What microbes in our soil (not dirt!) mean to us

Most people have no idea just how large the role of microbes play as a part in our world, in our soil, in our bodies. That was the introduction we received on the subject from Yale professor Jo Handelsman at New Horizons in Science (as part of #sciwri10).

As a molecular, cellular and developmental biologist, Handelsman takes issue with any scientist or science writer who dares refer to the world’s largest organ as simply “dirt” (a mistake I’ve already made and won’t make again).

In human health, microbes do a lot more than we thought, says Handelsman. There are interesting associations of feelings like anger and different composition of human gut microbiota. Microbes or microbial products or microbial interactions with host tissues are also shown in animals to be linked to diseases including obesity, diabetes, etc. (apart from genetics and diet).

We are “microbial organisms”! says Handelsman, noting that our bodies contain 10 times more microbes than cells. Similarly, the Earth is largely a microbial organism as the microbes affect climate, provide most of the nitrogen on the planet, and make up the soil that produces our food.

How much do microbes play in climate? A lot. The microbes in the ocean are what fix much of the carbon creating oxygen, but “the plants get most of the credit.”

Bacteria are also what stabilizes the soil, by living and forming the crust on the surface of sand — preventing erosion and providing planetary health.

So, in reality, microbes are good! They are not simply pathogens and toxic, as many people believe, says Handelsman.

Soil itself is mostly microbial with 10 billion bacteria per gram. Soil supports 95 percent of our food. And soil bacteria are our primary source for antibiotic drugs.

Antibiotics, in particular, present a reason why we must study soil. There are few antibiotics in the pharmaceutical industry pipeline, there’s bacterial resistance to most antibiotics in use, and overuse and abuse is worsening the problem.

“Now we’re facing a health crisis that is unprecedented,” says Handelsman. “But worse than that is that industry has abandoned the study of antibiotics (with the exception of Merck and Pfizer).”

This is scary considering the growth and density of the human population, which could lead to a major catastrophe that Handelsman says “we are not prepared for.”

She then shows a graph to illustrate an example of how resistant bacterial strains can spread rapidly, which cannot be treated — an area of “enormous concern” of which she studies.

Why does antibiotic resistance exist? It’s well established that excessive use, especially in livestock, creates the development of resistance. The antibiiotics used on animals leaks into the environment, into the soil, into the water.

About a decade ago, Handelsman and her team developed microbial observatories to study the soil. They asked questions about whether or not antibiotic resistance genes move from soil to humans, where are the origins, and is there contact between soil and wounds (such as in Iraq, Afghanistan).

Her team has three sites for microbial observation: West Madison, Alaska, and Epplegarden. The sites are strategically located to collect data on how antibiotics overuse could lead to antibiotic resistance.

Coming back now to soil bacteria, she notes that most bacteria that we know of can’t be cultured. They are dramatically different than bacteria we can culture. So, how to identify and study?

The team developed “metagenomics” (“bypassing the culturing step”) and going to genomic analysis. They also analyze the activities expressed by clones carrying fragments of genomic DNA extracted from the organism assemblage.

In other words, they take a sample of soil, place it in a vessel, extract DNA, clean uop the DNA (because it’s “dirty”!), and then replicate by introducing DNA fragments into E. coli.

For example, they take E. coli resistant to kanamycin (an aminoglycoside), penicillin resistance, then isolate genes that are responsible for the resistance. They found three kanamycin-resistant genes in orchard soil, which produced fusions of proteins that conferred the resistance.

Handelsman also described what they found when they looked at Alaskan soil bacteria with beta-lactam (amoxicillin, penicillin) resistance. The bacteria harbored a gene producing bifunctional enzyme, beta-lactamase.

“Interestingly, the resistance genes were relatively poorly related to other known resistance genes,” Handelsman says. So, the data reveal that bacteria don’t have specific “drug-resistant determinant.”

Antibiotic use in livestock, agriculture, “pig operations, in particular,” is an environment ripe for drug-resistant strains of microbes. An example is flurophenicol.

In apple orchards, sprayed with streptomycin, there was concern about strep resistance. But they found that there was little resistance since, perhaps, the strep didn’t penetrate the soil. Also, the strep-resistance genes in humans were not the same.

Takeaways? Bacteria are wonderful, should be revered. Most aren’t culturable, metagenomics provides us access to unculturable bacteria. Through metagenomics we’ve also discovered novel resistant genes, raising question about resistance origins, such as agricultural practices that raise more questions. In short, soil is super and needs more study.

In the Q&A session, Handelsman also commented on the unwillingness of the meat industry to understand, or do anything about, the evidence showing the problems with antibiotic resistance related to agricultural practices. Their defense, “the data are inconclusive.”

If you found the idea of metagenomics as neat as I did, then you might also find Jo Handelsman’s 2004 paper on the subject interesting, which is published in Microbiology and Molecular Biology Reviews.

Location:Chapel St,New Haven,United States

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