From 2011.igem.org

Revision as of 10:27, 19 September 2011

Informing Design

We consulted numerous experts in various fields to ensure that the design of the AuxIn system respects all relevant social, ethical and legal issues. One module of our system, Gene Guard, is a direct result of brainstorming around the issues involved in the release of genetically modified organisms (GMOs). Although we have only reached the proof of concept stage, we have put a lot of thought into how AuxIn may be implemented as a product and the legal issues that would be involved.

Ecology

As our project involves releasing bacteria into nature, we have to consider their impact on the environment and other soil organisms. This is vital in assessing the safety of release. We did a literature review of the impact of natural auxins on the rhizosphere and consulted ecologists to find out more about our organism’s impact.

Effect on soil fauna

Dr Alex Milcu demonstrating the Ecotron experimental setup (picture courtesy of Dr Milcu).

1. Goal

Many animals above and below ground are extremely important to existing ecosystems. We want to ensure that there is no significantly detrimental effect on these animals caused by our bacteria.

2. Action

We met Dr Alexandru Milcu, an expert in above/below ground interactions at Imperial College's Silwood Park campus to discuss the impact of our project on the soil ecosystem.

Dr Milcu informed us that there is no known negative effect of auxin on soil fauna. A more fibrous root network should not influence metazoans to a noticeable extent. However, earthworms take up nutrients through their coelom and may be affected by heightened auxin concentrations, although this has not been established in the literature. Earthworms act as „ecosystem engineers“ and are therefore extremely important to the soil. Affecting them negatively should definitely be avoided (Dr Alexandru Milcu, oral communication).

3. Result

We devised a development plant (see the Implementation page) that our project will undergo before release will become feasible. This plan includes extensive testing of the impact of AuxIn on several important organisms, including earthworms, fish and other animals.

Effect of protozoans on our project

1. Goal

An issue with dispersing bacteria in the soil is that they may be eaten by protozoa that naturally occur in the soil. Most bacteria are probably digested in this way. Grazing by protozoa has been shown to to increase plant growth [6]. There are competing theories that this may be due to promoting auxin-producing bacteria or by increasing the nitrogen in the soil. However, it is becoming more likely that the latter theory is true (Dr Alexandru Milcu, oral communication.

2. Action

We met with Dr Milcu to discuss the impact protozoans may have on the implementation of our project. To test the impact of protozoan grazing on our bacteria, Dr Milcu suggested ensuring that protozoa be in test compost with our bacteria and then measuring auxin levels. This would add to the complexity of trials but give a more realistic measure of density and auxin secretion than by simply plating out our bacteria on agar.

3. Result

Effect on plant population composition

1. Goal

Monocots such as grasses typically grow fibrous root networks while dicots tend to grow long, deep roots, from which other roots branch outwards. Auxin influences dicots and monocots differently. While it induces lateral root growth and inhibits deep root growth in both types of plants, only diots are influenced negatively by exogenous auxin, on which it can act as a herbicide [3]. Supplying auxin to the soil may therefore result in selecting against dicots and causing a predominantly monocot population to grow fibrous networks of plants. While this may be detrimental for crop usage, dense networks of roots lead to an exponential water erosion decrease [4]. Fibrous root networks are therefore advantageous when trying to prevent soil erosion. We want to ensure that our bacteria do not have a detrimental effect on plant population composition.

2. Action

Syngenta visit: Prof Stuart Dunbar showed us the greenhouses.

We met with soil and auxin specialists at Syngenta to discuss implications of our project. Dr. Torquil Fraser and Dr. John Paul Evans advised as that there are 4 main natural and 4 synthetic auxins. Synthetic auxins are very stable and persist for weeks to months and can be used as herbicides. Unlike synthetic auxins, natural auxins are rapidly degraded. In plants, the auxin concentration is tightly regulated by conjugation with aspartic acid and metabolic feedback loop. This is not the case with synthetic auxins because of a slight change in their molecular structure.

In addition, we discussed the issue of skewing the plant population with Dr. Milcu.

3. Result

Skewing the plant population may have negative impacts from an ecological perspective, affecting diversity, but this effect may be counterbalanced by the conservation of plant habitation in general. In addition, we are considering putting our bacteria into soil alongside plants that are able to revegetate desertified areas. Rather than putting our bacteria into soil and hoping for the best, we are planning to use existing programmes to "reclaim" deserts and use our bacteria to enhance the growth of these plants. Dr. Milcu agreed with us that this approach would counter-balance any possible negative effects on ecological balances in the affected areas.

In addition, inhibitory effects of auxin can be prevented by producing less than 106 CFU per mL [5]. While the system is yet to be optimised, one of the great advantages of synthetic biology is the modularity of engineered constructs. In particular, we have introduced a sequence between RBS and promoter that facilitates exchanging promoters without affecting the coding sequence. It will therefore be possible to change the amount of IAA secreted by our bacteria to ensure that the amount produced is not inhibitory.

To test the effects of heightened auxin on different kinds of plants, Dr Milcu suggested setting up lab experiments with different plant functional groups. These would be planted in compost with an increased auxin concentration (using synthetic auxin) and observe how they respond. This experiment would be performed in the later testing stages of the project when we would be testing the impact of auxin on the environment.

References

[1] UNCCD (2011) Desertification: a visual synthesis. (Online) Available from: http://www.unccd.int/knowledge/docs/Desertification-EN.pdf (Accessed on 12 August, 2011).

[2] Geist, H. & Lambin, E. (2004) Dynamic causal patterns of desertification. BioScience 54:817-829.

[3] McSteen, P. (2010) Auxin and monocot development. Cold Spring Harb Perspect Biol 2010;2:a001479.

[4] Gyssels, G. & Poesen, J. (2003) The importance of plant root characteristics in controlling concentrated flow erosion rates. Earth Surface Processes and Landforms 28:371-384.

[5] Spaepen, S. et al. (2007) Indole-3-acetic acid in microbial and microorganism-plant signalling. FEMS Microbiol Rev 31:425-448.

[6] Krome, K. et al. (2009) Soil bacteria and protozoa affect branching via effects on the auxin and cytokinin balance in plants. Plant Soil 328:191-201.