From 2011.igem.org

Revision as of 11:30, 14 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

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).

To investigate how earthworms are affected, we set up an experiment with Dendrobaena worms to investigate the effect of auxin on them. For this, we will be following the set up described by Zwahlen et al. (2003).

Effect on soil microorganisms

E. coli do not naturally occur in the soil, which makes it hard to predict its influence on other soil microorganisms. In addition, they are very likely to be outcompeted.

If we want to aim for endurance of our bacteria in the soil rather than ensuring as much containment as possible, using E coli as a chassis may not be viable. Accordingly, we have codon optimised all of our new BioBrick constructs for E coli as well as B subtilis. For future applications, it may therefore be useful to sample soil in the area and determine the dominant bacterial species. Methods for this have already been established and include shot-gun sequencing of all soil microorganisms (Dr Robert Griffiths, oral communication). These bacteria are very likely to persist in the soil and may be used as more applicable chassis.

Another aspect we need to consider is protozoan grazing on our bacteria.

Effect on plant population composition

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 (McSteen, 2010). 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 (Gyssels & Poesen, 2003). Fibrous root networks are therefore advantageous when trying to prevent soil erosion.

Auxin-producing bacteria can also parasitise plants and inhibit their growht. Several measures can be taken to ensure that our bacteria are beneficial. Inhibitory effects of auxin can be prevented by producing less than 106 CFU per mL and although it seems that pathogenic bacteria are more likely to invade the plants, beneficial bacteria can be found inside of plants as well. (Spaepen et al., 2007).

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 using existing programmes to „reclaim“ deserts and use our bacteria to enhance the growth of these plants.

References:
UNCCD (2011) Desertification: a visual synthesis. (Online) Available from: http://www.unccd.int/knowledge/docs/Desertification-EN.pdf (Accessed on 12 August, 2011).
Geist, H. & Lambin, E. (2004) Dynamic causal patterns of desertification. BioScience 54:817-829.
McSteen, P. (2010) Auxin and monocot development. Cold Spring Harb Perspect Biol 2010;2:a001479.
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.
Spaepen, S. et al. (2007) Indole-3-acetic acid in microbial and microorganism-plant signalling. FEMS Microbiol Rev 31:425-448.
Zwahlen, C. et al. (2003) Effects of transgenic Bt corn litter on the earthworm Lumbricus terrestris. Molecular Ecology 12:1077-1086.
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.