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CLOUD MICROBIOMES

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Posted on 2019/10/17 by secret santa

“Living bacteria were found on the surface of the International Space Station. Scientists explained that bacteria and plankton may have gotten there due to ionosphere lift, in which substances from our planet’s surface rise to the upper atmospheric layer. Following the discovery, Roscosmos suggested raising the upper border of the biosphere to 400 kilometers from the current altitude of 20 kilometers.”

AEROMICROBIOLOGY
https://microbewiki.kenyon.edu/index.php/Aeromicrobiology
https://www.cnet.com/international-space-station-bacteria-nasa-space-walk/
https://www.livescience.com/loads-of-bacteria-hiding-out-in-storm-clouds.html
https://www.wired.com/2011/05/microbes-make-rain/
Aerial Microbes Can Make Rain
by Janet Raloff / 05.24.11

“Even when the hosts are high-altitude parcels of air, microbes can be a source of inclement conditions, a Montana research team finds. Cloudborne bacteria might even pose climate threats by boosting the production of a greenhouse gas, another team proposes. Both groups reported their findings May 24 at the American Society for Microbiology meeting in New Orleans. These data add to a growing body of evidence that biological organisms are affecting clouds, notes Anthony Prenni of Colorado State University in Fort Collins, an atmospheric scientist who did not participate in the new studies. Right now, he cautions, “We still don’t know on a global scale how important these processes are.” But research into microbial impacts on weather and climate is really heating up, he adds, so “within a few years, I think we’re going to have a much better handle on it.” Alexander Michaud’s new research was triggered by a June storm that pummeled Montana State University’s campus in Bozeman last year with golf-ball–sized and larger hailstones. The microbial ecologist normally studies subglacial aquatic environments in Antarctica. But after saving 27 of the hailstones, he says, “I suddenly realized, no one had really ever thought about studying hailstones — in a layered sense — for biology.” So his team dissected the icy balls, along with hundreds of smaller ones collected during a July hail storm south of campus. Michaud now reports finding germs throughout, with the highest concentrations by far — some 1,000 cells per milliliter of meltwater — in the hailstones’ cores.

Since at least the 1980s, scientists have argued that some share of clouds, and their precipitation, likely traces to microbes. Their reasoning: Strong winds can loft germs many kilometers into the sky. And since the 1970s, agricultural scientists have recognized that certain compounds made by microbes serve as efficient water magnets around which ice crystals can form at relatively high temperatures – occasionally leading to frost devastation of crops. In 2008, Brent Christner of Louisiana State University in Baton Rouge and his colleagues reported isolating ice-nucleating bacteria from rain and snow. A year later, Prenni’s group found microbes associated with at least a third of the cloud ice-crystals they sampled at an altitude of 8 km. “But finding ice-nucleating bacteria in snow or hail is very different from saying they were responsible for the ice,” says Noah Fierer of the University of Colorado at Boulder. “I say that,” he admits, “even though as a microbiologist, I’d love to believe that bacteria control weather.” Pure water molecules won’t freeze in air at temperatures above about minus 40 degrees Celsius [minus 40 F], Christner notes. Add tiny motes of mineral dust or clay, and water droplets may coalesce around them — or nucleate — at perhaps minus 15 C [5 F]. But certain bacteria can catalyze ice nucleation at even minus 2 C [28 F], he reported at the meeting in New Orleans. Through chemical techniques, Michaud’s group determined that the ice nucleation in their hail occurred around minus 11.5 C [11.3 F] for the June hailstones and at roughly minus 8.5 C [16.7 F] for the July stones. Michaud’s data on the role of microbes in precipitation “is pretty strong evidence,” Prenni says.

Also at the meeting, Pierre Amato of Clermont University in Clermont-Ferrand, France, reported biological activity in materials sampled from a cloud at an altitude of 1,500 meters. The air hosted many organic pollutants, including formaldehyde, acetate and oxalate. Sunlight can break these down to carbon dioxide, a greenhouse gas, something Amato’s group confirmed in the lab. But sunlight didn’t fully degrade some organics unless microbes were also present. Moreover, certain cloudborne bacteria — the French team identified at least 17 types — degraded organic pollutants to carbon dioxide at least as efficiently as the sun did. Amato’s team reported these findings online Feb. 9 in Atmospheric Chemistry and Physics Discussions. This microbial transformation of pollutants to carbon dioxide occurs even in darkness. Amato has calculated the total nighttime microbial production of carbon dioxide in clouds and pegs it “on the order of 1 million tons per year.” Though not a huge sum – equal to the carbon dioxide from perhaps 180,000 cars per year – he cautions that this amount could increase based on airborne pollutant levels, temperatures and microbial populations.”

“Natasha DeLeon-Rodriguez shows agar plates on which bacteria taken from tropospheric air samples are growing”

BIOPRECIPITATION
https://www.bbc.co.uk/sounds/play/b00l0xxn
https://repository.library.noaa.gov/view/noaa/18059/Email
https://envs.au.dk/en//the-microbiology-of-the-air/how-to-collect-microorganisms-in-air/
https://www.nytimes.com/2015/02/15/magazine/its-buggy-out-there.html
by Ferris Jabr / Feb. 13, 2015

“Hunter Mountain, a three-hour drive northwest of New York, calls itself the Snow-Making Capital of the World. When operating at maximum capacity, the ski resort’s 1,100 or so snow guns can blanket 240 acres with as much as three feet of snow in just two days. The recipe for all that manufactured powder is pretty simple — mostly water and air. But there’s often another, rather surprising ingredient: a bacterial protein that works like Kurt Vonnegut’s ice-nine, the fictional substance that instantly freezes water. Scientists have long known that certain terrestrial microbes perform this alchemy. In recent years, however, new discoveries have increasingly persuaded them that such micro-organisms live a double life in the sky, manipulating the weather for their own benefit.

Pure water does not automatically freeze at 0 degrees Celsius; it will remain liquid to about minus 40 degrees. To freeze at higher temperatures, water needs a seed, or ice nucleus, a tiny particle that acts as a geometric template, aligning water molecules into a highly organized solid crystal. In the atmosphere, invisible water vapor condenses on dust, soot and salt to form globules of liquid water, which can in turn freeze. Clouds are visible agglomerations of condensed water or ice crystals or both. When the water and ice in clouds become heavy enough to overcome air resistance, they fall as rain or snow. Because suspended ice nuggets typically grow more quickly than water droplets, rain often starts as snow that melts as it drops. “Almost all rain that falls on land, even over the Sahara and along the tropics, is first an ice crystal,” says Russell Schnell of the National Oceanic and Atmospheric Administration.

In the 1970s, scientists discovered that evolution had produced its own ice-seeder: Pseudomonas syringae, a bacterium with an ice-nucleating protein that causes frostbite in plants, wounding their tissues to access their nutrients. These sterilized proteins became the primary component of Snomax, a powder used by ski resorts worldwide. Strong air currents routinely whisk P. syringae — and all kinds of bacteria, fungi and algae from land and sea — into celestial colonies for weeks at a time. It turns out that P. syringae is not the only one of them harboring ice-seeding proteins; many microbes move fluidly between land, sea and sky, returning to earth inside rain, hail and snow. In doing so, these Lilliputian aeronauts may influence the planet in profound ways that have been largely overlooked until now. “The whole concept has definitely gained a lot of traction in recent years,” says David Sands, a professor of plant pathology at Montana State University. “We need to recognize these microbes as a part — maybe even a major part — of meteorological processes.”

The possibility that the atmosphere teems with unseen life has intrigued scientists since the advent of microbiology in the 17th century. Antonie van Leeuwenhoek, one of the first people to document the existence of microbes, surmised the existence of “living creatures in the air, which are so small as to escape our sight.” In the 1800s, while aboard the H.M.S. Beagle, Charles Darwin collected windswept dust over the Atlantic that was found to be full of microbes. It was not until the late 20th century, however, that researchers began to consider these microbes as more than passive travelers. In 1978, searching for the origins of a P. syringae outbreak in Montana wheat fields, Sands flew a Cessna through the clouds above the crops, sticking petri dishes through a porthole. P. syringae soon grew in those dishes.

In the 1980s, Sands formally proposed the theory of bioprecipitation: the notion that some bacteria disperse themselves through an elaborate rain dance. “At the time, a lot of people thought it was crazy,” says Cindy Morris, who works for the French National Institute for Agriculture Research and is Sands’s longtime collaborator. The theory was largely neglected for more than two decades. Now, thanks to renewed interest, “no one is telling us we are crazy anymore,” Morris says. In 2005 and 2006, Sands, Morris and their colleagues collected fresh snow on three continents. Neary every sample contained ice-nucleating microbes, including plant-dwelling bacteria that had made it all the way to barren Antarctica. A few years later, scientists in Europe and the United States concluded that thunderclouds suck up a variety of microbes from below, many of which they later found in the very centers of hailstones. Other researchers analyzed cloud water and measured, on average, tens of thousands of bacteria in each milliliter. In the late 2000s, an international team of scientists discovered that the Amazon rain forest promotes its own rainfall in part by producing airborne salts, fungal spores and bacteria. And most recently, using a century of weather data, Morris and a couple of colleagues have found statistical support for a bioprecipitation feedback loop: The more intense a rainstorm, the more frequent and intense the storms in the days and weeks ahead, because heavy downpours kick up microscopic life into the air.

Scientists once believed that ice-nucleating proteins evolved primarily as a way for P. syringae and its ilk to feed on plants and only secondarily as an opportunistic means of air travel. But P. syringae does not always live on plants; it’s also found in rivers and lakes. Evolutionary relationships among different ice-making bacteria indicate that the first ice-nucleating proteins emerged 1.75 billion years ago, long before plants colonized land. Back then, Morris and Sands propose, these proteins probably helped microbes survive freezing water and major glaciations, perhaps by sequestering damaging ice crystals outside their cells. Over the eons, ocean waves and powerful winds would have carried microbes into the atmosphere, exposing them to intense ultraviolet light (which can mutate DNA), starvation and desiccation. Bacteria with ice-nucleating proteins would have enjoyed a huge advantage over others: a return ticket. And microbes that could survive long enough to travel great distances would have expanded their range and possibly found more favorable habitats, as the biologist W. D. Hamilton theorized. The types of bacteria that scientists are finding in precipitation today possess a number of skills that may be adaptations to an ancient familiarity with the high life: pigments that act like sunscreen, for example, and the ability to feed solely on molecules commonly found in cloud water. One study even concluded that certain bacteria can reproduce within clouds.

The phenomenon of weather-shifting microbes is at once global and regional: Each type of terrain — and its unique microbial community — interacts with the atmosphere in a particular way. At the same time, the continents “sneeze on each other,” as David J. Smith of NASA has written, flinging dust and microbes along streams of turbulent air that span oceans. To address this complexity, aerobiologists are turning to increasingly sophisticated tools: mountaintop laboratories that intercept transoceanic sneezes and nimble drones equipped with microbe-identifying sensors. “One reason there wasn’t a lot of progress for a while was technological limitations,” says Kostas Konstantinidis, a microbiologist at the Georgia Institute of Technology. “I think we will see a lot of exciting developments in the next few years.” Now that it’s been reinvigorated, aerobiology is churning up all kinds of questions in diverse fields, including agriculture. Razing a forest to create cropland has obvious ecological consequences on the ground, for example — what if these extend to the sky? Farming transforms a landscape’s microbiome, which in turn alters the density and diversity of micro-organisms swept into the surrounding atmosphere. “Maybe we can influence the feedback loops by changing the way we farm,” Morris says. “We already use agriculture for food, medicine and fuels. Why not try making rain?”

BIOAEROSOLS
https://en.wikipedia.org/wiki/Bioaerosol
https://health.ucsd.edu/2017-11-01-mapping-the-microbiome-of-everything.aspx
https://www.semanticscholar.org/paper/Microbiology-of-Aerosols-Delort-Amato/
https://www.asmscience.org/content/journal/microbe/10.1128/microbe.7.119.1
Clouds Disseminate Microbes, Which Can Drive Precipitation
by Pierre Amato with Marlene Cimons / January 2012

“When thermodynamic conditions prove favorable in the atmosphere, water vapor condenses on aerosol particle surfaces, forming micrometer-sized droplets or ice crystals constituting clouds. Even though clouds gather only 0.03% of the fresh water on Earth, they are important components of climate, acting as filters to solar and infrared radiation entering and leaving the planet. Moreover, they provide a multiphasic mixture of liquid, solid, and gas to support chemical reactions affecting the composition of the atmosphere. When scientists began collecting air samples at high altitudes from mountains, balloons, and, later, airplanes, they learned that living bacteria and fungi are present within the atmosphere. Because condensed water can protect airborne microbial cells against desiccation, aerobiologists consider clouds atmospheric oases. On a global scale, the total number of microorganisms in clouds reaches about 10 ¹⁹. Although this estimate seems low compared with the 10 ²⁶ microorganisms estimated to occupy lakes and rivers and to the 10 ²⁹ microorganisms in oceans, microbial levels in clouds appear sufficient to affect physicochemical processes in the atmosphere. Additionally, clouds could play a major role in disseminating microbes over long distances.

“Culture of bacteria from cloud water” (Pierre Amato)

Summary

Although low in number compared to the 10 ²⁹ microbes estimated in oceans, the 10 ¹⁹ microbial cells in clouds are sufficiently plentiful to affect the atmosphere.
Bacteria in clouds actively metabolize nutrients—for example, about 1 million tons of organic carbon per year—but only about 1% of such cells can be cultured.
Even though clouds play an important role dispersing microbes over long distances, they apparently do not serve as long-term microbial reservoirs.
In theory, a single ice-nucleating bacterium within a cloud can induce precipitation and thus cause its own deposition.
Little is known about rates of emission of bacteria from surfaces into the atmosphere, and such data are not easy to generate.

The concentration of microorganisms in clouds typically ranges from 10 2 to 10 5 cells per milliliter. Although only a small fraction—typically less than 1%—of such cells can be recovered by culture, bacteria actively grow in clouds, according to Birgit Sattler and colleagues of the University of Innsbruck in Austria. Because active growth entails the uptake of nutrients, living cells presumably change the chemistry in clouds, acting through processes that are likely driven by sunlight and that generate free radicals, notably hydroxyl and superoxide, OH and HO 2, respectively. Clouds are acidic, with pH ranging from 3 to 7, and have conductivity values ranging from 1 to 300 μ S cm ⁻¹. This chemistry results from compounds from gas and aerosols dissolving into the aqueous phase of clouds, and varies with underlying local terrestrial sources. The main ions within clouds—nitrates, sulfates, chloride, ammonium, and sodium—are present at micromolar concentrations. Cloud water also contains organic compounds, including carboxylic acids, aldehydes, and alcohols, from natural and anthropic origins that bacteria can use as nutrients. Additionally, other elements, including phosphorus, iron, copper, and magnesium, are dissolved within cloud water and can sustain microbial metabolism.

“The 1,465-m puy de Dôme mountain, situated near Clermont-ferrand in France, has hosted an atmospheric observatory for more than a century; it is also being used as a field laboratory for studying microorganisms in clouds.”

In 2003, my colleagues and I in Clermont-Ferrand, France, began sampling cloud water from samples that we collect along the puy de Dôme summit, which is 1,465 m above sea level. We are studying interactions between organic compounds and microbes in those samples, addressing whether cloudborne microbes affect atmospheric chemistry. To estimate biodegradation rates in clouds, we constructed microcosms in solution whose chemical compositions approximate what occurs in cloud water. We inoculated these microcosms with microorganisms isolated from cloud water, and then monitored their behavior as well as changes in organic compounds by ¹H and ¹³C NMR and by ion chromatography. Our observations surprised us: In some cases, microbes metabolize organic compounds at rates similar to or higher than they are changed by simulated solar light, on the order of 10 ⁻¹¹ M s ⁻¹. The relative contributions of biology and photochemistry vary for each chemical species, ranging from 0 to 100%. Where the two types of reactions combine, the rates are additive, as is the case in natural situations. Microorganisms catalyze some reactions exclusively—for instance, reducing formaldehyde to methanol. However, cloud-borne microbes do not take up oxalate, which was degraded exclusively photochemically. In addition and perhaps more importantly, microorganisms partly shut off photochemical reactions by lowering the concentration of hydrogen peroxide, the major source of free radicals in the atmosphere, likely degrading it via oxidative stress enzymes and antioxidant species. Although we continue to refine our estimates, we estimate that microorganisms in clouds metabolize about 1 million tons of organic carbon each year on a global scale.

“Schematic representation of the life cycle of microorganisms in the atmosphere”

Even though individual microbial cells are active in cloud droplets, microbial communities likely do not form within this, for them, transitory environment. Thus, clouds are not long-term microbial reservoirs, even though clouds can play an important role dispersing microbes over long distances. Indeed, wet deposition is the main process leading to removal of 1-μm particles, the size range of bacteria, from the atmosphere, and clouds likely are the best “shuttles” for moving airborne microorganisms back to the ground. To disseminate by air means that microbes must survive the harsh conditions that they encounter in the high atmosphere, including low temperature, desiccation, high levels of UV light, repeated freeze-thaw cycles, and osmotic shock. Hence, it is not surprising that microbes in clouds resemble those recovered from other harsh environments where such stresses occur, including along plant surfaces and glaciers.

“Concentration and Community of Airborne Bacteria in Response to Cyclical Haze Events During the Fall and Midwinter in Beijing, China”

Two genera of bacteria frequently recovered alive from cloud water collected at the puy de Dôme summit are Sphingomonas spp. and Pseudomonas spp. These hardy, cloud-borne microbes use the atmosphere and clouds as conveyors to reach distant terrestrial environments. The Sphingomonas species are oligotrophic organisms that produce yellow and red pigments, which contribute to their high resistance to UV. They also resist cold and salinity, and tolerate relatively high concentrations of oxidants. These traits help to explain how Sphingomonas species can survive in clouds until rain or snow brings them back to the Earth’s surface. By contrast, Pseudomonas species typically grow using a wide variety of carbon compounds, which can be advantageous in clouds where nutrient availability is limited. These bacteria are capable of autotrophy under some conditions, and some species produce siderophores to acquire iron. However, Pseudomonas species are less resistant to UV and oxidants than are many of the Sphingomonas spp. that we isolate from clouds. Some Pseudomonas species from clouds have properties that enable them to induce clouds to form and rain or snow to precipitate. Such cells produce biosurfactants, which facilitate the condensation of water on their surface, thus improving the chances of cells acting as cloud condensation nuclei (CCN).

In addition, thanks to a protein embedded in their surfaces and triggered by low temperatures and nutrient limitations, Pseudomonas syringae cells can induce freezing of supercooled water at temperatures as “warm” as −2°C, acting as ice nuclei (IN); typical abiologic aerosols act as IN around −10°C. Because freezing generally induces precipitation at mid-latitudes, through the Bergeron-Findeisen and Hallett-Mossop processes by which ice crystals grow and multiply within the cloud, respectively, these microbes could induce precipitation. In theory, a single ice-nucleating bacterium within a cloud can induce precipitation and thus cause its own deposition. This idea of bioprecipitation was launched in the 1970s by Gabor Vali of the University of Wyoming, Laramie, and supported by Dave Sands and Cindy Morris from Montana State University in Bozeman. Sands and Morris, who continue to study the abundance of the plant pathogen Pseudomonas syringae in water systems such as rivers, showed that its life cycle is intimately linked with and perhaps drives the water cycle. With many open questions concerning microorganisms in the atmosphere and clouds, numeric models will be useful for developing insights and answers. A key but difficult-to-obtain parameter that these models require is concentrations of airborne microbes. One recent aerobiology reference work, published in 2009 by Susannah Burrows and her collaborators at the Max Planck Institute for Chemistry in Mainz, Germany, presents airborne microbial communities as material transported from the surface via turbulent fluxes.

When this concept and published concentrations of airborne microorganisms are used in atmospheric models, the high spatial variability of the airborne biomass is not satisfyingly portrayed due to the lack of experimental data. Notably, we know very little about rates of emission of bacteria from surfaces (fluxes), and these data are not easy to generate for several reasons. For one, many different types of surfaces emit microbes, and they all behave differently. To develop a better understanding, we need to generate large datasets, and this effort necessitates the use of instruments that can continuously count bacterial aerosols. Several groups are developing such instruments, which are expected to be operational soon. Another challenge is that measuring flux requires one to make several meteorological measurements simultaneously, including sensible heat flux. This parameter can be measured directly using three-dimensional anemometers or approximated by monitoring horizontal wind speed and temperatures at two levels above the ground. Measuring emission fluxes of bacteria from surfaces and predicting their concentrations in clouds will entail complex experimental setups over different types of surfaces. Other challenging measurements include survival rates of microbes and modulations of their metabolic activity under different stresses in the atmosphere.

Although investigators long ago acknowledged that microbes are “everywhere,” it still took a while for them to recognize that microbes occupy clouds. Thus, we are in the early stages of thinking about the atmosphere as an extension of the biosphere, in which clouds appear to play an essential role distributing microbial species around the globe. This research has broad implications. While high levels of UV and the numerous selection pressures in the Earth’s envelope probably drove early microbial evolution, the arrival of humans doubtless changed those early dynamics. For instance, chemical data suggest that carbon is likely the main limiting nutritional factor in clouds, whereas it is considered to be closer to optimal concentrations in other aquatic environments. However, because recent anthropogenic atmospheric emissions are resulting in acidification and increased concentrations of organic carbon in cloud water, it is legitimate to ask what impact that has on microbes in clouds. A key question is whether humans are responsible for the “eutrophication” of clouds or are rendering them more hostile to microbial life.

“Life cycle of microorganisms in the atmosphere, by Pierre Amato”

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“Pierre Amato, a staff scientist at the Institut de Chimie de Clermont-Ferrand in France studies microorganisms in clouds. “My work should lead us to better understand and predict the formation of clouds, their behavior, and the chemical processes taking place in these floating aquatic environments,” he says. “What motivates me the most is the role these environments may have as filters to the long-distance dissemination of organisms. Some can survive, some can’t, and I believe this … is contributing, to the evolution of microorganisms.” Amato received a bachelor’s degree in science in 1996 from the Lycée Lafayette, Brioude, and then a series of graduate degrees leading to a doctorate in 2006, all from Blaise Pascal University in Clermont-Ferrand. Amato then moved to Louisiana State University in Baton Rouge to do postdoctoral research in 2007–2008, studying microbial activity in ice, including an excursion to the Dry Valleys, Antarctica. He spent the next two years studying landscape, microclimate, and dynamics of microbial populations of plants at the French Food Research Institute in Avignon. While a Ph.D. student, Amato recalls taking samples from clouds from an observatory at the summit of the Puy de Dôme, a volcano near Clermont-Ferrand. “There are places like this that you know have a history,” he says. “The wind, the fog, the cold, the ruins of the Roman temple of Mercury just in front of the building, the inside of the building, with old furniture and an old drawing of Emile Alluard, the director of the observatory at the earliest stages, made it very mystical. I guess this contributed to my desire to know more about what was going on in those clouds.”