# [Partners #19- The Soil Explorers]{.underline}

Microbial Observatory

Looking at this Wisconsin countryside, it's hard to imagine that much
could go wrong in such a pastoral landscape. But trouble arrived here
just a few years ago when a bacterial pathogen re-invaded the area,
causing widespread destruction.

**Patty McManus**- University of Wisconsin

*Fire blight is a disease that affects apples, pears, and related crab
apples, related ornamental trees. It is caused by a bacterium, or
Erwinia amylovora, and it although it's a sporadic disease, it can be
really devastating- taking out branches, flowers, fruit - entire trees
sometimes. The most noticeable signs are that when you look at the tree
it looks like a branch has been scorched by fire, and so it's brown or
black. And the leaves are dried up and the branch would be crooked up at
the end so it resembles a shepherds crook*. *It's a pretty big problem.*

**Narrator**

Patty McManus advised Wisconsin farmers on how best to combat the
disease. One of those was Verne Forest of Eplegaarden Farms.

**Verne Forest-** Eplegaarden Farms

*Very scary. I thought the way it suddenly hit and the fact that we had
it for two years in a row. I thought that we might lose the orchard.* *I
would say a total of 200 or 300 trees maybe we have lost, and of course,
we have cut back on some of the infected trees.* *Production was lost
for quite a while.* *From then on, we have been serious about trying to
cut out the ugly dead stuff and to manage it and get it under control.*

**Narrator**

One such control method that Verne and others use is the spraying of
streptomycin. Streptomycin comes from the bacterium *streptomyces
griseus* that's found in soil. It has proven to be a formidable foe
against fire blight.

But historically, streptomycin has been used as an antibiotic in the
medical world. It was here, in this building at Rutgers University, that
Albert Schatz and Selman Waksman first discovered the bacterium that
produces streptomycin. Streptomycin proved to be instrumental in
checking the spread of tuberculosis. Today, it is still used to fight TB
plus a number of other diseases including bubonic plague.

And herein lays the problem. Some in the medical community are alarmed
by the spraying of streptomycin for agriculture. They fear its overuse
will lead to a biological weakening of the medicine. If true, this could
have serious health implications.

**Dr. Jain-Johns Hopkins University**

*What streptomycin does is it inhibits the making of the protein from
the RNA. So basically it shuts down almost all the metabolism of the
bacteria.*

*If streptomycin is used extensively and in high concentrations, then I
think bugs which are in soil ... which will be exposed to high
concentrations will become resistant. So yes, it will have human
implications.*

*At least at this point in time one of the diseases we really need to
curb is TB. And if, for any reason... micro bacterial tuberculosis
becomes resistant to*

*streptomycin - which it is becoming- I think it will be a problem
because we will loose what people consider a second-line drug for TB. We
should be very careful how we use our antimicrobials.*

**Jo Handelsman-University of Wisconisn**

*Our concern is as the soil is treated with streptomycin -which is a
chemical that will kill organisms that are sensitive to it and allow
survival to the ones that are resistant. We're concerned that those
resistant ones may spread not only themselves, but the genes that they
carry that confer resistance to other organisms. And that would be a
risk for human health if those genes for antibiotic resistance moved
into microbes that could reside in the human body.*

**Patty McManus**

*They spray with streptomycin during bloom to prevent infections.*
*Growers are under scrutiny from people who don't understanding why they
are using it.* *But there is no data to help us figure out what the
effects are.*

**Jo Handelsman**

*We certainly don't want to be contributing to the antibiotic resistance
problem in that particular organism. But we don't know whether spraying
streptomycin in apple orchards actually does lead to clinically
important resistance.*

*Hi, Courtney. What's up?*

**Narrator**

Microbiologist Jo Handelsman and her team are trying to get answers to
this pressing question.

**Jo Handelsman**

*Did you see this?*

**Narrator**

With CSREES funding, they are exploring the soils in orchards and other
places for clues, establishing what she calls 'a microbial observatory'.

**Jo Handelsman**

*We all think of observatories as being places where we look at the
very, very largest parts of our universe. Microbial observatories are
places where we look at the tiniest parts of our universe - the
microorganisms that live around us.*

**Narrator**

It is in this world of microbes that Handelsman believes the answers may
lie.

**Jo Handelsman**

*No question about it - microbes rule. They run all of the major
chemical cycles on the earth. They make most of the oxygen that
available to us. They clean the systems that we live in. They clean the
soils. They clean the waters. But perhaps the most important use of the
microbes is their production of antibiotics that are used in medicine.
In fact, most of the antibiotics we use today in medicine are derived
from microorganisms that live in the soil.*

**Narrator**

For Jo Handelsman, the research has a personal meaning.

**Jo Handelsman**

*My mother had a long term illness that ultimately killed her, which was
caused by antibiotic resistant bacteria.* *Watching the ferocity of the
bacteria that killed her and the power of antibiotic resistant certainly
drove my work with a new passion. For me, it's just a way of keeping my
mother with me because every antibiotic experiment that we do connects
with her in some way. I think that human connection in science is really
important.*

*We use to think we knew a lot about the biology, but now we know that
99% or more of the bacteria in soil has never been heard from because we
have studied soil for so long culturing in Petri dishes. And know that
we know that most of the organisms are not succumbing to Petri dish
growth. We don't know anything about them. So there is way more to
learn.*

**Narrator**

It is in this vast, new frontier of uncultured bacteria where Handelsman
and her soil explorers work. Back at the lab, the samples are sifted.

**Jo Handelsman**

*The first thing we need to do is get rid of the rocks because it is
very hard to extract DNA in the presence of rocks. The hard part comes
when we try to extract the DNA from all the microorganisms in the soil.
This is the technology that we now know as metagenomics, which involves
studying all of the genomes of the organism in an entire community.*

*We simply extract the DNA. Then we cut it up into small pieces and
insert those pieces individually into a surrogate host like ecoli a very
common lab bacterium. And then we can study those DNA fragments and the
genes on them in that surrogate host.* *We now know after decades of
studying microbes in the environment using molecular methods that in
fact a very tiny percentage of the bacteria in the environment are
culturable - probably fewer that 1 percent.* T*hat tells us we need
another method to gain information about those micro-organisms that we
cannot capture in culture and metagenomics offers us one way to do
that.*

*Monumental doesn't begin to describe it. This is the most exciting time
in science that I've experienced.*

**Narrator**

But Handelsman's microbial observatory extends far beyond the borders of
Wisconsin. This is the Tanana River of the Alaskan interior. Today,
researcher Roger Ruess guides his boat down these wild waters toward a
remote island in the stream. His destination? the Bonanza Creek
Experimental Forest - one of the more biologically pristine environments
in the world.

**Roger Ruess-University of Alaska-Fairbanks**

*This is a braided river channel. It is a large river - one of the
largest rivers in Alaska. The landscape is a mosaic of islands that are
interrupted by back sloughs, and the vegetation represents various
stages of development in response to disturbances - principally fire and
flood dynamics. It's incredibly pristine relative to the lower 48. These
forests are undisturbed by humans essentially.*

**Narrator**

The very foundation of this 'laboratory under the sky' is why Roger
Ruess has traveled here. He is in search of soil -samples that may offer
clues to the streptomycin issue back in Wisconsin.

**Jo Handelsman**

*Roger has a fantastic ecological understanding system of the whole
ecosystem.* *The Alaskan soils are very interesting because of their
geological history because of the climate and the vegetation in the
islands that we study. But they also provide a very unusual habitat that
has been exposed to very little human effects. That gives a baseline of
antibiotic resistance in an environment that has not been pilfered by
humans, and provides a nice contrast to the site in Wisconsin that has
been managed by humans for quite a long time.*

**Roger Ruess**

*It offers her an unusual set of conditions in the soils. The soils are
characterized by extremely cold adapted organisms that are capable of
dealing with very recalcitrant organic matter. My thought for having her
work here is that there would be an unusual suite of organisms in the
soil just due to the tremendous variations we have in soil organic
matter.*

**Jo Handelsman**

*Ultimately, we hope by comparing the two soils we'll have a sense of
what antibiotic resistance genes are present even when humans have not
intervened. And that will give us some perspective on the apple orchard
because we won't know in the apple orchard if any of those genes would
have been discoverable in the absence of antibiotic use.*

**Narrator**

Over three thousand miles to the south, the work continues at the
University of Wisconsin's Microbial Observatory. Perhaps the answer to
the streptomycin issue will be found in one of the Alaska samples sent
by Roger Ruess.

**Jo Handelsman**

*We simply don't know if streptomycin is going to have an effect on
streptomycin resistance in the orchard. Of course, that is exactly what
we want to find out.*