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Article ; Online: The UK Crop Microbiome Cryobank

Matthew J. Ryan / Tim H. Mauchline / Jacob G. Malone / Susan Jones / Catriona M. A. Thompson / J. Miguel Bonnin / Helen Stewart / Payton T. O. Yau / Rodrigo G. Taketani / Ian M. Clark / Nicola Holden

CABI Agriculture and Bioscience, Vol 4, Iss 1, Pp 1-

a utility and model for supporting Phytobiomes research

2023 Volume 6

Abstract: Abstract Plant microbiomes are the microbial communities essential to the functioning of the phytobiome—the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to ... ...

Abstract	Abstract Plant microbiomes are the microbial communities essential to the functioning of the phytobiome—the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems.
Keywords	Rhizosphere ; Microbiota ; Biobank ; Metagenome ; Microbiome ; Soil health ; Agriculture (General) ; S1-972
Subject code	571
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness

Lilian S. Abreu Soares Costa / Mírian Rabelo de Faria / Josiane Barros Chiaramonte / Lucas W. Mendes / Edis Sepo / Mattias de Hollander / José Maurício Cunha Fernandes / Víctor J. Carrión / Wagner Bettiol / Tim H. Mauchline / Jos M. Raaijmakers / Rodrigo Mendes

Environmental Microbiome, Vol 18, Iss 1, Pp 1-

2023 Volume 15

Abstract: Abstract Background Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere ... ...

Abstract	Abstract Background Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. Results The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. Conclusion Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.
Keywords	Soilborne pathogens ; Plant disease suppression ; Soil microbiome ; Bacterial communities ; Fungal communities ; Environmental sciences ; GE1-350 ; Microbiology ; QR1-502
Subject code	630
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances

Rodrigo G. Taketani / Marta A. Moitinho / Tim H. Mauchline / Itamar S. Melo

PeerJ, Vol 6, p e

2018 Volume 5710

Abstract: Background Mangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is ... ...

Abstract	Background Mangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is produced by its vegetation and is decomposed in root associated sediment. This process involves a tight interaction between microbial populations, litter chemical composition, and environmental parameters. Here, we study the complex interactions found during litter decomposition in mangroves by applying network analysis to metagenomic data. Methods Leaves of three species of mangrove trees typically found in the southeast of Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were collected in separate litter bags and left on three different mangroves for 60 days. These leaves were subsequently used for metagenome sequencing using Ion Torrent technology. Sequences were annotated in MG-RAST and used for network construction using MENAp. Results The most common phyla were Proteobacteria (classes Gamma and Alphaproteobacteria) followed by Firmicutes (Clostridia and Bacilli). The most abundant protein clusters were associated with the metabolism of carbohydrates, amino acids, and proteins. Non-metric multidimensional scaling of the metagenomic data indicated that substrate (i.e., tree species) did not significantly select for a specific community. Both networks exhibited scale-free characteristics and small world structure due to the low mean shortest path length and high average clustering coefficient. These networks also had a low number of hub nodes most of which were module hubs. Discussion This study demonstrates that under different environmental pressures (i.e., plant species or mangrove location) the microbial community associated with the decaying material forms a robust and stable network.
Keywords	Metagenome ; Network analysis ; Mangrove ; Litter decomposition ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2018-10-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Exploitation of endophytes for sustainable agricultural intensification

Le Cocq, Kate / Sarah J. Gurr / Penny R. Hirsch / Tim H. Mauchline

Molecular plant pathology. 2017 Apr., v. 18, no. 3

2017

Abstract: Intensive agriculture, which depends on unsustainable levels of agrochemical inputs, is environmentally harmful, and the expansion of these practices to meet future needs is not economically feasible. Other options should be considered to meet the global ...

Abstract	Intensive agriculture, which depends on unsustainable levels of agrochemical inputs, is environmentally harmful, and the expansion of these practices to meet future needs is not economically feasible. Other options should be considered to meet the global food security challenge. The plant microbiome has been linked to improved plant productivity and, in this microreview, we consider the endosphere â a subdivision of the plant microbiome. We suggest a new definition of microbial endophyte status, the need for synergy between fungal and bacterial endophyte research efforts, as well as potential strategies for endophyte application to agricultural systems.
Keywords	agrochemicals ; economic feasibility ; endophytes ; food security ; fungi ; microbiome ; sustainable agricultural intensification
Language	English
Dates of publication	2017-04
Size	p. 469-473.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	2020755-4
ISSN	1364-3703 ; 1464-6722
ISSN (online)	1364-3703
ISSN	1464-6722
DOI	10.1111/mpp.12483
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Wheat dwarfing influences selection of the rhizosphere microbiome

Vanessa N. Kavamura / Rebekah J. Robinson / David Hughes / Ian Clark / Maike Rossmann / Itamar Soares de Melo / Penny R. Hirsch / Rodrigo Mendes / Tim H. Mauchline

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 11

Abstract: Abstract The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant ... ...

Abstract	Abstract The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of Plant Growth Promoting Bacteria on the Growth of Wheat Seedlings Subjected to Phosphate Starvation

Mariagrazia P. Cataldi / Sigrid Heuer / Tim H. Mauchline / Mark D. Wilkinson / Emily Masters-Clark / Nilde A. Di Benedetto / Maria Rosaria Corbo / Zina Flagella

Agronomy, Vol 10, Iss 978, p

2020 Volume 978

Abstract: Certain phosphorous solubilizing (PSB) and phosphorous mineralizing (PMB) bacteria may improve plant growth by improving nutrient availability. The aim of this work was to evaluate the effect of inoculation with two Bacillus spp. strains, 12A and 25A, on ...

Abstract	Certain phosphorous solubilizing (PSB) and phosphorous mineralizing (PMB) bacteria may improve plant growth by improving nutrient availability. The aim of this work was to evaluate the effect of inoculation with two Bacillus spp. strains, 12A and 25A, on wheat seedlings growth. To this aim, a durum and a bread wheat genotype were grown under controlled conditions in a low P compost medium to evaluate: (i) the effect of the bacterial isolates on plant growth and root system architecture; (ii) the expression of two key genes indicative of the P-starvation response and phosphate (Pi) uptake, TaIPS1 and TaPHT1.6-B1. The results showed that 12A Bacillus sp. significantly increased root length, surface area and biomass. Furthermore, an enhanced shoot dry weight and P content were observed. This might be explained by the capacity of strain 12A to produce indole-3-acetic acid (IAA) in addition to P mineralizing and P solubilizing capability. No effect on plant growth was observed for 25A strain. The semi-quantitative gene expression analysis showed an overall lower expression of TaIPS1 in the inoculated plants and highest expression of TaPHT1.6-B1 in 12A inoculated plants. This suggests that Pi-responsive genes might be useful molecular indicators for the effectiveness of PSB and PMB.
Keywords	PGPB ; wheat ; P-solubilizing bacteria ; P-mineralizing bacteria ; P-deficiency ; IAA ; Agriculture ; S
Subject code	580
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

Sally Hilton / Emma Picot / Susanne Schreiter / David Bass / Keith Norman / Anna E. Oliver / Jonathan D. Moore / Tim H. Mauchline / Peter R. Mills / Graham R. Teakle / Ian M. Clark / Penny R. Hirsch / Christopher J. van der Gast / Gary D. Bending

Microbiome, Vol 9, Iss 1, Pp 1-

2021 Volume 15

Abstract: Abstract Background The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between ... ...

Abstract	Abstract Background The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK’s third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers’ fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host. Results We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and ...
Keywords	Oilseed rape ; Microbiome ; Rhizosphere ; Roots ; Landscape ; Yield decline ; Microbial ecology ; QR100-130
Subject code	630
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability

Robinson, Rebekah J / Bart A. Fraaije / Ian M. Clark / Penny R. Hirsch / Robert W. Jackson / Tim H. Mauchline

Plant and soil. 2016 Aug., v. 405, no. 1-2

2016

Abstract: AIMS: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). METHODS: Endophytes were isolated from wheat grown under six fertiliser conditions in the ... ...

Abstract	AIMS: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). METHODS: Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues. RESULTS: Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants. CONCLUSIONS: Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture.
Keywords	Actinobacteria ; bacterial communities ; community structure ; developmental stages ; endophytes ; fertilizer application ; fertilizers ; Firmicutes ; isolation techniques ; leaves ; nutrient availability ; plant growth ; plant tissues ; Proteobacteria ; roots ; soil ; soil nutrients ; Triticum aestivum ; winter wheat ; United Kingdom
Language	English
Dates of publication	2016-08
Size	p. 381-396.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	208908-7
ISSN	1573-5036 ; 0032-079X
ISSN (online)	1573-5036
ISSN	0032-079X
DOI	10.1007/s11104-015-2495-4
Database	NAL-Catalogue (AGRICOLA)

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Article: Is there sufficient Ensifer and Rhizobium species diversity in UK farmland soils to support red clover (Trifolium pratense), white clover (T. repens), lucerne (Medicago sativa) and black medic (M. lupulina)?

Roberts, Rachel / Hannah E. Jones / Liz J. Shaw / Penny R. Hirsch / Robert W. Jackson / Thomas F. Döring / Tim H. Mauchline

Applied soil ecology. 2017 Nov., v. 120

2017

Abstract: Rhizobia play important roles in agriculture owing to their ability to fix nitrogen through a symbiosis with legumes. The specificity of rhizobia-legume associations means that underused legume species may depend on seed inoculation with their rhizobial ... ...

Abstract	Rhizobia play important roles in agriculture owing to their ability to fix nitrogen through a symbiosis with legumes. The specificity of rhizobia-legume associations means that underused legume species may depend on seed inoculation with their rhizobial partners. For black medic (Medicago lupulina) and lucerne (Medicago sativa) little is known about the natural prevalence of their rhizobial partner Ensifer meliloti in UK soils, so that the need for inoculating them is unclear. We analysed the site-dependence of rhizobial seed inoculation effects on the subsequent ability of rhizobial communities to form symbioses with four legume species (Medicago lupulina, M. sativa, Trifolium repens and T. pratense). At ten organic farms across the UK, a species-diverse legume based mixture (LBM) which included these four species was grown. The LBM seed was inoculated with a mix of commercial inocula specific for clover and lucerne. At each site, soil from the LBM treatment was compared to the soil sampled prior to the sowing of the LBM (the control). From each site and each of the two treatments, a suspension of soils was applied to seedlings of the four legume species and grown in axenic conditions for six weeks. Root nodules were counted and their rhizobia isolated. PCR and sequencing of a fragment of the gyrB gene from rhizobial isolates allowed identification of strains. The number of nodules on each of the four legume species was significantly increased when inoculated with soil from the LBM treatment compared to the control. Both the proportion of plants forming nodules and the number of nodules formed varied significantly by site, with sites significantly affecting the Medicago species but not the Trifolium species. These differences in nodulation were broadly reflected in plant biomass where site and treatment interacted; at some sites there was a significant advantage from inoculation with the commercial inoculum but not at others. In particular, this study has demonstrated the commercial merit of inoculation of lucerne with compatible rhizobia.
Keywords	alfalfa ; Ensifer meliloti ; genes ; inoculum ; Medicago lupulina ; Medicago sativa ; nodulation ; phytomass ; polymerase chain reaction ; Rhizobium ; root nodules ; seed inoculation ; seedlings ; sequence analysis ; soil ; sowing ; species diversity ; symbiosis ; Trifolium pratense ; Trifolium repens ; United Kingdom
Language	English
Dates of publication	2017-11
Size	p. 35-43.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1196758-4
ISSN	0929-1393
ISSN	0929-1393
DOI	10.1016/j.apsoil.2017.06.030
Database	NAL-Catalogue (AGRICOLA)

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Article: The genome of Rhizobium leguminosarum has recognizable core and accessory components

Young, J Peter W / Alison K East / Andrew RJ Curson / Andrew WB Johnston / Ann Cronin / Audrey Fraser / Carol Churcher / Claire Arrowsmith / Ester Rabbinowitsch / Halina Norbertczak / Heidi Hauser / Inna Cherevach / Jonathan D Todd / Julian Parkhill / Karen Mungall / Katherine H Hull / Kay Clarke / Kay Jagels / Lisa C Crossman /

Mandy Sanders / Margaret Wexler / Mark Simmonds / Michael A Quail / Nicholas R Thomson / Paul Davis / Philip S Poole / Sally Whitehead / Sharon Moule / Tim H Mauchline / Tracey Chillingworth / Zahra Hance / Zara F Ghazoui

Genome biology. 2006 Feb., v. 7, no. 4

2006

Abstract: BACKGROUND: Rhizobium leguminosarum is an Î±-proteobacterial Nâ-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow ... ...

Abstract	BACKGROUND: Rhizobium leguminosarum is an Î±-proteobacterial Nâ-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. RESULTS: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. CONCLUSION: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.
Keywords	Agrobacterium radiobacter ; chromosomes ; edaphic factors ; Ensifer meliloti ; legumes ; Mesorhizobium loti ; operon ; phylogeny ; plasmids ; Rhizobium leguminosarum ; ribosomal RNA ; symbionts ; transfer RNA
Language	English
Dates of publication	2006-02
Size	p. 1302.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2006-7-4-r34
Database	NAL-Catalogue (AGRICOLA)

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