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Dive into the research topics where Tim H. Mauchline is active.

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Featured researches published by Tim H. Mauchline.


Genome Biology | 2006

The genome of Rhizobium leguminosarum has recognizable core and accessory components

J. Peter W. Young; Lisa Crossman; Andrew W. B. Johnston; Nicholas R. Thomson; Zara F. Ghazoui; Katherine H Hull; Margaret Wexler; Andrew R. J. Curson; Jonathan D. Todd; Philip S. Poole; Tim H. Mauchline; Alison K. East; Michael A. Quail; Carol Churcher; Claire Arrowsmith; Inna Cherevach; Tracey Chillingworth; Kay Clarke; Ann Cronin; Paul Davis; Audrey Fraser; Zahra Hance; Heidi Hauser; Kay Jagels; Sharon Moule; Karen Mungall; Halina Norbertczak; Ester Rabbinowitsch; Mandy Sanders; Mark Simmonds

BackgroundRhizobium leguminosarum is an α-proteobacterial N2-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.ResultsThe 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.ConclusionOverall, 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.


Proceedings of the National Academy of Sciences of the United States of America | 2006

Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome

Tim H. Mauchline; J.E. Fowler; Alison K. East; A.L. Sartor; R. Zaheer; Arthur H.F. Hosie; Philip S. Poole; Turlough M. Finan

The number of solute-binding protein-dependent transporters in rhizobia is dramatically increased compared with the majority of other bacteria so far sequenced. This increase may be due to the high affinity of solute-binding proteins for solutes, permitting the acquisition of a broad range of growth-limiting nutrients from soil and the rhizosphere. The transcriptional induction of these transporters was studied by creating a suite of plasmid and integrated fusions to nearly all ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) transporters of Sinorhizobium meliloti. In total, specific inducers were identified for 76 transport systems, amounting to ≈47% of the ABC uptake systems and 53% of the TRAP transporters in S. meliloti. Of these transport systems, 64 are previously uncharacterized in Rhizobia and 24 were induced by solutes not known to be transported by ABC- or TRAP-uptake systems in any organism. This study provides a global expression map of one of the largest transporter families (transportome) and an invaluable tool to both understand their solute specificity and the relationships between members of large paralogous families.


Applied and Environmental Microbiology | 2002

Quantification in Soil and the Rhizosphere of the Nematophagous Fungus Verticillium chlamydosporium by Competitive PCR and Comparison with Selective Plating

Tim H. Mauchline; Brian R. Kerry; Penny R. Hirsch

ABSTRACT A competitive PCR (cPCR) assay was developed to quantify the nematophagous fungus Verticillium chlamydosporium in soil. A γ-irradiated soil was seeded with different numbers of chlamydospores from V. chlamydosporium isolate 10, and samples were obtained at time intervals of up to 8 weeks. Samples were analyzed by cPCR and by plating onto a semiselective medium. The results suggested that saprophytic V. chlamydosporium growth did occur in soil and that the two methods detected different phases of growth. The first stage of growth, DNA replication, was demonstrated by the rapid increase in cPCR estimates, and the presumed carrying capacity (PCC) of the soil was reached after only 1 week of incubation. The second stage, an increase in fungal propagules presumably due to cell division, sporulation, and hyphal fragmentation, was indicated by a less rapid increase in CFU, and 3 weeks was required to reach the PCC. Experiments with field soil revealed that saprophytic fungal growth was limited, presumably due to competition from the indigenous soil microflora, and that the PCR results were less variable than the equivalent plate count results. In addition, the limit of detection of V. chlamydosporium in field soil was lower than that in γ-irradiated soil, suggesting that there was a background population of the fungus in the field, although the level was below the limit of detection. Tomatoes were infected with the root knot nematode (RKN) or the potato cyst nematode (PCN) along with a PCN-derived isolate of the fungus (V. chlamydosporium isolate Jersey). Increases in fungal growth were observed in the rhizosphere of PCN-infested plants but not in the rhizosphere of RKN-infested plants after 14 weeks using cPCR. In this paper we describe for the first time PCR-based quantification of a fungal biological control agent for nematodes in soil and the rhizosphere, and we provide evidence for nematode host specificity that is highly relevant to the biological control efficacy of this fungus.


Fungal Biology | 2000

Detection of the nematophagous fungus Verticillium chlamydosporium in nematode-infested plant roots using PCR

Penny R. Hirsch; Tim H. Mauchline; Tom A. Mendum; Brian R. Kerry

PCR-based methods to detect Verticillium chlamydosporium on infected plant roots were developed. Arbitrary ERIC primers and those based on rRNA genes, to identify fungi grown in pure culture, were unsuitable for DNA extracted from nematode-infested roots, because of interference by plant and nematode DNA. A novel method utilizing specific primers designed from an amplified and cloned fragment of the V. chlamydosporium β-tubulin gene was developed. Although it could not discriminate between different isolates of V. chlamydosporium, one primer set could identify the fungus on tomato roots infested with root-knot nematodes. The V. chlamydosporium β-tubulin sequence data showed close homology to sequences from plant endophytic Acremonium and Epichloe species and the saprotrophic Trichoderma viride.


Fungal Biology | 2003

PCR-based DNA fingerprinting indicates host-related genetic variation in the nematophagous fungus Pochonia chlamydosporia

C. Oliver Morton; Tim H. Mauchline; R. Kerry; Penny R. Hirsch

The mitosporic fungus Pochonia chlamydosporia is a potential biocontrol agent for cyst (Heterodera spp. and Globodera spp.) and root knot (Meloidogyne spp.) nematodes, which are important agricultural plant pests. 54 isolates from diverse geographical regions and several nematode hosts were used in this study. Genetic variation was examined using enterobacterial repetitive intergenic consensus (ERIC) primed PCR and sequences from the internal transcribed spacer (ITS) rRNA region. ERIC PCR yielded 35 scorable binary characters from all the fungi tested and cluster analysis of the data showed that isolates from cyst nematodes were more genetically variable than those from root knot nematodes. The ITS regions were highly conserved, the only significant difference being an extra thymidine in isolates from Meloidogyne spp. Assays with nematode eggs indicated that isolates differ in their ability to infect different nematode genera. The results indicate host related variation in P. chlamydosporia. This finding has significant implications for the application of P. chlamydosporia as a biocontrol agent.


Plant and Soil | 2001

Methods for studying the nematophagous fungus Verticillium chlamydosporium in the root environment

Penny R. Hirsch; S. D. Atkins; Tim H. Mauchline; C. Oliver Morton; Keith Davies; Brian R. Kerry

In order to exploit fully the biocontrol potential of the nematophagous fungus Verticillium chlamydosporium, it is important to understand the ecology of the fungus in soil, and interactions with both plant and nematode hosts. Several approaches for studying the fungus in soil and the root environment are compared. These include a semi-selective medium for V. chlamydosporium, PCR primers specific for the fungal β-tubulin gene, and monoclonal antibodies. In addition to providing a target for species-specific primers, the β-tubulin gene is implicated in resistance to the fungicides used in the semi-selective medium, and the genetic basis for this is investigated. Culture and PCR-based methods were used to screen for the presence of the fungus in field soils known to have been suppressive to cereal cyst nematode and that contained V. chlamydosporium populations. Monoclonal antibodies specific for either hyphae or conidia of the fungus were obtained, and their application as a tool for visualising the infection process on the root was explored.


Fungal Biology | 2004

The biocontrol fungus Pochonia chlamydosporia shows nematode host preference at the infraspecific level

Tim H. Mauchline; Brian R. Kerry; Penny R. Hirsch

A RAPD-PCR assay was developed and used to test for competitive variability in growth of the nematode biological control fungus Pochonia chlamydosporia. Saprophytic competence in soil with or without tomato plants was examined in three isolates of the fungus: RES 280 (J), originally isolated from potato cyst nematode (PCN) cysts; RES 200 (I) and RES 279 (S), both originally isolated from root knot nematode (RKN) eggs. Viable counts taken at 70 d indicated that I was the best saprophyte followed by S, with J the poorest. RAPD-PCR analysis of colonies from mixed treatments revealed that there was a cumulative effect of adding isolates to the system. This suggested that the isolates did not interact and that they may occupy separate niches in soil and the rhizosphere. To investigate parasitic ability, soils were seeded with two isolates of the fungus: J and S, singly or in combination. Tomato or potato plants were grown in these soils: free of nematodes, or inoculated with PCN or RKN, and incubated for 77 d. The abundance of the PCN isolate J in PCN cysts was significantly greater than that of the RKN isolate S but in RKN egg masses, S was significantly more abundant than J. RAPD-PCR analysis of colonies from mixed treatments confirmed that J was more abundant than S in PCN cysts whereas the converse was observed on RKN egg masses. This substantiates the phenomenon of nematode host preference at the infraspecific level of P. chlamydosporia and highlights its relevance for biological control of plant parasitic nematodes.


Fems Microbiology Letters | 2008

In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere

Michelle Barr; Alison K. East; Mary Leonard; Tim H. Mauchline; Philip S. Poole

IVET was used to identify genes that are specifically expressed in the rhizosphere of the pea-nodulating bacterium Rhizobium leguminosarum A34. A library of R. leguminosarum A34 cloned in the integration vector pIE1, with inserts upstream of a promoter-less purN:gfp:gusA, was conjugated into purN host RU2249 and recombined into the genome. After removal of colonies that expressed the reporter genes of the vector under laboratory conditions, the library was inoculated into a nonsterile pea rhizosphere. The key result is that 29 rhizosphere-induced loci were identified. Sequence analysis of these clones showed that a wide variety of R. leguminosarum A34 genes are expressed specifically in the rhizosphere including those encoding proteins involved in environmental sensing, control of gene expression, metabolic reactions and membrane transport. These genes are likely to be important for survival and colonization of the pea rhizosphere.


Advances in Applied Microbiology | 2008

Biosensors for ligand detection.

Alison K. East; Tim H. Mauchline; Philip S. Poole

Publisher Summary Biosensors are such tools, which couple the ability of a biological sensor to precisely distinguish between inducer ligands, with a robust abiotic method of detection. The term biosensor can be used to describe devices for monitoring, recording, and transmitting information regarding physiological changes in living organisms. The most widely used are cellular and molecular biosensors. Cellular biosensors use reporter genes or proteins inside a cell, while molecular biosensors rely on a purified molecule, such as a protein. However, these definitions can become blurred as some molecular biosensors can be expressed inside a cell to generate a cellular biosensor. Another way of considering this is that cellular biosensors can be either induction biosensors or molecular biosensors, and one shall consider both these subclasses in this chapter. Induction biosensors rely on a ligand being detected by binding to a protein that induces expression of a reporter gene. The reporter gene codes for a protein that has an easily quantifiable activity, often relying on enzymatic and/or optical detection.


Pest Management Science | 2003

Development of a new management strategy for the control of root‐knot nematodes (Meloidogyne spp) in organic vegetable production

S. D. Atkins; L Hidalgo-Díaz; Helen Kalisz; Tim H. Mauchline; Penny R. Hirsch; Brian R. Kerry

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