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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 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.
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.
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.
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.
There are increasing efforts aiming to utilise endophytes as biological control agents (BCAs) to improve crop production. However, reliability remains a major practical constraint for the development of novel BCAs. Many organisms are adapted to their specific habitat; it is optimistic to expect that a new organism added can find a niche or even out-compete those adapted and already present. Our approach for isolating novel BCAs for specific plant diseases is therefore to look in healthy plants in a habitat where disease is a problem, since we predict that it is more likely to find competitive strains among those present and adapted. In vitro inhibitory activities often do not correlate with in planta efficacy, especially since endophytes rely on intimate plant contact. They can, however, be useful to indicate modes of action. We therefore screen for in planta biological activity as early as possible in the process in order to minimise the risk of discarding valuable strains. Finally, some fungi are endophytic in one situation and pathogenic in another (the mutualism–parasitism continuum). This depends on their biology, environmental conditions, the formulation of inoculum, the health, developmental stage and cultivar of the host plant, and the structure of the plant microbiome.
The fortuitous discovery of penicillin from Penicillium chrysogenum heralded the golden era of antibiotics. Since then, fungi have significantly contributed to the welfare of humans by producing bioactive compounds which have been used as antibacterial, anticancer, antioxidant and immunomodulatory agents. However, in recent years, microorganisms associated with plants have emerged as fountainheads of bioactive molecules with high therapeutic potential. In general terms, endophytes are an extremely diverse and ubiquitous group of microorganisms that resides within the living internal tissues of a host plant in a non-invasive manner. Endophytes communicate with their host plant through metabolic interactions which enables them to produce signal molecules with interesting biological activities. Further, the genetic recombination of endophytes with the host plant enables them to mimic the biological properties of the host and produce analogous bioactive compounds. Thus, they start producing the host plant phytochemicals when cultured independently. The endless need for potent drugs has prompted researchers to explore alternative avenues for finding novel bioactive molecules, and endophytes appear to be a plausible target for drug discovery. This chapter reviews the current research trends with these promising organisms.
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