Mini but mighty: How microbes make the world

François Aurat/Tara Ocean Foundation
Polar ice surrounds the research schooner Tara, which from 2009 to 2013 sampled oceanic plankton around the world. The expedition discovered 150,000 single-celled plants and creatures, 35,000 species of bacteria, and 5,000 new viruses.
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In the 1954 microbiology textbook, “Horton Hears a Who!” the title character, an elephant, must convince his friends not just that the Whos living on a speck of dust are important, but that they exist at all.

The same was true nearly three centuries earlier for Antonie van Leeuwenhoek, the Dutch draper who built microscopes that revealed an entirely new realm of life.

Why We Wrote This

People tend to seek out things that are bigger than themselves. But one of the most profound leaps in thought has been the recognition that life as we know it is made possible by the smallest creatures on Earth.

Leeuwenhoek’s revolution continues this week, as a pair of studies published in the journal Cell expand our understanding of ocean microbes, creatures whose behavior supplies us with the oxygen for one out of every two breaths. 

“Microbes are the stewards of the planet,” says Rutgers oceanographer Paul Falkowski. “They are the organisms in general that make life possible on Earth.”

The studies aim to establish a baseline for understanding the impact of climate change on the world’s oceans. They also reveal the diversity of creatures who, despite being in many ways the planet’s dominant form of life, are rarely seen.

“No matter what your religious background is,” says biologist Chris Bowler, an author on one of the studies, “life is beautiful.”

In the 1954 microbiology textbook, “Horton Hears a Who!” the title character, an elephant, must convince his friends not just that the Whos living on a speck of dust are important, but that they exist at all.

The same was true nearly three centuries earlier for Antonie van Leeuwenhoek. A Dutch draper with a knack for grinding and polishing lenses, Leeuwenhoek built tools that could magnify objects up to 400 times, about 20 times greater than his contemporaries’ microscopes. With these meticulously crafted instruments, Leeuwenhoek became the first person known to directly observe bacteria and protozoa, sperm cells and blood cells.

At first, not everyone bought Leeuwenhoek’s claims that the soil, water, and even our own bodies were teeming with life too small for human eyes to see. His 1676 letter to the British Royal Society, his 18th to the learned academy, includes testimonials from a Lutheran minister, a notary, a barrister, and five other witnesses. With the help of another pioneer of microbiology, the English polymath Robert Hooke, Leeuwenhoek brought to light a world previously unknown to science.

Why We Wrote This

People tend to seek out things that are bigger than themselves. But one of the most profound leaps in thought has been the recognition that life as we know it is made possible by the smallest creatures on Earth.

Today, Leeuwenhoek’s revolution continues, as a pair of studies published in the journal Cell this week expand our understanding of the tiny organisms that inhabit the world’s oceans, the invisible creatures whose ancient metabolic machinery supply us with the oxygen for one of every two breaths. As the scientists and policymakers prepare for the Decade of Ocean Science for Sustainable Development, a United Nations-backed effort set to launch in 2021 aimed at reversing the global decline in ocean health, many more of the world’s human eyes will be focusing on the oceans’ smallest inhabitants.

“Microbes are the stewards of the planet,” says Paul Falkowski, an oceanographer at the department of marine and coastal sciences at Rutgers University in New Brunswick, New Jersey. “They are the organisms in general that make life possible on Earth.”

Karl Bruun, Nostoca Algae Laboratory, courtesy of Nikon Small World/AP/File
Marine diatom cells, which are an important group of phytoplankton in the oceans, help soak up atmospheric carbon dioxide.

Both papers rely on data collected by the research schooner Tara, which from 2009 to 2013 sailed the oceans of the world to undertake the largest systematic sampling effort of oceanic plankton. The expedition brought back around 35,000 samples and discovered 150,000 single-celled plants and creatures, 35,000 species of bacteria, and 5,000 new viruses.

“Plankton actually represent about at least two thirds of the biomass in the ocean,” says Chris Bowler, a scientist at the Institut de Biologie de l’École Normale Supérieure in Paris and an author on one of the studies. “They’re just microscopic, so we don’t appreciate them. But actually, they are extremely abundant.”

“Plankton” is not actually a taxonomic category like “amphibian” or “gorilla.” Rather, the word refers to any organism – plant, animal, bacteria, you name it – that is unable to swim against ocean currents. Some plankton, like small jellyfish, can be seen with the naked eye. Most cannot.

The studies rely on both advanced microscopy and high-throughput DNA sequencing. Like Horton’s keen ears and Leeuwenhoek’s sharp lenses these modern instruments are revealing a world that previously existed only in the imagination.

In one paper, Dr. Bowler and his colleagues found that most planktonic groups follow a gradient of diversity along latitudes, with the lowest level of diversity closest to the poles. This finding mirrors an observation made by Alexander von Humboldt in the early 19th century. It’s one of the first patterns discovered in what would become the science of ecology.

“On land, things are pretty fixed,” says Dr. Bowler. “Whereas in the ocean, things are very mobile. ... We thought that, maybe we wouldn’t see these big global patterns that von Humboldt first noted on land. But yes, in fact, we do see them.”

The other paper complements this discovery by looking at not just which genes were present, which can tell what an organism is capable of, but which genes were expressed, which can explain what an organism is actually doing.

This study, conducted by an international team of researchers, examined how microbial communities – mainly bacteria and another domain of single-celled organisms called archaea – adjust to environmental change. Using data from 126 sampling sites from the equator to the poles, the team identified 47 million microbial genes and found that the microbial diversity and microbial gene expression vary across geographies. In warmer waters, where genetic diversity is rich, organisms adapt by switching genes on and off. In polar waters, where diversity is lower, the organisms may be more hard-wired to their environment.

“It’s quite safe to say that the Arctic presents itself as a biologically very unique ecosystem,” said Shinichi Sunagawa, a researcher at Eidgenössische Technische Hochschule Zürich and a co-author of the paper.

Taking a mental leap

It’s perhaps ironic that scientists ignored something so fundamental to biology for so long.

Most timelines of microbiology leave a huge gap after Leeuwenhoek.

“It took another 150 years almost before microscopes were rediscovered [by German biologist Ferdinand Cohn],” says Professor Falkowski, author of the 2015 book Life’s Engines: How Microbes Made Earth Habitable and a science adviser for the Tara expedition. 

Even then, the so-called Golden Age of Microbiology didn’t really get going until the mid-19th century, as science came to accept the existence of microorganisms and their ability to interact with the larger world.

“Interact” is an understatement. The breathable atmosphere as we know it was constructed by single-cell organisms. 

About 2.3 billion years ago, there were no animals, no leafy plants, and, in the planet’s atmosphere, very little oxygen. Then, rather suddenly as these things go, bacteria that had evolved with tiny solar-powered machinery to turn water and carbon dioxide into sugars and oxygen – that is, photosynthesize – forever altered the trajectory of life on Earth. 

These ancient cyanobacteria began dumping free oxygen into the air, killing nearly all life on the planet. Our ancestors were among the hardy microorganisms that survived what scientists today call the Great Oxidation Event, the first of two ancient bursts of oxygen that allowed animals to evolve.

“We’re the fragile species,” says Professor Falkowski. “Cyanobacteria will go a long, long time, long after we’re extinct.”

Today, ocean plankton serve as the lungs of our world, absorbing carbon dioxide and oxygen.

Scientists estimate that half the oxygen we breathe has been produced by microorganisms in the ocean. 

“There really are important ways that organisms, and in fact mostly very small microorganisms, can influence large-scale chemical cycles on Earth,” writes Zanna Chase, an oceanographer at the University of Tasmania, in Hobart, Australia, who studies the relationship between microbes and global climate, in an email to the Monitor. “The key mental leap is to recognize that they may be small, but there are lots of them, collectively they can do many things, chemically speaking, and they’re everywhere – in soils, in freshwater, in the surface ocean, the deep ocean, even in deep sea sediments and in the atmosphere.” 

Mighty microbes

Microscopic life can be found everywhere, from the upper stratosphere to miles deep in the Earth’s crust. Near-microscopic animals may even inhabit the moon as marooned colonists: A population of tardigrades – a kind of eight-legged animal that can measure up to the thickness of a credit card – is thought to have survived the crash of an Israeli lunar mission.

Even your own body is home to an entire ecosystem of microbes. Overall, scientists estimate that your microbiome – the 100-trillion-strong population of protozoa, viruses, bacteria, and fungi that make their homes in various parts inside and outside your body and are thought to be essential to your well-being – has 200 times the number of genes that you have. It may weigh up to five pounds. 

“We tend to focus on their immediate health effects on the human body, but microbes have so many more roles in our world,” writes Amy Lam, a postdoctoral fellow in bioengineering at Stanford University, in an email to the Monitor. “It’s kind of humbling to think that we humans could not exist without microbes, but likely a majority of microbial species would continue fine without us.”

Dr. Lam created an exhibit at the San Francisco Exploratorium that allowed visitors to interact with light-sensitive water-dwelling organisms called Euglena. Using projectors, the single-celled Euglena were scaled up to human size.

Dr. Lam’s single-celled participants didn’t always behave as expected, but, she writes, “when interacting with the completed exhibit, I definitely feel more kinship with the cells. Seeing them at my scale and being able to directly stimulate them (interact with them) makes them seem (falsely?) more relatable.”

An ocean of life

When it comes to microbe hospitality, the oceans lay out the welcome mat. In a single milliliter of seawater, one can find 10 million viruses, 1 million bacteria, 1,000 protists, and thousands of fungal cells. 

“In the upper ocean, microbes are extremely ubiquitous,” says Professor Falkowski. “In every drop of water, there are millions – literally millions – of microbes.  They’re everywhere. There’s no place on the planet where there are not microbes.”

These creatures form the basis of marine food webs. Phytoplankton and algae are consumed by zooplankton, small fish, and crustaceans, which are in turn eaten by larger fish, all the way up to top ocean predators like sharks, dolphins, and seals. 

As for humans, the U.N.’s Food and Agriculture Organization estimates that 1 in 10 depend on fish for their primary source of protein, meaning that the nutritional prospects of nearly three quarters of a billion people rest on the well-being of microscopic marine organisms.

Saving the oceans, then, means saving not just the whales, seals, and other animals that grace the marketing materials of ocean conservation advocacy groups, but also looking after all creatures, as Dr. Seuss would say, no matter how small.

Professor Bowler argues that microfauna can be just as charismatic. “No matter what your religious background is, life is beautiful, be it microscopic life, be it larger life.” he says “Life is beautiful with beautiful patterns, beautiful structures.”

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