Microbiome Engineering In Plants

Microbiomes are collections of all the microbes such as bacteria, fungi, viruses, and their genes that naturally live in our bodies and in plants, interacting to form a microbial ecosystem. Many companies, like Actimel and Yakult, produce and sell drinks containing ‘good’ bacteria that supports our immune systems and helps prevents us from being infected by harmful bacteria. Probiotics, like Lactobacillus acidophilus, can be naturally found in yoghurt or cheeses with live active cultures- the ‘friendly’ bacteria present in these foods or drinks work in many ways to out-compete harmful pathogens, specifically working to crowd dangerous bacteria out the gut and use the nutrients available, so there is none left for the pathogenic bacteria to use, disabling them from multiplying via binary fission, which requires nutrients such as glucose. Moreover, the beneficial bacteria in our guts also produce lactic acid, creating an environment that inhibits the growth of harmful bacteria, as the cytoplasm of the bacteria becomes acidified and hence prevents any further growth or replication. Probiotic strains can also release vitamins into the intestinal tract like vitamin B6 and B12 helping to strengthen and support normal function of the immune system and hence prevent infection. Using this knowledge of how building extensive microbial systems can benefit humans, scientists have applied this to microbiome engineering in plants, specifically focusing on finding out the ‘good’ bacteria naturally produced in plants that help defend them from bacterial infection.

The experiment conducted by a group of scientists from an international research team helped uncover the specific gene found in the ‘lignin biosynthesis cluster’ of the rice plant, which has aided in shaping its microbiome. The compound named 4-hydroxycinnamic acid (4- HCA), synthesised via the depolymerisation of lignin, by the host plants OsPAL02- which is linked to phyllo sphere microbiome assemblywas identified as the main driver of bacterial enrichment allowing a more extensive microbiome to be developed, preventing pathogenic bacteria from causing plant diseases. When the gene was deactivated, stopping the synthesis of 4-HCA, there was a noticeable decrease in the population of beneficial bacteria, and when the gene was overexpressed showed the reverse effect of producing the specific metabolite- 4-HCA- increasing the proportion of beneficial bacteria to outcompete pathogenic bacteria in the plant’s microbiome. The group of scientists had then exposed the modified plant, with the over-expressed gene, to Xanthomonas oryzae- a pathogen which causes bacterial blight in rice cops (see Fig.1) - they found it was ‘substantially more resistant to it than wildtype rice.’

This breakthrough could dramatically cut the use of pesticides and unlock opportunities in bolstering health for a range of plants. Pesticides are often associated with negative effects on the environment such as soil and water contamination, leading to intoxication of birds, insects, and even beneficial insects (see Fig.2). This naturally means a reduction in biodiversity in the area around crop fields, which is which is the intent of farmers when using pesticides, to increase crop yield. However, the integration of the plant gene which promotes secretion of 4-HCA, into plants, means less pesticides would have to be used hence farming can become less impactful on the environment. Moreover, the 4-HCA allows beneficial bacteria to divide and retain most of the plant’s nutrients taken up via the soil, that would otherwise be used up by harmful bacteria. This would, in turn, reduce the need for synthetic fertilisers too, as plants would be able to naturally grow without being harmedby pathogens. With a growing population, increasing demands for food and other crops need to be met- this is the start of the future to create an environmentally sustainable farming technique via microbiome engineering, and reduce the negative impact synthetic fertilisers and pesticides pose to the environment.

Binary Fission- asexual reproduction by a separation of the body into two new bodies. In the process of binary fission, an organism duplicates its genetic material, or deoxyribonucleic acid (DNA), and then divides into two parts (cytokinesis), with each new organism receiving one copy of DNA.

Probiotic- Probiotics are live bacteria and yeasts promoted as having various health benefits. They're usually added to yoghurts or taken as food supplements, and are often described as "good" or "friendly" bacteria.

Lignin biosynthesis cluster- A lignin biosynthesis cluster refers to a group of genes that are involved in the synthesis of lignin in plants. Lignin is a complex and rigid polymer found in the cell walls of plants, providing structural support and contributing to the resistance of plant cell walls against microbial attacks and environmental stresses. The biosynthesis of lignin involves a series of enzymatic reactions that are catalysed by various enzymes.

Lignin depolymerisation- refers to the process of lignin degradation with the assistance of bacteria, fungi, or isolated enzymes underrelatively mild conditions.

Phyllosphere microbiome- The phyllo sphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communitieson the leaf surface.

Metabolite- a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules.

Environmentally Sustainable- Environmental sustainability is the ability to maintain an ecological balance in our planet's natural environment and conserve natural resources to support the wellbeing of current and future generations.

References: [cited Jan 28/01/24]

1.Scientists engineer plant microbiome to protect crops against disease [Internet]. ScienceDaily. Available from: https://www.sciencedaily.com/releases/2024/01/240104122013. htm

1. Harvard Health Publishing. The benefits of probiotics bacteria - Harvard Health [Internet]. Harvard Health. Harvard Health; 2017. Available from: https://www.health.harvard.edu/stayinghealthy/the-benefits-of-probiotics
2. sis Viana Mendes, Mariana Botelho Garcia, Carolina A, Renata Henrique Santana, Philippe, Silveira R, et al. Bacterial diversity dynamics in microbial consortia selected for lignin utilization. PLOS ONE. 2021 Sep 13;16(9):e0255083–3.
3. Shavit JD. Farming breakthrough dramatically cuts the use of pesticides to protect crops against diseases [Internet]. Brighter Side News. 2024 [cited 2024 Jan 28]. Available from: https://www.thebrighterside.news/post/farming-breakthroughdramatically-cuts-the-use-of-pesticides-to-protect-crops-againstdiseases
4. Su P, Kang H, Peng Q, WicaksonoWA, Berg G, Liu Z, et al. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nature Communications [Internet]. 2024 Jan 2 [cited 2024 Jan 19];15(1):23. Available from: https://www.nature.com/articles/s41467-023-44335-3#Sec2
5. What Are Probiotics & What Do They Do? [Internet]. Cleveland Clinic. 2023. Available from: https://my.clevelandclinic.org/health/treatments/14598-probiotics

GCSE: 5.10- Plant Diseases (Bacterial Blight in rice crops caused by Xanthomonas oryzae) 5.11- Plant defence responses (Production of 4-HCA causes out-competition of bacteria causing blight, allowing plants to retain nutrients) 16.1- The importance in communities (Maintaining biodiversity by reducing the use of pesticides and synthetic fertilisers to aid crop growth) 18.1-The Human Population Explosion (Keeping up with relative demands of increasing populations + 18.12- sustainable food production)

A-Level: 13.4- Use of natural and artificial fertilisers (Reducing use of synthetic fertilisers and how that is helpful for the environment) 13.5- Environmental issues concerning use of nitrogen-containing fertilisers (negative effect of using synthetic fertilisers, and how integration of genes can reduce use) 21.4-Locating genes & genetic screening