Marine microbes in a changing climate

Events of the last few years have made Professor Dyhrman think about community resilience in new ways, both for human societies and for phytoplankton communities and the ecosystems they support. Roughly 50 Pg of carbon per year is fixed into organic forms by phytoplankton in the surface ocean and this resulting chemical-microbe network underpins ocean ecosystem structure and function. So-called ‘omic approaches are providing critical insight into how culture isolates, simple-communities, and even the complex field systems that represent this network can be driven by biotic factors like microbial interactions and abiotic factors such as temperature, resource availability, and CO₂ concentration among other factors. Yet, the over-arching rules that govern these processes are poorly constrained and this adds to the myriad challenges in predicting future ocean patterns in microbial diversity and biogeochemistry. What are the key drivers that shape the chemical – microbe network? How sensitive is this network to a changing ocean?  Here Professor Dyhrman will discuss field observations of microbial physiological ecology and the drivers of these patterns in the surface ocean. Leveraging multi-‘omic approaches the group is working to understand the drivers of phytoplankton diversity and activities in the chemical-microbe network. Moving beyond previous methodological constraints, and single domain perspectives, there is a confluence of need and opportunity to more fully resolve the rules which govern the chemical – microbe network in  the ocean. She will highlight the perspectives that come from our community discussion in this area. Collectively, this knowledge will help better predict marine ecosystem resiliency on a changing planet.

Professor Sonya Dyhrman, Columbia University, USA

Professor Sonya Dyhrman, Columbia University, USA

Professor Sonya Dyhrman is a microbial oceanographer who got her start in high school where an amazing teacher began an after school marine science program. She received her PhD in Marine Biology from the Scripps Institution of Oceanography, and was a Postdoctoral Scholar at the Woods Hole Oceanographic Institution, where she went on as a tenured member of the scientific staff until she joined the Columbia University faculty in 2013. Sonya is a Fellow in the American Academy of Microbiology, and serves on the executive committee of the US National Science Foundation Center for Chemical Currencies of a Microbial Planet. She has had the privilege of working in all the world’s oceans, visiting every continent, and getting to interact with an extraordinary group of students and collaborators, all the while learning about the tiny microbes that have such a large impact on our changing planet.

Earth System Models (ESMs) play a crucial role in assessing impacts on ocean biogeochemistry and biology in the global ocean. However, ESM projections of biological change neglect the growing insight from genomic datasets. Instead, metabolic models arise from advances in Systems Biology. They focus on the molecular functioning of organisms under different environmental conditions, suggesting that integrating ESMs with metabolic models would improve our ability to deliver a molecular, ecological, and evolutionary understanding of the links between environmental change and the phenology of organisms. This talk presents recent computational modelling that abstract the metabolic network capacity called the metabolic niche. This new formal definition of the fundamental niche is based on the genome-scale description of a given organism. It approximates the capacity of an organism to survive based on nutrient availability. It shows that the presence-absence of genes is insufficient to describe the niche and metabolic niche modelling allows for the investigation of the most important reactions for organisms survival of emblematic organisms such as diatoms or cyanobacteria. When intertwined with ESMs, the same concept predicts plankton's global scale metabolite production and the molecular response of organisms to environmental changes. In particular, these results highlight several acclimation strategies occurring globally that are characterized by nutritional stresses and their physiological consequences for maintaining growth rates. These include critical phenotypic traits such as energy storage via glycogen or lipids or mixotrophy, neglected so far by ESMs. This talk will demonstrate the potential of integrating genomic knowledge into biogeochemical modelling for including adaptation and evolutionary mechanisms in climate studies.

Associate Professor Damien Eveillard, Nantes Université, France

Associate Professor Damien Eveillard, Nantes Université, France

Damien Eveillard is a trained oceanographer from Sorbonne Université with a PhD in biological modelling from Lorraine Université. After a postdoctoral fellowship at Texas A&M University, he earned a faculty position in the computer sciences department at Nantes Université. Interdisciplinary and working on several complex biological systems, from HIV-1 alternative splicing regulation to ecosystem modelling, he is a computational biologist developing modelling techniques based on graph and constraints programming. These techniques allow the integration of heterogeneous knowledge for holistic reasoning and prediction across multiple scales. Damien Eveillard recently applied his expertise on modelling the plankton biocomplexity across scale (ie from molecules to the global ocean) via his implication in the Tara Océan initiative. His modellings assessed several benefits, such as identifying biomarker genes for biogeochemical processes or abstracting the genome-scale complexity of microbial phenotypes to understand their acclimation to climate perturbations. 

This talk presents the results of a project that aimed to understand the hidden molecular mechanisms underlying intraspecific thermal micro-diversity within a single coastal Synechococcus population. An estuarine microbial assemblage was collected, and incubated at 18^oC and 30^oC for two weeks to allow thermal selection and strain sorting to occur. Clonal Synechococcus isolates were then obtained from both temperature treatments using flow cytometry, and their thermal response curves were characterized in the laboratory. Isolates from the low and high temperature incubations were morphologically identical but thermally distinct, consisting of 'cool' or 'warm' thermotypes, respectively, based on their significantly different thermal optimum and upper thermal limit traits. These two contrasting Synechococcus thermotypes also exhibited consistent temperature-dependent differences in photobiology. Illumina sequencing was however completely unable to distinguish between these two thermally-divergent strains, with >99.9% average nucleotide identity across all the isolates. Application of long read sequencing technology ultimately showed that the relevant thermal adaptation mechanisms were not genomic at all, but differences in the two thermotypes instead correlated with m-5 cytosine methylation of the genes coding for C-phycocyanin. This thermally-significant epigenomic difference would be invisible to studies based on amplicon sequencing or metagenomics, and yet such cryptic, non-genomic, intra-specific micro-diversity could play a key role in providing thermal resiliency to cyanobacteria populations growing in a warming ocean. 

Professor David Hutchins, University of Southern California, USA

Professor David Hutchins, University of Southern California, USA

David AHutchins (PhD 1994, UC Santa Cruz), is a Professor of Marine and Environmental Biology at the University of Southern California, where he holds the George and Louise Kawamoto Chair in Biological Sciences. His research interests centre around global change processes in ocean ecosystems as they affect microbial assemblages and their associated cycles of carbon, nutrients such as nitrogen and phosphorus, and micronutrients such as iron. Hutchins uses experimental approaches in the lab and the field along with physiological, biogeochemical and molecular analyses to understand the responses of ocean microbiology and biogeochemistry to environmental changes including acidification, warming, deoxygenation and (micro)nutrient cycling. He has published ~210 peer-reviewed papers, was the founding chair of the Ocean Global Change Biology Gordon Research Conference, and is a Fellow at the American Association for the Advancement of Science (AAAS) as well as a Sustaining Fellow at the Association for the Sciences of Limnology and Oceanography (ASLO). 

Understanding the response of microbes to ocean global change requires an improved grasp of their underlying metabolic mechanisms, along with enhanced awareness of how altered microbial performance influences ocean biogeochemistry and ecology. Molecular biology offers a step change in the flow of information on the physiological potential of microbes. However, this unprecedented detail has been very difficult to translate into wider biogeochemical or ecological ramifications. To commence, Professor Boyd will make the case for a renewed focus on physiological rate measurements that is driven by the co-design of new ‘fit-for-purpose’ metrics by the omics and physiology research communities. Such metrics can help bridge the gap between omics and biogeochemistry.  Later, he will illustrate the need for a physiological ‘currency converter’ – by examining the wide-ranging strategies microbes employ to obtain fluctuating resources over the diurnal cycle. The superimposition of biological rhythms upon environmental heterogeneity poses major challenges for ocean sampling. There is emerging evidence of diel cycles across transcriptomics to lipidomics that brings important insights to the prior physiologically-based literature on the influence of diurnal cycles on ocean biogeochemistry. How can we best sample the ocean in a way that enables microbial metabolic responses to be understood mechanistically, then linked to the wider microbial community dynamics and their biogeochemical roles? New high-resolution datasets from robotic profiling floats, with both environmental and bio-optical sensors, may offer a framework to devise optimal sampling strategies for omics, rates, and biogeochemical fluxes.

Professor Philip Boyd, Institute for Marine and Antarctic Studies, Australia

Professor Philip Boyd, Institute for Marine and Antarctic Studies, Australia

Philip Boyd is a professor of marine biogeochemistry at the Institute for Marine and Antarctic Studies (IMAS) in Hobart, Tasmania. His interests range from the oceans’ iron biogeochemical cycle to the responses of oceanic phytoplankton to climate change. He has served as a member of the GEOTRACES and SOLAS scientific steering committees, and is currently active with the BioGEOTRACES project within GEOTRACES.

Additional interests include assessment of the feasibility, side-effects and societal implications of purposefully stimulating marine primary production using iron-enrichment to geoengineer the oceans.

Numerically abundant marine microbes hold great promise as model organisms for studying the ocean's response to a changing climate. Laboratory isolates representing genetically distinct lineages within the Prochlorococcus and SAR11 collectives have been essential in providing genetic reference information, linking genomic potential to physiological processes, and testing theories that arise from environmental sequences. The recent isolation of novel lineages from these collectives and the creation of stable semi-continuous co-cultures are expanding the utility of these organisms to inform our understanding of energy flow in the marine environment.

With substantial proportions of environmental sequence data still exhibiting poor recruitment to reference databases, Assistant Professor Becker will highlight what they believe to be the continued importance of domesticating wild marine microbes. They will define an appropriate level of taxonomic specificity for predicting microbial responses to global change (or not) and explore the potential of democratized sequencing for making informed sampling decisions at sea. They will look at several instances where laboratory isolates transformed our understanding of marine biogeochemical cycling before considering what knowledge gaps still exist as we navigate the bumpy journey from genome to biome. 

Finally, Assistant Professor Becker will share some nascent thoughts on pedagogical approaches to equip the next generation of oceanographers, modellers, and computational biologists with the necessary tools to collaborate with Earth's microbes and maintain a habitable Earth.

Assistant Professor Jamie Becker, Alvernia University, USA

Assistant Professor Jamie Becker, Alvernia University, USA

Jamie Becker is an Assistant Professor of Biology at Alvernia University, where he was recently appointed a Neag Junior Faculty Professorship. He received his PhD from the MIT/WHOI Joint Program and did a postdoc at MIT before finding his realized niche in the classroom. His research combines traditional cultivation techniques, genomic sequencing, and undergraduate students to examine microbial physiology and interactions. Jamie believes that the solutions to many of our most pressing environmental problems are invisible. He aims to understand how diverse microbes interact with each other and their surrounding environment to promote healthy marine ecosystems. Revealing an unseen world to his students (and coffee) gets him up each morning.

Microorganisms are primary drivers of biogeochemical cycles and thus centrally important for maintaining Earth as a habitable environment, but much remains unknown about their biogeography, controls on distribution, and metabolic potential and exchanges. Given multiple concurrent human- and climate-driven perturbations to the ocean environment, the habitats that exist now may be considerably different in only 10–15 years – predicting these shifts is essential to inform management and decision-making. As a result, there is an urgent need to elucidate interactions between microbes and their biogeochemical environments. In recent years, an international community effort has been underway to design a global-scale marine microbial biogeochemistry program 'BioGeoSCAPES: Ocean Metabolism and Nutrient Cycles on a Changing Planet' that combines rich biological (nucleic acid- and chemical omics) and chemical (nutrients, micronutrients, metabolites) sampling to map microbial communities and study ocean metabolism and its influence on ecosystem health and biogeochemical cycles. Recent advances in analytical and bioinformatics capabilities, combined with community-based momentum to organise ‘omics intercalibration and standardisation activities make this the ideal time to act. Dr Twining will describe a recently funded US NSF project to support planning and development of BioGeoSCAPES through a combination of meetings, workshops, working groups, student and postdoc exchanges, and summer school events. Planned community activities are envisioned to result in an international science plan, as well as plans for intercalibration assessment, methodological and sampling best practices, data management and informatics, and data-model integration strategies. 

Dr Benjamin Twining, Bigelow Laboratory for Ocean Sciences, USA

Dr Benjamin Twining, Bigelow Laboratory for Ocean Sciences, USA

Ben Twining is a marine biogeochemist who studies the interactions of metals with plankton, including the effects of metal availability on organism health and the ocean carbon cycle. Twining received an undergraduate degree in Environmental Science and Public Policy from Harvard University and a PhD in Coastal Oceanography from Stony Brook University. He conducted postdoctoral research at Yale University and then worked as an assistant professor of environmental chemistry at the University of South Carolina. He is currently a Senior Research Scientist and the Henry L. & Grace Doherty Vice President for Education at Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine.