Unravelling the contribution of the cereal bacterial microbiota to rhizosheath formation and functioning
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
The rhizosheath is the point of contact between plants and soil and is defined as the soil that adheres firmly to the roots. In small grain cereals, such as barley and wheat, the rhizosheath plays an important role in mitigating stress conditions, in particular towards nutritional drought. Rhizosheath therefore represents an attractive target to enhance the sustainability of crop production. Root hairs appear to be the major drivers of rhizosheath formation, although other plant traits contribute to this process. Preliminary data generated in my lab indicate that the structure of the root-associated microbial communities, the root microbiota, correlates with root hairs development, suggesting that the root microbiota might interfere with rhizosheath formation and functioning.
In this project, we will take advantage of experimental and bioinformatics approaches to develop plant genotype-tailored synthetic root microbiota enhancing rhizosheath formation and functioning under soil conditions. We are looking for an ambitious and highly motivated candidate with a background in plant biology or molecular microbiology with a strong interest in computational biology.
In this project, we will take advantage of experimental and bioinformatics approaches to develop plant genotype-tailored synthetic root microbiota enhancing rhizosheath formation and functioning under soil conditions. We are looking for an ambitious and highly motivated candidate with a background in plant biology or molecular microbiology with a strong interest in computational biology.
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M016811/1 | 01/10/2015 | 30/09/2019 | |||
| 1644361 | Studentship | BB/M016811/1 | 01/10/2015 | 30/09/2019 | Senga Robertson |
| Description | The thin layer of soil surrounding and influenced by plant roots, termed the rhizosphere, defines a distinct and selective microhabitat compared to that of the surrounding soil: the bulk soil. The microbial populations that reside in the rhizosphere, commonly referred to as the rhizosphere microbiota, participate in a variety of interactions with their host plant ranging from parasitic to mutualistic relationships. Due to the contribution of the microbiota to pathogen protection and nutrient uptake the rhizosphere microbiota has emerged as a determinant of crop yield. Consequently, a better understanding of plant-microbiota interactions in the rhizosphere can pave the way for novel applications enhancing sustainable crop yield and global food security. Experimental evidence indicates that the host plant is the driver of, at least in part, the rhizosphere microbiota, but genetic relationships underpinning these interactions are not fully understood. Filling this knowledge gap will allow plant breeders to select novel crops which better interact with the soil biota and, at the same time, biotechnologists can profit from microbial genetic information to develop a new generation of inoculants for agriculture. In this PhD project I used barley (Hordeum vulgare L.), the world's 4th and UK's 2nd most cultivated cereal, was used as an experimental model to dissect plant-bacteria interactions in the rhizosphere. I tested theThe hypothesis that root hairs: the tubular outgrowths of the root epidermis, modulate the physical and chemical environment in the rhizosphere to facilitate the colonisation of members of the microbiota implicated in mineral uptake was tested. To test this hypothesis, I developed three interconnected experimental approaches were developed:. By using 16S rRNA gene amplicon sequencing, it was I demonstrated that the presence and development of root hairs are a determinant offor nearly one fifth of the barley rhizosphere microbiota, with a bias for members of the order Actinomycetales, Burkholderiales, Rhizobiales, Sphingomonadales, and Xanthomonadales. In order to gain further insights into the molecular basis of this differential recruitment, the project I went on to investigate both the physical and chemical environment conditioned by root hairs. A pilot investigation of the rhizodeposition profiles using GC-MS of wild type and root hair mutants revealed that plant-genotype dependent patterns among the 69 amino and organic acids were detected and a further 23 sugars and sugar alcohols detected, pointing at root secretion as an additional selective layer in the barley rhizosphere. CongruentlyAdditionally, an amplicon sequencing survey of soil cores with different density, mimicking presence/absence of plant root hairs, revealed that this physical parameter is capable of triggering the differential enrichment of bacteria associated with the orders Bacillales, Burkholderiales and Xanthomonadales but not Actinomycetales. Thus, the physical perturbation of the soil environment alone cannot be the sole recruitment cue for the barley microbiota. However, it does indicate that soil density contributes, in part, to microbial recruitment. Finally, to discern the full genetic potential of plant-associated bacteria, I constructed an indexed bacterial collection of the barley microbiota was constructed by isolating, on synthetic media, individual rhizosphere bacteria. A total of 85 isolates were further selected for full genome sequencing including members of the orders Actinomycetales, Flavobacteriales and Xanthomonadales. A comparative genomic approach was deployed to identify plant-growth promoting traits among 53 of these isolates. This experimental work was complemented with a critical appraisal of my efforts to communicate to and increase the awareness of the general public on the importance of the plant microbiota for global food security. In the long term, I am confident the scientific outputs, of my research this project can be deployed to devise novel strategies aimed at enhancing sustainable crop production in the UK and to globally and increase the awareness of the general public to global food security, particularly with the potential of the bacterial isolate library to be used in collaboration with multiple research groups investigating a range of microbial approaches to improve crop sustainability. |
| Exploitation Route | The outcomes of this funding are currently being taken forward following the completion of my PhD in a short term ISSF funded bridging position where the indexed bacterial collection is being utilized in inoculation trials with barley. Further to this, the skills I have gained throughout my PhD coupled with the indexed bacterial collection are being taken forward in a post doctoral research position in the H2020 funded circles project detailed in my portfolio. |
| Sectors | Agriculture, Food and Drink,Environment |
| Title | Root hair mutations displace the barley rhizosphere microbiota database |
| Description | This database contains the raw data and open software scripts required to recreate the data presented in the paper: "root hair mutations displace the barley rhizosphere microbiota" (Robertson-albertyn et al 2017) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | this research article is approaching 5,000 views. |
| URL | https://www.frontiersin.org/articles/10.3389/fpls.2017.01094/full#supplementary-material |
| Description | ASM bring the magic of the microbiome to your classroom |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | blog article relating to the gut microbiome activity "microbe motels" |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.asm.org/index.php/education-blog/item/472-bring-the-magic-of-the-microbiome-to-your-class... |
| Description | ASM engage students active learning day |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Microbe motel gut microbiome activity selected to be delivered at the ASM active learning day |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.asm.org/index.php/education-blog/item/3039-engage-your-students-join-active-learning-day... |
| Description | Active learning day America: White House Stem initiative |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Microbe motels selected as one of the activities to be delivered as part of Active learning day: "On Active Learning Day, we encourage educators to provide opportunities for each of our Nation's daughters and sons to engage in active science, technology, engineering, and math learning and discover firsthand the power they have to bring their bold ideas to life. By using active learning techniques in our classrooms and out-of-school spaces, we are not only enabling students to take charge of their education, but also equipping them with the tools they need to solve our biggest problems and chart our country's course." President Barack Obama". Led by the Association of American Colleges and Universities (AAC&U) and its Project Kaleidoscope (PKAL), more than 165 colleges and universities and STEM-related professional societies-reaching more than 100,000 students-will support STEM faculty in adopting active-learning strategies by investing in faculty professional development and creating appropriate faculty rewards. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://obamawhitehouse.archives.gov/blog/2016/10/25/active-learning-day-america |
| Description | Bright Club (2016,2017,2018,2019) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Bright Club is a comedy club that runs in cities all over the UK, but started as an experiment in University College London. They asked: What would happen if we got a bunch of interesting comedians and musicians, and combined them with all of the fascinating people who work for one of the UK's best Universities? And what would happen if we did that combining on a stage, in front of an attractive and intelligent public audience? And what if we didn't worry about whether people were famous, or experienced, or had been on TV, and instead just picked people that we thought were brilliant at telling stories about what they know? The answer? Over 60 London Bright Club's, and 11 more cities later Bright Club has become a regular comedy night all over the country. |
| Year(s) Of Engagement Activity | 2016,2017,2018,2019 |
| URL | https://www.brightclubdundee.org/about/ |
| Description | Gatsby lectures |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | These free public lectures highlight how Plant Science is being applied to address problems of food and water inequality, climate change and health and well-being in a fast-growing world. Dundee is a centre of excellence for Plant Science research, which is based on the use of modern molecular biological techniques that are equally applicable to any of the Life Sciences. The role I played was speaking with the participants afterwards about my interest in plant science and the route I took to get in to this research field along with general careers advice. |
| Year(s) Of Engagement Activity | 2016,2017 |
| URL | https://www.lifesci.dundee.ac.uk/gatsby-plant-science-lectures |
| Description | I'm a scientist get me out of here |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | I'm a Scientist is an online activity where school students connect with real scientists about real science. It's a competition between scientists, where students are the judges. Students challenge the scientists over fast-paced online text-based live chats. They ASK the scientists anything they want, and VOTE for their favourite scientist to win a prize of £500 to communicate their work with the public. Senga Robertson-Albertyn won her zone and used the prize money along with funding awarded from the university of dundee ISSF seed fund for outreach then created her own medium scale outreach event which is described later in her profile |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://plutoniumn17.imascientist.org.uk/profile/sengarobertsonalbertyn/ |
| Description | Magnificent Microbes |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Magnificent microbes is an open event held at the dundee science centre organised by the molecular microbiology division of the school of life sciences, university of Dundee aimed at families. A variety of activities are presented on the day and foot fall is often around 1000 over the course of the day. Senga Robertson-Albertyn has participated in this event twice, with 2018 helping with the organisation of the event prior to delivery. She has delivered both the root printing and gut microbiome activity described in previous outreach work. |
| Year(s) Of Engagement Activity | 2017,2018 |
| URL | https://www.lifesci.dundee.ac.uk/impact/schools-outreach/media/magnificent-microbes |
| Description | Meet the expert |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Meet the expert is a free event held at the Dundee Science centre aimed at families. Activities are delivered by life scientists. Senga Robertson-albertyn held several training sessions for scientists participating to demonstrate the microbe motels activity and then assisted them with activity delivery on the day. This event specifically focused on connections between our food, our planet and our health. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://thecrunch.wellcome.ac.uk/get-involved/events/detail/families-event-meet-the-expert-at-dundee... |
| Description | Plant power day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | The free Plant Power Day event offers budding botanists the chance to see the University of Dundee Botanic Garden beautiful collection of trees and shrubs, glasshouses as well as its water and herb gardens. It also boasts a plethora of activities developed and delivered by scientsist from the division of plant science Dundee. During multiple occasions of participating in this event I have (as part of a team) delivered root printing, DNA extraction and animating science activities |
| Year(s) Of Engagement Activity | 2016,2017,2018,2019 |
| URL | https://www.hutton.ac.uk/events/plant-power-day-2018 |
| Description | Reviewer - School of Life Sciences public engagement strategy |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Reviewer of the production of the university of Dundee School of Life Sciences Public Engagement strategy which was developed to ensure clear focus and direction in outreach events that complimented the universities objectives of sharing aims, consulting and collaborating with audiences and partners, evaluating practices, and tracking the impact to people's lives in conjunction with ensuring that engagement needs are well resourced and provide long term stability and sustainability of impact, and to recognise and reward successes |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://discovery.dundee.ac.uk/ws/portalfiles/portal/42095431/University_of_Dundee_Public_Engagement... |
| Description | The James Hutton Institute Open Farm Day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | A family fun day aimed at the general public to disseminate the research being conducted at the james hutton institute and to convey key scientific concepts. Senga Robertson-Albertyn delivered a fun rhizosphere game translating the importance of root hairs in rhizosphere formation and in plant fitness. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.hutton.ac.uk/events/open-farm-sunday-2017 |
| Description | University of Dundee festival of the future comedy night performer |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | The very first stand up comedy event as part of dundees festival of the future intended to humorously translate your science to a general audience and to break down preconceptions about scientists/ normalize scientists. This event was well received and sold out and due to its success has become a regular feature in the dundee festival of the future. Senga performed a 10 minute stand up set to the audience, took part in multiple training events prior to the event and assisted performers with rehearsals. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.dundee.ac.uk/festival-future/programme/overview/ |
| Description | University of Dundee open doors day debate sessions |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | As part of a team set up, planned, coordinated and delivered multiple debate sessions for 14-16 years old learners around commonly misreported scientific topics such as Genetic Modification and artificial intelligence. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.doorsopendays.org.uk/media/3710/dundee-2017-dod-programme.pdf |
| Description | Women making waves in science |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | story telling event as part of Dundees womens festival telling the general public about our journey in life and our career. |
| Year(s) Of Engagement Activity | 2020 |
| Description | cell-ebration of science |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | cell-ebration of science was an event created and organised by Senga Robertson-Albertyn with £500 prize funding from the Wellcome Trust plus an addition £500 from the University of Dundee ISSF seed fund for outreach. pubils from two schools in underserved local ares were invited to take part in a range of activities devised and delivered by a broad variety of divisions of the school of life sciences including molecular microbiology, plant sciences, protein phosphorylation, forensic anthropology and computational biology. Free transport was provided to the schools to avoid potential expense or requirement of subsidisation from parents and a hot lunch was arranged with a local pizza restaurant to ensure there were no concerns for parents about providing a packed lunch. In addition to the activities created within the school of life sciences there was also an external drama coach who was employed to perform drama workshops with the participants. The event was highly successful, collaborative and covered all learning styles and approaches. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://about.imascientist.org.uk/2019/what-senga-robertson-did-with-her-prize-money/ |
| Description | hand printing - abernethy primary school |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Visited local primary school to deliver hand printing activity, the learners hands were placed on nutrient agar plates and then brought back to the university to be incubated. Images of the bacteria that have grown from the hands were sent to the learners. During the visit the importance of the hygiene was translated along with the impact that poor hygiene can have on health. Fluorescent handwashing was also conducted to show learners areas commonly missed on the hands when washing |
| Year(s) Of Engagement Activity | 2018 |
| Description | microbe motels - abernethy primary school |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Microbe motels activity delivered to primary 5 level learners at local primary school. Translating the importance of the gut microbiome and the impact this can have on health and lifestyle factors that can shape the microbiota. Hands on activity involving adding coloured "bacteria" to a fake gut along with food and water, mixing and then expressing to form a "poo". learners then discuss if poo looks healthy - if it doesn't this opens dialogue regarding dysbiosis |
| Year(s) Of Engagement Activity | 2018 |
| Description | microbe motels - doonfoot primary school - ayr |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Microbe motels activity delivered to primary 5 level learners at local primary school. Translating the importance of the gut microbiome and the impact this can have on health and lifestyle factors that can shape the microbiota. Hands on activity involving adding coloured "bacteria" to a fake gut along with food and water, mixing and then expressing to form a "poo". learners then discuss if poo looks healthy - if it doesn't this opens dialogue regarding dysbiosis. This school specialized in young people with additional learning needs - the activity was adapted accordingly |
| Year(s) Of Engagement Activity | 2017,2018 |
| Description | root printing - abernethy primary school, perthshire |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Visited local primary school to deliver root printing activity, the roots of barley seedlings were placed on nutrient agar plates and then brought back to the university to be incubated. Images of the bacteria that have grown from the roots were sent to the learners. During the visit the importance of the rhizosphere microbiome was translated along with the impact that over fertilization can have on the environment |
| Year(s) Of Engagement Activity | 2017 |
| Description | selected to be part JMBE's education blog |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Outreach activity microbe motels selected to feature as part of JMBEs spotlight education blog. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.lifesci.dundee.ac.uk/research/publications/public-engagement-publications/public-engagem... |