Endophytic bacteria have evolved to survive within plant leaf tissue while potentially providing benefits to their host. This relationship makes them uniquely applicable as agricultural biocontrol agents, sources of natural chemicals/products, plant growth promoters and mediators of phytoremediation. Foliar bacterial endophytes colonise leaf tissue through vertical transmission (i.e. through seed or pollen) or horizontal transmission (i.e. colonisation through environmental contact of the roots, wounds, stomatal infiltration, insect vectors, and airborne dispersal). The taxonomic diversity of foliar endophytes spans at least seven bacterial classes and they occupy hosts from all taxanomic groups of plants tested. Bacterial leaf endophytes can promote plant health by stimulating and producing plant hormones for growth and preventing pathogenic infection. Plant-pathogenic bacteria can be found residing within leaf tissue asymptomatically raising questions about the relationship between endophyte–host specificity. Similarly, human pathogenic enterobacteria not usually associated with plants have been found to persist as endophytes. Bioactive secondary metabolites produced by these endophytes have been broadly applicable as antifungals, antibiotics, and other compounds used for agricultural and human health. Endophyte research carries unique challenges that require novel and adaptive strategies for separation of plant and bacterial DNA. This chapter will focus on bacteria isolated from within plant leaf tissue with a focus on transmission, diversity, function and challenges associated bacterial leaf endophyte research.

Barley is an important crop worldwide with production largely used for animal feed and alcoholic beverages. Diseases are a major limiting factor to its production. These have, up until recently, been controlled by agrochemicals. However, legislation on the use of agrochemicals, especially within the European Union, is being tightened and there is growing interest in integrated pest management. This means that there is an increasing focus on controlling diseases using biological control. Living microorganisms that are applied as biological control agents (BCAs) to either soil, seed or leaves can have difficulty in persisting. Therefore, the focus of this review is on endophytes, which are microorganisms that live inside the plant without causing symptoms of disease and have the potential of staying protected as well as being beneficial to the plant and effective against multiple diseases. In this review, we discuss the different approaches for finding and testing beneficial endophytes and for determining the endophyte host range. Furthermore, we undertook a literature search to summarise previous studies that have investigated the use of endophytes as well as BCAs against barley diseases.

Endophytes are microorganisms that colonise the internal compartments of host plants without harming the host. In many cases, endophytic bacteria have been shown to provide several beneficial effects to their host plant, including growth-promoting activity, modulation of plant metabolism and phytohormone signalling that leads to adaptation to environmental abiotic or biotic stresses. Endophytic bacterial community structure is influenced by plant genotype, soil type, abiotic and biotic factors, such as environmental conditions and microbe–microbe/plant–microbe interactions. In addition, agricultural management practices, such as soil tillage, crop rotation, and fertiliser and pesticide applications have a major effect on the function and structure of the soil, rhizosphere and endophytic bacterial communities. Oilseed rape (Brassica napus L.) is an important break crop in cereal crop rotation and can significantly reduce the rate of ‘take-all’ fungal disease (Gaeumannomyces graminis var. tritici) and, as a result, improves the yield of subsequent cereal crops. Additionally, oilseed rape is the world’s third largest source of vegetable oil used for human nutrition and as a source of oil for biodiesel production. Therefore, the promotion of agricultural practices that maintain the natural diversity of B. napus endophytic bacteria is receiving attention as an important element for a sustainable agricultural system that ensures crop productivity and quality while reducing inputs. This chapter reviews the existing literature on the role of endophytic bacteria in oilseed rape crop production, agricultural factors influencing oilseed rape bacterial diversity and discusses how meta-omics is enhancing our understanding of the endophytic bacteria and their function.

There are increasingly restrictive EU regulations surrounding the use of chemicals in farming due to increased information linking environmental behaviour and ecotoxicity, such as the effect of the insecticide class neonicotinoids on bees. For this reason there will be a continued move towards a reduction of chemical use in farming throughout the EU. In this context, the use of plant growth-promoting bacteria (PGPB) offers an attractive alternative to chemical fertilisers. A range of commercially available PGPB products, consisting of different species of bacteria, offer a potential alternative to chemicals. This includes: rhizo power® by nadicom who provide bacteria-based organic fertilisers. In this chapter, we outline detailed findings of four field trials undertaken using PGPB in Europe on alfalfa, broccoli, faba beans and tomatoes. All trials using these products yielded positive results such as faster germination, higher yields, increased chlorophyll in leaves and improved tap root formation. Larger plants resulting in significantly higher yield of organic tomatoes were also observed in the tomato field trial. Longer tap root and deeper green colour was observed in the broccoli trial and a reduction in chocolate spot was shown when treated with Bacillus subtilis. Statistically significant higher yields were shown in treated alfalfa crops using Ensifer meliloti.

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.

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.