After writing my review of the Proceedings of the National Academy of Sciences USA article “Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death”, I vaguely wondered if the authors could have sequenced more than a single 10kb plasmid. If the single-copy chromosomal DNA was too scarce, maybe one of the other Yersina pestis plasmids that may exist at a higher copy number (e.g., pMT1) might be sequenced. Continue reading “Sequencing the Black Death is a Window to the Past”
Microorganisms: Infectious Disease and Ecology
Blog entries about bacteria, viruses, fungi and other microorganisms.
Dance Macabre: Will 14th Century Remains Reveal the Pandemic Secrets of the Black Death?
Last year, I reviewed a PLoS Pathogens paper that found European Black Plague victims from the mid 14th century were infected with more than one clone of Yersinia pestis. While the Y. pestis-specific sequences amplified from several skeletal samples from various countries were evidence of the bacterium as the etiological agent, questions still remained about the virulence of the outbreak. What allowed that ancient strain of Y. pestis to cause such widespread death? Another group of researchers decided to further analyze the causative agent of the Black Plague by enriching for and sequencing one of the extrachromasomal plasmids present in the bacterial genome: the 9.6kb virulence-associated pPCP1 plasmid. Continue reading “Dance Macabre: Will 14th Century Remains Reveal the Pandemic Secrets of the Black Death?”
Where Mycologists Go To Church On Sundays
When it comes to academic triumphs and laudatory honors it can be said that mycologist Paul Stamets has his fair share. Stamets has authored six books on mushrooms, holds over twenty patents, is a winner of the Collective Heritage Institute’s Bioneers Award. Today he also runs a facility that boasts twenty four laminar flow benches across four laboratories processing between 10-20 thousand kilos of mycelia each week. He has close to a thousand mycelium cultures growing at any given time and is renowned across the world for his view of fungi as the ‘grand molecular dissemblers of nature’. And so it was that the Biopharmaceutical Technology Center was pleased to host a lecture by Stamets almost two years ago with the promissory title: How Mushrooms Can Save the World. Continue reading “Where Mycologists Go To Church On Sundays”
Worms from Heaven and Hell
Worms from the heights of space and the depths of the earth were in the news last week, one well-known species soaring to the heavens as part of a space flight experiment and a previously undiscovered species revealing the surprising extent of multicellular life in the hidden depths of earth.
The Worm from the Heavens
Caenorhabditis elegans perhaps qualifies as the most well-known of all worms. This 1mm roundworm, is a staple model organism in molecular biology. It’s easy to grow and store, possesses a simple neuronal network, and is transparent, making it easy to study cell differentiation and development. It was the first multicellular organism to have its genome sequenced, and the developmental fate of all its somatic cells has been studied. In some ways we know C. elegans better than we know ourselves.
PCR-Based Diagnosis Wins by a Mile In the White-Nose Syndrome Race
Since the first photograph of bats with white muzzles in Albany, NY, was published, hibernating bat populations in the northeastern U.S. have been devastated by an emerging disease, White-Nose Syndrome (WNS), which continues to spread throughout the United States and now has been found in two Canadian provinces. Bats suffering from WNS are emaciated with little or no body fat and have a characteristic white fungal growth on their wing membranes, ears and muzzles. Instead of hibernating all winter, these bats can be seen active in the snow, when there is virtually no food available.
The infectious agent that responsible for WNS is a new species of the cold-loving fungus, Pseudogymnoascus destructans (formerly, Geomyces destructans) . Currently, WNS is confirmed either through histological analysis or by fungal culture. Both of these techniques have significant limitations. First, they have turnaround times of at least one week. Secondly, they require large amounts of tissue sample from affected bats, more than can be reasonably taken from live bats. Histological analysis is a laborious process that requires highly skilled and trained personnel. Fungal culture can be difficult because bats harbor many bacteria and fungi, and getting a pure culture of a causative organism is not simple. Furthermore, researchers need a quick method for assessing spread of the disease that can provide results quickly.
Polymerase Chain Reaction (PCR), already used for a host of diagnostic tests in humans, plants and animals, is a logical choice. In a paper published in the Journal of Veterinary Diagnostic Investigation, Lorch and colleagues design and evaluate a PCR-based diagnostic method for WNS. They compare the PCR method to a fungal culture method and the “gold standard” traditional histological analysis. Continue reading “PCR-Based Diagnosis Wins by a Mile In the White-Nose Syndrome Race”
Microbiome Studies: We Are More than the Sum of our Parts
What if you could help protect yourself from certain diseases by populating your gut with “good” bacteria, or selectively getting rid of “bad” ones? Two news articles suggesting this possibility caught my eye this week. The articles both summarized results from the microbiome project—a research effort geared towards developing a deep understanding of how the bacteria that live in and on our bodies influence our health. Analyses of these bacterial populations are providing new insights that suggest we are much more than the sum of our parts, and that our health may depend not only on our own genes and lifestyle but also on the contributions of the bacteria that colonize us.
Continue reading “Microbiome Studies: We Are More than the Sum of our Parts”Virophages: The Enemy of My Enemy is My Friend
Viruses are small DNA- or RNA-based infectious agents that can replicate only inside living cells of a host organism. Most people know what a virus is, and many of us harbor at least one or two of them at some point during the cold and flu season. However, I would guess that many of us do not know what a virophage is, even though they seem to be more common than previously thought.
Virophages were first discovered and characterized by LaScola et al. in 2008 (1) during studies with Acanthamoeba polyphaga mimivirus (APMV), the largest known virus—so large that it is visible by optical microscopy. Continue reading “Virophages: The Enemy of My Enemy is My Friend”
The Search for New Antibiotics: Looking for Achilles’ Heel (Again)
Some of the first available doses of penicillin were used to treat allied soldiers wounded on D-Day. It was the end of one war, but just the beginning of another–one that has gone on for a long time. The story of the development of antibiotics, and the emergence of resistant bacteria, followed by the renewed search for new antibiotics, seems neverending. As soon as a new antibiotic is discovered, it seems only a matter of time before a resistance mechanism emerges, and remaining one step ahead of the bugs can seem like a relentless challenge. Continue reading “The Search for New Antibiotics: Looking for Achilles’ Heel (Again)”
Metal Eaters Propel The Demise Of The Titanic
Oceanographer Robert Ballard’s literary showpiece The Discovery Of The Titanic today sits on a shelf in my bedroom collecting dust. Gone are the days when it was heavily leafed through by relatives and close friends mesmerized as they were by the glossy pictures and personal accounts of disaster contained within its covers. I had dismissed from mind images of the Titanic’s Captain Edward Smith and Marconi wireless operators Jack Phillips and Harold Bride that accompany the chilling story of the fateful night. I had forgotten about Ballard’s detailed chronicling of the turbulent expeditions that led to the eventual finding of the Titanic more than 70 years later. And I had put aside my fascination for the flagship submersible Argo that in 1985 had scoured the Atlantic at 13,000 feet below sea level until it finally met up with the eerie wreck of the luxury liner. But my interest in the book has recently been revived by the molecular characterization of a fastidious strain of bacteria that is “speeding up the decay of the historic wreck” (1).
When Ballard wrote his book over 25 years ago, biologists had already advanced the idea that micro-organisms were breaking down the iron cladding of the Titanic. His description of some of the first shuddersome glimpses of the ship’s contours give us an inkling of what was known at the time:
“As we rose in slow motion up the ghostly wall of the port bow, our running lights reflected off the still-unbroken glass of portholes in a way that made me think of cats’ eyes gleaming in the dark. In places, the rust about them formed eyelashes, sometimes tears. As though the Titanic were weeping over her fate. Near the upper railing- still largely intact- reddish –brown stalactites of rust hung down as much as several feet, looking like long needle-like icicles. This phenomenon, the result of iron-eating bacteria, was well known, but never had they been seen on such a massive scale. I subsequently dubbed them “rusticles”- a name which seems to have stuck” (2).
Now a joint effort from scientists in Spain and Canada has uncovered the DNA signature of one of a handful of bacterial agents that lie at the heart of the rusticle phenomenon. By removing stalactite pieces from the hull of the Titanic and performing a battery of elucidative phenotypic and chemotaxonomic tests, Christina Sanchez-Porro and others have homed in on the true identity of one salt-loving microbial wreck heister called Halomonas titanicae (3).
H.titanicae, dubbed BH1, is part of a larger family of bacteria that until now had never been observed so deep below the ocean surface. It uses iron as an inorganic source of energy, oxidizing it and leaving rust behind as a waste product. For many of the 27 bacterial strains now known to live in the rusticles, the deep sea conditions are not sufficiently acidic for growth (2). They get around this by manufacturing a more favorable dwelling of “highly viscous slime” that encapsulates them away from seawater and gives them an acidic habitat in which to flourish (2). But bacteria are not the only organisms feasting on the spoils of this particular maritime tragedy. Wood-borers have all but decimated much of the exquisite woodwork in the ship’s interior although the high density teak wood found in many of the railings, staircases and roof trims has proven to be remarkably unyielding to these voracious assailants (2).
Opinions differ over whether the havoc that bacteria such as BH1 are wreaking should be left to continue unabated (1) Ontario Science Center biologist Bhavleen Kaur believes that the bacterial goings-on aboard the Titanic could be used to help us better understand and halt the breakdown of other manmade sea structures such as offshore oil rigs and gas pipelines (1,4,5). Microbial ‘iron munching’ might even find application in recycling and disposal workflows (5). Some heritage devotees are less than happy about such proposals preferring instead to promote efforts to halt H.titanicae in its tracks and preserve the wreck for posterity.
While perhaps desirable, going head-to-head with nature’s forces seems impracticable given the sheer speed at which the wreck is succumbing to bacterial breakdown. Canadian civil engineer Henrietta Mann posited that twenty years from now there may be little more than a “rust stain on the bottom of the Atlantic” marking the location where the Titanic’s shadowy grave once lay (4,5). It is a sobering thought that such a fate should befall what was once a 50,000 ton steel leviathan of a ship (5). Extensive video footage and photographs may soon become the only means we have by which to remember the Titanic’s “very human story” (4,5).
Further Reading
- Rachel Kaufman (2010) New Bacteria Found On Titanic; Eats Metal, National Geographic News, December 10th, 2010, See http://news.nationalgeographic.com/news/2010/12/101210-new-species-bacteria-metal-titanic-wreck-science/
- Robert Ballard (1984) The Discovery Of The Titanic: Exploring The Greatest Of All Lost Ships, Madison Press Books, Toronto, ON, p.116, p.208
- Sánchez-Porro C, Kaur B, Mann H, & Ventosa A (2010). Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic. International journal of systematic and evolutionary microbiology, 60 (Pt 12), 2768-74 PMID: 20061494
- Graham Smith (2011) First it was an iceberg, now it’s bacteria: Rust-eating species ‘will destroy wreck of Titanic within 20 years’, Daily Mail, 12th January, 2011, See http://www.dailymail.co.uk/sciencetech/article-1346446/Titanic-wreck-completely-destroyed-20-years-new-rust-eating-bacteria.html
- Rosella Lorenzi (2010) Titanic Being Eaten By Destructive Bacteria, Discovery News, 7th December, 2010, See
What Caused the Black Death?
I was confident I knew a few things about the bubonic plague: It was caused by the bacterium Yersinia pestis, which was transmitted to humans by fleas hitching a ride on the back of traveling rats. It spread rapidly and devastated populations around the globe, and because cats, a natural predator of scurrying rodents, had been killed, rats proliferated along with their deadly, infectious cargo. However, until I read a recent PLoS ONE article, I did not realize there was still debate about whether Yersinia pestis was the infectious agent for Black Death, the disease that ravaged 14th century Europe and killed one third of its population.
