Hands in the soil

Grab a handful of soil. Go ahead, step outside and scoop up a small amount in your hand. It’s hard to imagine all that’s going on in there. You’re holding trillions of creatures, though that’s just an estimate. Nobody has done the actual counting.

Unless you happened to grab an earthworm or beetle in your handful, you’re not likely to see much of anything without the assistance of an optical device. But with a simple hand lens or magnifying glass, you’ll see some tiny animals, including mites, springtails, and potworms. Some are these animals are predators, but many are detritivores (eaters of dead things). They’re largely responsible for tearing holes in the tissues of the dead things and for spreading them around -- the first step of decomposition.

With a microscope, you can see even more minute animals. You’re likely to see tiny worms called nematodes and rotifers, as well as amoebae and miniscule, eight-legged animals called water bears. These organisms eat everything: other animals, dead things, bacteria, fungi. Some nematodes can infest plant roots by stabbing into them with hypodermic-needle-like mouth parts. (When gardeners plant marigolds because they are "good for pests," they are taking advantage of marigold roots’ nematicidal properties.)

You can also see root hairs, algae, cyanobacteria, fungi, actinomycetes, and bacteria.

They may not be very noticeable, but they are the source of most of the diversity in the soil, accounting for the bulk of the soil’s biomass and most of its metabolism.

Root hairs are tiny, single-celled extensions of a root’s epidermal layer. They anchor the roots, which are actively pushing through the soil, and increase the surface area with which to absorb water and nutrients. Algae need light to photosynthesize, so they are generally found near the surface of the soil. Green algae are most often found in moist (though not flooded) acidic soils; diatoms, another kind of alga, are often plentiful in garden soil that is rich in organic material. Cyanobacteria are similar and are often found in wetland soils.

Over 700 species of fungi have been found in the soil so far. They include single-celled yeasts, filamentous molds, mildews, and rusts. These various kinds of fungi are responsible for much of the humus formation, soil stabilization, and the breakdown of organic matter. Although we may think of mushrooms as above-ground organisms, this visible fruiting body is only a small portion of the whole organism; fungal strands called hyphae extend throughout the soil. Some fungi are even predators. One uses a lasso-like device to trap nematodes.

Fungi are the source of many plant diseases, including late blight, the disease that plagued tomato and potato plants in the region in 2009, but one fungus (a mold) is also the source of penicillin. Fungi are particularly important in bogs and forest soils, where they are able to withstand acidic conditions. Perhaps the most important fungi, however, are those that form mutually beneficial associations with plant roots, called mycorrhizae ("fungus root"). Most plants depend on mycorrhizae to survive.

Actinomycetes have some fungus-like characteristics and some bacteria-like ones. They are detritvores. Many produce antibiotics to kill other microorganisms. The drugs actinomycin and streptomycin are derived from actinomycetes. In forest soils, the genus Frankia (one type of actinomycete) is responsible for much of the nitrogen fixation that makes atmospheric nitrogen available to higher plants. Actinomycetes also produce volatile compounds that make the "good earth" smell you think of when you think of dirt. There are hundreds of millions of actinomycetes per gram of soil, weighing up to 5,000 kilograms per hectare.

Patients urged to test for infections after Chambersburg urology practice admits reusing instruments

Patients of a Chambersburg urology practice recently received a potentially unsettling letter, advising them to get tested for HIV and hepatitis because reused instruments had been used for their prostate biopsies.

Medical and legal experts say reusing biopsy needles is not recommended for several reasons, and that Urology Associates of Chambersburg could now face a range of legal repercussions.

While the risk of infection is statistically very low, experts advise that every man who received a letter should be tested. The tests are being conducted at Chambersburg Hospital and paid for by the urology practice.

A 68-year-old Chambersburg area man told Public Opinion that he received his letter in the past week and went in for the blood work Friday. Due to the potentially sensitive nature of his situation, Public Opinion agreed to keep him anonymous.

He had his biopsy done about four years ago by Dr. Christopher Klinko. While the procedure was typically less than comfortable, he was pleased with the doctor's care and said everything seemed to be done very professionally.

"Everything looked very sterile and clean, very efficient," he said.

When he received the letter, Klinko's patient wasn't too concerned at first. His wife convinced him to go for the test. A phlebotomist at the hospital told him there have been a significant number of other men getting the same test done in recent weeks.

"I hadn't given it much thought. My feeling

Quantcast was, with the time that elapsed, something would have shown up already," he said. "Then I realized it could take a long time for HIV to show up."

Dr. Jay Raman, a urological surgeon and assistant professor of surgery at Penn State Hershey Medical Center, said in some cases it takes between seven and 10 years for HIV to become apparent in an infected person. Symptoms of hepatitis typically appear within two to four years after initial infection.

"The most aggressive strains will show up early, but being asymptomatic does not mean you're in the clear," Raman said.

According to the letter sent to Urology Associates' patients, the practice used biopsy needles and guides that are labeled "single use only."

"We have recently discovered that some prostate biopsy instruments were reprocessed using a detergent scrub, sterilized and then re-used in our office," the letter states. "Corrective action was immediately taken and instrument reprocessing has been terminated."

Raman explained that an ultrasound probe and a tubular device called a cannula used in the procedure are not disposable. They are disinfected and sterilized after each use in a special liquid formulated to kill bacteria.

Since biopsy needles or "needle guns" actually pierce the patient's rectal wall and the prostate to collect tissue samples, they should not be reused, he said. At his hospital, the needles are immediately placed in a "sharps" container and disposed of as biohazardous waste.

Raman said chemical sterilization is "more than adequate to kill all conventional bacteria," but HIV and hepatitis are considered "more hardy viral agents." He was unable to provide a statistical likelihood of patients being infected by "reprocessed" instruments, but said it is a very low.

His personal risk of contracting hepatitis if he is accidentally stuck with a bloody needle during surgery is about 1 in 500,000, Raman said. The risk of catching HIV the same way is about 1 in a million.

Add to those long odds the fact that the needles at Urology Associates went through some form of sterilization, and the likelihood of infection becomes quite rare. Still, Raman recommends getting tested to anyone who received a letter.

"If it was me, I would. I think the risk is overall very low, but certainly it's higher than zero," he said. "In that case, I think it's worthwhile to be better safe than sorry."

There is another reason why reusing biopsy needles is not a very good idea, Raman said. Each use would make the device a little less sharp. Performing biopsies with a blunt needle decreases the procedure's accuracy and increases the risk of complications.

He said this is the first case of reused biopsy needles that he has heard of. Asked why any medical practice might do such a thing, he suggested that saving money was probably the motivating factor.

According to the website for a medical supply company based in New Jersey, urological biopsy needles range in price from about $100 to $240 for a box of 10. The instruments are typically 1-2 millimeters in diameter and 10-15 centimeters long, Raman said.

Public Opinion was unable to determine how many patients received letters from Urology Associates. A receptionist answering the phone at the office said the doctors are declining to comment on the matter.

According to their letter, Klinko and Dr. Louis Glass are practicing urology at the office on Fifth Avenue in Chambersburg. Some patients told Public Opinion they had been treated there in the past by Dr. William Haren, who apparently no longer works there.

A fourth urologist, Dr. Kambiz Tajkarimi, reportedly left Urology Associates earlier this year. He is now practicing exclusively with Summit Health, which operates hospitals in Chambersburg and Waynesboro, according to the organization's spokesperson, Jessica Walter.

After Glass and Klinko sent their letter, Tajkarimi mailed a letter to about 800 of his own former Urology Associates patients on May 11.

"I had no knowledge of the conduct described in that letter and resigned from employment with the practice when I learned of this matter," his letter states.