The currently reduced stratospheric ozone layer remains sensitive to destructive anthropogenic an... more The currently reduced stratospheric ozone layer remains sensitive to destructive anthropogenic and natural inputs. We hypothesised that a sudden increase in surface ultraviolet-B (UV-B) irradiation, as may have occurred in a past mass extinction event, would have a significant effect on the pollen grain morphology of the model angiosperm Arabidopsis thaliana L. Plants of A. thaliana in controlled-environment chambers were exposed to an increase in UV-B irradiation associated with an ozone column reduction of 70%. Pollen grains were examined with light and electron microscopy for morphological abnormalities. In this study, we found that a wild-type A. thaliana accession showed a significant increase in the proportion of pollen grain morphological abnormalities in response to the increase in UV-B irradiation. Plants exposed to normal daylight in early growth had less pollen morphological abnormalities when exposed to a subsequent increase in UV-B. Results here suggest that any future decrease in stratospheric ozone similar to that implicated in the end-Permian mass extinction event may increase angiosperm pollen morphological abnormalities, with uncertain and potentially negative consequences for plant reproductive success.
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...
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...
ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that... more ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that requires in-depth DNA sequencing for barcoding and phylogenetics, along with accurate morphological data. For identification using sequences it is essential to have data from well classified and studied reference collections so that genotype and phenotype can be compared. DNA from macroscopic fungarium sebacinalean fungi was extracted and characterized by DNA sequencing and phylogenetic analyses. Nuclear ribosomal ITS regions were successfully amplified and sequenced for 15 Sebacinales species. Likelihood of DNA amplification was negatively correlated with increasing age of the specimens. Phylogenetic analysis of these sequences combined with 187 sequences obtained from GenBank revealed significant cryptic diversity within Sebacinales. The type genus Sebacina was not recovered as monophyletic. These results suggest there may be a need for reclassification of some Sebacinales and that alternative approaches such as next generation sequencing may be required to efficiently obtain DNA sequences from older fungarium specimens. The reference ITS barcode sequences generated from this study will provide an invaluable tool for researchers working on applied and basic aspects of these fungi to infer ecological and evolutionary patterns.
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...
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.
ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that... more ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that requires in-depth DNA sequencing for barcoding and phylogenetics, along with accurate morphological data. For identification using sequences it is essential to have data from well classified and studied reference collections so that genotype and phenotype can be compared. DNA from macroscopic fungarium sebacinalean fungi was extracted and characterized by DNA sequencing and phylogenetic analyses. Nuclear ribosomal ITS regions were successfully amplified and sequenced for 15 Sebacinales species. Likelihood of DNA amplification was negatively correlated with increasing age of the specimens. Phylogenetic analysis of these sequences combined with 187 sequences obtained from GenBank revealed significant cryptic diversity within Sebacinales. The type genus Sebacina was not recovered as monophyletic. These results suggest there may be a need for reclassification of some Sebacinales and that alternative approaches such as next generation sequencing may be required to efficiently obtain DNA sequences from older fungarium specimens. The reference ITS barcode sequences generated from this study will provide an invaluable tool for researchers working on applied and basic aspects of these fungi to infer ecological and evolutionary patterns.
Abstract: This article describes a 1997 study funded by the AWWA Research Foundation in which a t... more Abstract: This article describes a 1997 study funded by the AWWA Research Foundation in which a team of international investigators began testing and evaluating techniques for rehabilitating or replacing small-diameter (less than 1 in.[25 mm]) lead piping in ...
Summary Pathogenic fungal infections of barley can lead to costly crop losses. However, not all f... more Summary Pathogenic fungal infections of barley can lead to costly crop losses. However, not all fungal infections are detrimental, and some are even beneficial. Beneficial root infections often involve symbiotic endophytic fungi. Benefits to barley and other pl ants infected with endophytic root fungi include an increase in seed yield, enhanced res istance to pathogens and improved stress tolerance. Here, we examine the mec hanisms and outcomes of fungal endophyte colonisation of barley roots and briefly dis cuss reported benefits for the host. The most important factors that determine the nat ure of the relationship are the specific combination of partner genotypes and dev elopmental stage, and the ecological and environmental setting. The full potential of these organisms is still to be determined and further studies are urgently required to develop speci fic beneficial root-endophyte associations, or combination of them, that are tailored to b arley cultivars for maximum impact i...
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...
Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminat... more Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminated sites and can exploit environmental microorganisms such as bacteria and fungi. These microorganisms are capable of removing and/or deactivating pollutants from contaminated substrates through biological and chemical reactions. Moreover, they interact with the natural flora, protecting and stimulating plant growth in these harsh conditions. In this study, we isolated a group of endophytic fungi from Agrostis stolonifera grasses growing on toxic waste from an abandoned lead mine (up to 47,990 Pb mg/kg) and identified them using DNA sequencing (nrITS barcoding). The endophytes were then tested as a consortium of eight strains in a growth chamber experiment in association with the grass Festuca arundinacea at increasing concentrations of lead in the soil to investigate how they influenced several growth parameters. As a general trend, plants treated with endophytes performed better compar...
Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminat... more Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminated sites and can exploit environmental microorganisms such as bacteria and fungi. These microorganisms are capable of removing and/or deactivating pollutants from contaminated substrates through biological and chemical reactions. Moreover, they interact with the natural flora, protecting and stimulating plant growth in these harsh conditions. In this study, we isolated a group of endophytic fungi from Agrostis stolonifera grasses growing on toxic waste from an abandoned lead mine (up to 47,990 Pb mg/kg) and identified them using DNA sequencing (nrITS barcoding). The endophytes were then tested as a consortium of eight strains in a growth chamber experiment in association with the grass Festuca arundinacea at increasing concentrations of lead in the soil to investigate how they influenced several growth parameters. As a general trend, plants treated with endophytes performed better compar...
The currently reduced stratospheric ozone layer remains sensitive to destructive anthropogenic an... more The currently reduced stratospheric ozone layer remains sensitive to destructive anthropogenic and natural inputs. We hypothesised that a sudden increase in surface ultraviolet-B (UV-B) irradiation, as may have occurred in a past mass extinction event, would have a significant effect on the pollen grain morphology of the model angiosperm Arabidopsis thaliana L. Plants of A. thaliana in controlled-environment chambers were exposed to an increase in UV-B irradiation associated with an ozone column reduction of 70%. Pollen grains were examined with light and electron microscopy for morphological abnormalities. In this study, we found that a wild-type A. thaliana accession showed a significant increase in the proportion of pollen grain morphological abnormalities in response to the increase in UV-B irradiation. Plants exposed to normal daylight in early growth had less pollen morphological abnormalities when exposed to a subsequent increase in UV-B. Results here suggest that any future decrease in stratospheric ozone similar to that implicated in the end-Permian mass extinction event may increase angiosperm pollen morphological abnormalities, with uncertain and potentially negative consequences for plant reproductive success.
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...
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...
ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that... more ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that requires in-depth DNA sequencing for barcoding and phylogenetics, along with accurate morphological data. For identification using sequences it is essential to have data from well classified and studied reference collections so that genotype and phenotype can be compared. DNA from macroscopic fungarium sebacinalean fungi was extracted and characterized by DNA sequencing and phylogenetic analyses. Nuclear ribosomal ITS regions were successfully amplified and sequenced for 15 Sebacinales species. Likelihood of DNA amplification was negatively correlated with increasing age of the specimens. Phylogenetic analysis of these sequences combined with 187 sequences obtained from GenBank revealed significant cryptic diversity within Sebacinales. The type genus Sebacina was not recovered as monophyletic. These results suggest there may be a need for reclassification of some Sebacinales and that alternative approaches such as next generation sequencing may be required to efficiently obtain DNA sequences from older fungarium specimens. The reference ITS barcode sequences generated from this study will provide an invaluable tool for researchers working on applied and basic aspects of these fungi to infer ecological and evolutionary patterns.
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...
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.
ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that... more ABSTRACT Sebacinales are a large, potentially useful and ecologically diverse order of fungi that requires in-depth DNA sequencing for barcoding and phylogenetics, along with accurate morphological data. For identification using sequences it is essential to have data from well classified and studied reference collections so that genotype and phenotype can be compared. DNA from macroscopic fungarium sebacinalean fungi was extracted and characterized by DNA sequencing and phylogenetic analyses. Nuclear ribosomal ITS regions were successfully amplified and sequenced for 15 Sebacinales species. Likelihood of DNA amplification was negatively correlated with increasing age of the specimens. Phylogenetic analysis of these sequences combined with 187 sequences obtained from GenBank revealed significant cryptic diversity within Sebacinales. The type genus Sebacina was not recovered as monophyletic. These results suggest there may be a need for reclassification of some Sebacinales and that alternative approaches such as next generation sequencing may be required to efficiently obtain DNA sequences from older fungarium specimens. The reference ITS barcode sequences generated from this study will provide an invaluable tool for researchers working on applied and basic aspects of these fungi to infer ecological and evolutionary patterns.
Abstract: This article describes a 1997 study funded by the AWWA Research Foundation in which a t... more Abstract: This article describes a 1997 study funded by the AWWA Research Foundation in which a team of international investigators began testing and evaluating techniques for rehabilitating or replacing small-diameter (less than 1 in.[25 mm]) lead piping in ...
Summary Pathogenic fungal infections of barley can lead to costly crop losses. However, not all f... more Summary Pathogenic fungal infections of barley can lead to costly crop losses. However, not all fungal infections are detrimental, and some are even beneficial. Beneficial root infections often involve symbiotic endophytic fungi. Benefits to barley and other pl ants infected with endophytic root fungi include an increase in seed yield, enhanced res istance to pathogens and improved stress tolerance. Here, we examine the mec hanisms and outcomes of fungal endophyte colonisation of barley roots and briefly dis cuss reported benefits for the host. The most important factors that determine the nat ure of the relationship are the specific combination of partner genotypes and dev elopmental stage, and the ecological and environmental setting. The full potential of these organisms is still to be determined and further studies are urgently required to develop speci fic beneficial root-endophyte associations, or combination of them, that are tailored to b arley cultivars for maximum impact i...
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...
Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminat... more Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminated sites and can exploit environmental microorganisms such as bacteria and fungi. These microorganisms are capable of removing and/or deactivating pollutants from contaminated substrates through biological and chemical reactions. Moreover, they interact with the natural flora, protecting and stimulating plant growth in these harsh conditions. In this study, we isolated a group of endophytic fungi from Agrostis stolonifera grasses growing on toxic waste from an abandoned lead mine (up to 47,990 Pb mg/kg) and identified them using DNA sequencing (nrITS barcoding). The endophytes were then tested as a consortium of eight strains in a growth chamber experiment in association with the grass Festuca arundinacea at increasing concentrations of lead in the soil to investigate how they influenced several growth parameters. As a general trend, plants treated with endophytes performed better compar...
Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminat... more Bioremediation is an ecologically-friendly approach for the restoration of heavy metal-contaminated sites and can exploit environmental microorganisms such as bacteria and fungi. These microorganisms are capable of removing and/or deactivating pollutants from contaminated substrates through biological and chemical reactions. Moreover, they interact with the natural flora, protecting and stimulating plant growth in these harsh conditions. In this study, we isolated a group of endophytic fungi from Agrostis stolonifera grasses growing on toxic waste from an abandoned lead mine (up to 47,990 Pb mg/kg) and identified them using DNA sequencing (nrITS barcoding). The endophytes were then tested as a consortium of eight strains in a growth chamber experiment in association with the grass Festuca arundinacea at increasing concentrations of lead in the soil to investigate how they influenced several growth parameters. As a general trend, plants treated with endophytes performed better compar...
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.
Endophytes are any microbes that can live within plants. We divide them into three major groups: ... more Endophytes are any microbes that can live within plants. We divide them into three major groups: endosyms (endosymbionts ), endopaths (pathogens) and endosympaths (those that exist in both forms along a mutualism – parasitism continuum). Within these groups, endophytologists recognise harmful pathogenic microbes and a diverse range of beneficial/ commensal microbes, including bacteria and archaea, such as diazotrophs, and fungi, such as the vertically transmitted clavicipitaceous endophytes, the generally horizontally transmitted class 2 fungal endophytes, mycorrhizal fungi and dark septate endophytes . This chapter introduces the science of endophyte biology and its application for a world population that is projected to grow to over 9 billion by 2050. It explores the potential of endophytes for improved agricultural and silvicultural sustainability including: yield improvement and nutrition; biocontrol of pests and diseases; and abiotic stress resistance in the context of climate change. It outlines how bioprospectors are using endophytes as sources of novel metabolites for the pharmaceutical and biochemical industries, and describes how endophytes can be used in vitro to elicit the increased production of known secondary metabolites from plants.
The book brings together papers covering the most recent scientific research from the top endophy... more The book brings together papers covering the most recent scientific research from the top endophyte researchers in the world. It presents the state of the art in our knowledge and technical capacity and explores future directions of this work. It is highly relevant and timely because of the need to improve global food security and its sustainability, and also to provide novel bioactive molecules for medicine. There is also a need to protect forestry in a changing and growing world. Endophytes offer a huge potential to reduce environmentally damaging agricultural inputs such as fertilisers and pesticides. They are also a largely overlooked group of organisms where much basic science remains to be undertaken. For example, new molecular tools of DNA profiling using high- throughput environmental sequencing are allowing the exploration of a previously largely unknown resource. There is a pressing need to convert scientific research on endophytes into practical application. This book describes how that will be achieved.
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Papers by Brian R Murphy