Dr. Bortrum
10/01/2015
Microbes Are Everywhere
CHAPTER 61 Microbiomes Above Ground and Below
Decisions, decisions. I was not even a year old when Alexander Fleming, in September of 1928, returned to his lab after a vacation to find a mold in one of his Petri dishes. The mold had killed the Staphylococcus aureus bacteria in the dish and penicillin was born. Years later, in the 1950s and early 1960s, here in New Jersey after coming to Bell Labs, our family doctor was a Dr. Williams, who prescribed penicillin for the flu or virtually any other illness that affected us. In those days, this was a common approach for many doctors. Some years later, I had an ear infection and the ear doctor prescribed penicillin. I don't remember if it cured my ear problem but I vividly remember my testicles swelling up and turning a bright red color! I was told that I was allergic to penicillin.
Some time later, I was diagnosed with a mitral valve prolapse. At the time, with this heart condition, an antibiotic was prescribed before undergoing a dental examination involving cleaning of the teeth. With my allergy to penicillin, I was prescribed clindamycin. It was later decided by the medical community that an antibiotic was not necessary and I stopped taking the clindamycin prior to my dental visits.
Fast forward to 2013, when I had a hip replacement. With the hip replacement, I once again was prescribed clindamycin before my dental visits. A couple of months ago, before my 6-month dental visit I obediently took my four tablets of clindamycin. A short time after this, I got my August issue of Consumer Reports, which contained an article titled "The Rise of the Superbugs". Needless to say, I was riveted upon reading the first two paragraphs of the article describing the case of a 56-year-old woman who took clindamycin to prevent a dental infection. Ten days later, she was dead! The antibiotic had killed off the good bacteria in her gut and the bad bacteria had run amok and a terrible infection resulted. Removal of her colon did not stem the tide and she died.
After reading this article, I had an appointment with my dermatologist to do a biopsy on a growth on my arm and before he did it he asked if I had taken my clindamycin. I told him of the article and that I had just taken clindamycin a couple months earlier and did not feel comfortable taking another dose so soon, if ever again! Incidentally, the biopsy showed a need for removal of more of the growth and this week I again had surgery without taking my clindamycin. So far, so good.
I've written before about the huge research effort to understand our gut bacteria, known as our microbiome. Much of the interest is due to the alarming number of hospital infections caused by antibiotics killing good gut bacteria that fight off the bad bacteria leading to serious infections and many deaths. That Staphylococcus aureus Fleming saw the penicillin kill has evolved into Methicillin-Resistant Staphylococcus aureus, MRSA, a deadly form of bacteria.
What brought up all this rant on the gut biome? Actually, it was an article by Jop de Vrieze in the August 14 issue of Science titled "The Littlest Farmhands". The article deals with another kind of microbiome, namely the thousands of microbes that are in the soil. As with our own microbiome these good microbes in the soil help plants survive and prosper. In many places years and years of poor farming practices and also years of drought have depleted topsoil and killed off good bacteria that form mutually profitable interactions with the plants. For example, there's a fungus that helps soybean plants absorb water and nutrients, while the plant helps the fungus by excreting nutrients that the fungus consumes.
Just as we harbor billions and billions of cells and who knows how many different kinds of microbes in our guts, scientists have found there can be up to 10 billion cells of bacteria in just a gram of soil around the roots of a plant. One study found over 30 thousand different species of bacteria on or around sugar beet roots! Many bacteria work with the plants by making compounds that ward off predators. Others promote the ability of plants to exist in salty conditions and in very dry conditions. Some produce toxins that kill caterpillars. Others consume heavy metals that are toxic to the plant. There are fungi that act like extended root systems by bringing to the roots of a plant water from deeper in the soil than the roots of the plant can go.
Pius Floris, a Dutch researcher, is leading an effort to restore severely damaged soil in a region of Spain by putting microbes to use. Without going into detail, the researchers planted three areas with oats, vetch (a plant that attracts bacteria that fix nitrogen) and olive trees. One zone was treated with chemical fertilizer and pesticides, the other two zones were treated with organic fertilizer and various amounts of fermented grape leftovers and a variety of bacteria and fungi along with doses of mychorrhiza spores. None of the zones was irrigated. The crops in chemical fertilized zone were negligible compare to the yield of crops in the zone which had the heaviest amount of organic fertilizer added. The really interesting thing was that in this organically fertilized zone the plant roots had found their way down 2 meters into the rocky soil to reach ground water. The reason the roots could do this was that the mychorrhiza penetrated the rock by excreting acid that dissolved the rock, allowing the roots to follow along to get at the water.
Speaking of water, longtime readers would be shocked if I didn't mention the big news from NASA that evidence for running salty water has been found on Mars. Is it a coincidence that the news is being released just at the time of release of the movie with Matt Damon being stranded on Mars? Actually, I wasn't particularly surprised at the confirmation of running water. The appearance and disappearance of features on Mars that could be streams of water have been around for some time. As far as life is concerned, I don't like it that the salt seems to be a perchlorate, not sodium chloride. I've used perchlorates in lithium battery electrolytes for a time when I was at Bell Labs and was not enthused about it.
I was much more enthused when last month NASA reported that, based on measurements from the Cassini spacecraft, there is a "global ocean" under the icy surface of Enceladus, one of the many moons of Saturn. This conclusion is based on years of observation of a very slight wobble as the moon orbits the planet. By precise observations of the positions of certain features on the moon's surface the scientists conclude that the wobble can only be explained by a fluid ocean underneath the solid surface. Previously, plumes of water vapor had been observed from one of the polar regions of Enceladus. If the salt in that ocean is sodium chloride, not perchlorate, I can visualize little critters swimming around underneath the icy crust.
Finally, it's getting to be a habit, not a pleasant one. Several of my recent columns have ended with mention of good friends or key figures in transitional points of my life. Last week, I noted the passing of a very good friend, Stanley Tannenbaum, a real rocket scientist. A couple of weeks ago, on the TV program Sunday Morning there was a segment on Milton Hershey of chocolate fame. There was mention of Hershey founding a school for orphaned boys to which Hershey left his entire fortune upon his death. I mentioned to my wife that Bill Gunderman, a fellow student at Dickinson College back in the 1940s, came to Dickinson from the Hershey orphans' school. Bill was a year or two behind me in college but we were the same age and became good friends. My wife had met him when he once visited us in New Jersey and we exchanged Christmas cards over the years.
I remarked to my wife that we hadn't had a card from him in a few years and wondered about him. So I Googled "William Gunderman obituary", hoping not to get a hit. However, the very first listing was my William Gunderman's obituary and he had died just a few weeks before the program, in August this year! I was surprised to find in the obituary that, during the Korean war he was in the military and was sent to Alabama, where he joined Werner von Braun's group building rockets. So, once again I mourn the passing of a friend who was, albeit briefly, a rocket scientist.
Next column, hopefully, on or about November 1.
Allen F. Bortrum
