A bid by Massey University researchers to showcase the latest DNA sequencing technologies for students around New Zealand may help compile a census of microbial life in the nation’s soils. It could also spark new interest in having a national database of soil microbe DNA of potential use for forensic work.
A senior lecturer in microbiology at Massey, Dr Justin O’Sullivan, is recruiting senior school students to take soil samples across the nation in April, and DNA from microbes in these samples will be extracted and analysed.
Dr O’Sullivan told the SMC that the project will store the extracted DNA. In Britain, researchers are already freezing a “libary” of soil samples from across the country to allow for future comparisons of microbial DNA, while others have looked at profiling the DNA of soil microbes for forensic purposes.
And the project has also caught the attention of researchers interested in the potential for a national database of DNA from soil microbes to be useful to crimefighters.
A New Zealand researcher, Rachel Parkinson — who last year finished five years of work showing how successive species of bacteria decomposed the bodies of dead pigs — wrote a masters thesis in 2004 on Forensic DNA Profiling of Bacterial Communities in Soil. Dr Parkinson is now working in Canada.
Two of her supervisors for that work, Dr Jacqui Horswell and Dr Steve Cordiner, told the SMC that researchers were no longer working on a national database of soil microbe DNA because it had been see as too risky in terms of the economics: comparatively few court cases would benefit.
Dr Horswell published a 2002 paper, Forensic Comparison of Soils by Bacterial Community DNA Profiling and led an ESR team which developed a technique for soil analysis that extracted DNA from the microbial, and analysed variations in a piece of genetic code common to all known bacteria: it was sensitive enough to show whether soil samples come from the same site – providing a ‘soil fingerprint’ of the specific location. Samples could be as small as a piece of dirt on the sole of a shoe or the thread of a tyre, or soil stains on clothing.
“Of course, every one else in the world has picked up on it … and internationally it’s certainly of great interest,” she told the SMC. The technology involved was very similiar to that needed for detecting human DNA.
Environmental microbiologist Dr Horswell, a senior scientist at ESR, and Dr O’Sullivan — who noted he was not looking at forensic applications — responded to questions from the SMC:
What is the feasibility of DNA sequencing of microbial soil DNA to point to locations in forensic work?
Dr Horswell:
“In a pilot study we found 90 percent similarity between microbes in soil on a shoe and microbes in the shoe print, compared with 40 percent on control sites. We then looked at whether you could profile the dirt on a spade and or in the boot of a suspect’s car and determine where to dig to find the body that had been buried. This was more complicated because of the diverse microbial community. We looked at a number of soil types in the Wellington region and found on the one hand you can pinpoint a soil to a region, but then you can get significant variability within a location. Probably the most useful thing would be where you have look for a match between a shoe and a shoeprint at a crime scene”.
Dr O’Sullivan:
” The question remains how useful it will really be? In our study we will be sampling at a depth of 30cm not surface soils so I would think it would be unlikely to make a significant contribution in instances where soil was obtained from simple foot prints. Secondly, our pilot study at Hot water beach demonstrated that the flora can alter dramatically over distances
of 2m-10 m. This supports other studies like this and may reflect point sources of heat or nutrients. Therefore, it is likely that our work will show similarities between soil types and similar coarse environments – i.e. forests, beaches, playing fields”.
What is the potential for quick and straightforward sequencing of soil microbes to help identify/locate the scene of an extensive assault or a buried body?
Dr Horswell:
“We looked at pigs and found that bacteria involved in decomposition come in particular successions. We know the microbial community changes when you add nutrients, and a body is nutrient. Not only are you looking at an input of body bugs, but you’ve got the impact of body fluids on the bugs in the soil. We again proved the hypothesis, but the amount of work is just pheonomenal : we just don’t know enough about the species that we find in the soil. The crossover of environmental science and foresnics is so interesting, but it would need a lot more work. In maybe 10 years time, it’s going to be really useful.
Dr O’Sullivan:
“It is possible but there are many caveats”.
Would it be possible to freeze a “library” of soil samples to allow for future comparisons against a collection of samples?
Dr Horswell:
“We’ve been working with a group of people from the Macauley Institute (UK) — they’re very interested in that side of it.
Dr O’Sullivan:
“We had not thought of this. We will store the extracted DNA. For a database … to be useful, we would have to perform temporal studies, as it is possible the population make up varies with the seasons and over time. It may turn out to be very useful depending on what we find”.
How do the bacterial communities vary according to associated plant communities, and the geology/pH of the soil?
Dr Horswell:
Most of the work on DNA profiling in soils has come from this environmental science field – the biggest influence on the bugs is the available nutrient.
Dr O’Sullivan:
” The flora change dramatically at different sites and this correlates with pH, temperature, salinity etc… Just like us bacteria have individual preferences for where they like to live and thrive: some like to live in hot places, some cold, some in dry environments and some in wetter ones, some with common food sources and others have different tastes”.