Composting vs. GMOs, the question: lateral gene transfer?

HowToBe

The Living Force
FOTCM Member
Here's a SOTT article about GMO's and horizontal/lateral gene transfer:
http://www.sott.net/article/240510-Why-GMO-And-Organic-Can-Not-Co-Exist-Lateral-Gene-Transfer
Here's another just about gene transfer (it mentions fungi, which are an important component of a successful compost):
http://www.sott.net/article/223254-Discovery-of-jumping-gene-cluster-tangles-tree-of-life
More on gene transfer, but less relevant:

https://en.wikipedia.org/wiki/Horizontal_gene_transfer
Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction. Also termed lateral gene transfer (LGT), it contrasts with vertical transfer, the transmission of genes from the parental generation to offspring via sexual or asexual reproduction. HGT has been shown to be an important factor in the evolution of many organisms.[1]

Horizontal gene transfer is the primary reason for bacterial antibiotic resistance,[1][2][3][4][5] and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides[6] and in the evolution, maintenance, and transmission of virulence.[7] This horizontal gene transfer often involves temperate bacteriophages and plasmids.[8][9] Genes that are responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms (e.g., via F-pilus), subsequently arming the antibiotic resistant genes' recipient against antibiotics, which is becoming a medical challenge to deal with.

[...]

Mechanism

There are several mechanisms for horizontal gene transfer:[1][25][26]
  • Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA).[27] This process is relatively common in bacteria, but less so in eukaryotes.[28] Transformation is often used in laboratories to insert novel genes into bacteria for experiments or for industrial or medical applications. See also molecular biology and biotechnology.
  • Transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or phage).[27]
  • Bacterial conjugation, a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact.[27]
  • Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales.[29]
A transposon (jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance.[27]
On the aside, I recall learning in high school that, basically, bacteria can more or less hook up to each other with tubes and swap DNA. Apparently this benefits the species in some way, and it may also occur between different species (I don't remember about that).

So, obviously composting involves very intense biological activity, especially the highly thermophilic, or thermogenic (heat-producing), composting which is best for killing unwanted diseases, bug eggs, weed seed, and, notably, pesticide residues on the plant materials (as an aside, this type of composting is even capable of breaking down plastics and motor oil to a certain degree , although that would make it not-garden-friendly). Given the higher temperatures reached that make chemical reactions more active, my guess and speculation is that thermogenic composting would be the method most likely to result in the most complete elimination of modified genetic material from GMO materials. On the other hand, this composting involves high concentrations of bacteria, fungi, and other organisms (I'm sure there are plenty of viruses in that ecosystem,) However, it seems there is limited research on this (no surprise). But, to my excitement, there is a little, so I thought I would share it here.

Here's what I just found:

1.
http://www.ncbi.nlm.nih.gov/pubmed/16594522
This one is just an abstract, as I can't view the full. Maybe someone with access can take a glance?
Crit Rev Biotechnol. 2006 Jan-Mar;26(1):1-16.
Composting: a potentially safe process for disposal of genetically modified organisms.
Singh A1, Billingsley K, Ward O.
Author information
Abstract

The widespread use of genetically modified organisms (GMOs) may result in the release of GMOs into the environment. The potential risks regarding their use and implementation of disposal methods, especially the possibility of novel genes from GMOs being transferred to natural organisms, need to be evaluated and better understood. There is an increasingly accepted public view that GMO products introduced into the environment should be degradable and should disappear after a limited period of time. Due to the risk of possible horizontal gene transfer, disposal methods for GMOs need to address destruction of both the organism and the genetic material. During the last two decades, we have developed a greater understanding of the biochemical, microbiological and molecular concepts of the composting process, such that maximum decomposition may be achieved in the shortest time with minimal negative impacts to the environment. The conditions created in a properly managed composting process environment may help in destroying GMOs and their genes, thereby reducing the risk of the spread of genetic material. When considering composting as a potential method for the disposal of GMOs, the establishment of controlled conditions providing an essentially homogenous environment appears to be an important requirement. An evaluation of composting as a safe option for disposal of GMOs is provided in this review.

PMID:
16594522
[PubMed - indexed for MEDLINE]
2.
http://www.darcof.dk/enews/june04/gmo.html
http://orgprints.org/5858/1/5858.pdf
Both link are the same article, but the second is in PDF form.
Until now, horizontal gene transfer from transgenic plants to bacteria has not been detected in natural systems when transgenic plant residues has been allow to decay in soils (Nielsen, 2003). However, the process has been detected in laboratory experiments (e.g., Gebhard and Smalla, 1998).

[...]

Different elements were investigated: i) the persistence of transgenic and wildtype DNA during composting of GM plant residues as compared to incorporating the residues into the soil, ii) the risk of naturally occurring bacteria (Bacillus, which is known to become dominant in compost) taking up and incorporating transgenic DNA during composting.

[...]

Composting of GM plants

Composting was performed at KVL in a laboratory composting system with PC-controlled compost-reactors (figure 1). The GM plant mixture consisted of dry barley straw and transgenic Arabidopsis transformed with the Sorghum gene for CYP71E1 via the Ti plasmid in Agrobacterium tumefaciens (the Arabidopsis plants were kindly provided by Prof. B. Lindberg Møller). The entire plant including the root of 5 weeks old Arabidopsis plants were used. Both straw and plant were cut into 2 cm pieces. The straw was re-wetted prior to mixing. The final mix had a water content of 86%.

Composting of GM plants were performed in litterbags (1 mm mesh size; 6.7 g/bag) which were placed in compost-reactors filled with a non-GM composting mixture (barley straw and white clover (I) or sugar beet leafs (II)). GM composting was performed at two separate occasions. Samples were taken at intervals (Compost I up to 111 days, Compost II up to 77 days) by harvesting an entire litterbag. To simulate ploughing down of the plant material a litterbag with 20 g of the GM plant mixture was kept in a bucket of soil at 17°C. Samples from this were taken until day 77. The presence of both transgenic and wildtype DNA was detected by DNA purification and PCR.

Rapid DNA degradation

In Compost I the temperature peaked at 58°C and the transgenic DNA could no longer be detected after 10-14 days (for one of triplicate samples, see figure 2).

In Compost II the maximum temperature was 68°C resulting in a faster decay of DNA which was no longer detected after 6-10 days (figure 2). In both composts the rate with which the transgenic DNA disappeared was much faster than the experiment where the plant material was kept in soil. Transgenic DNA was still detected after 77 days in the soil experiment (figure 2).

No DNA uptake by Bacillus

To determine if Bacillus were incorporating transgenic DNA during composting, all other bacteria had to be eliminated from the compost before spreading dilutions onto growth media. Boiling the compost leaving only the spore-forming Bacillus to survive can do this. Bacillus rapidly became dominating in the compost increasing in numbers from 103 to 107-108 per g compost.

Bacillus was screened for the presence of transgenic DNA by scraping colonies off the growth media, purifying the DNA and running a PCR. In several cases these screenings indicated that Bacillus contained transgenic DNA from Arabidopsis. This lead to the isolation of 300 colonies which were tested by PCR for the presence of transgenic DNA.

Of these, three isolates gave PCR products of the exact same size as the control DNA, but sequencing of these products revealed that they were not identical to the transgenic DNA. One sequence had highest homology with a Bacillus halodurans (one half of the sequence had almost 100% homology whereas the other half had no known homology), the two other isolated were identical and had 98% homology to Bacillus subtilis.

Conclusions and further studies

The experiments show that composting of GM plant residues greatly increases the rate of degradation of transgenic DNA compared to the rate for plant residues left in the soil. If this is considered as the only risk factor, composting is a 'DNA-safe' method to treat GM plant residues.

However, even though transgenic plant DNA was not detected in bacterial isolates in our experiments, we cannot conclude that horizontal gene transfer can not take place. The 300 isolates investigated proved to be too low a number to be conclusive.

The numbers of isolates tested were based on the screenings indicating high transfer, but the screenings were biased apparently because some Bacillus species gave PCR products matching the transgenic DNA. Thus, it is still an open question if composting constitutes a safe way of disposing of GM plant residues. Furthermore, these experiments give rise to other interesting questions, e.g., whether GM plant materials decomposing in waste piles or deposited in manure yards may be able to transfer genes to indigenous bacteria at the comparably lower temperatures present at these environments.

These questions need to be assessed if the risk associated with the use of GM plants is to be thoroughly investigated.
References

EU. 2001. Directive 2001/18/EC of the European Parliament and of the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms.

Gebhard, F. and Smalla, K. 1998. Transformation of Acinetobacter sp. strain BD413 by transgenic sugar beet DNA. Applied and Environmental Microbiology, 4: 1550-1554.

Nielsen, K.M. 2003. An assessment of factors affecting the likelihood of horizontal gene transfer of recombinant plant DNA to bacterial recipients in the soil and phytosphere. In: Collection of Biosafety Reviews, Vol. 1 pp. 98-149. International Centre for Genetic Engineering and Biotechnology (ICGEB). 2003. Printed by Editoriale Ergon.
3.
http://www.safecompostingtechnology.com/index.php?option=com_content&view=article&id=48&Itemid=21&lang=en
This one is questionable, mainly because it is written by a company that sells composting equipment, so they have reason to claim composting can "defuse" GMO's.
Concern arises due to the fact that some bacteria are able to take up DNA molecules from their environment and, under certain conditions, incorporate them into their own genome. This is called Horizontal Gene Transfer (HGT).

Extensive real environment tests have concluded that there is no evidence of HGT between GM plants and bacteria, although it has been conducted in laboratories. However, one field test has shown that HGT can occur between genetically modified microorganisms (GMMOs) and bacteria in the environment. [It is interesting that this appears to be (if I'm reading it correctly) the opposite of the claim in my second source above: "horizontal gene transfer from transgenic plants to bacteria has not been detected in natural systems when transgenic plant residues has been allow to decay in soils (Nielsen, 2003). However, the process has been detected in laboratory experiments"]

Experiments have been carried out since then to discover the impact of composting on GMMOs and transgenic DNA in compost.

These experiments have concluded that during the type of thermophilic composting process which occurs during in-vessel composting (such as that in the Rocket), GMMOs and transgenic DNA do not survive. Indeed, it was discovered that this type of composting eradicates the presence of GMMOs and transgenic DNA much more effectively than if GM plant material is simply turned back into the soil [2],[3]. Furthermore, the study carried out by University of Abertay Dundee, actually used one of our very own A500 Rockets™ in which to conduct their experiments.


[1] Genetically Modified Organisms, 2012.

[2] Schwarz-Linek, J. et al., 2007, The Fate of Genetically Modified Microorganisms During Thermophilic Composting, University of Abertay Dundee, Scotland.

[3] Rasmussen, L.D. et al, 2004, Composting Rapidly Degrades DNA from Genetically Modified Plants, Danish Research Centre for Organic Farming, Denmark.


So far it's not clear if "hot" composting takes care of the problem, because it is so hard to analyze a biological system genetically in great detail (at least that's what I'm seeing in this), but it is a hopeful possibility warranting further investigation.

Finally, there is at least one "sure-fire" method to eliminate the GMO genes in plant material: burn it to ash. Maybe one could use the ashes for lye to make soap? And in small amounts wood/plant ash can be a soil additive that increases acidity (lowers pH) and adds certain nutrients.
 
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