Microbes

Earth’s hot springs and hydrothermal vents are home to a previously unidentified group of archaea. And, unlike similar tiny, single-celled organisms that live deep in sediments and munch on decaying plant matter, these archaea don’t produce the climate-warming gas methane, researchers report April 23 in Nature Communications.

“Microorganisms are the most diverse and abundant form of life on Earth, and we just know 1 percent of them,” says Valerie De Anda, an environmental microbiologist at the University of Texas at Austin. “Our information is biased toward the organisms that affect humans. But there are a lot of organisms that drive the main chemical cycles on Earth that we just don’t know.”

Archaea are a particularly mysterious group (SN: 2/14/20). It wasn’t until the late 1970s that they were recognized as a third domain of life, distinct from bacteria and eukaryotes (which include everything else, from fungi to animals to plants).

For many years, archaea were thought to exist only in the most extreme environments on Earth, such as hot springs. But archaea are actually everywhere, and these microbes can play a big role in how carbon and nitrogen cycle between Earth’s land, oceans and atmosphere. One group of archaea, Thaumarchaeota, are the most abundant microbes in the ocean, De Anda says (SN: 11/28/17). And methane-producing archaea in cows’ stomachs cause the animals to burp large amounts of the gas into the atmosphere (SN: 11/18/15).

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Now, De Anda and her colleagues have identified an entirely new phylum — a large branch of related organisms on the tree of life — of archaea. The first evidence of these new organisms were within sediments from seven hot springs in China as well as from the deep-sea hydrothermal vents in the Guaymas Basin in the Gulf of California. Within these sediments, the team found bits of DNA that it meticulously assembled into the genetic blueprints, or genomes, of 15 different archaea.

The researchers then compared the genetic information of the genomes with that of thousands of previously identified genomes of microbes described in publicly available databases. But “these sequences were completely different from anything that we know,” De Anda says.

She and her colleagues gave the new group the name Brockarchaeota, for Thomas Brock, a microbiologist who was the first to grow archaea in the laboratory and who died in April. Brock’s discovery paved the way for polymerase chain reaction, or PCR, a Nobel Prize–winning technique used to copy small bits of DNA, and currently used in tests for COVID-19 (SN: 3/6/20).

Brockarchaeota, it turns out, actually live all over the world — but until now, they were overlooked, undescribed and unnamed. Once De Anda and her team had pieced together the new genomes and then hunted for them in public databases, they discovered that bits of these previously unknown organisms had been found in hot springs, geothermal and hydrothermal vent sediments from South Africa to Indonesia to Rwanda.

Within the new genomes, the team also hunted for genes related to the microbes’ metabolism — what nutrients they consume and what kind of waste they produce. Initially, the team expected that — like other archaea previously found in such environments — these archaea would be methane producers. They do munch on the same materials that methane-producing archaea do: one-carbon compounds like methanol or methylsulfide. “But we couldn’t identify the genes that produce methane,” De Anda says. “They are not present in Brockarchaeota.”

That means that these archaea must have a previously undescribed metabolism, through which they can recycle carbon — for example in sediments on the seafloor — without producing methane. And, given how widespread they are, De Anda says, these organisms could be playing a previously hidden but significant role in Earth’s carbon cycle.

“It’s twofold interesting — it’s a new phylum and a new metabolism,” says Luke McKay, a microbial ecologist of extreme environments at Montana State University in Bozeman. The fact that this entire group could have remained under the radar for so long, he adds, “is an indication of where we are in the state of microbiology.”

But, McKay adds, the discovery is also a testimonial to the power of metagenomics, the technique by which researchers can painstakingly tease apart individual genomes out of a large hodgepodge of microbes in a given sample of water or sediments. Thanks to this technique, researchers are identifying more and more parts of the previously mysterious microbial world.

“There’s so much out there,” De Anda says. And “every time you sequence more DNA, you start to realize that there’s more out there that you weren’t able to see the first time.” More

Clouds may be ecosystems — Science News, November 14, 1970
Clouds in the sky may contain living microbial ecosystems…. [Research] determined that metabolic activity, in the form of CO2 uptake into organic material, occurred in [airborne] dust over a 24-hour period, whereas it did not occur in sterilized control dust.
Update
The atmosphere is rich in microbial life. One census documented some 28,000 bacterial species in samples of water from clouds above a mountain in France, scientists reported in 2017. Research building over the last decade or so has supported the claim that some bacteria may indeed be metabolically active within their hazy abodes. One species of B­acillus, for example, eats sugar floating in the atmosphere to build a coating — perhaps to shield itself from ultraviolet radiation and low temperatures (SN: 2/7/15, p. 5). Some scientists suspect cloud bacteria contribute to Earth’s carbon and nitrogen cycles, and even influence weather (SN: 6/18/11, p. 12). The microbes can spur ice crystals to form, triggering rain and snow — and a ride back to Earth’s surface. More

Scientists have discovered the first bacteria known to use the metal manganese to grow. And the researchers had to look only as far as the office sink.
“It’s definitely an interesting story about serendipity,” says Jared Leadbetter, an environmental microbiologist at Caltech. He and Hang Yu, also an environmental microbiologist at Caltech, report their fortuitous find in the July 16 Nature.
Leadbetter had been working with a pink compound called manganese carbonate in a glass jar. After having trouble cleaning the jar, he filled it with tap water and left it to soak. When he returned 10 weeks later, after an out-of-town teaching stint, the contents of the jar had transformed into a dark, crusty material.
Leadbetter knew that scientists had long suspected that bacteria could use manganese to fuel growth. Over a century ago, researchers discovered that bacteria could borrow electrons from chemical elements like nitrogen, sulfur, iron — and manganese. In some cases, bacteria could even use these electrons to fuel growth in much the same way that humans use electrons from carbohydrates in the diet for energy. But no one had identified bacteria that could turn electrons from manganese into energy.  

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When bacteria do borrow electrons from manganese, they convert the metal to a dark material called manganese oxide. Manganese oxide is found all over the planet — from deposits in Earth’s crust to the seafloor to drinking water. And, as it turned out, in Leadbetter’s glass jar.
He wondered if the bacteria that had oxidized his manganese might be the elusive species that actually use manganese to grow. “Maybe I better not pour this down the sink,” he thought.  
Leadbetter and Yu first identified about 70 bacterial species in the jar, which likely came from the tap water. The pair then isolated two bacterial species that, when present together, generate manganese oxide. Given manganese carbonate, these bacteria multiplied exponentially. As the bacterial population size increased, the rate of manganese oxide production increased along with it, suggesting that the bacteria were using manganese as fuel.
The team dubbed the newly identified species ‘Candidatus Manganitrophus noduliformans’ and Ramlibacter lithotrophicus. The researchers don’t yet know the exact role of each species. Both might be integral in generating energy from the manganese or one could be the main driver.
Epifluorescence microscopy captures two newly discovered bacterial species (in magenta and green) on manganese oxide. Researchers don’t know yet whether the species work together to generate energy from manganese or whether one is just along for the ride.H. Yu and J.R. Leadbetter/Nature 2020
The findings could help researchers manage manganese oxide that pollutes drinking water, says Amy Pruden, an environmental scientist at Virginia Tech in Blacksburg who was not involved in the study. “Now that we have an idea of who the manganese oxidizers are, we can start looking for them in drinking water systems and maybe we can find better controls.”
Leadbetter suspects that similar bacteria may also be responsible for grapefruit-sized balls of manganese oxide on the ocean floor, first spotted in the 1870s, that have puzzled scientists. He wants to search there and other places for more examples of bacteria that use manganese for energy. 
“Let’s see if we can find these organisms in other environments,” Leadbetter says. “Not just my sink.” More