Posts Tagged ‘virus’
“The vast majority of terrestrial species are in fact microbes, and scientists have only begun scratching the surface of the microbial realm. It is entirely possible that examples of life as we don’t know it have so far been overlooked.”*…
Not only do we continue to find surprising new forms of microbial life, some of them challenge our very defintion of “life.” Alice Sun reports…
Scientists recently discovered a microbe with one of the tiniest genomes on Earth. More surprising, the creature is almost entirely dependent on its host: Its genes don’t support any of the functions of metabolism, one of the key processes of life. As such, it challenges fundamental notions of what it means to be a living organism. The discovery was “pure serendipity,” says Takuro Nakayama, an evolutionary microbiologist at the University of Tsukuba in Japan. Takayama wanted to study the many microbes that live within a single-celled marine dinoflagellate, Citharistes regius, a kind of plankton. But when he and his colleagues sequenced the genes of this microbial community, they kept turning up tiny, odd chunks of DNA.
It turns out that these DNA chunks belong to some unusual archaea—a branch on the tree of life populated by single-celled microbes that can often survive in extreme environments. (Archaea are similar to bacteria, but distinct in their structure, genetics, and metabolism.)
Nakayama and his colleagues proposed the name Sukunaarchaeum mirabile for the newly-discovered microbe: Sukunaarchaeum after the Japanese dwarf deity Sukuna-biko-na, and mirabile for marvelous. At only 238,000 base pairs, the number of genes in the DNA of Sukunaarchaeum is smaller than that of any other known archaea. The scientists described their finding in a bioRxiv preprint earlier this year.
So how did Sukunaarchaeum end up with such a strikingly tiny genome? Over the course of evolution, genetic instructions for life often become increasingly complex. But evolution can also go in the other direction, leading to greater simplicity in the genome. This so-called genomic reduction, where organisms end up with fewer genes than their ancestors, is typically observed in the domains of bacteria and archaea. What struck Nakayama and his colleagues about Sukunaarchaeum was the extent of reduction and specialization in its genes.
With its stripped down genome, Sukunaarchaeum appears to be completely dependent on its host, C. regius, for essential energy and nutrients. “It likely cannot produce its own cellular building blocks,” notes Nakayama. “No previously discovered microbe has shown such an extreme degree of metabolic dependence.”
Sukunaarchaeum seems to almost inhabit a new category of life, suspended somewhere between archaea and virus. It is like viruses—which aren’t typically considered to be “alive”—in that it has a tiny genome and is totally dependent on its host for metabolism. But unlike a virus, Sukunaarchaeum has its own ribosomes, cellular structures that synthesize proteins, and it can replicate itself without the help of a host.
To get a sense of just how unusual Sukunaarchaeum is, the researchers decided to scan the oceans for potential relatives. They analyzed environmental genetic sequence data from marine environments all over the world, focusing on spots where C. regius is known to live. Using a database called the Tara Oceans project, they discovered a vast array of sequences that are comparable to that of Sukunaarchaeum, which they hypothesize could represent a new, deeply branching archaeal lineage.
For Nakayama, this additional finding suggests that many more microbes that challenge the definition of life may be out there, living in what Nakayama calls “microbial dark matter,” or microbes that can’t be cultivated in the lab. “The extreme, virus-like lifestyle we hypothesize for Sukunaarchaeum is a perfect example of the surprising outcomes found in this ‘natural laboratory of evolution,’” he says.
Mart Krupovic, a virologist and microbiologist at Institut Pasteur in France who wasn’t involved in the study, called the finding “remarkable.” Krupovic has studied giant viruses that, like Sukunaarchaeum, defy categorization. These giant viruses have evolved larger and more complex genomes that include some of the genes for DNA translation, a characteristic thought to be reserved for cellular life. “I think that is fascinating,” says Krupovic, “how little we still know about the world which surrounds us.”…
How did Sukunaarchaeum end up with such a strikingly tiny genome? “A Rogue New Life Form,” from @alicesunreports.bsky.social in @nautil.us.
See also; “Candidatus Sukunaarchaeum Mirabile Is A Novel Archaeon With An Unprecedentedly Small Genome” (source of the image at the top).
The BioRxiv preprint is here.
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As we look again at “living,” we might spare a thought for Robert Huebner; he died on this date in 1998. A physician and virologist, his research into viruses, their causes, and treatment led to his breakthrough insights into the connections between viruses and cancer, which have led to new treatments. His hypothesized oncogene was discovered to be a trigger for normal cells turning cancerous.
“The past lives within the present, and our ancestors breathe through our children”*…
Indeed, that’s true all the way back. And as Jonathan Lambert explains, we now have more visibility on that distant past. The emerging understanding of our “last universal common ancestor” suggests it was a relatively complex organism living 4.2 billion years ago, a time long considered too harsh for life to flourish…
If you follow any path of ancestry back far enough, you’ll reach the same single point. Whether you begin with gorillas or ginkgo trees or bacteria that live deep in the bowels of the Earth — or yourself, for that matter — all roads lead to LUCA, the “last universal common ancestor.” This ancient, single-celled organism (or, possibly, population of single-celled organisms) was the progenitor of every varied form that makes a life for itself on our planet today.
LUCA does not represent the origin of life, the instance whereby some chemical alchemy snapped molecules into a form that allowed self-replication and all the mechanisms of evolution. Rather, it’s the moment when life as we know it took off. LUCA is the furthest point in evolutionary history that we can glimpse by working backward from what’s alive today. It’s the most recent ancestor shared by all modern life‚ our collective lineage traced back to a single ancient cellular population or organism.
“It’s not the first cell, it’s not the first microbe, it’s not the first anything, really,” said Greg Fournier, an evolutionary biologist at the Massachusetts Institute of Technology. “In a way, it is the end of the story of the origin of life.”
Still, understanding LUCA — whether it was simple or complex, and how quickly it emerged after life’s origin — could help answer some of our deepest questions about where we come from and whether we’re alone in the universe.
“[LUCA] tells our own story,” said Edmund Moody (opens a new tab), an evolutionary biologist at the University of Bristol. “It gives us a point from which we can look even further back.”
For half a century, biologists have focused on different kinds of physiological, genomic and fossil evidence to paint portraits of LUCA that sometimes clash dramatically. In 2024, Moody and a team of interdisciplinary researchers, including geologists, paleontologists, system modelers and phylogeneticists, combined their knowledge to build a probabilistic model that reconstructs modern life’s shared ancestor and estimates when it lived.
The analysis, published in Nature Ecology and Evolution in July, sketched a surprisingly complex picture of the cell. LUCA lived off hydrogen gas and carbon dioxide, boasted a genome as large as that of some modern bacteria, and already had a rudimentary immune system, according to the study. Its genomic complexity, the authors argue, suggests that LUCA was one of many lineages — the rest now extinct — living about 4.2 billion years ago, a turbulent time relatively early in Earth’s history and long thought too harsh for life to flourish.
The analysis reaches two conclusions that seem in conflict with each other, according to Aaron Goldman, who studies the molecular evolution of early life at Oberlin College and wasn’t involved in the new research. “The first is that LUCA was a complex cellular organism that likely lived in a complex ecological setting,” he said. “The second is that LUCA dates to a time that is pretty early in the history of Earth.” The results could mean that life evolved from a simple replicator into something resembling modern microbes remarkably quickly, he said. “That’s really exciting.”
“Our work suggests that those early steps of evolution weren’t hard; they’re pretty easy,” said co-author Phil Donoghue, an evolutionary biologist at the University of Bristol. “If you’re concerned with the origin of microbial-grade life, then that’s apparently very easy, and it should be quite common in the universe.”
Not all experts in the field agree, however. Some argue that a few hundred million years is not enough time for complex life to have evolved. The authors stress that their analysis is a first attempt to paint a fuller, admittedly fuzzy, picture of LUCA. “I fully expect and hope people prove us wrong in certain aspects,” said Moody, the paper’s lead author, especially if those new results offer a clearer view of the ancient ancestor of all life we know…
Eminently worth reading in full: “All Life on Earth Today Descended From a Single Cell. Meet LUCA,” from @evolambert in @QuantaMagazine.
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As we look back, we might send microscopic birthday greetings to Lewis Thomas; he was born on this date in 1913. A physician, poet, etymologist, essayist, administrator, educator, policy advisor, and researcher, he distinguished himself in medicine and microbiology both for his suggestion that an immunosurveillance mechanism protects us from the possible ravages of mutant cells (an idea later championed by Macfarlane Burnett) and for his proposal that viruses have played a major role in the evolution of species by their ability to move pieces of DNA from one individual or species to another.
But Lewis is more widely known for his writing, perhaps most especially for his first two books– The Lives of a Cell: Notes of a Biology Watcher (which won National Book Awards in two categories) and The Medusa and the Snail: More Notes of a Biology Watcher (which won another National Book Award)– which underscored the interconnectedness of life by sketching the ways that what is seen under the microscope is similar to the way human beings live.
“The most outstanding feature of life’s history is a constant domination by bacteria”*…
Jennifer Kahn interviews biochemist Jennifer Doudna (who won the Noel Prize for the gene-editing engine Crispr) on her new focus– our microbiomes, tackling everything from immune disorders and mental illness to climate change—all by altering microbes in the digestive tract…
… what isn’t the microbiome responsible for? It’s been all the rage for the past few years, with scientists hoping it could help treat everything from immune disorders to mental illness. How exactly that will work is something we’re just starting to explore. This spring, the effort got a boost when UC Berkeley biochemist and gene-editing pioneer Jennifer Doudna, who won a Nobel Prize in 2020 for coinventing Crispr, joined the pursuit. Her first order of business, spearheaded by Berkeley’s Innovative Genomics Institute: fine-tuning our microbiome by genetically editing the microbes it contains while they’re still inside us to prevent and treat diseases like childhood asthma. (Full disclosure: I teach at Berkeley.) Oh, she also wants to slow climate change by doing the same thing in cows, which are collectively responsible for a shocking amount of greenhouse gas.
As someone who has written about genetic engineering in the past, I have to admit that my first reaction was: No way. The gut microbiome contains around 4,500 different kinds of bacteria plus untold viruses, and even fungi (so far: in practice we’ve only just started counting) in such massive quantities that it weighs close to half a pound. (Microbes are so tiny that 30 trillion bacteria would weigh roughly 1 ounce. So half a pound is a lot.)
Figuring out which ones are responsible for which ailments is tricky. First you need to know what’s causing the problem: like maybe something is producing too much of a particular inflammatory molecule. Then you have to figure out which microbe—or microbes—is doing that, and also which gene within that microbe. Then, in theory, you can fix it. Not in a petri dish, but in situ—meaning in our fully active, roiling, squishing stomach and intestines while they continue to do all the stuff they usually do.
Until recently, it would have seemed insane—not to mention literally impossible—to edit all the microbes belonging to a species within a vast ecosystem like our gut. And to be fair, Doudna and her collaborator, Jill Banfield, still don’t know quite how it will work. But they think it can be done, and in April, TED’s Audacious Project donated $70 million to support the effort. My own gut feeling (right?) was that this was either brilliant or terrifying, or possibly both at once. Brilliant because it had the potential to head off or treat diseases in an incredibly targeted and noninvasive way. Terrifying because, well, you know … releasing a bunch of inert viruses equipped with gene-editing machinery into the vital ecosystem that is our gut microbiome—what could go wrong? With that in mind, I invited Jennifer Doudna to my house for a chat about the future of microbiome medicine…
Fascinating– and encouraging: “Crispr Pioneer Jennifer Doudna Has the Guts to Take On the Microbiome,” in @WIRED.
(Image above: source)
* Stephen Jay Gould
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As we investigate our intestines, we might spare a thought for Guido Pontecorvo; he died on this date in 1999. A geneticist, he discovered the process of genetic recombination in the common soil fungus Aspergillus— and as a result the parasexual cycle— in what became the model for the genetic studies in many other fungi. This cycle gives rise to genetic reassortment by means other than sexual reproduction; its discovery provided a method of genetically analyzing asexual fungi…. which, as noted above, populate our microbiomes.
“There are more things in heaven and Earth, Horatio, than are dreamt of in your philosophy”*…
And some of them were recently found in the woods near Boston…
Researchers have unearthed a trove of wonders in the soil of a Massachusetts forest: an assortment of giant viruses unlike anything scientists had ever seen. The find suggests this group of relatively massive parasites has an even greater ecological diversity and evolutionary importance than researchers knew.
Giant viruses can exceed 2 micrometers in diameter, on par with some bacteria. They can also harbor immense genomes, which reach 2.5 megabases—larger than the genomes of far more complex organisms. Between the discovery of these impressively sized viruses in algae and the culturing of amoeba-infecting Mimiviruses, most of the research on the group has focused on viruses that inhabit freshwater environments. But DNA sequencing has long indicated that giant viruses are diverse and abundant elsewhere, too—especially in sediments and soils, which are estimated to host some 97% of all the viral particles on Earth. Indeed, genomic sequencing of the soils of Harvard Forest—a roughly 16-square-kilometer area west of Boston—indicated the presence of numerous, novel giant viruses.
Now, electron microscopy has allowed scientists to see what others had only sequenced. The diversity of forms was astounding, they report in a bioRxiv preprint. Not only did the researchers see the 20-sided icosahedral shapes they expected, they spotted ones with myriad modifications—tails, altered points, and multilayered or channeled structures abounded. There were even viruses with long tubular appendages, which the team dubbed “Gorgon” morphology [photo above]. Furthermore, many of these putative viral particles were coated with almost hairlike projections, which varied in length, thickness, density, and shape.
The findings suggest virologists have much to discover about how giant viruses interact with their host cells. That likely means the ecological roles these viruses play in soils—and elsewhere they’re found—are woefully underappreciated…
Microbes come in a variety of shapes, hinting at undiscovered ecological diversity: “Alien-looking viruses discovered in Massachusetts forest,” in @ScienceMagazine.
* Shakespeare, Hamlet
As we marvel at multifariousness (and note that viruses, while generally considered to be non-living and thus not considered microorganisms, are colloquially lumped in with microbes), we might spare a thought for Sidney Walter Fox; he died on this date in 1998. A biochemist, he was responsible for a series of discoveries about the origin of life. Fox believed in the process of abiogenesis, by which life spontaneously organized itself from the colloquially known “primordial soup,” poolings of various simple organic molecules that existed during the time before life on Earth. In his experiments (which possessed, he believed, conditions like those of primordial Earth), he demonstrated that it is possible to create protein-like structures from inorganic molecules and thermal energy. Dr. Fox went on to create microspheres that he said closely resembled bacterial cells and concluded that they could be similar to the earliest forms of life or protocells.
“The welfare and the future of our societies depend on our capacity to remain mobilized so as to improve the health of every mother and child”*…
Preparing for a world post Roe v Wade…
The red states poised to ban or severely limit abortion already tend to have limited access to health care, poor health outcomes and fewer safety net programs in place for mothers and children.
If the U.S. Supreme Court overturns Roe v. Wade, as it’s expected to, the ensuing increase in births will likely leave families in tough circumstances and strain systems that are already hanging by a thread.
“What we’re facing as a country is hundreds of thousands of births, probably disproportionately located in the states that have been most limited in what they do for pregnant women, infants and children. So this is the great paradox that we are dealing with,” said Sara Rosenbaum, a health law and policy professor at George Washington University. “We have not ever designed these programs for a world without Roe,” she added. “You need a child welfare system, the likes of which we’ve never seen.”…
A growing shortage of obstetricians, higher maternal mortality rates and worse health care outcomes generally, increased pressure on U.S. foster and adoption systems— it all bodes ill…
We know from focus on health outcomes that kids born into poverty, kids born into unstable social circumstances, tend to have higher incidence of early onset chronic diseases,” Shannon said. “We also know that when those children are raised in unstable circumstances and have to be cared for in foster care, the outcomes there are really sobering.
Richard Shannon, chief quality officer for Duke Health
“Red states aren’t prepared for a post-Roe baby boom,” from Caitlin Owens (@caitlinnowens) in @axios.
* Jean Ping
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As we contemplate care, we might sending healing birthday greetings to Thomas Huckle Weller; he was born on this date in 1915. A virologist, he developed a technique for cultivating poliomyelitis viruses in a test tube, using a combination of human embryonic skin and muscle tissue– which enabled the study of the virus “in the test tube,” a procedure that led to the development of polio vaccines. He was awarded the Nobel Prize in Physiology or Medicine in 1954.
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