Streptomyces bacteria: Antibiotic production in the wheat endosphere

Lead Research Organisation: John Innes Centre
Department Name: Molecular Microbiology

Abstract

Plants use photosynthesis to fix carbon dioxide from the air into glucose which they use as food. However, up to 40% of the carbon they fix is released into the soil from their roots and this appears to be a mechanism to attract beneficial bacteria from the surrounding soil. The bacteria use the root exudates as food and this helps the plants assemble a healthy microbiome. Some of these microbes protect the plants against disease and others help them get important nutrients from the soil. The root microbiome is therefore essential for plant health, but crop breeding over hundreds of years has selected traits such as bigger plants with more grain while perhaps neglecting the (unknown) effects on the microbiome. There is now growing interest in manipulating the microbiomes of crop plants such as wheat to make them more resistant to disease and to abiotic stresses like drought and salinity. Wheat is a staple crop for about 4 billion people and one of the most important crops in the world so increasing yields is essential if we are to support a growing world population.

Our project focuses on a genus of soil bacteria called Streptomyces. The ~600 known species of Streptomyces make numerous secondary metabolites, and these account for half of all the known antibiotics. They are easy to isolate from soil but also form stable interactions with plant roots and can colonise the rhizosphere and endosphere of a wide range of different plants. We have found they are abundant inside wheat roots and that some strains can protect wheat against fungal diseases such as Take-all which can cause devastating crop losses. For one of these strains we have identified the molecules and genes responsible for this antifungal activity and shown it is increased two-fold when we add indole 3 acetic acid, a plant hormone present in wheat root exudates, to the growth medium. In this proposal we aim to look in more detail at the colonisation of wheat roots by soil dwelling, antibiotic-producing Streptomyces bacteria. We will sequence the genomes of 10 strains we have isolated from wheat plants which inhibit the take-all fungus on agar plates, identify the antifungals made by these strains and determine if they can protect wheat plants against take-all disease. We will also try to discover which molecules in wheat root exudates can feed these bacteria and switch on their production of secondary metabolites. Since Streptomyces bacteria form spores which can be dried and stored for long periods, we are interested in developing wheat seed coatings containing these spores so the bacteria grow into the roots of germinating wheat plants and protect them against disease. We will also test the role of the type VII secretion system in root colonisation by these strains since we have preliminary evidence that this system helps them outcompete other bacteria for wheat root colonisation.

Our ultimate aim is to develop streptomycetes as seed coatings to protect wheat plants against fungal disease and to discover molecules from wheat root exudates that we can use to switch on secondary metabolite production in vitro because we know that 90% of the secondary metabolites they encode are not made under laboratory conditions. This could help us discover new and useful molecules from these bacteria.

Technical Summary

Increasing food production to feed a growing world population is essential for the future survival of the human race. Our proposal focuses on wheat, one of the most important crops in the world, and a genus of antimicrobial-producing bacteria called Streptomyces that are abundant inside wheat roots. Streptomyces bacteria make numerous specialised metabolites (SMs), many of which have antimicrobial activity, and they also form mutually beneficial symbioses with insects, marine invertebrates and plants, which exchange food and housing for antimicrobials, to protect themselves against disease. We are interested in exploiting Streptomyces bacteria as biological fungicides to protect wheat against disease and we are also interested in unlocking the biosynthesis of the estimated 90% of their SMs that are encoded but not produced under laboratory conditions. Their SMs already account for 50% of all known antibiotics and genome sequencing has indicated there are many more waiting to be discovered.

We have shown streptomycetes are highly enriched in the endosphere of wheat variety Paragon grown in Church Farm soil (Norfolk) relative to the rhizosphere and surrounding soil. Some Streptomyces strains have beneficial effects on wheat plants, including protection against the Take-all fungus and we have also shown that the wheat root exudate molecule IAA can increase the antimicrobial activity of a Streptomyces endophyte strain. Here we will determine which root exudate molecules attract and feed streptomycetes and test whether they induce production of SMs not made under laboratory conditions. We will also genome sequence 10 streptomycetes isolated from wheat roots which inhibit the growth of the Take-all fungus and determine if the fungus or plant can activate production of their antifungal molecules and whether these strains can be used as seed coatings to protect wheat plants against fungal disease.

Planned Impact

The proposed work will generate significant impacts for a broad range of end users and we describe below who will benefit and the mechanisms in place to show how that impact will be achieved.

1. TRAINING. This project will offer excellent training and career opportunities to the named PDRA Sarah Worsley and the chemistry PDRA we recruit. The project will lead to high quality publications and the researchers will be encouraged to present at national and international academic conferences and take part in public engagement events, including at least one big public exhibition during this project plus six SAW Trust workshops in local schools. The technician will also be offered broad training as will visitors to the lab, including A-level students, undergraduates and Masters students who regularly volunteer to gain work experience or carry out research projects as part of their degrees.

2. DISSEMINATION TO SCIENTISTS AND THE GENERAL PUBLIC. It has long been known that soils can be disease suppressive and this is due to the prevalence of antibiotic-producing bacteria in those soils which presumably colonise and protect plant roots. Research has largely focused on plant symbiotic pseudomonads and bacilli and their antifungal compounds and streptomycetes have been overlooked, perhaps because they are difficult to work with. Our project will be of general interest to groups working on Streptomyces bacteria and on plant root microbiomes. There is a lot of interest in this area amongst academic groups and industrial scientists as high throughput sequencing techniques have enabled advances in understanding the core root microbiomes of many plants. We will share our results freely with scientists through publication in high quality open access journals, dissemination at academic conferences and more widely through Twitter (@actinobase and @matthutchings10) and press releases and on our group websites. Hutchings has a strong track record in public engagement in schools, through public lectures and at major public science events including the Royal Society Summer Science Exhibition 2014, the BBSRC Great British Bioscience Festival 2014, Big Bang Science Fair 2015 and Norwich Science festival 2016. He won a UEA award in 2015 for his outstanding contribution to public and community engagement and the Microbiology Society Outreach prize 2019 and will continue to engage widely with the public through all available avenues to talk about his group's work on Streptomyces natural product antibiotics and their role in protective symbioses.

3. ECONOMIC - NEW TOOLS. Materials, strains and knowledge developed during this project will be made freely available to academics and industrial scientists (subject to MTA) to stimulate and assist efforts to promote beneficial root microbiome formation. As the project progresses, we will engage with seed companies such as Elsoms and agritech to explore the possibility of including streptomycete spores in seed coatings. Companies interested in developing plant root synthetic communities (syncomms) include AgBiome, Syngenta, BioAg and Bayer AG and we will make contact with these companies via our IP officers who will protect this work through patent filing.

Publications

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Worsley SF (2020) Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. in Applied and environmental microbiology