New Studies Point to ‘Carbon Starvation’ as a Cause for Tree Mortality
Tree death rates could increase globally because of rising temperatures and prolonged droughts linked to climate change, according to multiple studies.
The reasons for tree mortality in a warmer, drier world have been narrowed down to three main scenarios — greater prevalence of insects and diseases in a warmer world, the drying out of plants, and a third mechanism where water-stressed trees stop photosynthesizing, called carbon starvation.
In Search of Chlamydia
The cement trough yawns below me, an abyss filled with streaming sewage hundreds of feet below. The smell is pungent and faintly urine-like as wastewater from streams and rivers mixes with household waste to create a haven for the bacterium that is my nemesis: Chlamydia.
“You know what’s in the sewage?” asks the beefy engineer at the Woodward Avenue water purification plant in Hamilton, a small city in Ontario once famous for its steel. These days, it is more known for its non-achievements: steel mill layoffs; Ti-Cats football fanatics who shout “Oskie-Wee-Wee! Oskie-Wa-Wa! Holy mackinaw! Tigers…ha! Ha! Ha!” even as their team repeatedly loses; and an underdeveloped downtown core with an overdeveloped pigeon problem.
But Hamilton is also a city of waterfalls and streams, rivers and harbors, all a natural home for Chlamydia. As, of course, is sewage.
“Corn,” the engineer answers himself seriously. “Corn doesn’t get digested. It passes through the intestine intact.”
He hands me five liters of the waste water.
Under a darkening sky, I drive back to my research laboratory at the McMaster University hospital and lug the jugs of water upstairs, past the red zone where just-born infants rest peacefully in plastic incubator cages, under individual yellow bulbs.
Rather like plants.
Children are at great risk of infection by Chlamydophila pneumoniae, which causes pneumonia. Its cousin Chlamydia trachomatis is infamous for causing the sexually transmitted disease Chlamydia, which can result in blindness. Prachlamydia and Simkania cause respiratory illness. Waddlia causes abortion in cows.
I run through the list, memorized for my upcoming thesis defense. The next sentence in the presentation goes so:
New species of the bacterium are still being found, in places as far-flung and extreme as Antarctic salinity lakes. Wherever they are found, they are pathogenic. And yet, their presence in our environment, in our water sources—rivers, ponds, and lakes—has been largely ignored.
My job is to figure out a way to detect them that lab technicians can employ easily, an amazingly difficult task as I’ve found out over the past four months. I have trudged through forests and swamps and manmade reservoirs located next to deserted hiker’s trails and country roads and highways. I have watched the Red Hill Expressway, intended to cut travel time between Hamilton and Toronto in half, grow from a muddy road to a cemented monster, all the while collecting water from the Red Hill Creek. The different water sources have distinctive fauna and flora that comes to life under a microscope.
A single drop of water is a universe unto itself, inhabited by creatures of reduced proportions. Magical shapes drift in and out under 40 times magnification—translucent amoebas, paramecia, rotifers, sun animalcules (“little animal”) with hair-like flagellum around them like a halo, and other strangely beautiful blobs. These are the visible creatures.
My target is the inhabitant of a world of less than a single micrometer—invisible.
Invisible is what I feel as I pass into the purple zone of the hospital. Fluorescent bulbs cast shadows in the deserted hallway. Graduate students have fled their labs to quell their boredom in alcoholic beverages. I am alone in my quest for what I have come to view as an ethereal creature, my yeti. It exits, but has eluded me repeatedly. I do not know if this is because of human error, or because the water samples lack Chlamydia.
I do not know which answer I would prefer.
So filtering sewage is what it comes down to.
–
Every day, for the past four months I have performed the same set of experiments.
One. Collect sample. Spin sample in a centrifuge at 500 times the speed of gravity. This weighs down all the debris that can be thrown away.
Two. Take the “soup”—the resulting sample—and filter using paper with pore size of 1000 micrometers under strong vacuum. All but the biggest microorganisms will go through.
Three. Filter through a paper with one micrometer-sized pores. Only the smallest organisms will pass through.
Four. Add phenol and chloroform, chemicals that will cause the beautiful, mysterious living blobs to burst open, spilling out their genetic secrets—DNA and RNA—into the water.
Five. Amplify regions of DNA where the four bases—adenine, guanine, cytosine, and thymine—have come together in a sequence that, out of all the organisms in the world, are present only in the Chlamydial genome. The sequence is a signature as unique as a thumbprint, which, after many steps inside the nucleus of the bacterium, results in the “signature protein” CT429. No one knows the function of this protein, one of the thousands that allow these bacteria to grow and multiply and infect.
Six. Amplify regions of DNA that correspond to Heat shock protein 70, a protein present in most organisms on Earth. It helps fold other proteins into shapes that must be painfully conserved for proper function. Misfolded proteins can result in disease—dementia and Lou Gherig’s, for example.
Seven. Separate amplified DNA fragments according to size and charge using agarose gel electrophoresis.
If the heat shock protein amplifies but the Chlamydia protein doesn’t, it means the water sample contained organisms of many varieties, but not Chlamydia.
Or it could mean that there is a glitch in the experimentation.
This uncertainty is ever present in the lab, I have found. Why did something not work? Or why did something work? Was the result an outlier? Could it be possible that the wrong sequence got amplified due to primer mismatch? Perhaps the AGTCCCT primer, instead of attaching to TCAGGGA, attached to a region of the DNA that goes TCACGGA. Now the wrong region is amplified, a size of 600 base pairs instead of the 400 base pairs that I am expecting.
Or perhaps, serendipitously, the wrong region is also 400 base pairs long, creating the illusion of the perfect match. Voila! The protein is found! Chlamydia exists!
But clone the region into a vector and re-amplify. Sequence. The protein sequence is not the same as for CT429. The wrong protein got amplified. Chlamydia doesn’t exist.
–
I pour the sewage into 1000 ml centrifugation bottles. The lab vibrates as the ancient machine spins. I bounce slightly on my toes in rhythm with the rocking cultures of bacteria grown by my colleagues.
This is a world of objectivity, ruled by the gods of precision and accuracy. But much as life itself, the world of experimentation is ruled by uncertainties, with a result true to perhaps a 90th percent of certainty, or 95th percent. There are no final answers.
But there is always the quest.