Tag Archives: Ecology

Microbiology

Scientists Discover Unique Microbial Community on Short-Lived Former Island

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In 2015, an underwater volcano in the South Pacific erupted, giving rise to the short-lived Hunga Tonga Hunga Ha’apai island. The University of Colorado Boulder and the Cooperative Institute for Research in Environmental Sciences (CIRES) spearheaded a research team that seized the uncommon chance to investigate the initial microbial inhabitants of a recently formed landmass. Surprisingly, they detected a unique microbial population that can metabolize sulfur and atmospheric gases, akin to organisms present in deep-sea hydrothermal vents or geothermal hot springs.

“These types of volcanic eruptions happen all over the world, but they don’t usually produce islands. We had an incredibly unique opportunity,” said Nick Dragone, CIRES Ph.D. student and lead author of the study recently published in mBio. “No one had ever comprehensively studied the microorganisms on this type of island system at such an early stage before.”

“Studying the microbes that first colonize islands provides a glimpse into the earliest stage of ecosystem development – before even plants and animals arrive,” said Noah Fierer, CIRES fellow, professor of ecology and evolutionary biology at CU Boulder and corresponding author on the study.

A multi-institutional team of researchers on the ground collected soil samples from the island, then shipped them to CU Boulder’s campus. Dragone and Fierer could then extract and sequence DNA samples from the samples.

“We didn’t see what we were expecting,” said Dragone. “We thought we’d see organisms you find when a glacier retreats, or cyanobacteria, more typical early colonizer species—but instead we found a unique group of bacteria that metabolize sulfur and atmospheric gases.”

And that wasn’t the only unexpected twist in this work: On January 15, 2022, seven years after it formed, the volcano erupted again, obliterating the entire landmass in the largest volcanic explosion of the 21st century. The eruption completely wiped out the island and eliminated the option for the team to continue monitoring their site.

“We were all expecting the island to stay,” said Dragone. “In fact, the week before the island exploded we were starting to plan a return trip.”

However, the same fickle nature of the Hunga Tonga Hunga Ha’apai (HTHH) that made it explode also explains why the team found such a unique set of microbes on the island. Hunga Tonga was volcanically formed, like Hawaii.

“One of the reasons why we think we see these unique microbes is because of the properties associated with volcanic eruptions: lots of sulfur and hydrogen sulfide gas, which are likely fueling the unique taxa we found,” Dragone said. “The microbes were most similar to those found in hydrothermal vents, hot springs like Yellowstone, and other volcanic systems. Our best guess is the microbes came from those types of sources.”

The expedition to HTHH required close collaboration with members of the government of the Kingdom of Tonga, who were willing to work with researchers to collect samples from land normally not visited by international guests. Coordination took years of work by collaborators at the Sea Education Association and NASA: a Tongan observer must approve and oversee any sample collection that takes place within the Kingdom.

“This work brought in so many people from around the world, and we learned so much. We are of course disappointed that the island is gone, but now we have a lot of predictions about what happens when islands form,” said Dragone. “So if something formed again, we would love to go there and collect more data. We would have a game plan of how to study it.”

Reference: “The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga” by Nicholas B. Dragone, Kerry Whittaker, Olivia M. Lord, Emily A. Burke, Helen Dufel, Emily Hite, Farley Miller, Gabrielle Page, Dan Slayback and Noah Fierer, 11 January 2023, mBio.
DOI: 10.1128/mbio.03313-22

University of Colorado at Boulder

Microbiology

Scientists have found that a gene that has been previously identified in many animals and their associated microbes …

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Scientists have found that a gene that has been previously identified in many animals and their associated microbes can enable resistance to antimicrobial drugs. The resistance gene encodes for an enzyme called EstT, which can deactivate antibiotic drugs known as macrolides. The enzyme can disrupt the chemical ring structure of these antibiotics through hydrolysis. When the ring is broken or opened with water, the antibiotic loses both its active shape, and its target affinity, explained study leader Dr. Tony Ruzzini PhD, an assistant professor at the Western College of Veterinary Medicine (WCVM) of the University of Saskatchewan. The findings have been reported in the Proceedings of the National Academy of Sciences.

Image credit: Pixabay

This gene can take macrolide antibiotics out of commission, and illnesses can no longer be treated effectively. Macrolides such as tylosin, tilmicosin and tildipirosin are often used to treat cattle with bovine respiratory disease or liver abscesses, and may also be used to treat other diseases in livestock and companion animals.

In this study, the researchers analyzed genes that were found within microbes that were living in watering bowls at a beef cattle feedlot in western Canada. The investigators isolated the microbes that were in the water, and compared the genes in the microbes to databases of antimicrobial resistance genes.

A bacterium called Sphingobacterium faecium WB1 was found to carry the EstT gene, which was contained within a cluster of three antibiotic resistance genes (ARGs). It was also near plasmids and retrotransposons, suggesting it can move easily from one microbe to another. EstT is commonly found in microbes in the human microbiome too.

“This gene, even though we found it in an environmental organism, it is also present in pathogens that are responsible for causing bovine respiratory disease,” noted Ruzzini.

“Our finding adds to the considerable database of ARGs, which can be crossmatched to a bacteria’s DNA to determine if the bacterium has the potential to be resistant to a particular antimicrobial,” said first study author Dr. Poonam Dhindwal PhD, a postdoctoral fellow at WCVM.

The researchers are continuing to study EstT to learn more about how it works.

“As [antimicrobial resistance] surveillance systems rely more on molecular tools for detection, our knowledge of this specific gene and its integration into those systems will help to better inform antimicrobial use,” said Ruzzini.

Sources: University of Saskatchewan, Proceedings of the National Academy of Sciences (PNAS)


Carmen Leitch

Microbiology

In a first, scientists have used bat cells to create bat induced pluripotent stem cells (iPSCs), which can …

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In a first, scientists have used bat cells to create bat induced pluripotent stem cells (iPSCs), which can now serve as a tool to study the connections between bats and the viruses they host. Many viruses, including Ebola, Marburg, Nipah, MERS-CoV, SARS-CoV, and SARS-CoV-2 have been linked to different species of bats, even if other animals have acted as infection reservoirs. Bats are known to harbor more viruses than other mammals, and bats themselves are the second most diverse order of mammals on Earth (after rodents). Even though we know that novel pathogens may emerge from bats to infect humans, bat virus ecology has been poorly understood. This model can help change that.

Scanning electron micrograph of Ebola virus particles (purple) both budding and attached to the surface of infected VERO E6 cells (green)/ Image captured at the NIAID Integrated Research Facility in Fort Detrick, Maryland. Credit: NIAID

Researchers can now use bat iPSCs to learn more about the growth and spread of viruses that bats carry. Bats also have special characteristics that enable them to carry these viral reservoirs without getting sick, and this model may help us understand how they defend themselves from disease. The work has been reported in Cell.

The scientists used cells from the wild greater horseshoe bat (Rhinolophus ferrumequinum), the most common asymptomatic host of coronaviruses, including relatives of SARS-CoV-2, to create induced pluripotent stem cells. These cells are made by changing the expression of a few genes of skin or blood cells, such that they resemble newborn stem cells. The bat iPSCs can be used to generate any other bat cell type.

Bat iPSCs were compared to iPSCs from other mammals, revealing a unique biology, noted study co-author Adolfo García-Sastre, Ph.D., a Professor of Medicine and Director of the Global Health and Emerging Pathogens Institute at Icahn Mount Sinai. “The most extraordinary finding was the presence of large virus-filled vesicles in bat stem cells representing major viral families, including coronaviruses, without compromising the cells’ ability to proliferate and grow. This could suggest a new paradigm for virus tolerance as well as a symbiotic relationship between bats and viruses.”

This study has suggested that bats have certain biological mechanisms that allow them to tolerate many viral sequences, and bats could be more entwined with viruses that we knew, noted senior study author Thomas Zwaka, MD, Ph.D., a Professor at the Icahn School of Medicine at Mount Sinai. Bats can survive the presence of viruses that often kill humans, such as Marburg, which may be due to a modulation of their immune response, added Zwaka.

This study could help researchers answer some crucial questions, and protect humans from emerging viruses; we may be able to use tactics like those in bats to prevent viral infection or illness. Ultimately, it could help scientists learn why bats hold a unique position as viral reservoirs, noted Dr. García-Sastre. “And that knowledge could provide the field with broad new insights into disease and therapeutics while preparing us for future pandemics.”

Bat stem cell research will “directly impact every aspect of our understanding of bat biology, including bats’ amazing adaptations of flight and ability to locate distant or invisible objects through echolocation, the location of objects reflected by sound, as well as their extreme longevity and unusual immunity,” Zwaka concluded.

Sources: The Mount Sinai Hospital, Cell


Carmen Leitch

Microbiology

Wood-Wide Web: Do Forest Trees Really “Talk” Through Underground Fungi?

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University of Alberta expert challenges popular claims about the “wood-wide web.”

The idea that forest trees can “talk” to each other, share resources with their seedlings — and even protect them — through a connective underground web of delicate fungal filaments tickles the imagination.

The concept is so intriguing, it’s taken root in popular media — even being raised in the popular Apple TV show Ted Lasso — and been dubbed the “wood-wide web,” but the science behind those ideas is unproven, cautions University of Alberta expert Justine Karst.

In a peer-reviewed article published today (February 13) in the journal Nature Ecology & Evolution that also shares their personal point of view, Karst and two colleagues contest three popular claims about the capabilities of underground fungi known as common mycorrhizal networks, or CMNs, that connect roots of multiple plants underground. Fungi are living organisms such as molds, yeast, and mushrooms.

“It’s great that CMN research has sparked interest in forest fungi, but it’s important for the public to understand that many popular ideas are ahead of the science,” says Karst, associate professor in the U of A’s Faculty of Agricultural, Life & Environmental Sciences.

While CMNs have been scientifically proven to exist, there is no strong evidence that they offer benefits to trees and their seedlings, the researchers suggest.

To evaluate the popular claims, Karst and co-authors Melanie Jones of the University of British Columbia Okanagan and Jason Hoeksema of the University of Mississippi reviewed evidence from existing field studies.

They found that one of the claims, that CMNs are widespread in forests, isn’t supported by enough scientific evidence. Not enough is known about CMN structure and its function in the field, “with too few forests mapped.”

The second claim, that resources such as nutrients are transferred by adult trees to seedlings through CMNs and that they boost survival and growth, was also found to be questionable.

A review of 26 studies, including one in which Karst is a co-author, established that while resources can be transferred underground by trees, CMNs don’t necessarily bring about that flow, and seedlings typically don’t benefit from CMN access. Overall, their review revealed roughly equal evidence that connecting to a CMN would improve or hamper seedlings, with neutral effects most commonly reported.

The third claim, that adult trees preferentially send resources or “warning signals” of insect damage to young trees through CMNs, is not backed up by a single peer-reviewed, published field study, Karst and her co-authors note.

The researchers say overblown information can shape and distort the public narrative about CMNs, and that could, in turn, affect how forests are managed.

“Distorting science on CMNs in forests is a problem because sound science is critical for making decisions on how forests are managed. It’s premature to base forest practices and policies on CMNs per se, without further evidence. And failing to identify misinformation can erode public trust in science.”

Reference: “Positive citation bias and overinterpreted results lead to misinformation on common mycorrhizal networks in forests” by Justine Karst, Melanie D. Jones and Jason D. Hoeksema, 13 February 2023, Nature Ecology & Evolution.
DOI: 10.1038/s41559-023-01986-1

University of Alberta

Microbiology

Researchers were able to take advantage of “an incredibly unique opportunity” to study the microbial life that rapidly …

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Researchers were able to take advantage of “an incredibly unique opportunity” to study the microbial life that rapidly colonized a short-lived island that formed in the South Pacific after a volcanic eruption. This work, reported in mBio, revealed a variety of unique microbes that could metabolize sulfur and gases in their local atmosphere, like the extremophile microbes that are sometimes found near hydrothermal vents or in hot springs. The lead author of a report on the findings, CIRES graduate student Nick Dragone noted that, “These types of volcanic eruptions happen all over the world, but they don’t usually produce islands.”

Hunga Tonga-Hunga Ha'apai in 2017 / Image credit: NASA/Damien Grouille/Cecile Sabau

But in 2015, an eruption of a submarine volcano created the Hunga Tonga Hunga Ha’apai Island, which existed for seven years. The formation of the island is described in the NASA video below. During the island’s lifetime, the study authors collected soil samples from the site and sent them off to the laboratory so that DNA in those samples could be extracted. By analyzing the genetic sequences, the scientists determined that some unusual bacteria were living on the island.

The investigators said they were surprised by the findings. Instead of revealing organisms that accompany the retreat of glaciers, or marine microbes like cyanobacteria, they found something else — an unusual bunch of microbes that metabolize sulfur and atmospheric gases.

On January 15, 2022, the research team got another surprise; there was another eruption near the island, which destroyed the entire landmass in the 21st century’s largest volcanic explosion (so far). Now, the site can’t be monitored ever again.

“We were all expecting the island to stay,” said Dragone. “In fact, the week before the island exploded we were starting to plan a return trip.”

Luckily the team was able to make use of the island while it existed. “No one had ever comprehensively studied the microorganisms on this type of island system at such an early stage before,” added Dragone.

The short life of the island, and its volcanic origins, fostered an unusual community of microbes, as well as an international group of researchers working together. Learning more about this unique type of microbial community can provide insights into how ecosystems might start to develop, even before organisms like plants or animals arrive on the scene, noted corresponding study author and CIRES fellow Noah Fierer, a professor of ecology and evolutionary biology at CU Boulder.

Sources: University of Colorado Boulder (CU Boulder) and Cooperative Institute for Research in Environmental Sciences (CIRES), mBio


Carmen Leitch

Microbiology

Shaking Up Our Understanding: Ethereal Variant of Mysterious Plant Is Actually a New Species

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It was once thought that green leaves and photosynthesis were essential for plants, however, some plants have evolved to obtain their nutrients from other organisms instead. One such plant is Monotropastrum humile, a ghostly-looking species that is widely found across East and Southeast Asia. This mycoheterotrophic plant thrives in woodlands with limited sunlight, obtaining its nutrients by feeding off the hyphae of fungi.

Despite its wide distribution, it was previously believed that only one species of this plant existed in the world. However, Professor Suetsugu Kenji and colleagues have discovered that a variant found in Japan is actually a new species, shaking up our understanding of this unusual-looking genus of plants.

It has rosy pink petals and stems resembling milk glass, giving it a beautiful, otherworldly appearance. As it was first found around Kirishima in Kagoshima Prefecture, Japan, the new species has been named Monotropastrum kirishimense.

Originally, this new species was tentatively treated as a color variant of M. humile, known as M. humile f. roseum. Thus began an extensive and multifaceted 20-year study to determine how exactly these plants differed. Specimens were collected from throughout Japan and Taiwan, as well as Vietnam.

Results of various analyses revealed morphological differences (Figures 1-3), including the following; M. kirishimense flowers and ovaries are more rounded than those of M. humile, and its rootball is more obscured by the surrounding soil (in contrast to M. humile’s protruding root tips). M. kirishimense individuals are shorter above ground (under 5cm) and longer below ground (over 10cm).

The flowering season is different too; M. humile flowers bloom approximately 40 days earlier than M. kirishimense. As the two plant species have the same primary pollinator (the bumblebee Bombus diversus), this difference in flowering times can reduce heterospecific pollen deposition, helping to ensure conspecific mating, and thereby preventing them from producing hybrids.

There are several other possible reasons why M. kirishimense and M. humile may have evolved into separate species. One possibility is that they have become specialized in feeding on different fungi, which has led to reproductive isolation, or the inability to produce offspring together. This process is known as resource partitioning and is one of the major ways that species can evolve from a common ancestor. Genetic analysis of mycobionts revealed that M. kirishimense has a consistent, specialized association with a particular lineage of fungi, whereas M. humile is associated with different lineages (Figure 4).

Therefore, this study suggests that M. kirishimense may have evolved into a new species by relying on a specific type of fungus. In fact, the phylogenetic tree (a ‘family tree’ of the evolutionary history of a group of organisms) of the plants themselves shows that the genetic characteristics of M. kirishimense and M. humile can be separated into two clades (Figure 5). Based on the researchers’ analysis of various characteristics, it has been revealed that M. kirishimense is distinct from M. humile in terms of its appearance, flowering patterns, evolutionary history, and ecological relationships. Therefore, the researchers concluded that it should be recognized as an independent species.

Overall, the research group not only revealed that M. kirishimense is a distinct species but also deepened the understanding of plants in the Monotropastrum genus. Mycohetrotrophic plants are very vulnerable to extinction as they rely on specific ecosystems to survive and are usually found in old-growth forests. The newly recognized species, M. kirishimense, is rare and presumably endangered.

Now that it has been identified as a new species, conservation efforts can be made to protect it. This study emphasizes the importance of combining various analysis methods, called integrative taxonomy, to fully understand and protect biodiversity.

Reference: “Monotropastrum kirishimense (Ericaceae), a new mycoheterotrophic plant from Japan based on multifaceted evidence by Kenji Suetsugu, Shun K. Hirota, Tian-Chuan Hsu, Shuichi Kurogi, Akio Imamura and Yoshihisa Suyama, 29 November 2022, Journal of Plant Research.
DOI: 10.1007/s10265-022-01422-8

Kobe University

Microbiology

Scientists have discovered a signaling pathway that links an arthropod parasite with its host, in which molecules in …

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Scientists have discovered a signaling pathway that links an arthropod parasite with its host, in which molecules in the host animal’s blood trigger the development and immunity of a parasite. When ticks feed on mouse blood that carries the bacterial pathogen Borrelia burgdorferi, which causes Lyme disease, a mouse immune protein binds to tick cell receptors, causing organs in the tick to develop faster. An immune response is also activated long before the bacterial pathogen infects the tick. This is the first interspecies biochemical signaling pathway that’s ever been identified, according to the researchers. The findings have been reported in Science.

Image credit: Pixabay

This work has shown that species can develop biochemical dependencies on one another, and reveals a combination of immunity and development that has never been observed before. It also involved an ancient signaling pathway that is found in plant and animal cells, which cells utilize to sense and respond to their environments. The study may also reveal new targets for therapeutics or vaccines against ticks and tick pathogens.

“This adaptive flexibility of a conserved cell signaling pathway was surprising,” said senior study author Utpal Pal, a professor in the Virginia-Maryland College of Veterinary Medicine at College Park. “It is remarkable that this pathway that is present in everything from sponges to humans is so flexible it can adapt to accept a [binding partner] from another distant species. This tool that everybody has is being used in a way that we didn’t imagine.”

There could be other cell signaling pathways that have been harnessed for new purposes in different species, and these findings could open up a new area of immunological study.

The researchers were investigating tick immunity, which is not well-understood. They exposed ticks to blood from healthy mice and mice infected with Borrelia bacteria. A protein linked to the JAK/STAT signaling pathway, which is involved in energy production was activated only in the ticks that fed on infected blood.

The investigators injected Borrelia bacteria into ticks, and found that the bacteria alone did not activate the JAK/STAT pathway. Next, the researchers collected blood from mice infected with Borrelia, and removed the bacteria. When ticks were exposed to this ‘decontaminated’ blood, the JAK/STAT pathway was activated once more.

A protein in the digestive systems of ticks was found to be acting as a JAK/STAT receptor. This protein evolved to bind with interferon, a molecule that is produced by the immune system when mammals are infected with a bacterial pathogen like Borrelia.

The JAK/STAT receptor and pathway also influence normal tick development, even when infected blood does not trigger the pathway. When a gene that produces the JAK/STAT receptor was eliminated from ticks, the genetically-engineered ticks were abnormal, and could not complete development; their growth was arrested.

The study authors suggested that JAK/STAT has integrated immunity and development in ticks. In an infected host, pathogenic microbes and ticks compete for nutrients, and if a tick senses infection in a blood meal, it may start quickly growing so it can consume nutrients that may soon be scarce.

“Understanding that this pathway integrates immunity and development has important implications for potential strategies to prevent tick-borne disease transmission,” Pal said.

Sources: University of Maryland, Science


Carmen Leitch

Microbiology

A New Ancient Branch on the Tree of Life: The “Lions of the Microbial World”

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A new branch has been discovered on the tree of life, and it is composed of predators that nibble their prey to death.

These microbial predators are divided into two groups, one of which has been referred to as “nibblerids” due to their use of tooth-like structures to bite off pieces of their prey. The other group, known as “nebulids,” consume their prey whole. Both groups form a distinct ancient branch called “Provora,” according to a recent study published in the journal Nature.

Like lions, cheetahs, and more familiar predators, these microbes are numerically rare but important to the ecosystem, says senior author Dr. Patrick Keeling, professor at the University of British Columbia department of botany. “Imagine if you were an alien and sampled the Serengeti: you would get a lot of plants and maybe a gazelle, but no lions. But lions do matter, even if they are rare. These are lions of the microbial world.”

Using water samples from marine habitats around the world, including the coral reefs of Curaçao, sediment from the Black and Red seas, and water from the northeast Pacific and Arctic oceans, the researchers discovered new microbes. “I noticed that in some water samples, there were tiny organisms with two flagella, or tails, that convulsively spun in place or swam very quickly. Thus began my hunt for these microbes,” said first author Dr. Denis Tikhonenkov, senior researcher at the Institute for Biology of Inland Waters of the Russian Academy of Sciences.

Dr. Tikhonenkov, a long-time collaborator of the UBC co-authors, noticed that in samples where these microbes were present, almost all others disappeared after one to two days. They were being eaten. Dr. Tikhonenkov fed the voracious predators with pre-grown peaceful protozoa, cultivating the organisms in order to study their DNA.

“In the taxonomy of living organisms, we often use the gene ‘18S rRNA’ to describe genetic differences. For example, humans differ from guinea pigs in this gene by only six nucleotides. We were surprised to find that these predatory microbes differ by 170 to 180 nucleotides in the 18S rRNA gene from every other living thing on Earth. It became clear that we had discovered something completely new and amazing,” Dr. Tikhonenkov said.

On the tree of life, the animal kingdom would be a twig growing from one of the boughs called “domains,” the highest category of life. But sitting under domains, and above kingdoms, are branches of creatures that biologists have taken to calling “supergroups.” About five to seven have been found, with the most recent in 2018 – until now.

Understanding more about these potentially undiscovered branches of life helps us understand the foundations of the living world and just how evolution works.

“Ignoring microbial ecosystems, like we often do, is like having a house that needs repair and just redecorating the kitchen, but ignoring the roof or the foundations,” said Dr. Keeling. “This is an ancient branch of the tree of life that is roughly as diverse as the animal and fungi kingdoms combined, and no one knew it was there.”

The researchers plan to sequence whole genomes of the organisms, as well as build 3D reconstructions of the cells, in order to learn about their molecular organization, structure, and eating habits.

Culturing the microbial predators was no mean feat since they require a mini-ecosystem with their food and their food’s food just to survive in the lab. A difficult process in itself, the cultures were initially grown in Canada and Russia, and both COVID and Russia’s war with Ukraine prevented Russian scientists from visiting the lab in Canada in recent years, slowing down the collaboration.

Reference: “Microbial predators form a new supergroup of eukaryotes” by Denis V. Tikhonenkov, Kirill V. Mikhailov, Ryan M. R. Gawryluk, Artem O. Belyaev, Varsha Mathur, Sergey A. Karpov, Dmitry G. Zagumyonnyi, Anastasia S. Borodina, Kristina I. Prokina, Alexander P. Mylnikov, Vladimir V. Aleoshin and Patrick J. Keeling, 7 December 2022, Nature.
DOI: 10.1038/s41586-022-05511-5

University of British Columbia

Microbiology

There are many microbes that perform essential functions that we don’t even have to think about. For example, …

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There are many microbes that perform essential functions that we don’t even have to think about. For example, the ocean is full of Prochlorococcus bacteria, which generate huge amounts of the oxygen in the seas, from the poles to the tropics. They are thought to be the most abundant photosynthetic organisms in the world. Now scientists have learned more about how these microbes are able to survive in so many places. Prochlorococcus bacterial cells can exchange genetic information with one another, which is no surprise; but they can do so in a way that has never been observed before. Huge segments of DNA with blocks of genes can be transmitted from one Prochlorococcus cell to another, enabling them to take on new abilities such as metabolic reactions or viral defense strategies even when few of the microbes are present in one location.

A TEM image of Prochlorococcus marinus - a globally important marine cyanobacterium./ Public domain image courtesy of Luke Thompson from Chisholm Lab and Nikki Watson from Whitehead, MIT

Scientists have now described this new process of horizontal gene transfer, in which one organism passes genetic material directly to another in a way that does not involve inheritance. The findings have been reported in Cell.

Sequences of DNA that contain several genes and their surrounding sequences that get transferred through this method have been called tycheposons. They can separate from their original location spontaneously and then migrate to another organism, probably through cellular sacs known as vesicles, which bud from cell membranes.

“We’re very excited about it because it’s a new horizontal gene transfer agent for bacteria, and it explains a lot of the patterns that we see in Prochlorococcus in the wild, the incredible diversity,” said Professor Sallie “Penny” Chisholm of MIT, who aided in the discovery of Prochlorococcus in 1988 and is featured in the video below.

This work started with an analysis of genetic sequences from hundreds of different Prochlorococcus species. The researchers wanted to know how they quickly gained or lost functions, while they did not display any of the known mechanisms of horizontal gene transfer, or features of mobile genetic elements. The researchers found genetic regions or islands that were hotspots of variation, which often contained genes that conferred abilities to deal with certain nutrients.

These islands often varied significantly between Prochlorococcus species, but they kept appearing in the same part of the Prochlorococcus genome, and sometimes they were almost the same, even in very different species; this was all evidence of that some kind of horizontal transfer was occurring.

The scientists have discovered something that was like a genetic LEGO set, according to MIT postdoctoral researcher Thomas Hackl. The microbes could use this system to quickly adapt to their environment, such as by acquiring a gene that improved their ability to absorb an important nutrient that was scarce. The researchers were even able to collect some of these vesicles and capsids from the open ocean, and they were “actually quite enriched” with tycheposons.

The team discovered that there are several mechanisms that Prochlorococcus uses to transport genes. They might use membrane vesicles as little sacs containing tycheposons, or they may hijack a viral infection that can then move the tycheposons along with the virus. These modes of transport are especially valuable in the open ocean, where cell to cell contact is very challenging, noted Hackl.

This phenomenon may also occur in other marine bacteria, suggested Hackl. The researchers have already found genetic elements in other bacteria that are similar to those found in Prochlorococcus.

Sources: Massachusetts Institute of Technology (MIT), Cell


Carmen Leitch

Microbiology

Viruses can infect cells, and take them over to produce more viruses. But can viruses serve as a …

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Viruses can infect cells, and take them over to produce more viruses. But can viruses serve as a source of nutrition? It seems that, yes, some aquatic microbes are able tocan consume viruses and use them as a source of energy that fuels the microbe’s growth. In new research reported in the Proceedings of the National Academy of Sciences (PNAS), investigators showed that a species of microbe called Halteria, which are ciliates that live in freshwater ecosystems around the world, can survive on a diet of viruses alone; the researchers termed this phenomenon “virovory.” The microbes can eat thousands, even a million particles of chloroviruses in a single day, the researchers found.

Image credit: Pixabay

Chloroviruses infect green algae, which eventually causes the microscopic algal cells to burst, releasing carbon and other elements that other microorganisms can use in a kind of recycling process. The carbon is thought to be retained in a layer of microbial soup, without moving up the food chain, noted senior study author John DeLong, an associate professor at the University of Nebraska–Lincoln.

But vivory, noted DeLong, could be helping carbon escape that cycle, and those tiny organisms may be having a big impact.

By taking a rough estimate of the number of viruses and ciliates in the volume of water there is, a massive amount of energy could be moving up the food chain, said DeLong, who estimated that in a small pond, ciliates could eat 10 trillion viruses every day. “If this is happening at the scale that we think it could be, it should completely change our view on global carbon cycling.”

DeLong had suspected that some microbes could use viruses as a form of nutrition that almost anything would want to eat. “They’re made up of really good stuff: nucleic acids, a lot of nitrogen and phosphorous,” he explained. Lots of organisms will consume anything they can, so “surely something would have learned how to eat these really good raw materials.”

To see whether any microbes had indeed started to eat viruses, he did a simple experiment. After collecting samples from a local pond, he added chlorovirus to droplets of water that contained microbes from the pond. After one day, he could see that Halteria used chlorovirus as a snack food; there were so many more Halteria that he was able to start counting them. This was happening as the chlorovirus level was dropping precipitously. In two days, there were 100 times fewer viruses, and Halteria cells were growing to be about 15 percent larger. Halteria that had no access to chlorovirus weren’t getting any bigger.

Another experiment confirmed that Halteria cells were eating the virus. The researchers labeled chlorovirus DNA green, then watched as an organelle in Halteria cells that were exposed to these chloroviruses began to turn green. The ciliates were eating the virus.

After collecting additional data, DeLong found that Halteria can convert about 17 percent of the chlorovirus mass they consume into a new mass of their own.

DeLong is planning to return to the pond as the weather warms to confirm that this is also occurring in nature.

Sources: University of Nebraska-Lincoln, PNAS


Carmen Leitch