World population growth has generated a demand for increased healthy food production and the development of sustainable agricultural technologies to replace environmentally damaging farming practices, including the overuse of pesticides. Biological control using entomopathogenic fungi, as natural pathogens of arthropod pests, is an alternative method to meet this objective. These fungi have been traditionally studied to control insects, but recent studies have begun to examine their activity as plant endophytes to protect plants against phytopathogens and improve other aspects of crop production. This chapter reviews the importance of these entomopathogenic fungi as endophytes in the context of biological control. Our studies focus on determining the ability of native strains of entomopathogenic fungi for endophytic colonisation and their potential application for the control of diseases in tomato. The chapter also discusses aspects to consider for their development as commercial biopesticides and suggests ways to make this control method available to producers of agricultural crops.

Phosphate belongs to the major mineral nutrient category in plants and is a non-renewable resource. Many natural soils are phosphate deficient, and phosphate fixation into insoluble mineral complexes limits plant growth by decreasing root uptake. Different strategies have appeared during the evolution of land plants to cope with this situation, one of which is to interact with various microbes (bacteria and fungi) located in the plant rhizosphere. This chapter will focus on three major groups of fungi that colonise the roots of most land plants: arbuscular mycorrhizal fungi (Glomeromycotina), fungi from the order Sebacinales (Basidiomycota) and the diverse form-group of dark septate endophytes (Ascomycota). Three major mechanisms of fungal contribution to plant nutrition will be discussed. First, fungi are able to solubilise phosphate from inorganic sources that are not available to plants. Second, fungi can set free mineral nutrients from organic compounds/sources. Third, fungi are able to transport phosphate along their hyphae towards the plant, thereby bridging phosphate depletion zones around the roots. In this chapter, we summarise published knowledge on this topic and present some new non-published data to complete our current model.

Dark septate endophytes (DSEs) are ascomycetous fungi whose structure is characterised by dark melanised hyphae and microsclerotia located in plant roots. Associations with DSEs are commonly found in various biomes and plant taxa. Although DSEs are commonly recorded, the effects of their colonisation on plant growth and fitness are unclear. This chapter summarises the state of knowledge about DSEs from the literature and personal data. The effects of DSEs on plant growth range from parasitism to mutualism. They can promote plant growth by improving nutrition (e.g. solubilisation of minerals, degradation of complex carbon compounds), producing secondary metabolites (e.g. phytohormones, volatile organic compounds) and protecting against phytopathogens. More particularly, the high tolerance of DSEs to abiotic stress and their relatively high abundance in trace element-contaminated and other stressful habitats suggest that they may have an important function for host survival under these conditions. Finally, this chapter outlines why additional research is required in the emerging field of plant–DSE interactions to address future challenges.

A study to detect the diversity of endophytic Actinobacteria from Australian rice was conducted using culture-dependent and culture-independent methods. Rice samples were collected from the rice growing area near Yanco, New South Wales, Australia. Isolation of the endophytic Actinobacteria was done over two consecutive growing seasons. The results demonstrated that most isolates were obtained from plants 10 weeks and older, and only a few were found in younger plants. Microbispora spp. were the most commonly isolated endophytic Actinobacteria (94%) with Streptomyces spp. and other genera present at lower numbers (6%). The culture-dependent method findings were confirmed by T-RFLP profile analysis. Restriction digests using HhaI and RsaI also showed an abundance of terminal restriction fragments (TRFs) profiles related to the genus Microbispora. Furthermore, other biological properties of the endophytic Actinobacteria isolates were also determined. Four isolates, Saccharothrix OSH21, Saccharopolyspora OSR26, Streptomyces OSR46 and Microbispora OSR61, were found to suppress the growth of the pathogenic fungus Rhizoctonia solani. Moreover, these isolates might be able to promote plant growth by producing indole acetic acid or to solubilise phosphate making this nutrient available for plant uptake.

Endophytes have the potential to contribute to the sustainable production of bioenergy crops such as the perennial rhizomatous grass Miscanthus. They can improve plant growth on marginal land that is otherwise unsuitable for conventional agriculture and can also reduce the need for environmentally damaging chemical inputs including fertilisers and pesticides. This chapter outlines current knowledge of Miscanthus endophytes and presents new data on the diversity of root and shoot fungal endophytes isolated from three Miscanthus species (M. sacchariflorus, M. sinensis and M. ×giganteus). Malt extract, potato dextrose and Czapek Dox media were compared for isolation and growth of the endophytes. The endophytes were then identified using DNA barcoding with three DNA loci (nrITS, nrLSU and TEF). nrITS and nrLSU were found to be the most reliable and consistent barcoding regions. Internal transcribed spacer (ITS) had the highest discriminating potential and is thus recommended for single locus barcoding of endophytes in Miscanthus. Most new isolates were Ascomycota belonging to Pezizomycotina with representatives from Dothideomycetes, Eurotiomycetes and Sordariomycetes. One Basidiomycota species was recovered (a known soil yeast Rhodotorula). Comparisons between Miscanthus endophyte species composition and its better-known sister genus Saccharum (including sugarcane) are provided.

Endophytes are any microbes that can live within plants. We divide them into three major functional 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.

In vitro tissue culture systems are required for plant–microbe interaction studies on European ash, Fraxinus excelsior. Methods are needed for plant micropropagation and for physiological experimentation including pathogen/resistance testing and biocontrol studies. For example, systems are required for experiments on ash dieback disease, caused by the ascomycete fungus Hymenoscyphus fraxineus, that is killing ash plantations and natural populations across its native range. Methods are also needed to optimise the number of endophytes cultured from ash tissue and to taxonomically identify them. We present endophyte isolation protocols and media for ash, provide an optimised DNA barcoding procedure for endophyte identification and describe in vitro tissue culture methods suitable for ash–microbe interaction studies in both roots and shoots. Methods for both embryo culture and seed culture (with precutting) and for the bulking up of genotypes via single node culture are outlined. We also discuss the potential of tissue culture for establishing microbe/endophyte-free cultures.

Endophytes are any microbes that can live within plants. We divide them into three major functional 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.

Quercus suber L. is an evergreen tree species with high economic, ecological and social importance within the Mediterranean Basin. Cork oak forests occupy more than 2 million hectares worldwide, being mainly located in Algeria, Morocco, Portugal and Spain. As in other Mediterranean ecosystems, cork oak forests have been reported as important reservoirs of biological diversity, including endemic species that are currently under threat due to abiotic and biotic stress. Despite the adaptation of cork oak to the Mediterranean climate, which is characterised by warm, dry summers and wet winters, the growth and productivity of this species is sensitive to climatic change and variability. Extended periods of high temperature and/or low precipitation leading to low level of available water in the soil, can trigger the decline of cork oak and increase vulnerability to pathogen attack. Plant microbiomes are major factors for preserving plant health and productivity under challenging climates and their endophytic components can have dual ecological function, both as detrimental microbes or as beneficial symbionts. Endophytes can play beneficial roles for plant health and productivity but some can become opportunistic pathogens that take advantage of weakened plants that are stressed by environmental conditions. This review discusses endophytes in the context of Mediterranean bioclimates, the geographic distribution of cork oaks and the spread of opportunistic disease-causing agents. Some studies have begun to characterise and isolate endophytes from cork oak, which represents the first steps towards understanding how cork oak endophytes might help ameliorate the negative impacts of climate change for this tree species.

In some environments, the survival and production of ryegrass and fescue is heavily reliant on its mutualistic association with Epichloë endophytes. Epichloë endophytes produce a range of bioactive alkaloids, or secondary metabolites that can be effective in deterring insect pests, although some have also been shown to be toxic to grazing animals. These endophytes are being used in grassland farming systems in Australia, New Zealand, USA and some parts of South America. However, to achieve this outcome there has been considerable investment into developing a research pipeline for delivery of animal-safe endophyte strains that are still capable of deterring insect pests and providing protection against abiotic stresses. The pipeline starts with the discovery and isolation of endophytes from wild populations of ryegrass and fescue, characterisation of the known alkaloids they produce, use of genetic markers to determine the relationship between known well-characterised strains and new strains entering the collection, determination of their bioactivity against insect pests of economic significance, understanding issues of compatibility of a strain of interest with the elite germplasm into which it has been inoculated, determining ease of transmission to subsequent seed generations, and ensuring there will be no or minimal animal health and welfare issues associated with using the strain in grazing systems.

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.

Fungal endophytes are a vital component of the plant microbiome. The symbiotic relationship between endophytic fungi and medicinal plants can considerably influence plant secondary metabolism pathways, thus affecting their metabolite production and the quality and quantity of crude drugs produced. This chapter focuses on how fungal endophytic symbiosis can increase production of secondary metabolites during in vitro culture. Other than promoting secondary metabolite accumulation, endophytic fungi can also promote the growth of host plants and improve their resistance to abiotic and biotic stresses. Therefore, an understanding of the relationship between endophytic fungi and their host medicinal plants is of utmost importance. This knowledge can be applied in the production of novel and improved drugs from medicinally valued plants. In vitro elicitation of secondary metabolites by endophytic fungi has been reported in several medicinal plants. A case study is documented in this chapter which shows enhancement of asiaticoside by an endophytic fungal (Colletotrichum gloeosporioides) elicitor isolated from in vivo grown plants of Centella asiatica. These findings may motivate further exploitation of fungal endophytes as an effective and beneficial way to enhance the production of pharmacologically important compounds from medicinal plants.

In some environments, the survival and production of ryegrass and fescue is heavily reliant on its mutualistic association with Epichloë endophytes. Epichloë endophytes produce a range of bioactive alkaloids, or secondary metabolites that can be effective in deterring insect pests, although some have also been shown to be toxic to grazing animals. These endophytes are being used in grassland farming systems in Australia, New Zealand, USA and some parts of South America. However, to achieve this outcome there has been considerable investment into developing a research pipeline for delivery of animal-safe endophyte strains that are still capable of deterring insect pests and providing protection against abiotic stresses. The pipeline starts with the discovery and isolation of endophytes from wild populations of ryegrass and fescue, characterisation of the known alkaloids they produce, use of genetic markers to determine the relationship between known well-characterised strains and new strains entering the collection, determination of their bioactivity against insect pests of economic significance, understanding issues of compatibility of a strain of interest with the elite germplasm into which it has been inoculated, determining ease of transmission to subsequent seed generations, and ensuring there will be no or minimal animal health and welfare issues associated with using the strain in grazing systems.