PhyloChip Helps Scientists Identify Communities of Microbes Suppressing Disease Pathogens in Soil.

Ask any organic gardener and they will tell you that microorganisms are a fundamental part of soil health and overall fertility. That is why we go to such extents to provide compost and organic amendments for our gardens and why we abhor the use of chemicals which kill these microbes. We want to provide the most amiable environment possible so as to propagate these critical components of nature.

We know of several specific microbes that perform incredible feats with near magical properties as they work to support plant growth in our gardens.Microbes breakdown organic matter and make nutrients available for plants to absorb. Species such as Rhizoba form synergistic relationships with roots, absorbing carbohydrates from the host and in return providing moisture and nutrients for the plant. There are species that convert gaseous nitrogen from the air and fix it into a useable form of nitrogen for plants and even microbes that are capable of extracting minerals from ore.

Scientist estimate that there may be hundreds of thousands even millions of microbe species that have yet to be identified. The difficulty researchers have historically encountered is that some 99% of all microorganisms cannot survive the current process of culture testing. But that problem seems to have been eliminated with the introduction of the PhlyoChipTM.

Recently scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory and Wageningen University in the Netherlands were able to identify an intricate community of soil microbes that fight disease pathogens in the soil. “Individual organisms have been associated with disease suppressive soil before, but we demonstrated that many organisms in combination are associated with this phenomenon” said Gary Anderson of Berkeley Labs. Berkeley Labs Anderson was part of the team from Berkeley which also included Todd DeSantis and Yvette Piceno. The full report was published in the May 5 issue of Science Express.

For the first time in history scientists have both observed and identified communities of microbes working together synergistically to fight off disease pathogens in soil using the revolutionary technology called the PhyloChipTM which has been in development for over ten years.

The research centered around a field used to grow sugar beets, located in the Netherlands. The beets are normally susceptible to a pathogen known as Rhizoctonia Solani which causes root fungus that can decimate an entire crop. This pathogen is also known to attack potatoes and rice crops additionally. The particular field that was tested had somehow developed an immunity to this pathogen. After researchers tested this field they found 17 different soil microbes that were actively engaged in fighting the pathogen and that all the other microbes indicated were working together to reduce the incidence of outbreak. The sugar beets in turn funneled about one fifth of the total carbon that they photosynthetically captured through their roots to supply fuel for the microbes.

The PhyloChipTM is a credit card sized chip that can detect over 59,000 species of bacteria and archaea in samples of air, soil or water. It not only detects the most common organisms but the rarest known. Testing and analysis are provided by Second Genome.

The PhyloChip compared the field sample to 1.1 million referenced DNA targets in it’s micro array that includes probes that can determine the relative amounts of all bacteria 16S gene sequences present in a sample without culturing. Second genenome provided processing and detailed statistical analysis of samples. The PhyloChip now enables researchers to identify signatures of disease or environmental contamination.

This is truly an exciting scientific advance, not just for understanding how microorganisms act in the soil but in many other applications as well. Researchers have been able to identify the specific microbes that feed on the hydrocarbons that help to clean up from oil spills. This technology also permits air sampling to rapidly determine contaminates, pollutants and bio threats. This breakthrough has a number of applications in the medical field as well and research has already been conducted in a number of fields such as gastroenterology, asthma and cancer research.

Now that scientists able to identify specific microbes which can help remediate a number of problems, one can only hope that it only becomes a matter of time before mankind can incubate and combine selected species as a prescription for any number of maladies from soil deficiencies to water pollution and even cancer.




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