Phosphorus cycling in the soil-microbe-plant continuum of agri-ecosystems

Lead Research Organisation: University of Reading
Department Name: Sch of Agriculture Policy and Dev

Abstract

The element phosphorus (P) is an essential nutrient required by crops to ensure good growth and yields. Crops get their P from the soil via their roots in the form of phosphate (a phosphorus atom surrounded by four oxygen atoms, Pi). The availability of Pi for the crop in the soil depends on the soil type, its pH, the growth of bacteria and fungi in the soil and the amount of Pi the crop takes up. Unfortunately, P is very reactive and can get locked away in the soil either with other elements or in organic compounds, making it hard for the crop to acquire sufficient Pi. To overcome this, farmers add Pi fertilisers to the crop. However, Pi fertilisers are made from rock phosphate, a non-renewable resource, the availability of which is set to decline, and the price increase, over the coming decades. Excessive use of Pi fertilisers is also a problem as the Pi can be washed into local rivers and lakes and contributes to the process of eutrophication.

Since plants evolved over millions of years without Pi fertilisers, they are well equipped with adaptations to help improve the availability of Pi near their roots. Many of these adaptations have not been selected for directly when breeding crop varieties or they are not optimised for rapidly growing, high yielding crops. These adaptations included making more roots, releasing acids from their roots to free Pi bound to the soil, releasing enzymes from their roots to release Pi trapped in organic compounds and recruiting soil bacteria and fungi to help acquire Pi.

To help reduce our need for Pi fertilisers we will study these plant adaptations and the bacteria that grow near the roots of oilseed rape. We will begin by identifying the bacteria that live near the roots of these crop plants using next generation sequencing technology. This allows us to sequence the genomes of most of the bacteria living in the soil near the roots and identify them. We will also investigate the enzymes and proteins made by the bacteria and the root. These approaches will tell us about bacterial activity in the soil near the root and which processes they are contributing towards. Since the P can be in different forms in the soil, such as bound to the soil or trapped in organic compounds, we will use 31P-NMR spectroscopy to investigate what forms the P is in and how they change.

The growth of bacteria around the roots of the crop is largely controlled by sugars and other products released by the roots; the content and concentrations of these are genetically determined. We will reduce the expression of some of the genes that determine the release of these compounds and study the effects on the types of bacteria present near the roots and the processes they affect in relation to P availability.

Finally, the P requirement of the crop changes during the growing season, declining towards harvest. We will study how the root and the bacteria growing near to it change overtime and regulate the availability of P to the crop.

These studies will provide valuable information on how a crop controls the bacteria growing near its root, how the bacteria help the crop acquire P and how these processes change during the growing season. This information will help develop agricultural systems that use existing P in the soil more efficiently and optimise the amount of Pi fertiliser required to grow a successful crop. It will also provide targets for breeding crops that are more efficient at acquiring Pi from the soil, either by themselves, or with help from some soil bacteria.

Technical Summary

To provide a holistic understanding of phosphorus (P) cycling in the rhizosphere of a non-mycorrhizal crop, we will use metagenomics, transcriptomics, metaproteomics and 31P-NMR analyses on the rhizospheres of soil grown Brassica rapa and Brassica napus plants. This will deliver novel insights into the structure and function of rhizosphere microbial communities and their role in P cycling for a crop plant (Objective 1). We will utilise TILLING resources available for B. rapa to manipulate the expression of genes regulating the amount or content of root exudates and quantify the impact on rhizosphere P pools and microbial community structure and function. This will provide knowledge on the role of root exudates in making P directly and indirectly available through their contribution to microbial growth (Objective 2). Since the demand for P by the crop changes during development, we will evaluate changes in rhizosphere P pools and microbial community structure and function during the development of B. rapa under controlled environment conditions and B. napus (oilseed rape) under field conditions, with and without P fertiliser. This will deliver temporal information on crop P demand and how this impacts on root exudates and P cycling. The addition of P fertilisers and their effects on labile and non-labile P pools, specifically organic P pools, will also be evaluated (Objectives 3 & 4).

Knowledge gaps on P cycling in the rhizosphere of a major crop and the roles of the crop and microbial community will be addressed. This will deliver information on the microbes functionally responsible for P cycling, the enzymes involved and the role of the root in delivering carbon for these functions. Novel opportunities for breeding crops that are more efficient at acquiring P, either directly or indirectly through the rhizosphere microbial community will be possible, together with potential biotechnological applications for microbes and enzymes identified by this research.

Planned Impact

The proposal will deliver novel insights into 1) the structure and function of rhizosphere microbial communities and their roles in rhizosphere phosphorus (P) cycling of a crop plant, 2) the role of root exudates in making P available directly and indirectly through their contribution to microbial community growth and 3) temporal information on crop P demand and how this impacts on root exudates and rhizosphere P cycling. The results of the project will highlight the predominant bacterial genes actively expressed in the rhizosphere and provide data on proteins to be isolated through metagenomic clone library screening approaches. We hope to enhance collaboration with industry with the new approaches to understanding microbial activity in soil and further develop techniques for analysis of the soil bacterial metagenome and metaproteome. The latter will improve understanding of soil enzyme activity and impacts of plant growth on bacterial activity below ground. We will also improve understanding of how soil conditions impact on microbial diversity both at the structural and functional levels. This project will provide vital information to farmers and government agencies, such as Defra, on the potential effects of soil conditions on plant health. The relevant individuals from Defra and HGCA (cereals and oilseeds division of the Agriculture and Horticulture Development Board (AHDB)) already have strong contacts with Warwick School of Life Sciences so this represents an opportunity to extend these contacts. In addition to the academic beneficiaries to these advancements in our knowledge, the following could benefit from this research:

PDRAs: PDRAs recruited to the project will benefit from formal training supplied through University centres for continuing professional development, which includes management and leadership training, and through the development of skills in metagenomics, metaproteomics, plant genetics and rhizosphere biology. These will generate future research scientists focused on rhizosphere processes with the skills required to develop and lead their own research programs.

Industry: Potential immediate impacts will result from the identification of novel microbes and/or enzymes from the rhizosphere and improved knowledge on the role of a microbial inoculant in plant nutrition. These may be of interest to biotechnology companies for use in bioprocessing or for the development of biofertilisers. Research on the genes involved in root exudate production could be of interest to breeding companies for the development of new crops with enhanced abilities to acquire P or encourage the growth of beneficial bacteria in their rhizosphere. Knowledge of these rhizosphere processes could lead to the development of improved cultural practices for crop production or reduced inputs of P fertilisers, benefitting growers. Savings in input costs could be passed on to consumers. Capacity building for young researchers in the exploitation of metagenomics for discovery of novel microbial enzymes and metabolic processes which will improve UK based commercial exploration and exploitation of the uncultured microbial diversity in soil.

Public: Ultimately, potential impact will be felt by the wider society in the longer term. To feed the world's burgeoning population, agricultural production must double in the next three decades within unpredictable environmental constraints. Better understanding of how crops interact with the soil they grow in will facilitate improvements in crop varieties and growing practices to improve yields and increase the food supplied from a given area. This will contribute to agricultural sustainability and greater food security.

Increasing the efficiency with which crops acquire P could reduce inputs of P fertilisers, which will help sustain this non-renewable resource and benefit society through greater food security and lower production costs.

Publications

10 25 50

 
Description Global food production is reliant on the application of finite phosphorus (P) fertilisers. Numerous negative consequences associated with intensive P fertilisation have resulted in a high demand to find alternative sustainable methods that will enhance crop P uptake. To better understand how plant-growth promoting bacteria make phosphate available for themselves and nearby plants, we performed comparative exoproteomics on soil bacteria from the Pseudomonas species grown with and with phosphate. Our approach helped identify a number of novel phosphate-responsive proteins and revealed significant genus-level heterogeneity in their adaptation to phosphate depletion and thus their potential phosphate recycling capabilities. We have identified and experimentally confirmed the function of two secreted glycerolphosphodiesterases from two species of bacteria Pseudomonas stutzeri and Pseudomonas fluorescens. These are a class of enzymes that can release phosphate from glycerolphosphorylcholine in the soil, and thus make it available for bacteria and plants. Using a series of co-cultivation experiments we revealed that in these Pseudomonas strains, cleavage of glycerolphosphorylcholine and its metabolites occurs extracellularly allowing other bacteria to benefit from this metabolism. We have also characterised a group of bacteria that are commonly found in the rhizosphere, called Flavobacterium. We show that these Flavobacterium strains possess novel mechanisms for phosphate mobilisation and subsequent uptake. These include the completely novel and phylogenetically distinct phosphatases that were expressed all the time, novel genes that were the expressed in response to phosphate starvation and finally the involvement of outer membrane SusCD transport complexes, which are usually associated with carbohydrate transport, in the transport of phosphate. The genes encoding these unusual inducible phosphate starvation proteins were specifically enriched in plant-associated Flavobacterium strains suggesting that this machinery represents niche-adaptive strategies for overcoming P scarcity in this group of bacteria. We propose that abundant rhizosphere-dwelling Flavobacterium spp. have evolved rather unique mechanisms for coping with Pi-stress which may provide novel solutions for future sustainable agricultural practices. Finally, we have generated a collection of plants that have altered root exudate profiles. These are currently being used to identify the impact of these altered profiles on phosphate uptake and the soil bacterial community that inhabit the rhizosphere of these crops.
Exploitation Route Reduce reliance on NPK inorganic fertilizers and phosphates which are a mined finite resource by improved understanding of the plant root microbiome and its exploitation for P supply. Ultimately this is be the beginning of our aims to exploit flavobacteria as a group of highly useful rhizobacteria which can contribute to vital plant Pi nutrition and be exploited as plant inoculants into the rhizosphere. Ian Lidbury will continue this approach in fellowship application.
Sectors Agriculture

Food and Drink

Environment

Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

 
Description During his recent work Dr Ian Lidbury has demonstrated that in Flavobacteria spp. one of a SusCD-like complexes (outer membrane transporters for various oligosaccharides) is required for phosphate transport, instead of the classic high-affinity phosphate ABC-transporter. He discovered a completely novel mechanism for bacterial phosphate acquisition whereby high affinity nutrient uptake is governed at the outer membrane (SusCD) instead of the inner membrane (ABC).He performed a comprehensive comparative genomic analysis on the distribution of various ABC transporters, thought to be found in all major bacterial groups7 and discovered that Bacteroidetes, including Flavobacteria, lack numerous ABC transporters associated with ecologically important nutrients. In addition a novel gene cluster involved in synthesis of a non-ribosomal peptide compound was discovered and further analysis proved this peptide had antimicrobial activities. Detailed study of genomes from the Bacteroidetes group indicated a wide range of clusters and biosynthetic enzymes covering peptides, polyketides, aromatic peptides, polyenes, terpenes and many other metabolite classes.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology
Impact Types Economic

 
Description EIT-Food KIC
Amount € 461,348 (EUR)
Funding ID 18112 
Organisation European Institute of Innovation and Technology (EIT) 
Sector Public
Country Hungary
Start 08/2017 
End 12/2018
 
Description Interplay Between Different Wheat Cultivars and Novel Biostimulants to Increase Quality and Yield in Wheat - EIT-Food KIC
Amount € 309,787 (EUR)
Funding ID 19164 
Organisation European Institute of Innovation and Technology (EIT) 
Sector Public
Country Hungary
Start 01/2019 
End 12/2019
 
Description Remediation of Cocoa Soils in Ghana as a Route to more Sustainable Cocoa Production
Amount £595,682 (GBP)
Funding ID BB/S014454/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2021
 
Description University of Reading Undergraduate Research Opportunities Programme
Amount £1,320 (GBP)
Organisation University of Reading 
Sector Academic/University
Country United Kingdom
Start 06/2016 
End 08/2016
 
Description University of Reading Undergraduate Research Opportunities Programme
Amount £1,320 (GBP)
Organisation University of Reading 
Sector Academic/University
Country United Kingdom
Start 05/2018 
End 08/2018
 
Description Collaboration with Dr Ron Smirnik at the University of Adelaide 
Organisation University of Adelaide
Country Australia 
Sector Academic/University 
PI Contribution Visit to lab to work on analytical possibilities for soil and rhizosphere phosphorus analysis
Collaborator Contribution Analysis of solution 31P samples from selected soil samples.
Impact None as yet
Start Year 2016
 
Description A radio interview on soil nutrients for the Naked Scientist radio program. 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A radio interview was pre-recorded on location at the University of Reading farm. The pre-recorded segment featured in the Naked Scientists radio broadcast on the 15 December 2015 in a section focused on soils entitled "Dishing the Dirt on our Soils". The program was broadcast on BBC Radio Cambs, BBC 5 Live, ABC Radio National (Australia) and is available as a podcast. This has raised the interest in the topic and plans for future contributions were discussed.
Year(s) Of Engagement Activity 2015
URL http://www.thenakedscientists.com/HTML/typo3conf/ext/naksci_podcast/jplayer/player.php?podcast=10012...
 
Description BBC Radio 4 Farming Today Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Following on from press releases around the work on this project and the stand at the Royal Society exhibition, we featured as the main article on the 4th July edition of the BBC Radio 4's Farming Today programme. The interview discussed the importance of phosphorus and the work we are doing with soil bacteria and crops to improve cycling within the rhizosphere. Several members of the public, which heard the interview, subsequently visited the Soils; our buried treasure at the Royal Society Summer exhibition to find out more.
Year(s) Of Engagement Activity 2018
 
Description Inovative Farms Wilts Soil and Root Innovators 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This is a farmer led activity focused on investigating practical and cost effective methods to measure soil biological activity. The activity is being supported by Dr Hammond (University of Reading). We will be looking at the optimum balance of green manures, composts and tillage to encourage a healthy soil food web, within the context of the wide range of soil types found in North Wiltshire and South Gloucestershire. Methods to include root studies, novel assays, and experiences gained in the identification of within-field soil variation. The group are particularly interested in increasing the availability of phosphate in their soils.
Year(s) Of Engagement Activity 2016
URL https://www.innovativefarmers.org/groups/group/?id=b0ae96f9-a4be-e511-80c6-005056ad0bd4
 
Description Nuffield International Triennial Conference 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Over 70 Nuffield Scholars from around the world attended field trial demonstrations at the University of Reading's farm at Sonning. All participants received information about this project as part of the tour, and several requested to be kept informed about future developments.
Year(s) Of Engagement Activity 2017
 
Description Open Farm Sunday 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Approximately 300 members of the public visited our research farm as part of the national Open Farm Sunday initiative. This was intended to provide information about farming and included information on the importance of soils and the work we are doing as part of this project to better understand the soil microbiology and the roles they play in recycling nutrients for crops.
Year(s) Of Engagement Activity 2018
URL https://research.reading.ac.uk/research-blog/in-pictures-open-farm-sunday/
 
Description Podcast about soils and the project 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A podcast was recorded about soil and the role of phosphorus and how the project will address some of the unknowns about how phosphorus is made available to plants by soil microorganisms.
Year(s) Of Engagement Activity 2015
URL https://www.soilsecurity.org/nerc-soil-security-interview/
 
Description Poster presentation at SSP Outcomes Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Work from the project was presented as a poster and within a plenary talk.
Year(s) Of Engagement Activity 2019
URL https://soilsecurity.org/ssp-outcomes-event/
 
Description Presentation at the Soil Security Program Annual Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A presentation outlining the objectives of the project and early findings to the Soil Security Program annual meeting held at Reading.
Year(s) Of Engagement Activity 2015
 
Description Presentation to the South West England Soils Discussion Group (SWESDiG) at Rothamsted North Wyke 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presentation on the objectives of the project was given to the South West England Soils Discussion Group (SWESDiG) at Rothamsted, North Wyke. Approximately, 30-40 people attended.
Year(s) Of Engagement Activity 2015
 
Description Presentation to the UK Brassica Research Community Annual Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation given at the UK Brassica Research Community Annual Meeting at York attended by research scientists, policy makers and industry. Approximately 40 people were present.
Year(s) Of Engagement Activity 2015
 
Description Press release from Innovative Farmers 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A press release was issued by the Innovative Farmers on the progress of the Wiltshire Innovators group working with Dr John Hammond to improve phosphate availability on their soils. The press release was picked up by a number of special interest groups.
Year(s) Of Engagement Activity 2018
URL https://innovativefarmers.org/news/2018/march/05/phosphate-concentration-up-to-20-higher-with-co-com...
 
Description Reading Fringe Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Approximately 50 members of the public attended a debate about the Future of Food, inviting questions about sustainability of production systems and impacts of modern farming on soils.
Year(s) Of Engagement Activity 2019
URL https://merl.reading.ac.uk/event/future-food-symposium/
 
Description Royal Society Summer Exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact As part of the Soil: our buried treasure stand at the Royal Society Summer Exhibition we discussed the importance of soil and the microorganisms that live within it with members of the public and groups of school children that visited the exhibition.
Year(s) Of Engagement Activity 2018
URL https://royalsociety.org/science-events-and-lectures/2018/summer-science-exhibition/exhibits/soil-ou...
 
Description Talk to Secondary School Children on science careers, soil science and phosphate 
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 National Science Week, I gave a presentation and engagement activity with 30 secondary school children form Chiltern Edge Secondary School, Sonning Common. The activity included aspects on a career on science and our research into soil bacteria and phosphate uptake by plants. The presentation included online quizzes and and question and answer session, generating questions about soil bacteria and the need to conduct research into food production systems.
Year(s) Of Engagement Activity 2016
 
Description Used method for part of a workshop on metagenomics network sponsored by BBSRC 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Training in methods needed for metagenomics and this included how analysis of habitat or sample total DNA, RNA and protein can be analysed for community functional studies. The primary focus was on bacteria and fungi but as proteins were analysed data was presented on total sample components including proteins from plants and animals. Purpose was to inform participants of the benefits of protein analysis and pitfalls when trying to identify proteins. Many attendees were motivated to try these new approaches.
Year(s) Of Engagement Activity 2009,2015,2016
URL http://www.metagenomics.uk
 
Description Workshop on Organic Phosphorus in the Environment: Solutions for Phosphorus Security 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We convened more than 100 international experts in organic P (Po) and asked them to consider the importance and benefits of Po in organisms and the environment and to identify priorities for research. It was highlighted that Po is central to a number of global issues such as food security, agricultural sustainability, environmental pollution, climate change mitigation and natural ecosystem services and biodiversity. Priorities were suggested including: the need for more integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of Po in natural and managed systems; the role of microorganisms in controlling Po cycles; and the implications of the emerging science. Each priority is discussed and we conclude with a statement of intent for the Po research community.
Year(s) Of Engagement Activity 2016