Mysterious Microbes – Full Episode

They are some the ocean’s smallest inhabitants…and
on coral reefs, microorganisms are copious creatures. Microbes are very prolific on the surface
of corals, both in healthy and diseased corals. But in a world that’s invisible to the naked
eye, drastic changes are taking place. Whether it’s Australia or the Bahamas or
the Florida Keys, the scientists sees this microbial power shift. With healthy corals, when temperatures increase, pathogenic bacteria
go up and the beneficial bacteria go down. Just like when we get stressed out, we’re
more likely to get a cold. When you stress out these corals, they could
potentially be more susceptible to bleaching or getting a disease. Throughout Florida, scientists painstakingly
work to identify key players within this microbial community. It’s estimated that you can only culture
one percent or less of the bacteria that are out there but yet corals have thousands of
different kinds of bacteria associated with them. While some of the bacteria found on corals
are important to their health, others can lead to disease outbreak. This bacterium was killing the coral. We could hypothesize based on what we knew
about the bacterium that it might be coming from humans. Usually we hear about pathogens from wildlife
to humans. Examples are HIV, Swine flu, avian flu. But we haven’t had the reverse and so this
is a new disease mechanism that we’re not familiar with, especially in the marine environment. With experimental sites in the lab and in
the sea, what will microbes reveal about coral health? How do human activities impact the microbial
balance on the reef? Major funding for this program was provided
by the Batchelor Foundation, encouraging people to preserve and protect America’s underwater
resources. And by Diver’s Direct, inspiring the pursuit
of tropical adventure scuba diving. They help protect our coastal communities
from massive storm surge. Their beauty and bounty fuels a multi-billion
dollar tourism and fishing economy. Coral reefs are the underwater oases of the
oceans. But rising water temperatures and pollution
are taking their toll on the health of these gardens of the sea. In Summerland Key, Florida, researchers from
Mote Marine Laboratory are studying the microbial communities that surround corals. We’re leaving to go off shore about five
nautical miles to the famous Looe Key special protected area in the Florida Keys National
Marine Sanctuary. Leading today’s excursion is Dr. Kim Ritchie,
Manager of the Marine Microbiology Program at Mote Marine Laboratory. I’m most interested in corals that are reef
building corals. Some of the bigger corals, some of the corals
that grow fast and actually build the reef structure because these are the ones that
are more susceptible to diseases. Dr. Ritchie has been studying coral microbes
since the early nineties, a period of time that coincided with visible changes on reefs
throughout the keys. That happened to be at a time of increased
ocean temperatures and coral bleaching events and increased diseases. Water temperatures rise, they get higher than
usual, corals bleach, and by bleaching I mean they lose the coloration, the plant type of
algae. These symbiotic algae live within the coral’s
tissue. But if the algae are absent for too long,
the corals can die. For the past seven years, Dr. Ritchie and
her staff have traveled to Looe Key to collect mucus from various corals. We will agitate very gently the coral’s
surface and it will give off this mucus the surface slime, this protective layer that
harbors a lot of the bacteria. Experts are hoping that a closer look at microbes
living in the mucus will provide better clues about the health of these marine invertebrates. Corals are very ancient animals so they have
an ancient immune system. What ancient organisms often use to help them
with their immunity are bacteria that they utilize to help them fight off diseases. Over time, experts have observed a pattern
of change related to bleaching events. One thing that we know from studies that we’ve
done since the nineties are that corals have a particular balance of bacteria associated
with them. Well what we see is when temperatures increase,
even before the corals bleach, these pathogenic bacteria populations go up and the beneficial
bacteria go down. In recent years, Dr. Ritchie has noticed an
imbalance among a group of pathogens or disease-causing bacteria. One thing that we see when corals are stressed
are vibrio type bacteria. Vibrio are a large group of bacteria typically
found in marine environments. The most common strains are known to cause
foodborne illness through consumption of undercooked seafood. If you find a majority of vibrios when you
culture them that’s a sign that the corals are sick. Because I was measuring monthly we were actually
able to show that vibrio levels increased when temperatures are increasing, even before
the corals show signs of distress, even before you see that they’re bleaching. Most people realize how hard it is to keep
a reef tank in their home. They can’t have temperatures going all over
the place; they have to have good water quality. Well it’s the same with the corals here. Scientists at Mote hope their research will
continue to provide clues about bleaching events and other microbial activities. Meanwhile, other experts are studying how
a unique disease is destroying an iconic species of coral. Its majestic branches resemble the shape of
Elk or Moose antlers. And Years ago, it was one of the most common
corals in the Florida Keys, Bahamas and the Caribbean. But in two-thousand six, Elkhorn corals were
added to the Endangered Species List. Now a devastating disease threatens what few
living stands remain. Elkhorn coral has declined by ninety percent
since the mid nineteen nineties. White pox has been a major contributor to
the decline. At Rollins College in Winter Park, Florida,
coral disease microbiologist Dr. Kathryn Sutherland has studied white pox disease since its first
appearance in nineteen ninety-six on reefs off Key West. It was actually discovered within a photo
monitoring station that I had been monitoring for a year at that point. And I had been expecting to see increase in
coral size, because Elkhorn coral grows relatively fast. But instead I saw a slowing of growth and
then the appearance of white pox disease within these monitoring stations. So white pox disease exclusively affects Elkhorn
Coral, it appears as patches or spots of white on the coral. And the white is the dead skeleton that is exposed
when the tissues dies and sloughs away. In 2002, Dr. Sutherland and other
scientists discovered the pathogen responsible for white pox, a bacterium called Serratia
marcescens. It’s a common inhabitant of human guts. So it’s found in human intestines and it’s
found in our waste. Strains of Serratia marcescens manifest as
pink biofilm on areas such as tile grout, toilet bowl water lines and as slime on contact
lens cases. It also is associated with respiratory tract
infections, urinary tract infections and wound infections, all common in hospital settings. Once the coral pathogen was identified, a
search began to locate the source of this bacterium. So we started a widespread search for the
pathogen in the Florida Keys, collecting samples from multiple potential sources. Human sewage from the Key West waste water
treatment facility as well as waste of other animals like sea birds and key deer, but our
genetic analyses showed that only the strain of the bacterium that was found in human sewage
matched the same strain that we found in diseased corals on the reef. Once scientists inoculated healthy corals
in the lab with the matching strain, they were able to replicate disease symptoms. We saw disease signs in five days. And so this was our definitive evidence that
humans are a source of this devastating disease of Elkhorn coral, causing white pox. This is new because usually we hear about
passage of pathogens from wildlife to humans, right? Examples are HIV, Swine flu, avian flu. But we haven’t had the reverse going from
humans to a marine invertebrate in this case Elkhorn coral. And so this is a new disease mechanism that
we’re not familiar with, especially in the marine environment. Researchers were able to trace the human pathogen
back to its source, leaking septic tanks. Septic tanks were not designed for areas in
the Florida Keys, they were designed for areas where you have soil and also where you have
low population density. And the soil is extremely important because
if you have a leaky septic tank, the soil acts as a filter. But in the Florida Keys what we have is lots
of people and we have not soil but limestone bedrock. And limestone bedrock is very porous, it’s
like Swiss cheese and the leaking septic waste can very quickly move through the porous bedrock, into the near shore environment. The good news is that there is a solution. And the solution is using wastewater treatment
facilities that actually process the waste and remove the microbes
In 2001, the city of Key West switched to an advanced wastewater treatment
facility. Since then, the remainder of the Florida Keys
have started the process of upgrading their sewage treatment systems. Today, experts have described approximately
20 coral diseases but only the causes for five of these have been identified. To get a better understanding of coral disease
behavior, scientists from the University of Florida are looking at a sea anemone for help. Aiptasia is a little weedy polyp; it’s a
distant relative of corals. It’s a good laboratory model because it multiplies
really fast, it’s sturdy, it’s easy to work with. Unlike corals, which are protected and are really
difficult to harvest in the wild, we can set up a lot of real interesting experiments with
Aiptasia in the laboratory. You can simply take the coral pathogen that
you cultured in the lab and infect the animal with a predetermined dose of that pathogen,
and then over time you can monitor disease progression…which takes about a week. At the end of the experiment, macerate the
polyp, break it up and we can plate it on this, and determine whether or not the cause
of the sickness was actually from the pathogen that you infected the sea anemone with. Experts hope that by testing a variety of
coral microbes on sea anemones, they can better understand which organisms play a role in
disease infection. Scientists also conduct DNA experiments with
genes from bacteria as a potential way to biologically protect corals from disease. In order to understand how pathogens establish
on the surface of a polyp or on the surface of a coral, the first thing we wanted to understand
is what are the early events in the interactions. So the first thing that a pathogen comes in
contact with is the mucus… To test how effective the mucus is in protecting
a coral from harmful bacteria, researchers focus on the genes from pathogens. They try to identify the function of specific
genes and how those genes interact with the mucus. Scientists hope to understand the genetic
mechanisms that make pathogens stronger or weaker and how those can be manipulated in
favor of the coral’s health. And the long term goal of this experiment is to
figure out a way to black or inhibit—the virulence potential. To do this, scientists isolate and genetically
modify specific genes. They’re testing how important the newly
mutated gene is for virulence or the bacteria’s ability to cause disease. These mutations are compared to the genes
of the original bacterium, or wild type. What I do is test that mutation against the
wild type in terms of its ability to grow, growing them together. So once we incubate the plates overnight, the resulting growth looks something like
this. And just using sterile toothpicks, we can
pick an individual colony from the plate and then simply patch it onto this media that
contains the antibiotic “Kanamycin.” The antibiotic Kanamycin is commonly used
in molecular biology to treat a variety of bacterial infections. In this case, Kanamycin represents the native
or beneficial bacteria found in the coral’s mucus which fight off disease. So after we incubate these patch plates over
night, then we can look at them. So the ones growing on this plate are our
mutant strains Normally, the antibiotic Kanamyacin would
have prevented the bacteria from growing, instead, the mutated gene allowed the bacterium
to colonize the plate. So this mutant is now going to be resistant
to the antibiotic Kanamycin and those that didn’t grow are our wild type. This will tell us how competitively fit the
mutant strain is compared to the wild type. In this case, the mutation caused the bacteria
to potentially be more harmful to corals it might come in contact with. In the future, more tests will be performed
to identify which mutations can do the reverse and block disease growth. Once we know which behaviors the pathogen
relies on for the infection of the coral and the establishment on the mucus, we can then
find ways to inhibit these behaviors in the pathogen, either by harnessing the potential
of native coral associated bacteria or maybe by learning something more about coral immunity. And if we can prevent the pathogens from establishing
on the coral surfaces, that would be the first and the easiest way to prevent or stop the
disease progression. Experts are still in the early stages of research,
but they hope their long-term findings will be a useful tool for future management and
protection of coral reefs. In Key Largo, scientists from Florida International
University are using underwater cages and garden fertilizer to gain a better understanding
of the microbial health of corals. It’s kind of like a chess board when you
go out there and dive on the reef, We’ve got essentially eight different large
plots. We have four with nutrients and four with
no nutrients. One of the major stressors on reefs is fertilizer
that makes its way from land to sea. Dr. Deron Burkepile and his team study how
coral reef communities are affected by nutrients such as nitrogen and phosphorous. Those are the two big key elements that humans
impact the ocean by putting them in a lot via fertilizer and sewage. So we essentially go buy common garden fertilizer
that we put in PVC tubes, So we put these enrichment treatments at every
corner of three foot sections and then one in the middle. Within these large plots are also experimental
cages that keep herbivorous fish away from select corals
They’re essentially made out of plastic-coated chicken wire and the mesh is about an inch
in size so small fish can move through, but it keeps all the grazers out. By keeping grazers away and allowing seaweeds
to grow at faster rates with the help of fertilizers, scientists are able to mimic stress factors
such as pollution and overfishing. Using these experiments, Dr. Burkepile has
observed a change in the Mustard Hill coral, Porites astreoides. Seaweed competition causes the porites astreoides
to lose an important bacteria, its Gama proteobacteria. So this one bacteria is always
found on porites astreoides, its thought that it’s important for the health and growth
of this coral. But when seaweeds start competing against
the coral, this bacteria actually disappears from the microbial community. Researchers are still investigating what the
effects of this disappearance will have on the coral’s health. Scientists from FIU not only monitor shifting
microbial groups, but they also examine parrotfish for their potential to spread microbes. So the Parrotfish are important herbivores,
but some of the parrotfish also eat coral. So we stretch barrier nets out on the bottom
of the ocean, herd these parrot fish into the barrier nets with hand nets, catch them,
take them up to the boat, and then we swab their mouths with a q-tip essentially; put
it in a preservative and then we can extract the DNA off that parrot fish’s mouth sample,
see if we can match the bacteria on the parrot fish mouth to the corals that they just preyed
on. They could take a bite out of a diseased coral
and potentially move a diseased microbe from a diseased coral to a healthy coral. Determining whether or not parrotfish transport
microbes from one coral head to another could give experts important insights into how coral
diseases spread. Florida scientists aren’t just studying
the microbial communities of shallow water corals. Dr. Christina Kellogg from the U.S. Geological
Survey in St. Petersburg, Florida, examines microbes from deep sea corals. In shallow water corals, if they’re unhappy
it’s like they change colors, they start to bleach, you can tell. The deep sea corals don’t bleach, they’re
already white… To access cold water corals from the depths
of the Gulf of Mexico, scientists use manned submersibles. To collect specimens and prevent contamination,
Dr. Kellogg created a sampling device which has been dubbed the “Kellogg Box.” It was a big acrylic box that could fit on
the front of the submersible and it had ten separate bins; it’s sort of like a little
kid you know, my spaghetti can’t touch my sauce. Well my corals can’t touch another coral,
or sediment or water. By isolating each sample, researchers can
maintain the true microbial diversity of each coral and prevent cross contamination of microbes. Once samples are brought to the lab, Dr. Kellogg
can begin the process of DNA extraction. And so when I’m ready to do extractions,
I take the tubes out, keep them cold on ice, quickly measure out a very small amount of
that powder, which that powder used to be the coral and the mucus and the bacteria. And you keep doing extractions where you make
it purer and purer and in the end you end up with just pure DNA and that’s what we
end up using to put on the micro-ray phylochips. Initially developed by the Lawrence Berkley
National Laboratory to scan airborne microorganisms scientists like Dr. Kellogg now use the PhyloChip
to identify the types of bacteria found on coral DNA samples
On those tiny little chips which are like glass slides, robots spot little dots of DNA…
which corresponds to about fifty-thousand different bacterial types. It allows me to get sort of a top down view
of the community that we haven’t had in coral before. If any of the spots that are on the chip match
a bacteria that’s in my sample then that spot lights up. The first way people looked at bacteria in
general was to culture them. The problem is maybe one to ten percent of
the bacteria that are in the environment actually will agree to be cultured and so you only
see this tiny little subset of the whole world that’s out there. And the problem with disease is, what if what’s
causing the disease doesn’t happen to be one of that one to ten percent, you’d never
know. Experts believe that it is important to know
the microbes that live on corals and how they interact, because they are the earliest warning
signs of serious changes on a reef If something changes in the environment, the
water temperature or the level of nutrients, the microbial community will shift. By doing that they’re basically our first
diagnostic tool before you even see something with your eyes is wrong with the coral, you
could see that change if you were looking at the microbiological level. Major funding for this program was provided
by the Batchelor Foundation, encouraging people to preserve and protect America’s underwater
resources. And by Diver’s Direct, inspiring the pursuit
of tropical adventure scuba diving.

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