New research takes scientists a step closer to identifying important characteristics of the communities of ocean organisms we rely on to aid the planet – as well as understanding how a warming climate could affect the functions of those communities.
The work is part of an international effort to reliably predict how the world’s oceans will respond to climate change by getting acquainted with the organisms that live there and do most of the work of absorbing half the human-generated carbon in the atmosphere and producing half of the oxygen we breathe.
The research shows that water temperature has a significant influence on how these floating creatures, called plankton, structure their communities and on how diverse these communities are. Specifically, in warmer water near the equator, most plankton communities are more diverse, and organisms living there are more likely than their peers in polar waters to change their gene activation, a sign they are likely better at adapting to their environment.
Models created by the international team of researchers predict that warming temperatures in the polar regions of the oceans could significantly change the characteristics and diversity of microbial communities, potentially making them less useful as food sources and less likely to absorb carbon from the air.
“It’s important for us to understand these patterns and the idea that things will shift,” said Matthew Sullivan, professor of microbiology at The Ohio State University and a co-author on the two articles published today (Nov. 14) in the journal Cell. “I think we are at a point where we have to go so far as to develop such a roadmap for the oceans in the hopes we can engineer the oceans to help us mitigate the rapidly accelerating problem of climate change. Such studies are needed if we are to know which knobs we need to turn.”
The reports represent the latest findings from the Tara Oceans Consortium, a three-year global study of the impact of climate change on the world’s oceans that involves hundreds of scientists from nearly 30 countries around the world.
In this work, the methods used to get to the findings are a noteworthy part of the story. Tara itself was an unprecedented effort – not even Charles Darwin’s worldwide sea voyage on the HMS Beagle between 1831 and 1836 collected samples for microbes and viruses, and only one other global ocean expedition has occurred since – but without viruses. The expedition team collected 35,000 water samples with the goal of learning everything they could about some of the busiest creatures in the ocean: plankton, the tiny plants and animals that float throughout the sea.
The sizes of the datasets related to this work alone are hard to fathom: For example, this single research effort generated a new catalog of 47 million microbial genes. (For comparison, consider the first estimates of the entire human genome put the number at 100,000 genes.)
Assessing gene expression patterns was the primary purpose of one of the papers, and the analysis showed a noticeable pattern driven by water temperature. Plankton communities in polar waters were more likely to change their composition while communities in warmer waters were more likely to remain the same but change the activation of their genes.
“In the polar regions, community changes are what dominate, and in non-polar regions, gene expression changes are what dominate. Community change suggests a limit to adaptability. That’s really striking because it says something about polar waters: Their microbes may not be ready for climate change,” said Sullivan, who also holds a faculty appointment in civil, environmental and geodetic engineering and is co-director of Ohio State’s Infectious Diseases Institute Microbial Communities Program.
To identify the diversity of groups among the plankton, scientists used two types of data: “barcode” gene markers unique to specific groups of organisms not visible to the naked eye, and imaging data of bigger and more complex organisms. Artificial intelligence was used to interpret the imaging data – only after more than two dozen experts analyzed hundreds of thousands of images to classify what they depicted.
After identifying the diversity trends, scientists generated tens of thousands of models to project how warming of the oceans and related microbial shifts might affect the organisms’ functions. Their estimates, comparing current figures to future predictions, suggested the shifts could bring severe reductions to fish catches and carbon absorption.
In a May 2019 Cell paper, Sullivan’s lab discovered that one group of plankton buck the trend of lower diversity in polar regions, when they identified and mapped nearly 200,000 new viral species throughout the global oceans. While microbes are essential contributors to all life on the planet, viruses that infect or interact with them have a variety of influences on microbial functions.
Sullivan is the virus coordinator for Tara. He suspects that a virus type that infects bacteria known as a phage, when scaled up in an engineering framework, could be used as a therapeutic device to correct microbial problems – in humans and plants to fight pathogens and superbugs, and in the world’s oceans to combat climate change. Analyzing the feasibility of this concept in a variety of settings is a key component of his lab’s work.
Additional Ohio State co-authors on the papers were former graduate student Ahmed Zayed, now a postdoc at Ohio State; former graduate student Ann Gregory, now a postdoc at KU Leuven, Belgium; and former postdoc Simon Roux, now at the Department of Energy Joint Genome Institute. These studies were led by Shinichi Sunagawa of the Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, and Chris Bowler and Lucie Zinger from the École Normale Superieure, Paris.
The work is sponsored by multiple international organizations and agencies, including the Gordon and Betty Moore Foundation and the National Science Foundation. The Ohio Supercomputer Center provided computational support.