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Author

Kate Le Cocq

Other affiliations: University of Exeter
Bio: Kate Le Cocq is an academic researcher from Rothamsted Research. The author has contributed to research in topics: Agronomy & Cropping system. The author has an hindex of 6, co-authored 14 publications receiving 236 citations. Previous affiliations of Kate Le Cocq include University of Exeter.

Papers
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Journal ArticleDOI
TL;DR: A new definition of microbial endophyte status is suggested, the need for synergy between fungal and bacterialendophyte research efforts, as well as potential strategies for endophytes application to agricultural systems are suggested.
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 – 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.

122 citations

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TL;DR: It is shown that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12.
Abstract: Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-β-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits.

84 citations

Journal ArticleDOI
TL;DR: The hypothesis that Sclerotinia biocontrol is mediated by the synthesis and secretion of antifungal compounds and that GD12's unique reservoir of uncharacterized genes is actively recruited during the effective biological control of a plurivorous plant pathogen is supported.
Abstract: The free-living soil fungus Trichoderma hamatum strain GD12 is notable amongst Trichoderma strains in both controlling plant diseases and stimulating plant growth, a property enhanced during its antagonistic interactions with pathogens in soil. These attributes, alongside its markedly expanded genome and proteome compared with other biocontrol and plant growth-promoting Trichoderma strains, imply a rich potential for sustainable alternatives to synthetic pesticides and fertilizers for the control of plant disease and for increasing yields. The purpose of this study was to investigate the transcriptional responses of GD12 underpinning its biocontrol and plant growth promotion capabilities during antagonistic interactions with the pathogen Sclerotinia sclerotiorum in soil. Using an extensive mRNA-seq study capturing different time points during the pathogen-antagonist interaction in soil, we show that dynamic and biphasic signatures in the GD12 transcriptome underpin its biocontrol and plant (lettuce) growth-promoting activities. Functional predictions of differentially expressed genes demonstrate the enrichment of transcripts encoding proteins involved in transportation and oxidation-reduction reactions during both processes and an over-representation of siderophores. We identify a biphasic response during biocontrol characterized by a significant induction of transcripts encoding small-secreted cysteine-rich proteins, secondary metabolite-producing gene clusters and genes unique to GD12. These data support the hypothesis that Sclerotinia biocontrol is mediated by the synthesis and secretion of antifungal compounds and that GD12's unique reservoir of uncharacterized genes is actively recruited during the effective biological control of a plurivorous plant pathogen.

34 citations

Journal ArticleDOI
TL;DR: The potential for soils to produce nitrous oxide (N2O) is impacted by past moisture conditions; however, the extent of this impact is not fully understood as mentioned in this paper, and there is still a large uncertainty regarding how microbial population structure, relative gene abundances and gene expression profiles change according to antecedent dry/wet cycles.
Abstract: The potential for soils to produce nitrous oxide (N2O) is impacted by past moisture conditions; however, the extent of this impact is not fully understood We conducted the first review of this, using two literature searches and a meta-analysis We found 36 studies out of a possible 735 that described experiments where soil moisture conditions had been controlled, such that the impact of antecedent moisture levels could be separated from contemporary moisture levels and attributed to N2O emissions Of those studies, 14 (130 data points) used the appropriate experimental design and presented suitable data that could be standardized for the meta-analysis We found that the degree to which the soil was rewetted and the water filled pore space (WFPS) the soil was brought to were significant explanatory variables (p = < 00001) The larger the difference between the dry and wet states of the soil and the higher the WFPS of the soil after rewetting, the larger the hot moment, with an exponential increase once the soil is anaerobic Substrate availability and fertiliser quantity and type were also important controls on the amount of N2O emitted during the hot moment (p = < 00001) However, controls with a constant WFPS can have the same anaerobicity and substrate concentrations, yet much lower emissions, so we suggest that it is the bioavailability of and how the substrates are utilized by the microbial community, and thus how they are primed by the drought, that is the main causal mechanism Unfortunately, there is still a large uncertainty regarding how microbial population structure, relative gene abundances and gene expression profiles change according to antecedent dry/wet cycles We suggest several areas of improvement for future studies and the development of drought-impact curves These would show the relationship between N2O emissions and the length of drought (we found no studies that have investigated this) and N2O emissions and the severity of drought (eg the difference between 20% and 40% WFPS)

29 citations

Journal ArticleDOI
TL;DR: It is demonstrated how the mAbs can be used in combination with a semiselective isolation procedure to track these opportunistic pathogens in environmental samples containing mixed populations of human pathogenic fungi.
Abstract: This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1111/1462-2920.12470

23 citations


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TL;DR: A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria.
Abstract: One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only ‘passengers’ with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as ‘gatekeepers’ to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage ‘priming’ plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

423 citations

Journal ArticleDOI
TL;DR: The use of Trichoderma-based biological products will have an important role in agricultural production of the future, in light of changing worldwide perspectives by consumers and governing bodies.
Abstract: Governing bodies throughout the world, particularly in Europe, are now implementing legislative mandates with the objective of decreasing dependence on pesticides in agriculture to increase consumer and environmental safety. In order to reduce the risks associated with pesticide applications and reduce dependency on their use, Directives will promote low pesticide-input by implementing integrated pest management (IPM), and provide the means to establish the necessary conditions and measures to employ these practices, as well as to ensure security of commercial products. One approach includes the use of biological control agents and their products as alternatives to synthetic agro-chemicals. Trichoderma spp. are widely studied fungi and are among the most commonly used microbial biological control agents (MBCAs) in agriculture. They are presently marketed as bio-pesticides, biofertilizers, growth enhancers and stimulants of natural resistance. The efficacy of this fungus can be attributed to their ability to protect plants, enhance vegetative growth and contain pathogen populations under numerous agricultural conditions, as well as to act as soil amendments/inoculants for improvement of nutrient ability, decomposition and biodegradation. The living fungal spores (active substance) are incorporated in various formulations, both traditional and innovative, for applications as foliar sprays, pre-planting applications to seed or propagation material, post-pruning treatments, incorporation in the soil during seeding or transplant, watering by irrigation or applied as a root drench or dip. Trichoderma-based preparations are marketed worldwide and used for crop protection of various plant pathogens or increase the plant growth and productivity in diverse cultivated environments such as fields, greenhouses, nurseries; in the production of a variety of horticultural, fruits, trees and ornamental crops. A survey was conducted of Trichoderma-containing products found on the international market to obtain an overall perspective of the: 1) geographical distribution, 2) product composition and identity of Trichoderma species selected, 3) contents combined with Trichoderma in the products - other microbial species or substances in the mix, 4) number of products available globally and geographically, 5) number of products registered or having use specifications, 6) product formulations and applications, 7) manufacturer claims - target use, target pests, product type and effects of applications. The largest distribution of Trichoderma bioproducts is found in Asia, succeeded by Europe, South- Central America and North America. The majority of the labels indicated fungicidal properties, but only 38% of the marketed merchandise are registered. Ten Trichoderma species are specifically indicated, but many labels indicate a generic Trichoderma sp. or spp. mix in the list of ingredients. The most common formulation is a wettable powder, followed by granules. Generally, Trichoderma are applied to the seed or propagation material at the time of planting, then the secondary use is during plant development. On the whole, the target use is for the control of soilborne fungal pathogens such as Rhizoctonia, Pythium and Sclerotinia, and a few foliar pathogens such as Botrytis and Alternaria; whereas the minor use indication is for plant growth promotion. The use of Trichoderma-based biological products will have an important role in agricultural production of the future, in light of changing worldwide perspectives by consumers and governing bodies.

410 citations

Journal ArticleDOI
TL;DR: Recent proteomic and genetic data suggest that Trichoderma activates the mitogen activated protein kinase 6, transcription factors and DNA processing proteins, which represent promising targets toward formulation of more efficient products.

293 citations

Journal ArticleDOI
TL;DR: Results indicate that root responses to 6-PP involve components of auxin transport and signaling and the ethylene-response modulator EIN2.
Abstract: Plants interact with root microbes via chemical signaling, which modulates competence or symbiosis. Although several volatile organic compounds (VOCs) from fungi may affect plant growth and development, the signal transduction pathways mediating VOC sensing are not fully understood. 6-pentyl-2H-pyran-2-one (6-PP) is a major VOC biosynthesized by Trichoderma spp. which is probably involved in plant-fungus cross-kingdom signaling. Using microscopy and confocal imaging, the effects of 6-PP on root morphogenesis were found to be correlated with DR5:GFP, DR5:VENUS, H2B::GFP, PIN1::PIN1::GFP, PIN2::PIN2::GFP, PIN3::PIN3::GFP and PIN7::PIN7::GFP gene expression. A genetic screen for primary root growth resistance to 6-PP in wild-type seedlings and auxin- and ethylene-related mutants allowed identification of genes controlling root architectural responses to this metabolite. Trichoderma atroviride produced 6-PP, which promoted plant growth and regulated root architecture, inhibiting primary root growth and inducing lateral root formation. 6-PP modulated expression of PIN auxin-transport proteins in a specific and dose-dependent manner in primary roots. TIR1, AFB2 and AFB3 auxin receptors and ARF7 and ARF19 transcription factors influenced the lateral root response to 6-PP, whereas EIN2 modulated 6-PP sensing in primary roots. These results indicate that root responses to 6-PP involve components of auxin transport and signaling and the ethylene-response modulator EIN2.

208 citations

Journal ArticleDOI
TL;DR: This paper aims to demonstrate the efforts towards in-situ applicability of EMMARM, as to provide real-time information about the phytochemical properties of phytonutrients found in fruit fruits and vegetables.
Abstract: Department of Pharmacy, University of Naples Federico II, Naples, Italy, National Research Council, Institute for Sustainable Plant Protection, Portici, Italy, 3 Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy, CIRAM-Interdepartmental Center for Environmental Research, University of Naples Federico II, Naples, Italy

165 citations