Trevor Hodkinson | Trinity College Dublin (original) (raw)

Papers by Trevor Hodkinson

Perennial Biomass Crops for a Resource-Constrained World, 2016

A greater range of germplasm is required to increase the genetic base of Miscanthus and to adapt ... more A greater range of germplasm is required to increase the genetic base of Miscanthus and to adapt it to a range of climates and soil types, including on marginal land. We undertook a major collecting expedition in Primorsky Krai in the Russian Far East to collect Miscanthus growing in a diverse range habitats. Miscanthus was found to be locally abundant, and a total of 361 genotypes were collected. Ten populations were sampled at high intensity and the remaining genotypes were spot sampled from a further 39 populations to maximize geographic and environmental range. Taxa were identified using morphology in the field and with subsequent stereomicroscopy where required. A total of 287 M. sacchariflorus and 70 M. sinensis plants were sampled. Potential hybrids have been identified using morphology and are currently being investigated further using molecular analysis including DNA sequencing and ploidy determination.

Endophytes for a Growing World, 2019

The wild relatives of agricultural crops represent a largely untapped source of beneficial microb... more The wild relatives of agricultural crops represent a largely untapped source of beneficial microbial endophytes that have potential for agricultural applications. Much of the research into the effects of endophytes on crop species has focused on a relatively small selection of well- characterised bacterial or fungal strains. However, many of these strains can have inconsistent and even unpredictable agronomic effects depending on the complex relationship between host, endophyte, microbiota and environment . We argue that a more focused approach to endophyte selection and application to crop production can generate more predictable results. We show that the appropriate identification of novel fungal endophyte strains from defined source host populations along with the consideration of the target crop species, cultivar and site can improve the chances of a successful endophyte- induced benefit. We discuss the implications for agriculture and suggest further research that will provide more robust support for this approach.

Global Journal of Science Frontier Research, 2015

Abstra ct- Sustainable farming systems are required to allow crops to better cope with the simult... more Abstra ct- Sustainable farming systems are required to allow crops to better cope with the simultaneous multiple stresses that they grow under or are likely to be exposed to under future climate change. Fungal endophytes could form part of the solution. They have been shown to improve important agronomic traits under a single stress, but few studies have investigated the impact of endophytes on growth or disease resistance when exposed to multiple stresses. We compared the performance of the barley cultivar Propino when inoculated with five fungal root endophytes, either individually or combined, derived from wall barley (Hordeum murinum) and grown in optimal conditions (OC) and under a combined drought, heat, nutrient and pathogen stress (MS). We found a greater endophyte-induced improvement in important agronomic traits in the MS plants compared with the OC plants. For the MS plants only 13% of the controls survived to the end of the experiment compared with 80% of the endophyte t...

Journal of Fungi, 2021

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxin... more Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richnes...

The root endophyte community of the grass species Elymus repens was investigated using both a cul... more The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe end...

Journal of fungi (Basel, Switzerland), Jan 11, 2018

The development of endophyte inoculants for agricultural crops has been bedevilled by the twin pr... more The development of endophyte inoculants for agricultural crops has been bedevilled by the twin problems of a lack of reliability and consistency, with a consequent lack of belief among end users in the efficacy of such treatments. We have developed a successful research pipeline for the production of a reliable, consistent and environmentally targeted fungal endophyte seed-delivered inoculant for barley cultivars. Our approach was developed de novo from an initial concept to source candidate endophyte inoculants from a wild relative of barley,(wall barley). A careful screening and selection procedure and extensive controlled environment testing of fungal endophyte strains, followed by multi-year field trials has resulted in the validation of an endophyte consortium suitable for barley crops grown on relatively dry sites. Our approach can be adapted for any crop or environment, provided that the set of first principles we have developed is followed. Here, we report how we developed t...

Journal of Agronomy and Crop Science, 2015

Crops often face severe and damaging local drought events, and in some regions, these episodes ar... more Crops often face severe and damaging local drought events, and in some regions, these episodes are predicted to become more frequent due to climate change. Some micro-organisms have been shown to improve drought tolerance and improve yield in crop plants. Here, we show that fungal root endophytes isolated from a wild barley species (Hordeum murinum subsp. murinum) induced significant improvements in agronomic traits for a severely drought-stressed barley cultivar grown in a controlled environment, including number of tillers, grain yield and shoot biomass. Five endophyte strains were tested, and the trait that showed the greatest significant difference in the drought-stressed plants was the number of tillers, where all of the endophyte treatments induced a greater number of tillers per plant. However, except in one case, the mean dry root weight for all plants was greater in the control plants, indicating preferential allocation of resources to aboveground parts in the endophyte treatments. Results were not consistent across all endophyte treatments, with some endophytes performing much better than others. As these growth studies were conducted using soil-based compost, the results may translate to the field and suggest that some of these endophytes have potential as barley inoculants in arid growing conditions.

The Journal of Agricultural Science, 2017

SUMMARY The use of chemicals to fertilize crops incurs economic and environmental costs and it is... more SUMMARY The use of chemicals to fertilize crops incurs economic and environmental costs and it is widely recognized that the current level of chemical fertilizer use is unsustainable in many intensive farming systems. Any methods that can reduce fertilizer input and still maintain acceptable yields would be of great benefit to both the farmer and the environment. The use of beneficial endophytes as crop inoculants may go some way towards improving crop yields beyond that achievable using fertilizer increases alone. Field trials were conducted over two seasons on three contrasting field sites to test the effects of fungal endophytes from a wild barley relative on three barley cultivars (Mickle, Planet and Propino). Seeds were either untreated or dressed with a consortium of four endophyte strains, and three levels of nitrogen (N) were applied to both treatments: full N, 50% N and 0 N. On the field site with the lowest overall N input, the endophyte treatment with 50% N restored yield...

Symbiosis, 2016

The use of beneficial fungi as crop inoculants is constrained by the need for application of fung... more The use of beneficial fungi as crop inoculants is constrained by the need for application of fungicides because the pathogen controlling fungicides often concurrently suppress the efficacy of the beneficial mycobiont. Root endophytic fungi have been shown to improve agronomic traits in spring barley and may be less sensitive to the regularly applied foliar fungicides. We hypothesised that a consortium of fungal endophyte species applied as a seed spore dressing may improve the germination and subsequent growth of barley and oat seedlings. We tested a range of seed dressings to evaluate the effects of the endophytes: untreated seed, regular fungicidal dressing (triticonazole and prochloraz), endophyte seed spore dressing and a combination of endophyte and fungicide. We found significant increases in mean barley seedling length induced by the endophytes after 28 days of seedling growth at time points of up to 6 months from seed dressing. The increases in mean seedling length were greatest for the combined fungal endophyte and fungicide treatment. For the oat cultivar, we found even more substantial endophyte associated increases in mean seedling length. These results indicate that the endophytes tested here are persistent in a seed dressing, enhance early seedling growth, are fungicide tolerant and are competent in two different genera of cereal crops.

Symbiosis, 2015

ABSTRACT Overuse of chemical fertilisers in barley crops carries large economic and environmental... more ABSTRACT Overuse of chemical fertilisers in barley crops carries large economic and environmental costs and can lead to ecosystem degradation and loss of biodiversity. Methods of reducing chemical crop inputs using endophyte treatments have been demonstrated elsewhere. Here, we show that inoculation with six different fungal root endophytes isolated from wild populations of Hordeum murinum ssp. murinum increased grain yield in a nutrient-starved barley cultivar by up to 29 %. Furthermore, we also show that inoculation with the isolates induced increases of up to 70%in shoot dry weight in the nutrient-starved barley. The greatest increases in grain yield and shoot dry weight were achieved under the lowest nutrient input. Several of the isolates may be new species, and one particularly effective isolate has previously been shown to completely suppress seed-borne infections of barley. Our results indicate that novel fungal root endophytes derived from a wild relative of barley may help to reduce fertiliser inputs while maintaining acceptable yields. If this potential can be realised in field crops it may result in more sustainable, economically cost-effective and environmentally friendly crop treatments and a reduction in chemical fertiliser use.

BioControl, 2014

ABSTRACT Ten fungal root endophytes were isolated from wild populations of Hordeum murinum ssp. m... more ABSTRACT Ten fungal root endophytes were isolated from wild populations of Hordeum murinum ssp. murinum L. and inoculated onto untreated seeds of a barley cultivar using five artificial and one soil-based growth media. A co-inoculant of all ten isolates as well as two individual isolates successfully suppressed the development of seed-borne fungal infections on germinated and ungerminated seed. The two most successful isolates were also the most persistent as re-emergents and may provide real potential for development as crop inoculants. All isolates were more persistent in barley exposed to light after germination. The soil-based compost was associated with the greatest degree of seed-borne infection suppression, and the most successful artificial medium for suppressing seed-borne infections was also the medium with the most similar pH to the soil at the sampling sites. These results suggest a direct antagonistic effect of the fungal isolates on seed-borne pathogens without the induction of plant defences.

ABSTRACT Purpose: The fungus Piriformospora indica was first isolated from plants growing in arid... more ABSTRACT Purpose: The fungus Piriformospora indica was first isolated from plants growing in arid, hot desert conditions and has been shown to have significant potential as a biocontrol and biofertilising organism in barley under optimal growth conditions. However, it was not thought to be effective in plants grown in low temperatures and has consequently not been well tested in cold-stressed crops. This study sought to determine the effects of inoculating barley plants with this fungus in cool growth conditions with variable nutrient input. Methods: We grew three barley varieties inoculated with P. indica and two other fungal root endophytes in a controlled environment under low temperature stress with variable nutrient input, and measured growth, development and yield. Results: Under higher nutrient input, the P.indica-inoculated plants flowered earlier and had 22% greater grain yield than the control. The other two endophytes, Chaetomium globosum and Epicoccum nigrum, conferred no significant benefits under either nutrient regime. Conclusions: Piriformospora indica is easy to culture and propagate, and may have significant biofertilisation potential as a crop treatment for barley grown in cool climates provided that a threshold level of nitrogen is supplied. Such treatments may enable the profitable cultivation of barley in previously marginal sites and reduce the carbon footprint of barley through increased nitrogen use efficiency.

The Journal of Agricultural Science, 2013

SUMMARYFungal infections of barley have tremendous agricultural significance, and can be detrimen... more SUMMARYFungal infections of barley have tremendous agricultural significance, and can be detrimental or beneficial. Beneficial root infections often involve endophytic fungi, but endophytic associations do not always confer benefits on their hosts. Endophyte infection can be negative, positive or neutral for the host. Benefits to barley and other plants infected with endophytic root fungi include an increase in seed yield, enhanced resistance to pathogens and improved stress tolerance. Even if an endophyte is never pathogenic, it is not always beneficial. The most important factors that determine the nature of the relationship are the specific combination of partner genotypes and developmental stage, and the ecological and environmental setting. The nutrient status of the plant and the availability of soil nutrients may have little effect on the degree of beneficial endophyte colonization and, unlike mycorrhizae, there is no apparent increase in endophyte-associated phosphorous tran...

Systematic Botany, 2012

ABSTRACT Phylogenetic relationships of 34 species and 11 out of 14 Vitaceae genera, were evaluate... more ABSTRACT Phylogenetic relationships of 34 species and 11 out of 14 Vitaceae genera, were evaluated using parsimony and Bayesian analyses of four plastid DNA sequence regions (trnL intron, trnL-trnF spacer, atpB-rbcL spacer, and rps16 intron). Vitaceae were shown to be monophyletic and at infrafamilial level, well-supported groups included a Cayratia-Cyphostemma-Tetrastigma clade, an Ampelopsis-Cissus striata-Rhoicissus clade, and a Nothocissus-Pterisanthes clade. However, the relationships among the remaining genera remained unresolved. Cyphostemma, Tetrastigma, and Vitis were clearly monophyletic, while both Ampelopsis and Cayratia were paraphyletic and Cissus was polyphyletic. Parsimony based studies of character evolution suggested that 5-merous flowers, leaf-opposed inflorescences, and a hermaphroditic sexuality are ancestral character states in the family.

Symbiosis, 2014

ABSTRACT The fungal root endophytes Chaetomium globosum, Epicoccum nigrumand Piriformospora indic... more ABSTRACT The fungal root endophytes Chaetomium globosum, Epicoccum nigrumand Piriformospora indicahave value as biocontrol and biofertilising organisms in barley, but have not been well tested at low temperatures. This study assessed the efficacy of the endophytes on barley varieties grown under low temperature stress with variable nutrient input. Seed from three cultivars of spring barley were inoculated with one of the three fungal root endophyte isolates – C. globosum, E. nigrum or P. indica - and grown in low temperature under higher and lower nutrient input regimes. Compared with the control, for P.indica-inoculated plants with the higher nutrient input, flowering was earlier and grain dry weight significantly greater for all barley varieties by a mean of 22 %. The nitrogen and carbon content of the grains did not differ significantly between treatments. Chaetomium globosum and Epicoccum nigrum conferred no significant benefits under either nutrient regime. Piriformospora indica is amenable to axenic culture, sporulates readily and can be multiplied rapidly, suggesting that it could be developed as an effective crop treatment in low temperature stressed barley and may have the potential to increase crop yield in colder growing conditions provided that adequate nutrients are supplied.