and explore the area near the Helmholtz Institute of Functional Marine Biodiversity (HIFMB) campus. Credit: Alejandra Prieto-Davó
Yet, we are confident that a means to achieve these goals will present itself eventually if we simply continue the discussion with meaningful priorities, recognition of challenges, and motivation to push forward. During one of our scheduled walking breaks, our route back to campus took us to a closed bridge. All of us were just staring at the fence, some reading the sign in German that said in no uncertain words “Do not cross”. Then someone said, “Well, we have a session to get to”, and over we went. All of us. Fence-hopping our way back to the workshop. It set a tone: we are here to solve problems, and we are not letting obstacles stop us.