Victoria Orphan has loved the ocean for as long as she can remember. She used to snorkel in the Pacific Ocean near her family’s home in San Diego, Calif. She’d grab her mask and snorkel tube to visit the hidden world of plants and animals beneath the ocean’s surface. Orphan went to college at the University of California, Santa Barbara in the early 1990s. There she discovered something that changed the way she thought about the oceans — and life on Earth.
Another student showed her a small vial of seawater. Orphan didn’t think it looked all that interesting. It was just plain old water. Then the other student added a fluorescent chemical to the water and shined ultraviolet light on it. The tube lit up as millions of tiny bacteria began to glow. Just moments earlier, the microbes had been invisible. “These tiny organisms were all over the place,” says Orphan, “and yet we couldn’t see them. We knew almost nothing about them.”
She now spends her days exploring this hidden single-celled world. As a geobiologist at Caltech in Pasadena, Calif., she studies how bacteria and other microscopic life shape the deep sea.
Bacteria play central roles in many ecosystems. These include the oceans, soil and atmosphere. They’re also a big part of the global food web. Bacteria make it possible for all other life on Earth to exist. That’s why scientists say these single-celled organisms are the invisible backbone of all life — at least on Earth.
Yet there’s plenty we don’t know about them. Scientists think they’ve identified fewer than one percent of all bacterial species. That’s been driving Orphan and others to explore the mysteries of their one-celled world. They suspect bacteria will prove key to understanding — and protecting — Earth’s most important natural resources.
The methane eaters
Some bacteria eat really weird things. Scientists have found bacteria that eat rocks, sewage — even nuclear waste. Orphan studies a type of bacteria that live on the sea floor and gobble up methane.
Methane is a greenhouse gas. Like carbon dioxide and some other greenhouse gases, it enters the air when people burn oil, gas and coal. There are also natural sources of methane, such as natural gas, rice production and cow manure. Greenhouse gases trap heat in the atmosphere. An excess of these gases in Earth’s atmosphere has been warming the global climate.
Methane can seep out of the Earth on the sea floor. Some scientists say that even more methane would escape into the atmosphere if it wasn’t for marine bacteria. Certain of those bacteria dine on methane. That allows the oceans to trap a huge amount of the gas. “These microorganisms are the gatekeepers. They prevent ocean methane from getting into the atmosphere where it can change greenhouse-gas levels,” Orphan explains.
Finding single-celled organisms on the vast sea floor can be a challenge. Through the window of a submarine, she looks for clusters of clams and giant tube worms. These organisms signal that invisible marine bacteria live there, too. Wherever those methane-eaters live, they create new molecules as they dine. Other organisms use those new molecules as food. An entire food web springs up on the ocean floor.
Orphan and her team have found methane-eating bacteria along cracks on the sea floor, where this gas is seeping out. These cracks often happen where two tectonic plates bump into each other.
Some bacteria, they learned, can eat methane only by partnering with other single-celled organisms called archaea (Ar-KEE-uh). That important detail could help scientists better predict how much methane is escaping into the air, says Orphan.
In the trenches
Methane eaters aren’t the only deep-sea bacteria to interest scientists. “The deep sea is home to some pretty cool microbes,” says Jennifer Biddle. She’s a marine microbiologist at the University of Delaware in Newark. Biddle studies bacteria that live in deep ocean trenches.
These underwater canyons are some of the least-studied places on Earth. They are incredibly hard to reach. Challenger Deep wins the record for the deepest-known spot on the planet. At the bottom of the Mariana Trench, in the western Pacific, Challenger Deep sits some 11 kilometers (more than 7 miles) below the ocean surface. If Mount Everest, the world’s tallest mountain, sat in the Mariana Trench, its peak would still be more than a mile beneath the waves.
The Mariana Trench is one of the toughest places for life to survive. Zero sunlight reaches it. Its temperatures are frigid. Large animals, such as whales or fish, can’t visit because the intense pressures there would crush them. Little surprise, then, that most of the locals are microscopic. They have adapted its extreme conditions.
Biddle and other scientists teamed up with deep-ocean explorers to send a submarine to Challenger Deep. James Cameron piloted the vessel. (He’s the movie director famous for Avatar and Titanic.) Cameron visited the bottom of Challenger Deep in March 2012 while making a documentary called Deepsea Challenge 3D. But the sub’s trek wasn’t just to get mesmerizing video for the Big Screen. The vessel also brought back sediment from the bottom of the trench.
Biddle and the other scientists screened that sediment for DNA. They were scouting for genes of familiar bacteria. They turned up evidence of some known as Parcubacteria.
Scientists didn’t even know this big group of bacteria existed until 2011. Back then, they found some in groundwater and dirt from a few places on land. But Biddle’s group now showed it also survives in one of the most inaccessible depths of the ocean.
Here, on the trench floor, the microbes were breathing nitrogen, not oxygen (as they did on land). And that makes sense. They had adapted to nitrogen since their home had little access to oxygen.
The more places we find such little-known bacteria, says Biddle, the more we can learn about what they do for their ecosystems.
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From bread to biofuels
Even the bacteria in our kitchens and compost heaps interest scientists.
Sourdough bread gets its unique tart flavor when a mix of bacteria munches on the sugars in bread flour. Those bacteria make carbon dioxide, acids and other flavorful compounds. But to function, sourdough bacteria need their friends. Isolate just one bacterial species from the mix and the chemical reaction won’t happen. No sourdough.
Microbiologist Steve Singer lives near San Francisco, a California city famous for sourdough bread. He works for the Department of Energy at Lawrence Berkeley National Laboratory. And he suspected he could use the lessons of sourdough to make better biofuels. These plant-based fuels can power cars or trucks. They are considered “green,” meaning more Earth-friendly, than fossil fuels.
To make biofuels, scientists must break down plants into sugars. These sugars can then be turned into fuels such as ethanol (a type of alcohol). The chemical reactions that break down the plants require help from enzymes. These are molecules that jump-start or speed up chemical reactions.
The enzymes currently used to make biofuels are expensive. They also don’t work well, Singer says. That’s why researchers all over the world are searching for enzymes that might lower the cost and speed the production of biofuels.
He turned his search for them to the compost pile. There, bacterial communities were hard at work breaking down rotting fruits and veggies.
Singer took a small sample of the compost back to his lab. There, he let bacteria from the compost grow in a beaker. Later, he collected enzymes that these bacteria made and tested them on other plant bits. It worked: The enzymes broke down the plants into sugars.
Just as the sourdough bacteria need their friends to function, Singer discovered that these microbes produced the useful enzymes only when they were part of robust communities of different compost bacteria. Singer is now scaling up his project. His team is growing bacteria in huge vats called bioreactors. After he makes lots of the new enzymes, he can test whether they work better than existing ones for converting plant wastes into fuels.
“Taking something from the environment and trying to figure out how it works is one of the best parts of being a microbiologist,” Singer says.
Singer is studying his new enzymes without knowing which bacteria are making them. This isn’t all that unusual. Bacteria are invisible to the unaided eye. Even with a microscope, telling two species apart can be hard. They don’t look as different as might two species of birds or flowers.
Scientists needed a different way to tell bacteria apart and know when they’ve stumbled upon new ones. Key to this sleuthing: DNA.
All organisms shed a little DNA throughout their environment. “It’s like a fingerprint. Each is unique,” explains Kelly Ramirez. She studies bacteria at the Netherlands Institute of Ecology in Wageningen.
Swab your kitchen counter and you might find human DNA (from you and your parents). There might be some plant DNA (from the veggies you just cut up) and from a fungus or two. There might even be some dog or cat DNA if you have a pet. You’ll also get a bunch of bacterial DNA because, well, bacteria a everywhere!
All of the cast-off genetic bits are known as environmental DNA, or eDNA.
Scientists can use these genetic fingerprints to discover new bacteria, notes Ramirez. They just need to bring any little bit of dirt or seawater or compost to a lab and check out what’s in it.
The sum of all the genetic material in an environment is called the metagenome (MET-uh-GEE-noam). Think of it as a DNA soup. All the molecules used to build the genes of different organisms are jumbled together.
Scientists use computers to untangle the mess.
Like a sieve, computer programs filter the soup. They look for familiar patterns known as genetic sequences. They form an organism’s DNA fingerprint. If scientists find a fingerprint they don’t recognize, it may be because it’s from some new species.
Scientists can compare these patterns to the fingerprints of familiar bacteria to see where the new bacteria fall within the tree of life. “We can now discover new microbes without ever seeing them,” explains Biddle at the University of Delaware.
The bacterial limb of the tree of life is sprouting new shoots and branches faster than at any time in history. Thirty years ago, all known single-celled organisms on the planet fit into a dozen major groups. Now there are about 120 known groups, or phyla (FY-lah). And the number of named bacteria in each group grows daily.
Little life, big data
What do you get when you add up the DNA sequences of millions of new bacteria? Lots and lots of data.
You can think about the planet as a machine, and all the ecosystems on Earth as the machine’s parts, says Jack Gilbert. All these data on bacterial DNA are key to “understanding the parts that make up the machine and how they all work together,” he says. Gilbert is a microbiologist at Argonne National Laboratory near Chicago, Ill.
His team is trying to organize those data into a virtual catalog of all the bacteria on Earth. It’s called the Earth Microbiome Project. More than 1,000 scientists around the world are helping collect samples. They’re looking in a host of different environments, then testing them for bacterial DNA.
So far the researchers have collected 100,000 samples. They’ve catalogued bacteria from the deepest ocean. They’ve found bacteria on the International Space Station, some 350 kilometers (220 miles) above Earth. They’ve discovered bacteria in exotic locations like the Amazon rainforest and ordinary places like public toilets.
Discovering which bacteria lurk there — and why — is the first step to understanding how different ecosystems drive the vast machine we think of as life on Earth. Learning about bacteria may help us answer questions about how our planet works, Gilbert says. Bacteria may explain why coral reefs in the ocean teem with life. Or they could explain why the soils of the North American prairie are so good for planting crops.
That’s why this search is so important, he says: “This is knowledge that can help us take better care of the planet.”
archaea (singular: archaeon) A domain of life that includes single-celled organisms. Although archaea superficially resemble bacteria, they are distinct. Archaea inhabit many harsh environments.
Argonne National Laboratory A federal laboratory owned by the U.S. Department of Energy, outside of Chicago, Ill. It was formally created on July 1, 1946. Today, its roughly 1,400 scientists and engineers (and 1,000 students) conduct research across a broad range of fields, from biology and physics to materials science, energy development and climate studies.
atmosphere The envelope of gases surrounding Earth or another planet.
bacteria (singular: bacterium; adj. bacterial) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals).
biofuels Energy sources derived from carbon stored in living organisms. Although wood is a biofuel, most people who support “green” sources of energy consider biofuels to be liquids that can substitute for gasoline. Examples include bioethanol, an alcohol derived from crops such as corn or sugarcane. Engineers are also developing ways to make biofuels from nonfood crops, such as trees and shrubs. Renewable biofuels are an alternative to nonrenewable fossil fuels.
carbon dioxide (or CO2) A colorless, odorless gas produced by all animals when the oxygen they inhale reacts with the carbon-rich foods that they’ve eaten. Carbon dioxide also is released when organic matter burns (including fossil fuels like oil or gas). Carbon dioxide acts as a greenhouse gas, trapping heat in Earth’s atmosphere. Plants convert carbon dioxide into oxygen during photosynthesis, the process they use to make their own food.
chemical A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.
chemical reaction A process that involves the rearrangement of the molecules or structure of a substance, as opposed to a change in physical form (as from a solid to a gas).
climate The weather conditions that typically exist in one area, in general, or over a long period.
compost The end product in the breakdown, or decomposition, of leaves, plants, vegetables, manure and other once-living material. Compost is used to enrich garden soil, and earthworms sometimes aid this process.
compound (often used as a synonym for chemical) A compound is a substance formed when two or more chemical elements unite (bond) in fixed proportions. For example, water is a compound made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.
computer program A set of instructions that a computer uses to perform some analysis or computation. The writing of these instructions is known as computer programming.
DNA (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.
documentary A type of movie or television program that takes its name from the fact that it attempts to document actual real-life events.
ecology A branch of biology that deals with the relations of organisms to one another and to their physical surroundings. A scientist who works in this field is called an ecologist.
ecosystem A group of interacting living organisms — including microorganisms, plants and animals — and their physical environment within a particular climate. Examples include tropical reefs, rainforests, alpine meadows and polar tundra. The term can also be applied to elements that make up some an artificial environment, such as a company, classroom or the internet.
environment The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of components in some electronics system or product).
environmental DNA (also eDNA ) A tool for detecting the presence of a species solely from the genetic material (DNA) it has left in the environment.
enzymes Molecules made by living things to speed up chemical reactions.
ethanol A type of alcohol, also known as ethyl alcohol, that serves as the basis of alcoholic drinks, such as beer, wine and distilled spirits. It also is used as a solvent and as a fuel (often mixed with gasoline, for instance).
exotic An adjective to describe something that is highly unusual, strange or foreign (such as exotic plants).
filter (in chemistry and environmental science) A device or system that allows some materials to pass through but not others, based on their size or some other feature.
fluorescent (v. fluoresce) Adjective for something that is capable of absorbing and reemitting light. That reemitted light is known as fluorescence.
food web (also known as a food chain) The network of relationships among organisms sharing an ecosystem. Member organisms depend on others within this network as a source of food.
fossil Any preserved remains or traces of ancient life. There are many different types of fossils: The bones and other body parts of dinosaurs are called “body fossils.” Things like footprints are called “trace fossils.” Even specimens of dinosaur poop are fossils. The process of forming fossils is called fossilization.
fossil fuel Any fuel — such as coal, petroleum (crude oil) or natural gas — that has developed within the Earth over millions of years from the decayed remains of bacteria, plants or animals.
fuel Any material that will release energy during a controlled chemical or nuclear reaction. Fossil fuels (coal, natural gas and petroleum) are a common type that liberate their energy through chemical reactions that take place when heated (usually to the point of burning).
function A relationship between two or more variables in which one variable (the dependent one) is exactly determined by the value of the other variables.
fungus (plural: fungi) One of a group of single- or multiple-celled organisms that reproduce via spores and feed on living or decaying organic matter. Examples include mold, yeasts and mushrooms.
gene (adj. genetic) A segment of DNA that codes, or holds instructions, for a cell’s production of a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.
genetic sequence A string of DNA bases, or nucleotides, that provide instructions for building molecules in a cell. They are represented by the letters A,C,T and G.
greenhouse gas A gas that contributes to the greenhouse effect by absorbing heat. Carbon dioxide is one example of a greenhouse gas.
groundwater Water that is held underground in the soil or in pores and crevices in rock.
host (in biology and medicine) The organism (or environment) in which some other thing resides. Humans may be a temporary host for food-poisoning germs or other infective agents.
International Space Station An artificial satellite that orbits Earth. Run by the United States and Russia, this station provides a research laboratory from which scientists can conduct experiments in biology, physics and astronomy — and make observations of Earth.
Mariana trench A deep, crescent-shaped canyon running along the Pacific Ocean floor east of the Philippines. It’s massive, some 2,550 kilometers (1,500 miles) long and 70 kilometers (43 miles) wide, on average. The trench marks where two of Earth’s tectonic plates are colliding, forcing one to dive beneath the other.
marine Having to do with the ocean world or environment.
metagenome The sum of all genetic material in an organism.
methane A hydrocarbon with the chemical formula CH4 (meaning there are four hydrogen atoms bound to one carbon atom). It’s a natural constituent of what’s known as natural gas. It’s also emitted by decomposing plant material in wetlands and is belched out by cows and other ruminant livestock. From a climate perspective, methane is 20 times more potent than carbon dioxide is in trapping heat in Earth’s atmosphere, making it a very important greenhouse gas.
microbe Short for microorganism. A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.
microbiology The study of microorganisms, principally bacteria, fungi and viruses. Scientists who study microbes and the infections they can cause or ways that they can interact with their environment are known as microbiologists.
microbiome The scientific term for the entirety of the microorganisms — bacteria, viruses, fungi and more — that take up permanent residence within the body of a human or other animal.
microscope An instrument used to view objects, like bacteria, or the single cells of plants or animals, that are too small to be visible to the unaided eye.
molecule An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).
nitrogen A colorless, odorless and nonreactive gaseous element that forms about 78 percent of Earth's atmosphere. Its scientific symbol is N. Nitrogen is released in the form of nitrogen oxides as fossil fuels burn.
organism Any living thing, from elephants and plants to bacteria and other types of single-celled life.
oxygen A gas that makes up about 21 percent of Earth's atmosphere. All animals and many microorganisms need oxygen to fuel their growth (and metabolism).
Pacific The largest of the world’s five oceans. It separates Asia and Australia to the west from North and South America to the east.
prairie A type of fairly flat and temperate North American ecosystem characterized by tall grasses, fertile soils and few trees.
pressure Force applied uniformly over a surface, measured as force per unit of area.
rainforest Dense forest rich in biodiversity found in tropical areas with consistent heavy rainfall.
reef A ridge of rock, coral or sand. It rises up from the seafloor and may come to just above or just under the water’s surface.
sea An ocean (or region that is part of an ocean). Unlike lakes and streams, seawater — or ocean water — is salty.
seawater The salty water found in oceans.
sediment Material (such as stones and sand) deposited by water, wind or glaciers.
sewage Wastes — primarily urine and feces — that are mixed with water and flushed away from homes through a system of pipes for disposal in the environment (sometimes after being treated in a big water-treatment plant).
species A group of similar organisms capable of producing offspring that can survive and reproduce.
submarine A term for beneath the oceans. (in transportation) A ship designed to move through the oceans, totally submerged. Such ships — especially those used in research — are also known as submersibles.
tectonic plates The gigantic slabs — some spanning thousands of kilometers (or miles) across — that make up Earth’s outer layer.
tree of life A diagram that uses a branched, treelike structure to show how organisms relate to one another. Outer, twiglike, branches represent species alive today. Ancestors of today’s species will lie on thicker limbs, ones closer to the trunk.
ultraviolet light A type of electromagnetic radiation with a wavelength from 10 nanometers to 380 nanometers. The wavelengths are shorter than that of visible light but longer than X-rays.
unique Something that is unlike anything else; the only one of its kind.
virtual Being almost like something. An object or concept that is virtually real would be almost true or real — but not quite. The term often is used to refer to something that has been modeled — by or accomplished by — a computer using numbers, not by using real-world parts. So a virtual motor would be one that could be seen on a computer screen and tested by computer programming (but it wouldn’t be a three-dimensional device made from metal).
waste Any materials that are left over from biological or other systems that have no value, so they can be disposed of as trash or recycled for some new use.
wave A disturbance or variation that travels through space and matter in a regular, oscillating fashion.
Journal: S.E. McGlynn et al. Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy. Applied and Environmental Microbiology. Apr. 6, 2018. doi: 10.1128/AEM.00399-18.
Journal: K.S. Ramirez et al. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology. Vol. 3, Nov. 20, 2017, p. 189. doi: 10.1038/s41564-017-0062-x.
Journal: S. Kolinko et al. A bacterial pioneer produces cellulase complexes that persist through community succession. Nature Microbiology. Vol. 3, Nov. 6, 2017, p. 99. doi: 10.1038/s41564-017-0052-z.
Journal: R. Leon-Zayas et al. The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1). Environmental Microbiology. Vol. 19, Jul. 2017, p. 2769. doi: 10.1111/1462-2920.13789.