Soil Health & Frog Decline

What is the link between soil and sick frogs?

Hardly anyone thinks about the ground under their feet. If you are a keen gardener or work in the nursery industry, you are at least aware that the better your soil is, the better your plants will grow. But the condition of the soil on the property you own or rent very seldom keeps you awake at night! We're suggesting that maybe you should dedicate 30 minutes to thinking in depth about the ground under your feet, even if you are just a tenant on a rental property. There are many reasons why!

Did you know that soil functions as a living thing and is a complex mixture of all kinds of minerals, nutrients, bacteria, fungi, protozoa, microscopic creatures (such as mites, insects and worms, etc.) and decaying matter?

Did you know that our survival is based on soil containing all these things in good balance (because this is what makes the plants grow which then provide our oxygen, shelter, raw materials, and food)?

Did you know that when soil is neglected for a period of time or is subjected to extended periods of drought, it can change its microbial composition, ph and structural properties?

Did you know that the more acidic your soil becomes, the more diseases its breeds?

Did you know that when soil diseases get out of control, they can attack anything such as gardens, agriculture, farm animals, wildlife, your pets and even YOU?

Do you still think soil is boring and irrelevant?

Without healthy soil, it would be very difficult to grow our food crops. Once a disease problem has been triggered, it can be extremely costly and very UNfriendly to the environment to get rid of, requiring large scale destruction or toxic chemicals. (For example, just look at the costs of controlling the citrus canker (bacterial) outbreak in Emerald years ago.) Rusts and fungi in your garden can ruin your expensive landscaping projects and remove the privacy and noise reduction that plants offer a property. Even worse, the tiniest cut which gets infected with a soil disease while playing or walking in the yard can lead to substantial personal costs in the forms of mobility issues, lost school or work time, medical expenses and long term damage or loss of a limb. We need to be concerned about the loss of wildlife as well since the complex environment we live in depends on each of the participants (big, small and microscopic) fulfilling their roles in the ecology.

How can you tell quickly if soil might be bad? You might pick up a hint of soil problems if you move to a property and try to grow just a few veggies but they keel over and die quickly or the entire property is a mass of weeds. The fruit trees might look okay but they don't seem to produce very much fruit, or the fruit is there but becomes discoloured or attacked by an assortment of things which leave holes and deformities in it. So it is easy to make a connection that poor soil leads to poor plant growth and health. But is the soil bad enough to be creating disease issues?

Since 1998, our frog hospital activity has been cataloging problems in Queensland frogs and toads and this amount of time has been sufficient to detect several patterns in the kinds of problems present, when they appear and how each might be connected to environmental variables such as drought or excessive wet seasons. To explain some of the patterns we have observed and experienced firsthand and how they can effect frogs (and toads), let's take a little journey down 'memory lane' to the time before the severe drought which started in this region in 2000.

From Too Much To TOO MUCH!!

We normally have an annual wet season with a few metres of rain falling in a relatively short period of time. This flows through soils and washes them clean, so to speak. It also means that whatever has been accummulating in those soils for the year is shifted to the water runoff rushing down streams and rivers and is carried out to sea. This could include the good things in the soil such as nutrients and the bad things such as pesticides.

From 2000 to 2003, this region was in severe drought. Keep in mind that human activities did not stop during this time - agriculture and whatever fertilisers and chemicals it depends upon continued to be applied as did whatever pesticides and herbicides households normally use. However, the annual "flushing of the soils" did not occur so these additives would have continued to accummulate. What was also happening in soils is that they thoroughly dried out. Those microbials (microscopic organisms) which need moisture to survive would have died off while drought-tolerant organisms would have thrived and overpopulated to fill the gap left by the loss of moisture dependent species.

First Soil Related Outbreak in Frogs and Toads

After the drought had been in progress for over two years, we catalogued an outbreak of a new disease problem which we named the "respiratory/nervous system condition" until a lab could name the specific causitive agent. This outbreak killed frogs and toads in such huge numbers that reports started coming in from parts of Queensland that cane toads completely disappeared from some areas where they had been densely populated before. Many callers in Queensland contacted us to report that they were finding sick and dead frogs, toads and snakes concurrently. We obtained the newest soil survey maps from the government and noticed that the Cairns phone calls and sick frogs we were receiving came from areas having three very specific soil types (out of more than 30 soil types in this area). As the drought continued and even clay soils evenutally dried out, then the outbreak spread to those soil areas as well.


During the first five months of the outbreak, skin symptoms were worst and included sliming and ulcers; once ulcers opened up, bacterial infection followed which killed the frog if it hadn't already died. We tried to get an identification of this disease pathogen from labs in three states but no-one could identify it. That is because the right diagnostic tools were not used. Whatever the pathogen is, it is a toxin and needs special equipment - such as a gas chromatograph - to find it in the body. However, very few labs in Australia have that kind of equipment and the testing costs for those that do were and still are way beyond our small group to pay for. We believe, based on the consistency of culture results since 2002, that the pathogen responsible for the "respiratory/nervous system condition" is a drought-tolerant soil fungus in the Fusarium genus. This clearly was a problem caused by the drought itself and suggests that soil changes can be responsible for deaths in frogs. This is important information for climate change modelling and for understanding better the process of global frog decline - but we find that whenever we have approached relevant professionals to introduce this information, the usual response is the equivalent to being "shown the door", so to speak!

Churning things up with Larry

We digress from our historical journey, however. The drought was officially "broken" in 2003 but the wet seasons that followed were still short of what is normal rainfall for the area so soil "flushing" was probably still a bit limited. After category 4/5 cyclone Larry in March 2006, several new problems suddenly appeared in the frogs and we enlisted the help of the DPI vet diagnostics lab in Townsville (since closed by the Newman govt and never restored by the current Labor govt). When comparing culture results pre- and post- cyclone, we noticed a sharp increase in the species of "environmental" bacteria being found on/in the frogs including some species of concern such as three that cause bacterial meningitis in humans. ("Environmental pathogens" are those bacteria and fungi that are supposed to be in local soil and water but aren't normally supposed to cause disease in frogs or other animals - unless those animals are immuno-compromised.)


We also discovered that a plant disease not known to be in the local area before Larry (the cane smut Ustilago spp.) caused an outbreak in local frogs immediately after Larry. Not normally a disease of animals, Ustilago can become pathogenic to them under periods of immune stress. (Luckily, as soon as we had a lab result, we found a treatment and all incoming frogs were treated for Ustilago until the outbreak subsided in the wild.) (NB: It is worth nothing that by 2010, Ustilago had spread to cane fields throughout FNQ when it had been unheard of in this region before cyclone Larry - more evidence that severe cyclones can cause biosecurity problems!)

After La Nina returned sometime in 2007, we received the best wet season rainfall we had since the late 1990's (our summer wet season is usually Dec to March/April). There was the typical monsoonal flooding in low lying areas and some serious flooding in some places like Mackay. Everything that had been accummulating in the area's soils since the start of the drought would have been flushed right out of the soils and spread through the runoff before reaching the sea. Some of it was mixed up like pea soup in the areas where flood waters accummulated and this would have likely just descended into those soils (e.g., the lower northern beaches of Cairns) as the water levels dropped.

Bacteria on the move

Three things happened during the wet season of 2007/08:

Gropers off the coast of FNQ started to be found washed up dead on local beaches (spelled grouper in the USA; these are not small fish but reach about 5 feet/1.4 m in length); since the initial deaths, sporadic dead gropers have been found along the coast from Cooktown to Cardwell
A bacteria we had never seen before (photo at right) which causes dramatic skin changes and death showed up in January on frogs coming in for care and the labs couldn't tell us what bacteria it was
A wave of really sick frogs started arriving in March (wrong time of year for frogs in such condition) and all had a cryptic change in skin secretions; these cases suffered excessive mortality rates and did not respond to any of the antibiotics we tried; again, it could not be identified but behaved like a bacteria

We did learn later that DPI investigated the groper deaths and found that a bacteria, Streptococcus agalactiae, was the cause. This same bacteria was found in dead grunters found floating in Trinity Inlet after the wet season of 2008/09. This is not the same as the Strep that causes Strep throat. Streptococcus is a large genus and some of the species it contains are serious "flesh-eaters" (they can dissolve various bodily tissues including tendons, cartilage, bone, etc.) which are often referred to as Invasive Streptococcus or Streptococcus Groups A and B. The species of Streptococcus that killed the fish is one of the Group B species. (Addendum, Sept. 11th, 09: a DPI bacteriologist has informed us that the specific strain of S. agalactiae involved in the fish deaths was a different strain than that of humans and was a strain of the marine environment. This does not appease our suspicions that terrestrial diseases are still finding their way into runoff and the fish deaths occured primarily during the periods of greatest runoff from the land and would have to be connected to something in the runoff. Another DPI veterinarian has also commented to us that S. agalactiae was not the only pathogen in the dead fish so it is still inconclusive what was the actual cause of death.)

Some of these aggressive bacteria can also cause death by invading the blood (this is called scepticaemia) and a very well known one which has made the headlines in recent years is Staphyloccus aureus (Staph aureus, Golden Staph). Bacteria are growing more resistent all the time to our pharmaceutical weapons and Staph aureus now has a powerful strain called MRSA (Methicillin Resistant Staph aureus) which no longer responds to penicillin drugs but has limited response to gentamycin.

Getting Even Closer to the Problem

The wet season of 2008/09 was very short but good rainfalls took place while it lasted and it was just before the wet that we relocated to a 1/4 acre block in older Edmonton, south of Cairns. We threw in some prefab ponds to take advantage of some in situ breeding opportunities by the local frogs but we observed that every single frog found in the yard (even the calling males) was very ill with the same cryptic problem that had turned up in frogs last year. Some adult frogs were being found with the skin entirely eaten off parts of their bodies. Then the four big 'photo op' cane toads we had in captivity for three years became deathly ill with what appeared to be the same dramatic bacterial skin problem (see photo at left) that first turned up the previous year. Although they were in captivity, we had used mulch and leafy materials from the backyard in their tank. Impression smears were done on the sick toads and, lo' and behold, Streptococcus was present (most likely Strep. pyogenes). This is another of the invasive Strep. species but is in Group A.


What riveted our attention and allowed us to finally connect all the dots was when our own Curator picked up an infection during the wet season while walking around in the backyard's muddy soil. This infection was dramatic, fast, and needless to say, very painful - the clinical symptoms and behaviour of the infection pointed to only one possible culprit: Streptococcus. After not being able to walk for a month and only partial response from the massive amounts of antibiotics used (she was treated for Streptococcus and Staph aureus), it became obvious that hospital admission and surgery was required. After surgery, culture results showed that there was another stowaway hidden deep in the joint - Pseudomonas auruginosa was also present and ate away all the cartilage in a joint. Pseudomonas has been a known problem in frogs for many years, is extremely difficult to treat and usually kills them pretty quickly - sometimes only 48 hours after clinical symptoms first appear.

Our Curator discovered in hospital that her infection was not a rare event. The woman in the bed across had the same infection in her arm and nearly lost the arm to amputation. Someone in the same queue at the chemist as our Curator was picking up the same drugs for the same infection in her husband's foot. Hospital doctors commented that these infections have become common in the area which again supports our concerns about how and where so many infections from soil pathogens are being picked up. When volunteers in the group became aware of what caused the Curator's infection, several relayed horror stories about friends and relatives they know who have also had these kind of infections. It seems that if you mention these diseases to half the people you know, at least half of them will know someone who has had one. Not a rare problem at all.

Speculation or Important Evidence

Based on our observations going back to the drought, we believe that soils in the region have changed and are supporting the growth of diseases. That is our conclusion but, sadly, surveying techniques presently used for analysis of water runoff do not include any diseases (other than possibly E-coli which is not relevant to this discussion). These diseases of concern are also not on the Commonwealth or state Notifiable Disease Lists so nobody is monitoring their occurence. (NB: Strep Group A only is on the QLD Health notifiable list only and for human cases only.) Considering what we are finding on the frogs (and toads) we receive, and the ease with which humans can be affected, we feel that there is more than enough evidence to show that investigation of soil diseases is warranted by several relevant government agencies and that a more proactive response from the community is justified. We issued a press release in April 2009 to educate the public about these diseases and to call upon the state and Commonwealth governments to add Strep Groups A and B, Pseudomonas, and Staph aureus/MRSA to their Notifiable Diseases lists for both human and veterinary cases. Sadly, almost all the major media refused to run the story.

The information must get out to protect the community and the wildlife, so we set about finding someone who knows about soil ecology who could help us create this section for our website. We wanted to work through a simple process of analysis that any resident can do themselves and a process of "fix-its" that anyone can implement for their own property. There is a questionaire in this section which you can use to determine if your soil is healthy or if it is ailing and needs correction. There is a recommendations page for how to correct soil problems which are relevant to your situation.

We hope that if you discover that your soil needs attention, that you will follow the recommendations. Healthier soil will benefit you by making your garden more attractive and productive, reduce disease threats to your family, animals and wildlife, and will help reduce the potentially damaging affects of the region's runoff onto the Great Barrier Reef. In other words, everybody wins!

Always remember to ALWAYS handle all frogs and toads, no matter how healthy they look, with gloves or a plastic bag over your hands!

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