What Agresearch found in the offal pits (15/9/2005)

Allegations have been made by GE Free NZ that AgResearch soil tests suggest 'horizontal gene transfer' could have occurred with soil micro-organisms in land where transgenic cattle have been grazing for 6 years.

However, AgResearch has strongly contested this claim. Its Bio-technologies Manager says tests have not found the specific gene used in the cattle in the soil bacteria.

Here the scientist Dr Jack Heinemann of the Institute of Gene Ecology, at the University of Canterbury in New Zealand, discusses the evidence available and puts it into context.

That context seems to be that we have miniscule knowledge of the factors we would need to understand in order to make sense of the data available. In other words, we're dancing in the dark - taking uncomputable risks which could have far reaching consequences.

The Nature Biotechnology paper he refers to can be found here:

What Agresearch found in the offal pits
Agresearch Annual Report; p25 (GMF 98009
Paragraph on monitoring horizontal gene transfer (HGT)

"A sensitive real time assay is currently being developed in collaboration with a research group in Italy."

"Soil samples have been taken from the offal hole and control site within the animal containment unit. The samples were analysed for bacterial populations and the presence of puromycin and kanamycin resistant bacteria and puromycin resistance genes."

"Preliminary results indicate that the bacterial community from the offal hole is different from that found in the surrounding soil. In addition we found a high proportion of resistant bacteria and the presence of puromycin and kanamycin resistance genes in both soils, indicating the presence of resistance genes in the natural bacterial soil population."

Jack Heinemann answers GiantExperiments questions:

*What does the presence of resistant bacteria and puromycin and kanamycin resistance genes in both soils (offal pit and control) indicate?

It could indicate bacteria made recombinant by the uptake of transgenes that confer resistance to these antibiotics. But that is not the first conclusion you would come to because the soil carries many bacteria that are intrinsically tolerant of various antibiotics as well as those that are naturally resistant. The latter may be so because they use the same or similar biochemical mechanisms of resistance that are conferred by the transgenes.

Currently, the only definitive test that horizontal transgene transfer, from GMO to soil microorganisms, was occurring would be to identify the genes responsible for resistance in the soil bacteria and then sequencing them to see if they were identical to the modified genes used in the GMO.

*What does the presence of a "different" bacterial community in the offal pit indicate?

For me this is the most interesting question. We still know very little about the relationship between the soil ecology and disturbance. The offal pits undoubtedly differ from control sites in a number of ways, not just in the presence or absence of dead GMO animals. The variance could be normal or it could be indicative of an important impact. I don't know.

So it is very important to settle such basic ecological questions, such as establishing both baseline analyses on the soil ecology and normal variations, before an experiment such as the offal pit monitoring is even contemplated. Obviously that means before making GMOs to be buried in them!

*Can we say there is preliminary/any evidence of HGT?

To the degree that you cannot, from present data, eliminate HGT as the cause, then yes. It would be extremely weak evidence though. But I caution you: unless AgResearch is prepared to sequence the genomes of every bacterium in every gram of soil (and there are as many as 2 billion bacteria per gram), they also cannot exclude HGT as a cause of some of the resistance.

From our own calculations (see Nature Biotechnology in September, 2004), we know that extremely rare occurrences of HGT can ultimately develop into high numbers of recombinant organisms. This development may take time. Our analysis used antibiotic resistant organisms developing under nearly constant antibiotic selection and it still took decades before it could be routinely detected.

In an environmental situation such as the offal pits, where selection is uncertain, then it could take more time before they reached detection levels but that doesn't mean there won't be a problem in the end.

*The Agresearch spokesperson said on the radio that soil bacteria are naturally resistant because they make the antibiotics and use them to "attack" other soil bacteria.

This justification is a double-edged sword. While it explains a high level of resistance not arising from acquisition of a transgene, it also establishes the conditions necessary for selecting a population of bacteria that became resistant because of a transgene. Again, this could take many many years, but that does not exclude an ultimate impact on human health or the environment just because it takes time.

*What further monitoring should be done for HGT?

The first and foremost should be investment in basic research directed toward understanding HGT, how it works and how it happens in relevant environments, before creating risks that might become harms by HGT. Currently, there is no validated technology for monitoring HGT in real environments (again, see our Nature Biotechnology paper in Sept 2004).

*What will the real time assay show?

My prediction is that it will show nothing. It is like using a fighter jet to catch butterflies. Lots of technology ill applied. Moreover, as we established in that Nature Biotechnology article, you have to look for small internal changes to the DNA sequence, not just for the sequences that mark the transgene for amplification by PCR.

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