With global temperatures on the rise, replacing industrial nitrogen fixation—a major source of the greenhouse gas nitrous oxide—with biological nitrogen fixation represents one of many ways to mitigate climate change (Thomson et al., 2012). As the world’s growing population needs to be met with growing sources of food, biological nitrogen fixation will need to be enhanced such that agricultural yields remain unaffected. The first obstacle in determining how to enhance nitrogen fixation carried out by biological organisms today is understanding the exact genes that enable it.
Ensifer meliloti is a nitrogen-fixing rhizobacterium (soil bacterium) that interacts with legume plants like Medicago sativa (alfalfa) in a symbiotic relationship (Jones et al., 2007). Harnessing symbiotic nitrogen fixation (SNF) from this naturally-occurring system (Figure 1) such that it can be amplified or even transferred to other bacteria or plants via synthetic biology approaches necessitates establishing a “minimal symbiotic genome,” composed of the least number of genes required for SNF.
To date, derivatives of E. meliloti with reduced genomes have been constructed to provide genomic backgrounds for assaying reintroduction of genome subsets (diCenzo et al., 2014). Here, E. meliloti was stripped of its megaplasmid pSymA and/or chromid pSymB, producing ΔpSymA, ΔpSymB, and ΔpSymAB (where Δ represents deletion) (Figure 2). Subsequently, screening a pSymA deletion library revealed three regions (A117, A118, A121) important for SNF (diCenzo et al., 2016). The re-introduction of the A117-A118-A121 region into pSymA recovered the plant growth-promoting phenotype in alfalfa, marking the achievement of a first generation minimal symbiotic genome, later termed minSymA1.0 (Huang, 2019). Further minimizations have produced minSymA2.1, minSymA3.1, and minSymA3.2 (Geddes, unpublished). Overall, it is expected that genome minimizations will impair SNF to some degree. However, studies should indicate whether the impairment is drastic. If so, previously uncharacterized genes may surface as genes with important functions. If the impairment is negligible, the minimization will be a step towards the least number of parts required for SNF, a suitable framework for creating synthetic symbioses.
Altogether, synthetic biology approaches potentiate reorganization and enhancement of minimal symbiotic genomes for increased yield in both legume and non-legume plants (Mus et al., 2016). The framework for configuring non-legume plant hosts to interact with rhizobacteria has already been laid out (Geddes et al., 2019). Alternatively, transferring minimal symbiotic genomes harboured by E. meliloti to rhizobacteria that already interact with non-legume plant hosts would establish similar synthetic symbiotic phenotypes.
Ultimately, transferring nitrogen-fixing ability to plants, such that rhizobacteria are permanently integrated as an organelle OR such that all nitrogen-fixing machinery from rhizobacteria is incorporated into existing organelles like mitochondria, could define the emergence of a super-plant. This approach would also require a deeper developmental understanding of plant hosts; after all, breaking the evolutionary barrier that has kept rhizobacteria from permanent symbiosis with plant hosts would be no small task. And though we are currently far from a synthetic N2 fixation pathway in planta, the establishment of a synthetic pathway for CO2 fixation in vitro suggests that integrating nitrogen-fixing machinery is possible from a chemical standpoint (Schwander et al., 2016). Nevertheless, amplifying existing symbioses, crafting synthetic symbioses, and integrating synthetic parts into agriculturally-important crops will be an exciting task with significant implications for a more sustainable alternative to industrial nitrogen fixation.
References
diCenzo, G.C., MacLean, A.M., Milunovic, B., Golding, G.B. and Finan, T.M., 2014. Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction. PLOS Genetics, [online] 10(10), p.e1004742. Available at: <https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004742> [Accessed 6 Jan. 2020].
diCenzo, G.C., Zamani, M., Milunovic, B. and Finan, T.M., 2016. Genomic resources for identification of the minimal N2-fixing symbiotic genome. Environmental Microbiology, [online] 18(8), pp.2534–2547. Available at: <http://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.13221> [Accessed 6 Jan. 2020].
Geddes, B.A., Paramasivan, P., Joffrin, A., Thompson, A.L., Christensen, K., Jorrin, B., Brett, P., Conway, S.J., Oldroyd, G.E.D. and Poole, P.S., 2019. Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nature Communications, [online] 10(1), pp.1–11. Available at: <http://www.nature.com/articles/s41467-019-10882-x> [Accessed 23 Sep. 2019].
Huang, J., 2019. Towards The Minimal Symbiotic Genome Of Sinorhizobium Meliloti. [Thesis] Available at: <https://macsphere.mcmaster.ca/handle/11375/25093> [Accessed 6 Jan. 2020].
Jones, K.M., Kobayashi, H., Davies, B.W., Taga, M.E. and Walker, G.C., 2007. How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model. Nature Reviews Microbiology, [online] 5(8), pp.619–633. Available at: <http://www.nature.com/articles/nrmicro1705> [Accessed 6 Jan. 2020].
Mus, F., Crook, M.B., Garcia, K., Garcia Costas, A., Geddes, B.A., Kouri, E.D., Paramasivan, P., Ryu, M.-H., Oldroyd, G.E.D., Poole, P.S., Udvardi, M.K., Voigt, C.A., Ané, J.-M. and Peters, J.W., 2016. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Applied and Environmental Microbiology, [online] 82(13), pp.3698–3710. Available at: <http://aem.asm.org/lookup/doi/10.1128/AEM.01055-16> [Accessed 21 Feb. 2020].
Schwander, T., Borzyskowski, L.S. von, Burgener, S., Cortina, N.S. and Erb, T.J., 2016. A synthetic pathway for the fixation of carbon dioxide in vitro. Science, [online] 354(6314), pp.900–904. Available at: <http://science.sciencemag.org/content/354/6314/900> [Accessed 21 Feb. 2020].
Thomson, A.J., Giannopoulos, G., Pretty, J., Baggs, E.M. and Richardson, D.J., 2012. Biological sources and sinks of nitrous oxide and strategies to mitigate emissions. Philosophical Transactions of the Royal Society B: Biological Sciences, [online] 367(1593), pp.1157–1168. Available at: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306631/> [Accessed 15 Mar. 2020].
Comments
9 Responses to “Soil bacteria to the rescue”
Hi everyone!
Since IP is running at full power about now, I thought why not write about some of the big implications of these few months of contributions.
My topic is plant-microbe (legume-bacterium) symbiosis and it bridges content from plant biology, microbiology, genetics, synthetic biology–and as one of the main applications of this work is reducing nitrous oxide emissions–the topic is linked to CC as well.
Hope you enjoy reading about this cool system, accomplishments to date, and aims for sustainable agricultural intensification!
Thanks,
Aakanx
Hello Aakanx,
Cool post! I really liked the application of genetics and molecular biology to climate change.
I have a few minor suggestions, as follows:
– In your first sentence, I would write “with global temperatures on the rise” – to make it clearer from the get-go what you’re implying.
– In the following sentence: “Ensifer meliloti is a nitrogen-fixing bacterium that interacts with legume plants like Medicago sativa (alfalfa) in a symbiotic relationship (Jones et al., 2007).”, I would change “bacterium” to “bacteria”, since you’re referring to the whole population of that species and and not a single individual.
– I think you should consider explaining a few of the genetic terms you mention, such as “minimal symbiotic genome”, “gain-of-function analysis”, “super-plant”. These are not terms that everyone will be familiar with and I think it would help to explicitly explain them in-text.
I liked your conclusion, I thought it tied the post together nicely and gave you a nice food-for-thought finish. Overall, great job!
Happy editing,
Jessica
Hi Jessica,
Thanks for the comments! I’ve made changes according to your first and third points. (I explained “minimal symbiotic genome” further, replaced “gain-of-function analysis” with something more descriptive, and kept “super-plant” because that’s a term I came up with to distinguish plants that have received enhancement, which is explained in the term’s sentence already.) As for your second point, I have seen more often that single bacterial species are described in the singular (i.e. Genus species is a bacterium that…) and multiple bacterial species are described in the plural (i.e. Gs1 and Gs2 are bacteria that…) so I will keep what I have. Glad you liked my conclusion! 🙂
Thanks,
Aakanx
Hi Aakanx,
First of all, a good blog post! I enjoyed reading about soil bacteria.
Here are some suggestions for editing.
1. I would consider dividing the last paragraph as it is on the longer side.
2. I think you forgot to cite for your figure in the figure caption.
3. Don’t forget to add your references at the end!
I look forward to reading your more updated blog post! Happy editing!
Kate
Hi Kate,
Thanks for the suggestions. I’ve split up my last paragraph where I found appropriate, cited my figure caption, and added my references (totally forgot)!
Thanks,
Aakanx
Hi Aakanx,
I really enjoyed reading your post! The idea of using synthetic symbiosis in order to create these nitrogen-fixing super-plants is fascinating, and I liked your connection to a climate change application. This was super well-written as well, I thought the flow was great and you clearly have a deep understanding of the topic — I also liked your descriptions of things, such as ‘super-plants,’ and the challenges of incorporating E. meliloti SNF activity into other plants as ‘breaking an evolutionary barrier’.
Overall, it looks great, but I have a couple of suggestions as you finish up with editing:
– This is more of a style choice, but I found the switch from using the BNF acronym in the first paragraph to SNF for the rest of the post a little awkward — is using the acronym in the first paragraph worth it if you only use it a couple of times?
– The section on establishing a minimal symbiotic genome was really interesting, and I found the purpose & implications to be really well-explained. However, I was a little confused by what exactly replicon-curing is, and what ΔpSymAB, etc. represent (the plasmid DNA without the replicon maybe??) — it might be helpful to define these terms a little more to make the post a little more accessible!
– The post was really well-researched — you have a lot of sources, and I like the focus on recent research! A couple things to keep in mind, though: remember that DOI is preferred over URLs for article sources. Also, when you cite “Geddes, unpublished” in text, I think you need an end reference for it even though it’s unpublished — just use whatever information you do have about it, and simply indicate (unpublished) for the date.
Good luck with your final edits, and happy summer!
Helen MacDougall-Shackleton
Hi Helen,
Thanks for the suggestions! Glad you enjoyed my post 🙂
I did feel the BNF to SNF switch was awkward, but was kind of on the fence about whether I should include both. I’ve removed the BNF abbreviation and made some related changes in that paragraph. I clarified those terms a bit – thanks for letting me know! I don’t think I can reference that Geddes article because it doesn’t exist quite yet haha, but will in the near future (it’s not “in press” either which is something the Harvard reference style has instructions for); Geddes is referring to a post-doc in my lab who has built those minimized strains. (Is there still a way to cite something like that though? Please let me know if you’re aware of one.)
Thanks,
Aakanx
Hi Aakanx,
This was a really great post! It was very well written and very informative! You start off immediately with the relevance of your topic and some background information, setting tone and pace for the post. Very well done! I don’t have much to comment on besides making sure to capitalise your title and the content of your third paragraph. Your third paragraph is rather information-heavy, and could benefit from either a nice graphic helping to explain the concepts, or some of the protein/plasmid names removed for easier understanding.
Other than that, really great post with lots fo great sources!
Thanks for the awesome read,
Paula
Hi Paula,
Thanks for the comment! I’ve added another figure – hope it helps with visualization of the information in the third paragraph.
Thanks,
Aakanx