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

Lead Research Organisation: University of Warwick
Department Name: School of Life Sciences

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.
 
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. Bacteroidetes, primarily from the genus Flavobacterium, have recently been shown to be abundant members of the plant microbiome, but their general ecological role and potential to mobilise P in the rhizosphere remains very poorly characterised. Here, we sought to determine the P mobilisation potential of Flavobacterium strains isolated from the rhizosphere of Oil Seed Rape. In contrast to other abundant rhizosphere bacteria such as Pseudomonas, all Flavobacterium strains exhibited constitutive phosphatase activity independent of external phosphate (Pi) concentrations. Interestingly, a combination of exoproteomic analysis and classical molecular microbiology techniques revealed that Flavobacterium have a complex and largely unique repertoire of mechanisms to mobilise and acquire Pi. This includes the expression of novel, as yet unidentified, phosphatases, and numerous proteins of unknown function. We also discovered that Flavobacterium expresses various SusCD-like transporters, whose role is usually associated with specialised carbon acquisition, in response to Pi-starvation. Furthermore, the genes encoding these unusual Pi-responsive proteins were enriched in plant-associated Flavobacterium strains suggesting that these mechanisms represent niche-adaptive strategies for overcoming P scarcity in this genus. 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.
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

 
Description Potential for economic exploitation of biodiversity in the rhizosphere. 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 groups 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,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
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 04/2019 
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 06/2018 
End 08/2018
 
Title Metaexoproteomics 
Description New way to extract proteins from soil involving a series of extractions steps 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact Acquired new funding from BBSRC 
 
Title Novel enzymes 
Description Novel enzyme assay and enzyme activity relating to phosphate solubilisation 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2017 
Provided To Others? No  
Impact Important for commercial exploitation of bacteria in the rhizosphere of plant for improved supply of inorganic phosphate 
 
Description Korean partnering on metagenomics and microbiome analysis 
Organisation Chung-Ang University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution Understanding the risk posed by the widespread dissemination of antimicrobial resistant bacteria (AMRB) and pathogenic variants (AMRP) in the environment depends on persistence of the bacteria and the resistance genes (ARGs). ARGs can move into indigenous environmental bacteria but risks of infection will be reduced or removed. What has been observed is the high diversity of resistance genotypes in waste water polluted environments coupled with the expansive diversity of the environmental resistome and so the extensive mixing of human and animal wastes with environmental bacteria particularly in the presence of antibiotics could produce AMRP capable of extensive resistance phenotypes. Uncertainty exists over the longevity and activity of AMRP in the environment outside of their hosts and to what extent they may participate in gene exchange so current work in both the Cha and Wellington groups is focused on this aspect and finding new ways of monitoring AMRP and their activities. Thus we identified two major challenges in understanding risk in environmental exposure to AMRP which relates to viability and ARG acquisition. In the form of two workshops and exchange of personnel the Wellington group members Dr Chiara Borsetto and Dr Robert James demonstrated their methods for using long read sequencing to gain an improved analysis of resistance genes in the environmental resistome, Chiara Borsetto talked about using mesocosms to establish if sublethal levels of antibiotics in the environment select for resistance phenotypes or are simply collocated with already resistant bacteria in waste water effluent. By characterizing the host genome it is possible to establish if the resistant bacteria are human adapted or environmental bacteria. From our work on river flumes used to model impact of waste water effluent in UK rivers it appears that sublethal antibiotic has a distinct impact on the prevalence of the relevant resistance genes.
Collaborator Contribution Professor Chang-Jun Cha's group have expertise in bioinformatics and hold a resistance gene database in addition to having a WaferGen SmartChip machine and the arrays which can detect very sensitively over 300 types of resistance genes using PCR conducted in hundreds of minicells.We were given access to this machine and were able to compare results and also establish diversity and new combinations of various mobile genetic elements. We aim to write a position paper comparing our results on anthropogenic impacts on Thames riverine microbiome compared with the study they are conducting on the Han river in South Korea. They provided access to databases and SmartChips plus shared sequences and databases.
Impact Two papers are in progress and one submitted currently: Submission no: ENVINT_2019_218, Submission title: A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria Corresponding author: Professor Chang-Jun Cha, Listed co-author(s): Dr Kihyun Lee, Dr Cung Nawl Thawng, Professor Elizabeth Wellington, Dr Dae-Wi Kim.
Start Year 2018
 
Description Presentation to MRC sponsored scientists and panel members 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Gave a presentation entitled "AMR in Soil" MRC workshop Antimicrobial Resistance Cross Council Initiative, London July 4-5th.
Year(s) Of Engagement Activity 2017
 
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 Micrbiome Stakeholders meeting, Manchester 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Meeting to discuss the current status of Micrbiome work in the UK. Discussing future directions with industrial partners, funders, researchers and end users.
Year(s) Of Engagement Activity 2017
 
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 Oral presentation at Micro Soc Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Focused meeting between researchers and policy makers discussing microbial tools for sustainable agriculture. Focus on phosphorus cycling management.
Year(s) Of Engagement Activity 2017
 
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 International meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave presentation entitled "Metagenomics and culturomics: The environmental resistome" FEMS 2017 7th Congress of European Microbiologists Valencia Spain July 9-13th.
Year(s) Of Engagement Activity 2017
 
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 Public Science Evening 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation given at an evening event on the Microbiome event to inform the public about the importance of bacteria in the human gut, in the soil and in the bioremediation of polluted environments.
Year(s) Of Engagement Activity 2017
 
Description Public science evening 
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 At the public science evening "The microbes on us and around us: We can't see them but can't live without them" hold at the university, the general public was introduced to the issue of AMR dissemination in the environment through oral and poster presentations followed by discussion in small groups with member of the team working on AMR. The Department reported an increased interest and understanding in the related subject area.
Year(s) Of Engagement Activity 2017
 
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...