Keywords

1 Introduction

The bioactive compounds, also known as “biologically active compounds”, are extra nutritious components found in a minute quantity in various products of plants and foods rich in lipids (Cammack et al. 2006). Bioactive compounds are mostly formed by microbes and plants, having broad pharmaceutical characteristics including cardiovascular, anti-thrombotic, anticancer, antidiabetic, anti-glycaemic and antihypertensive (Villaescusa et al. 2015; Atanasov et al. 2015; El-Beltagi et al. 2018, 2019a, b, c; Hamed et al. 2019; Aminkhani et al. 2020), and are used as favoured medicines, made synthetically to cure different diseases with minimum side effects (Chang et al. 2013). Currently, these are demanded highly in the naturopathy and pharmaceuticals, because of their benefits to plants and human’s health. These compounds are synthesized by microorganisms and nearly by few enzymes either with plant association or alone. Microbes living inside the tissues of plants are called endophytes, producing a wide range of these compounds (Singh et al. 2017).

Endophytes are known to be the class of endosymbiotic microbes which are distributed widely among the plants and make colonies in intra- or intercellular spaces of entire plant parts. They do not cause deceptive disease infection or substantial change in morphology (Fouda et al. 2019). Plant endophytes extending from a range of bacteria to fungi form a quality class of organic compounds, volatile in nature, and considered to be significant for the symbiotic relationship development under an environment with high competition with their host (Chowdhury et al. 2015). Endophytes spend most of their life inside the tissues of a plant with no visible injury or elicitation in any defence reaction in plant host (Liarzi et al. 2016), and they exhibit wide-ranging symbiotic relationship with the host plants and different lifestyles, also possessing beneficial long-term association to both the host and microbes (Card et al. 2016). Endophytes could be found in most of the ecosystems while reducing biotic and abiotic stressors of plant crops; stimulate immunity responses, excluding pathogens of plants by niche competition; and take part in the metabolism of phenylpropanoid and antioxidant activities, the activation of which produce defence in plants, molecules for survival and structural support (Ek-Ramos et al. 2019).

Endophytic bacteria have reported with many different useful benefits to their host plant including plant metabolism modulation, activity of promoting growth and signalling of plant hormones leading to ecological biotic and abiotic stress adaptation. Their use grants special concern for agricultural application development ensuring the improved performance of crops under drought, cold, contaminated soil and salinity stress conditions and enhanced resistance to disease (Lata et al. 2018).

The need to uplift human lifestyle using advance, new and beneficial compounds is ever growing. Despite the advancement in research and so much efforts to cope up with many medical problems (appearance of bacterial drug resistance, viruses threatening life, enhancement in fungal infections, problems with organ transplant, etc.), mankind is still unable to control these problems. Also, mankind faces different problems like land and water pollution, environmental degradation and biodiversity loss, but more importantly, there are hurdles to produce enough food for people in certain parts of the world which has become a threat to human life. The endophytic population is greatly affected by climatic conditions and the location where the host plant grows. They produce a wide range of compounds useful for plants for their growth, protection to environmental conditions, and sustainability, in favor of a good dwelling place within the hosts. They protect plants from herbivory by producing certain compounds that will prevent animals from further grazing on the same plant and sometimes act as biocontrol agents. A large number of bioactive compounds produced by them not only are useful for plants but also are of economical importance to humans. They serve as antibiotics, drugs or medicines, or compounds of high relevance in research or as compounds useful to the food industry. This chapter provides an in-depth detail of occurrence, microbial biological by-products of endophytes, their mechanism, discovery, and significances and uses them to enhance plant health and human life.

2 Needs for New Medicines and Agrochemical Agents

To explore new chemotherapeutic agents, antibiotics and highly effective agrochemicals with low toxicity and less environmental effect is the need of the day. This research is accelerated by developing resistance against infectious microorganism (e.g. Mycobacterium, Streptococcus and Staphylococcus) to recent compounds and threatened naturally resistant organism present in the result of this search. Detection and development of new medicines to tackle new diseases such as SARS and AIDS in humans. New treatments are used as well as medications to treat illnesses such as AIDS and ancillary (due to weak immune systems). Unscrupulous pathogens (Aspergillus spp., Cryptococcus spp. and Candida spp.) usually attack more on an immunocompromised human population, which is another major risk to human life. For treating nematode infections (malaria, trypanosomiasis, leishmaniasis and filariasis) and parasitic protozoans, new and more drugs are required. Generally speaking, a single malaria can kill more lives every year among all the aforementioned diseases except AIDS virus and Mycobacterium tuberculosis (National Institute of Health 2001). Alternative methods to control farm pathogens and pests are required to be searched to remove many synthetic agricultural agents from the market due to environmental and safety problems (Demain 2000), where, opportunities for innovative drugs and agrochemical discovery are possible due to novel natural products and organisms.

3 Natural Products and Their Traditional Approaches in Medicinal World

These are the naturally derived metabolites and by-products of plants, microorganisms and animals (Baker et al. 2000). China is the largest traditional medicine users producing plants of approximately 5000 and obtained products in their pharmacopoeia. Aspirin (salicylic acid) is considered the most known and widely used medicine in the world, reported in various plant species of different genera, i.e. Populus and Salix. Salicylic acid is naturally originated from glycoside salicin. Mayans nearly 3000 years ago treat intestinal ailments using fungi grown on roasted green corns which indicated the benefits of medicinal plants in now-extinct civilizations (Buss and Hayes 2000). Around 800 AD, the Benedictine monks use Papaver somniferum for a pain reliever, which was done way back by Greeks. In the past, products obtained from the mixture of leaf, stem and roots are considered very helpful to treat certain diseases, reduce pain and sufferings and provide relief and quality improvement in life, but understanding the complex nature and function of these bioactive compounds remained a mystery. The mystery was partly solved from Pasteur discovery (fermentation caused by living cells). By then people thought seriously to search the sources of these bioactive compounds which were microorganisms. Later, the discovery of penicillin from Penicillium notatum (a fungus) provided motivation and observance power to Flemings, who led the antibiotic era. By then scientists are busy to overcome plant and human pathogens by applying different microbial metabolites. Since many of the beneficial micro-organisms had been found, the work in medicine (immunosuppressing functions and anti-cancer) which is used to combat various harmful illnesses and therefore in agriculture, has been made simple, a revolutionary and sophisticated screening method developed in medicine as well as agriculture.

4 The Endomicrobiome

Microbial community could be studied within plants using next-generation sequencing (NGS) technology and is together termed as “endomicrobiome”. Various factors like geographical location and different genotypes of plants, etc. are somewhat less diverse than rhizomicrobiome (Edwards et al. 2015). The mechanism for microbe acquisition is still ambiguous in a particular ecosystem. A reasonable supposition suggests a two-step acquisition of microbiomes. During the first step, microorganism is first introduced in the rhizosphere which is followed by entrance mechanism within root tissue. This entrance depends upon general factors and is species-specific (Bulgarelli et al. 2013). Based on the time-staged profiling experiments in rice plants, it was concluded that microbial colonization starts within a day and reaches a steady state within 2 weeks. This shows the fast-growing process of microbial colonization in the endosphere. Root wounds, lateral roots, root hairs, lenticels or leaf stomata and cracks are usually the entry points of bacteria (Edwards et al. 2015). It is reported that Proteobacteria are found more in bulk soil as compared to endosphere while there is a reverse followed by acid bacteria, and Gemmatimonadetes are more in endosphere than in bulk soil. Pseudomonas-like operational taxonomic unit (OTU) which is gammaproteobacterial is found to be approximately 34% in endophytic bacterial sequence of Populus . After the analysis of sequencing approaches of different plant parts, a similar trend was observed in the whole community, not only in plant roots. When tomato leaf was analysed using 16S-rRNA pyrosequencing, it was reported the predominance of Actinobacteria (1.5%), Proteobacteria (90%), Verrucomicrobia (1.1%), Planctomycetes (1.4%) and Acidobacteria (0.5%). The phylum Proteobacteria is reported to dominate about 98% among the microbial communities which mostly consist of Enterobacteriales, Pseudomonadales, Flavobacteriales, Actinomycetales, Xanthomonadales, Sphingomonadales and Rhizobiales (Shi et al. 2014). All these studies assumed the endosphere of most land plants.

5 Definition, Classification and Origin of Endophytes

Endophytes are defined as the organisms residing inside the plant’s internal tissues in its whole life period, no matter whether it was unbiased, beneficial or harmful to its host plant (Bacon and White 2000). They reside within plants for some part of the life cycle without initiating any signs of diseases (Sikora et al. 2007). Thus, endophytic microbes are an ecology concept and are an essential part of a plant-microecology system (Li 2005). About 270,000–4,000,000 different kinds of endophytic fungi live in the intercellular spaces and microtubule plant cells. Furthermore, a high density of about 104–106 CFU/g of endophytic bacteria live in plant roots (Dreyfuss and Chapela 1994). Moreover, McInroy and Kloepper (1996) discovered that Neotyphodium coenophialum (endophytic fungi) produced a syndrome called “fescue toxicosis” in cattle eating the grass Festuca arundinacea, providing new insights in this field.

6 Types of Endophytes

Endophytes are classified based on microbes into endophytic fungi, bacteria and actinomyces (Strobel et al. 2004).

6.1 Endophytic Fungi

An endophytic fungus can multiply asymptomatically in the tissues of plants including stems, leaves, and roots. Bacon and White (2000) reported that an endophytic fungus lives in the mycelial form in the biological organization within the living plant, at least for some time. Endophytic fungi are found to associate with above ground tissue of liverworts, hornworts, mosses, lycophytes, equisetopsids, fern, and seed plants from the arctic to the tropics and from agriculture fields to the most diverse tropical forest (Arnold 2007). They found that endophytic fungi could produce tolerance against drought and saline conditions (Waller et al. 2005). They act as stimulator against stress conditions more rapidly in comparison to the non-symbiotic plants (Redman et al. 2002). Red and chilli peppers contain a bioactive compound, capsaicin , that has been used as a remedy against pain and different types of human cancers. The endophytic fungus named Alternaria alternata, separated from Capsicum annuum (chilli), produces capsaicin, while Eurotium sp. from the rhizome of Curcuma longa (turmeric) produces asparaginase which can usually be used as an anticancerogenic enzyme (Jalgaonwala and Mahajan 2014).

6.1.1 Plant-Associated Fungi that Produce Bioactive Compounds

To adopt sustainable agriculture by maintaining a healthy ecosystem and reduce the residual effect of inorganic fertilizer and pesticides, the use of beneficial microorganism, i.e. fungi, as a biocontrol agent and growth promoter can be an effective alternative to various chemical pesticides and controlling pathogens in plants (Vurukonda et al. 2018; Aswani et al. 2020). Fungi interact with plants in a different way, playing a key role in the maintenance of ecosystems’ well-being while developing associations with various plant tissues positively or negatively. These metabolites adopt different protective measures in protecting plants from herbivores, inducing systematic resistance to pathogens, and stimulate the synthesis of phytohormones and nutrient and water transport efficiency during different stress conditions (Zeilinger et al. 2016). They increase resistance against stress conditions in the plants by producing bioactive compounds like Paecilomyces formosus LWL1 , an endophytic fungus in japonica rice cultivar ‘Dongjin’ that produced secondary metabolites under heat stress and improves growth-related attributes (Waqas et al. 2015). They promote accumulation of different secondary metabolites in the host plants under stress conditions (Venieraki et al. 2017).

6.1.1.1 Mycorrhizal Fungi

Mycorrhiza” the term used to describe the symbiotic association between a fungus and a root of higher plant. Endomycorrhizal fungi are involved in colonization of roots causing significant changes in their chemicals, produced by roots that influence the health status of plant, their performance under competitive condition, soil aggregate formation, increasing resistance against any biotic or abiotic stresses and activation of stimulated response (Jamiołkowska et al. 2017). Endophytes provide extensive types of bioactive secondary metabolites with a selected structure including flavonoids, alkaloids, chinones, phenolic acids, steroids, quinones, tetralones, terpenoids, xanthones, and others. Bioactive secondary metabolites are also isolated from conifer-associated endophytic fungi which are having anti-inflammatory, antimicrobial, antiproliferative, or cytotoxic activity toward human cancer cell lines and activity against plant insect pests or plant pathogens [96]. Such bioactive metabolites find wide-ranging application as anticancer, antiparasitics, agrochemicals, antibiotic, immune suppressants, and antioxidant agents (Stierle and Stierle 2015). Also, mycorrhizal fungi produce various bioactive compounds such as glomalin as defensive strategies that perform different functions by immobilizing contaminants on the hyphal cell wall and reduces predator infection (Souza et al. 2012). Under drought conditions, the association of plants with mycorrhizal fungi withstand drought-induced oxidative stress by the increased production of antioxidant compounds that scavenge reactive oxygen species and activate the activities of antioxidant enzymes (Rapparini and Penuelas 2014).

6.1.1.2 Fungi-Promoting Plant Growth

Such types of fungi living inside the soil can colonize the roots of plants. These fungi function as biocontrollers and growth promoters while improving the development and growth, as these microbes destroy pathogenic microorganisms and produce substrates of minerals. Furthermore, a series of metabolic responses were also observed in the plants through the volatile organic compounds’ (VOCs) production by these fungi (Naznin et al. 2013). Plant defense is then achieved by priming for enhanced expression of sequences regulated by the production of jasmonic acid, ethylene, or salicylic acid. In other cases, the functions of mycorrhizal fungi are to produce active VOCs and antibiotics, both in plants and soil, which can be helpful in the identification of active biomolecules against plant pathogens and enhanced vegetative and reproductive performance of the plant (Vurukonda et al. 2018).

6.2 Endophytic Bacteria

Almost a diverse array of endophytic bacteria have some beneficial effects, i.e. as biocontrol agent, and act as an enhancer of N2 fixation, plant hormone production, phosphate solubilization and inhibitors of ethylene (C2H2) biosynthesis against different biotic and abiotic stresses, having biocontrol activity (Fig. 11.1). They get multiplied at low-density population compared to bacterial pathogens and rhizospheric bacteria (Rosenblueth and Martinez Romero 2004), providing better protection than rhizospheric bacteria against abiotic stress. They help in repressing nematode proliferation in the rotation of other crops with other plant hosts (Sturz and Kimpinski 2004). They grow usually inside cellular space and plant vascular tissues. According to an estimation, about 129 or more endophytic bacterial types have been isolated from different kinds of plants, particularly, gram-positive and gram-negative bacteria representing about more than 54 genera. Gaiero et al. (2013) reported that bacterial endophytes promote the growth of plant, but have not obtained productive success to influence the growth of plants in the field conditions. Endophytes act as plant growth promoters, suppress pathogens, remove contaminants and help in solubilizing phosphate or contributing to plant nitrogen assembly (Rosenblueth and Martínez-Romero 2006).

Fig. 11.1
figure 1

Mechanism, classification and significance of endophytic bacteria

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6.2.1 Bacteria Associated with Plants Produce Bioactive Compounds

Bacterial endophytes have several potential applications in drug discovery and pharmaceutical (Tang et al. 2008) and serve as a key source of natural products for application in oxidative stress and as new bioactive agents (Nongkhlaw and Joshi 2015). They also act as antimicrobial agents that counteract the multidrug resistance in pathogenic microbes. The use of beneficial metabolites isolated from endophytes i.e. Amines and amides as the natural protective defense against pathogens which shows the toxic effect on insects but not mammals are increasing day by day and have shown a significant response compared to antimicrobial compounds that are environmentally friendly. Many endophytes adopt resistance mechanisms against plant pathogens by producing extracellular hydrolases, e.g. proteinase, cellulases, esterases and lipases establishing resistance against plant invasions (Tan and Zou 2001). The endophytic fungi enhance growth attributes of a dwarf mutant which is gas deficient, such as Dongjinbeyo and Waito-C rice through plant growth regulator production (Waqas et al. 2012).

6.2.1.1 Pseudomonas Species

They are facultative aerobic microorganisms and gram-negative bacteria; they can grow, both under aerobic and anaerobic conditions; however, their growth is fast in the aerobic condition under suitable nutritive ecological conditions. The physical appearance of this bacterium could be changed by using tools of molecular biology (Chin-A-Woeng et al. 2002). These bacteria with a minimum pathogenicity potential are saprophytic in nature, and show adaptation to changed environmental conditions, where they are found in all types of ecosystems, i.e. soil, water, plants and animals (Madigan et al. 2010).

6.2.1.2 Phenazines

These are heterocyclic compounds with aroma, produced by Xanthomonas, Streptomyces, Mycobacterium, Burkholderia and Brevibacterium (Pierson III and Pierson 2010), which could be extracted easily from microbial culture and have significant nitrogen and brightly coloured pigments. According to a hypothesis, as a subsistence capability approach, phenazines are used by bacteria for a competition of nutrients or improving the ability of survival (Laursen and Nielsen 2004) that is not easily understood. They also affect negatively electron flow and functional enzymes that play a vital role in the cellular respiration (Yu et al. 2018).

6.2.1.3 Pyrroles

Pyrrole pyrrolnitrin is considered to be a very prominent bacterial compound which is produced by Burkholderia and Pseudomonas in some of the bacteria in secondary metabolism (Kilani and Fillinger 2014). Pyrroles in general function in electron transportation to a respiratory chain of complex III in mitochondria and play a key role in preventing protein and lipid oxidation (Gomes 2012).

6.2.1.4 Siderophores

These are compounds diversely produced by genus Pseudomonas with low molecular weight and tendency of high affinity towards iron, helping in the metabolism and growth of organisms (Fedrizzi 2006). Pyoverdin and pyochelin have the ability to remove iron to perform the biological control of plant pathogens and decline in population (Scavino and Pedraza 2013).

6.2.1.5 Hydrogen Cyanide

It is a highly volatile compound which produces cyanide anions and is highly toxic when it comes in contact with air or water. A number of biocontrol PGPB have the ability to synthesize hydrogen cyanide (HCN). If the HCN produced by these bacteria were the only biocontrol mechanism being used in most instances, the low level of HCN would not be particularly effective at preventing the proliferation of most fungal phytopathogens. However, it is often the case that biocontrol PGPB that can produce HCN also synthesize some antibiotics or cell wall degrading enzymes (Fernando et al. 2005). Moreover, it has been observed that the low level of HCN synthesized by the bacterium improves the effectiveness of antifungals directed against fungal pathogens thereby ensuring that the fungi do not develop resistance to the particular antifungal in question. Thus, HCN synthesized by PGPB appears to act synergistically with other methods of biocontrol employed by the same bacterium (Fernando et al. 2005). It also stimulates ISR in plants and is also involved in the cytochrome oxidase inhibition playing a key role in electron transport during cellular respiration to prevent adenosine triphosphate production (Spence et al. 2014) and also acts as antinematode agent. The model nematode Caenorhabditis elegans was repelled by using HCN together with pyrrolnitrin (Nandi et al. 2015). Likewise, Kang et al. (2018) observed a positive correlation of HCN production with nematode biocontrol.

6.2.1.6 Bacillus Species

Biocontrol agents such as antibiotics are used to suppress pathogens that produced substances with the competition of antimicrobial activity, enhancing the growth of a plant and simulating resistance induction (Xu et al. 2013). They have an antimicrobial role formed by Bacillus sp. or ribosomal antibiotics like subtilin, chitinase, sublancin, Tas A and subtilisin A. They adopt environmental variations by forming endospore-resistant structures (Hoyles et al. 2012). Enabling polyketide synthases or NRPS formed various other compounds, e.g. mycobacillin, bacilysin, difficidin, chlorotetain, bacillaene, cyclic lipopeptides, and rhizocticins with a wide-ranging biotechnological significance (Shafi et al. 2017).

Iturins, consisting a subgroup of iturin, mycosubtilin and bacillomycin, through pore formation in the cytoplasmic membrane, affect cells (Gong et al. 2015). The isomers of iturin A have a high antifungal activity against several microorganisms (Ye et al. 2012). Bacillomycin belongs to the family iturin lipopeptide, with a ring structure. It helps in spore germination, mycelial growth inhibition, antifungal action and productivity and also has high ultrastructural variations, i.e. cell wall and membrane damage (Gu et al. 2017). Mycosubtilin considerably affected some of the crops like F. oxysporum, B. cinerea, R. solani and Pythium sp. by targeting cells of cytoplasmic membrane (Leclère et al. 2005). Fengycins, also called plastathins, consisted of fatty acids which are hydroxylated, having solid antifungal activity (Gong et al. 2015). Surfactins are hydroxylated fatty acids, which are not toxic fungi themselves. A combination of surfactins with iturin A shows the tendency for antifungal action (Deravel et al. 2014).

6.2.1.7 Actinobacteria, Beta- and Gammaproteobacteria

Actinobacteria are gram-positive bacteria generally found abundant in soil, water environment, animals and any other natural place and in anaerobic conditions with important morphological variations (El-Tarabily and Sivasithamparam 2006). The use of actinomycetes has been started by a human in the recent few decades assuring the quality of agricultural products. They have high potential as biological controlling agents of pathogens of plants. Antimicrobial compounds can be produced by actinomycetes acting as inhibition promoters against phytopathogens, as they also are producers of 70% of antibiotics (Lasudee et al. 2018).

Betaproteobacteria consisted of more than 400 species and 75 bacterial genera. They are mostly heterotrophic, while a few of them are known to be autotrophic and photo-heterotrophic, helping in soil pH maintenance and nitrate usage as a side acceptor of an electron. The majority of taxa within this class contain HPUT, which has been reported only for selected species of the gammaproteobacterial genus Shewanella and a Colwellia species, However, a few taxa have been reported to lack the Betaproteobacteria-specific HPUT (Ionczewski and Foster 2014).

However, Gammaproteobacteria consisted of a variety of polyamine patterns such as PUT, DAP, SPD and CAD in combinations and in a single form. Majority of Shewanella sp. contains HPUT and in common a diamine which is a clear seen trait for most of the beta bacteria. However, these species within the genus Shewanella did not show any relationship with this diamine. Species of the family Pseudomonadaceae consist of major polyamines PUT and SPD and often also CAD. Species of the genus Aeromonas contain DAP and PUT as major components, and significant amounts of CAD may also be present. The family Enterobacteriaceae requires separate consideration. Almost all species of the assigned genera contain the major diamine PUT, and the majority of them also contain major amounts of DAP and/or CAD and some also contain SPD. The physiological age of the biomass from which polyamines were extracted can greatly influence the resulting polyamine pattern. In late exponential phase cells of K. pneumoniae, PUT is predominant, and DAP is a second major polyamine. In contrast, CAD is predominant in late stationary phase cells, and PUT is a second major polyamine. These changes in the polyamine contents are reflected by a twofold reduction of relative amounts of DAP and PUT in late stationary phase cells, whereas the amount of CAD increases tenfold. Applying the same test conditions, DAP is the major polyamine in E. cloacae, and its relative amount is almost unaffected (reduced from 51 to 45%) by the growth phase of the cells. At the same time, CAD is increased from 2 to 22%, and relative amounts of PUT are unaffected as well. In late exponential phase cells of Y. regensburgei, PUT is the major polyamine (54%), whereas in stationary cells, PUT and CAD are predominant (33.5 + 1.3%) (Hamana and Kishimoto 1996).

7 Volatile Organic Compounds

Compounds which are organic, have high vapour pressure, and easily evaporate at room temperature and are produced by actinobacteria having great potential as biopesticides in the field of agriculture (Sharma and Salwan 2018) are known as volatile organic compounds (VOCs). They are also known as solvents having variable volatility and lipophilicity. A small amount of VOCs is present in correction fluid, graphics, copier and printer and carbonless copy paper. These are also found in craft material (adhesives, photographic solutions, glues and permanent markers) as well. These compounds have some major health concern from the last three decades due to their carcinogenic property (presence of predominant solvent, i.e. CHCl3, trichloroethylene, tetrachloroethylene, benzene xylenes and ethylbenzene). VOCs volatilize during production, transport, storage and processing activities; hence their entry point to the environment is through evaporation process.

7.1 Ecological Role of VOCs and Interspecies Interactions

Loss in biodiversity and changes in ecosystem behaviour due to environmental pollution are major concerns to mankind causing different physiological disorders and diseases in human. Volatile organic compounds, with physical and chemical properties and mean life in the atmosphere, are introduced through biogenic and anthropogenic activity forming tropospheric ozone and less than 2.5 μm particles in big cities, degrading the quality of air and causing air pollution (Robinson 2005). According to World Health Organization, compounds with less than 250 °C boiling point (at a standard pressure of 101.3 kPa) are known as volatile organic compounds (Habre et al. 2014). Their life span is usually from few minutes to several months; hence transport through large distance from the emission source to the living body through air or skin causes several pathogenic diseases like atopic dermatitis, asthma, neurologic problem, etc. The International Agency for Research on Cancer (IARC) considered VOCs of group 1 as carcinogenic for humans (Rumana et al. 2014).

Direct and indirect interaction in community-wide scenario greatly depends on chemical traits of plants, which have a key role in running of these processes. Plant-mediated interaction has several effects (allelopathy, natural communities, resource competition and facilitation) on plant community organization (Callaway 1995), while the structure of a community is due to mutualistic and antagonistic interaction of plants with other organisms. Such interactions directly alter physiology of another organism by plant traits or indirectly affect the third party (which is not involved in the interaction) due to the interaction of two organisms (Ohgushi et al. 2007). As a result, plant-mediated interaction adds complexity within community interactions and links potential organism of different trophic levels (Utsumi et al. 2010). It is well known that the effect of plant-mediated interaction on the agricultural system is of great importance. These effects include herbivore, pathogen and pollinators which affect plant productivity (Schiestl 2015).

7.2 Microbial VOCs (mVOCs) in Bacteria and Plant Interactions

Microbial interaction plays an important role within and outside kingdom interaction due to a variety of compounds and secondary metabolites released by these microorganisms. Plant and soil-related microbes produced a group of secondary metabolite which was reported; however, there are many more groups which are still unexplored. These compounds are small and odorous with high vapour pressure, low boiling point, a lipophilic moiety and low molecular weight, which has facilitated above and below ground diffusion and evaporation processes due to pore spaces in the ecological rhizosphere and soil (Effmert et al. 2012). The mVOCs produced belonging to several classes (ketones, alchohols, pyrazines, alkenes, sulfides, benzenoids, terpenes, etc.) are influenced by different factors which include nutrient and oxygen availability, the growth stage of microbes, temperature, soil moisture, pH, etc. (Schulz-Bohm et al. 2015). mVOCs benefit the plants in several ways which include induced resistance against plant pathogen, source of nutrients and plant secondary metabolite production and induce soil fungistasis and suppressiveness (Wintermans et al. 2016). There is a decrease in spore formation of B. cinerea and Alternaria alternata, and increase in plant defence reactions is due to a 6-pentyl-pyrone, a distinguishing compound of Trichoderma asperellum (Kottb et al. 2015). VOCs extracted from roots have multiple roles, i.e. as defence metabolites, chemical attractants, carbon sources, etc. (Van Dam et al. 2016).

7.3 Microbial VOCs in Fungi-Plant Interactions

Recent studies have shown the capability of soil fungi to produce volatile organic compounds that enhance growth (Lee et al. 2015). There are beneficial effects of Trichoderma strains found in root ecosystem and soil to enhance plant growth by mimicking themselves as secondary metabolites. This mimicry effect significantly improves biomass, plant size, chlorophyll concentration and root size of tomato and Arabidopsis (Lee et al. 2016). 1-Hexanol at low concentration had a growth-promoting effect on Arabidopsis while at high concentration it inhibited plant growth (Jelen et al. 2014) showing the change of volatile fungal profile with maturation and growth. Moreover, the survival of plants in certain habitats is also mediated by VOCs of endophytic fungi. VOCs enhance the growth of host by reducing the availability of nutrients to endophytic fungi showing the toxic effect of VOCs on endophytic fungi (Macias-Rubalcava et al. 2010).

7.4 Microbial VOCs in Fungi-Bacteria Interaction

There are different phenotypical responses in the interacting behaviour of fungi and bacteria due to fungal VOCs. Some of the recent studies showed the role of fungal VOCs in the suppression of bacterial growth, for example, VOCs formed by mushroom (oyster) have an inhibitory effect on B. subtilis and B. cereus (Werner et al. 2016). Transcriptomics and proteomics studies showed that there was a change in protein and gene expression (associated with energy metabolism, motility, secondary metabolite production, signal transduction and cell envelope biogenesis) of S. plymuthica when kept open to VOCs produced by Fusarium culmorum, a fungal pathogen (Schmidt et al. 2017). All the results indicate the significance of VOCs as molecules of signalling in bacterial and fungal interaction. In response to fungi, bacteria can also produce some VOCs which have an inhibitory effect on fungal growth. This phenomenon is known as soil fungistasis (Garbeva et al. 2011). VOCs produced by Streptomyces spp. have an inhibitory effect on the growth of a fungus Rhizoctonia solani thereby reducing the chances of diseases on the plant (Cordovez et al. 2015).

7.5 Endophytic Plants Secreting Microbial VOCs with Potential Aspects

The progress in biological, chemical and genomic analysis has led us to improve these mysterious natural volatile organic compounds produced by plant endophytes. We are at the beginning to explore the properties and nature of secondary metabolites, and by now several metabolites positively affect biocontrol, the stimulants of plant growth, biofuel and biopharmaceuticals. The significant volatile organic compounds produced organics of endophytes with the key role and their effect on socio-economic development (Table 11.1).

Table 11.1 Volatile organic compounds and their functions
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7.6 VOCs of Endophytes as a Plant Growth Stimulant

Plant endophytes ranging from bacteria to fungi produce a diverse class of volatile organic compounds (VOCs) that are important for the development of symbiotic relation under highly competitive environment with the host. They provide for an alternative to chemicals used to protect plants from pathogens and thus allow for better crop welfare. Microbial volatile organic compounds (mVOCs) act as a biocontrol agent to control phytopathogens and as biofertilizers to promote plant growth. Various recent studies have proven the importance of mVOCs (eco-friendly) like a cost-effective sustainable strategy in the use of agriculture, which improves productivity, plant disease resistance and growth. Moreover, mVOCs can also be used as the substitutes to bactericides, fungicides and pesticides which are harmful (Ryu et al. 2003). It was evident that VOCs enhance plant nutrition, growth, health processes and resistance to stress, coined by a group of scientists who reported improvement in growth of Arabidopsis thaliana by volatile organic compounds released by Bacillus subtilis GB03. Furthermore, Bacillus species release volatiles that modify root architecture (Gutiérrez-Luna et al. 2010). Among the first volatiles produced by bacteria was 2,3-butanediol, which confers resistance in plants (Ryu et al. 2004).

7.7 VOCs of Endophytes as Aroma and Flavour Compounds

Some endophytes that live in aromatic plants are of commercial importance and produce abundant VOCs which produce aroma and fragrance. Terpenes, terpenoids and ester molecules are used in the preparation of beverages and food which has valuable aroma and flavour. Many fungal VOCs are found to be identical to natural flavouring and fragrance produced by plant molecules and are therefore of huge importance in chemical, feed, pharmaceutical, food and cosmetic industries. The fungal endophytes, which are volatile, produce a desirable aroma and flavour property which is used in many nonalcoholic beverages, jellies, backed goods, cheese, puddings, candies and other food products. The major component of rose oil, methyl eugenol (having a high demand in industries), has been identified in fungal endophytes Aspergillus niger and Alternaria sp. which were extracted from Rosa damascena (Abrahao et al. 2013). A remarkable molecule of terpene (β-caryophyllene) with spicy flavour has been reported in endophytic fungus volatile (Phialocephala fortinii) and extracted from Pinus sylvestris (Molina et al. 2012).

7.8 VOCs of Endophytes as Mycofumigation Agents and Biopharmaceuticals

Endophytic compounds are known to have anticancerogenic, antibacterial, immunosuppressant and antioxidant activities, reported from different researches of the last few decades. VOCs enhance plant defence and are discovered to have new antimicrobials to treat many diseases in medical science. Fungal endophytes produced different secondary metabolites used in pathogenic and pests attack control (Hung et al. 2015). Muscodor albus (an endophyte fungus) produce more than 25 volatile compounds extracted from cinnamon tree and are thought to have strategic defence against many pathogens (Stinson et al. 2003). The first ever fungus endophyte, M. albus, was thought of having potential antimicrobial function against humans and phytopathogens. The volatiles of M. albus are also used to treat different diseases like silver scurf, bacterial soft rot and dry rot in potatoes (Solanum tuberosum) inhibiting the three infectious fungi (T. indica, T. tritici and Tilletia horrida) causing many diseases in rice and wheat plants (Schalchli et al. 2016). Moreover, a special volatile, 2-phenylethanol, found in Aspergillus niger (endophyte fungi of rose) has great importance as preservatives in pharmaceuticals (Wani et al. 2010).

7.9 Significance of mVOC and Future Perspectives on Commercial Basis

Since the improvement in the analysis of gas-phase molecules, it can be observed that endophytic VOCs change biologically and chemically in a more active way. Gas chromatography-mass spectrometry (GC-MS) is known to be the most common and effective method that identifies volatile components but limited to the column used in this spectrometry. These columns used are selective for detecting some chemical groups of VOCs but not the total VOCs (Insam and Seewald 2010). Recently, quantitative analysis of VOCs becomes easy using a technique called proton transfer reaction-mass spectrometry (PTR-MS) that is a very sensitive method (Strobel et al. 2011). Hydronium ion in gas phase is used as a sourcing agent to monitor VOCs in ambient air. Nowadays, the most effective tool to detect and identify VOCs is the combination of PTR-MS and GC-MS (Insam and Seewald 2010).

Various environmental factors such as the composition of a microbial community, nutrient content, pH, humidity and temperature influence microbial volatile production (obtained as a complex mixture). These factors made it difficult to identify whether the effect is on an individual molecule and what is the mechanism. Hence, the commercial application of this volatiles is very limited as compared to the economic implications. Now it is well understood that there are varying differences of volatile compound effect from lab to field (Song and Ryu 2013). However, volatile compounds as a biocontrol and growth-promoting agent are effective against human and plant pathogens (Grimme et al. 2007). Endophyte developed strategies to overcome the challenges related to climate change (salinity, water and drought stress and high temperature) faced by agriculture crops. Moreover, the use of volatile compounds proves to be important in overcoming adversities on plant communities.

8 Signalling Pathway of Secondary Metabolism in Endophytes

To establish a stable biological community collaboration between plants and organisms is required. An ultimate model of studying the benefits of the interaction of fungi and plant is the relation between cool-season grasses and fungi (Schardl et al. 2013). The infection of endophytes and its effect in the light of expression profile relay on the sequencing of RNA. The reprogramming of infection of endophytes results in metabolism which makes secondary metabolism easier compared to primary metabolism. These types of infections can also produce variations in host development such as trichome formation and biogenesis of cell wall. The endophytic diazotrophic bacteria result in nitrogen signalling with endophytic bacteria. The diazotrophic bacteria help in growing a different variety of root associations and fixing N2 to plant-available ammonium. The biogenesis pathway of swainsonine was reported to be beneficially important in the medical treatment of cancer and plays a significant role in anticancer activities and in regulating the immune system (Carvalho et al. 2014).

The mechanism for the signalling of ethylene reported that this signalling pathway helps in the production of endophytic fungus, the Gilmaniella sp. AL12, through induced production of ethylene in Atractylodes lancea (Yuan et al. 2016). Plantlet pretreatment with inhibitor aminooxyacetic acid (AOA) suppressed endophytic fungi-induced accumulation of sesquiterpenoids. The amino oxyacetic acid with ethylene inhibitor helps in the pretreatment of plantlets which inhibits the endophytic fungi (Ren and Dai 2012). The biosynthesis of sesquiterpenoid gives a theoretical base for active compound development in A. lancea and other compound biosynthesis like menthol, ginseng saponins, glycyrrhizic acid, artemisinin and paclitaxel. Jasmonic acid functions in the signalling pathway of fungal endophyte induced volatile oil for the plant Atractylodes lancea. Reports from research observed that jasmonic acid also helps in molecule signalling in mediated volatile of nitric oxide and hydrogen peroxidase by an endophytic fungus (Table 11.2).

Table 11.2 Mechanism of metabolite production by endophytic fungi
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9 Molecular and Metabolic Cooperation of Hosts and Endophytes

Many endophytes have the capability of producing different bioactive metabolites, which may be used as the agent for heals, either directly or indirectly, against a wide-ranging disease (Kharwar et al. 2011). Their vast biodiversity combined with the capability of biosynthesizing secondary metabolites has provided the impetus to many endophytic studies (Alvin et al. 2014). A symbiotic association between asexual endophytes of fungus and tall grasses from Epichloe exposes alkaloid biosynthesis that produces either beneficial or damaging effects (Ekanayake et al. 2017).

10 Uses and Importance of Endophytes in Plant Health

10.1 Antibiotics Prepared from Endophytic Microbes

Endophytes are a good source of antibiotics (organic natural products having low molecular weight) produced from active microorganisms. These natural products not only kill inclusive diversity of harmful pathogen (phytopathogen) but also those (bacteria, virus, protozoa and fungi) affecting humans and animals. The imperfect stage of Pezicula cinnamomea is Cryptosporiopsis quercina , known to be a fungus (isolated from an endophytic medicinal plant of Eurasia, i.e. Tripterygium wilfordii) which is associated with various deciduous species in European countries. Echinocandins, pneumocandins and antifungal are the major sources of bioactive compounds. A group of fluorescent bacteria (Pseudomonas viridiflava), mostly related to plants (linked with a portionof grass leaf present in or on the tissues), produce ecomycins (Strobel et al. 1999).

10.2 Antiviral Compounds

Another charming use of endophytic fungal antibiotic products is viruses’ inhibition. sp. is an endophytic fungus, isolates two different cytomegalovirus protease inhibitors Cytospora (Ctyonic acid A and B) by solid-state fermentation process. Using mass spectrometry and NMR methods, structures of isomers can be fully elaborated. There is a still long way to detect the potential of endophytic compounds having antiviral activities. Inadequate screening systems of a virus limit the detection of antiviral compounds, but still some detected compounds have shown encouraging results against viruses.

10.3 Volatile Antibiotics from Endophytes

Muscodor albus (fungus), isolated from a cinnamon tree, is a newly studied fungus from endophytic group (Worapong et al. 2001). A fungus having no spores (xylariaceaous fungus) produces a mixture of volatile compounds (having antibiotic effect) that can alter different types of fungi and bacteria (Strobel et al. 2011). A non-Muscodor species, Gliocladium sp. (G. sp), for the first time has been discovered to be a producer of volatile antibiotics (different from volatile compounds of M. albus and M. roseus). Indeed, annulene could be found as the most abundant volatile inhibitor; previously, this was the first discovered natural product in an endophytic fungus and was used as rocket fuel (Stinson et al. 2003).

10.4 Biocontrol Activity of Endophytes

A large number of microorganisms are present inside plants producing microbe-plant interaction (some are destructive while others are beneficial). These microorganisms are rich sources of nutrients. Rhizobia, mycorrhiza and actinobacteria help the plants to get nutrients from the soil in a symbiotic interaction. Many bacterial species reduce the activity in the root system, stem, leaves and another plant organ by blocking plant tissues and vessels, but most of them are beneficial (metabolites producer) and help to increase plant defence mechanism against pathogens, nutrient uptake, growth promotion and hence crop productivity. Streptomyces belonging to actinomycetes are species-specific (having symbiotic relationship with plants) and are very much helpful to produce a variety of antibiotics. They protect the plants to fight against a pathogen, in response to boost up plant exudate production which is important for the growth of Streptomyces (El-Shanshoury 1991). Endophytic actinobacteria produce a chelated iron compound (siderophores), and chitinolytic enzymes have a supplemental role to hinder fungal growth. They also produce chitinase which damages fungal cell wall. About 90% of chitinolytic microorganisms are actinomycetes (Hastuti et al. 2012). A large number of bacteria (especially streptomycetes) obtain nutrients and degrade environmental chitin and soil-borne fungal cell wall by producing chitinases. Numerous bacteria, and especially streptomycetes, also form a variety of chitinases. Thus, selection and exploitation of chitinolytic mediators helps to control phytopathogenic fungi.

10.5 Endophytic-Mediated Plant Growth

Plants face hostile and unfavourable conditions in normal conditions, collectively called abiotic stresses which cause prevention in growth and homeostasis. Below or above optimum levels, severe ecological conditions often cause an effect on plant growth and development. Abiotic stress includes high or low temperature stress, nutrient stress, heavy metal stress, hunger stress, acidic, salt and drought stress that badly affect plant growth (Chaves and Oliveira 2004). Biotic stresses may consist of damage to plant caused by viruses, bacteria, fungi, pests, parasites, native or cultivated plants and weeds. Several microorganisms containing fungi, protozoa and bacteria make a symbiotic or beneficial association with plants, providing benefits to avoid various environmental stresses and support the development and growth of the plant as well (Shahzad et al. 2018). These endophytes contribute significantly to regulate many crucial physiological processes and enhance the overall growth and vigour of plants. For example, the endophytic fungi facilitate the cuticular cellulose degradation by improving the consequence of carbon absorption and promoting the germination of seed (Jerry 1994).

10.5.1 Production of Growth-Induced Compounds and Phytohormones

Plant growth, defence response and physiological processes are positively affected by phytohormones (regulatory molecules) (Egamberdieva et al. 2017). IAA homeostasis affects various physiological processes, comprising germination of a seed, cell differentiation, development of vascular tissues, vegetative growth, development and elongation of root, photosynthesis and pigmentation (Ahmad and Kibret 2013). Microbial representatives of this group enhance plant growth and development by producing a variety of proactive substances such as siderophores, 1- aminocyclopropane-1-carboxylate deaminase (ACC), phytohormones, e.g., indol acetic acid (IAA), gibberellic acid (GA), volatile organic compounds (VOCs), antibiotics, cyanides, and fungal cell-wall-degrading enzymes (Long et al. 2008). The enzyme ACC deaminase is thought to be a key trait in the arsenal that PGPB uses to promote plant growth. ACC and IAA deaminases produced by the rice plants cultivated in the fields of coastal areas recognized six endophytic bacteria in a study reported by Bal et al. (2013). Gibberellic acid-producing endophytic microorganisms often contribute to the improvement of the host plant yield.

Phoma herbarum (an endophytic fungus) obtained from soybean roots under salt stress, showed growth enhancing properties, leading to increased active GAs production and biomass (Hamayun et al. 2010). Strains (SF2, SF3 and SF4) of bacterial endophytes from sunflower under stress condition produced salicylic acid which was helpful to enhance plant growth (Forchetti et al. 2010). Root colonization by endophytic fungus Piriformospora indica caused stimulation in the growth and development of Arabidopsis due to the production of cytokinins (Vadassery et al. 2008).

10.5.2 Potential Role of Endophytes in the Acquisition of Nutrients

One of the key roles is the acquirement of plant nutrients from its natural habitation where most of the plants do not have the mechanism naturally to get vital nutrients. Nitrogen is essential for the plant growth and development but they can not obtain from the atmosphere, and dependent fertilizers containing nitrogen. Whereas, some other plants make a strong association with nitrogen-fixing bacteria, helping out the plants to consume atmospheric nitrogen. Others make symbiotic associations with the nitrogen-fixating bacteria, mostly seen in legumes, which help the plants to utilize the atmospheric nitrogen. However, the colonization of endophytes is markedly different than those of rhizobial nitrogen-fixating symbionts (Doty 2011) or an exchange offer by photosynthesis producing carbohydrates is given for available nitrogen. Through energy involvement and nitrogenase enzyme, ammonia is formed from atmospheric nitrogen by symbionts. Herbaspirillum spp., Acetobacter spp. and Azoarcus spp. help to fix nitrogen from the atmosphere in an association with the actinorhizal and rhizobial symbiosis of plant and bacteria. As like rhizobial bacteria, endophytic organisms adopt various strategies to protect nitrogenase, an enzyme that is sensitive to oxygen. In rhizobial condition, oxygen is usually at very low concentration, where, the haemoglobin in the legs provides help to clean free oxygen traces in the nodules. The endophytic associations between Gluconacetobacter diazotrophicus and sugarcane and pines are the well-studied symbiotic associations where the endophyte helps the host plant in nitrogen fixation (Hardoim et al. 2015). A high chelating iron compound, siderophores, functions in the absorption of iron (Johnson et al. 2013).

10.5.3 Endophytic-Mediated Tolerance to Abiotic Stress

Environmental stresses often disrupt the growth and development of plants. To overcome the challenges in such a situation, the endophytes present inside the host plant help out. Though endophytes have a very short life in comparison to its host, the short life cycle helps the host cope with its diversity. In association with plant endophytes, different strategies are then adopted to reduce the abiotic stresses emanating from the natural habitation of the host. Interaction between plants and microbes can be mostly classified as detrimental or neutral. In most of the cases, the interaction is considered as beneficial, because microbes consume the plants organic product for respiration and metabolism and at the same time help in nutrient recycling and tolerance against various stresses. Beneficial microbes encourage plant growth development and inhibit the plant diseases by enhancing different types of the mechanisms which mainly include production of growth regulators, hormones, and pathogen-inhibiting compounds (Lata et al. 2018). For example, Phoma spp. and Penicillium help to promote growth (uptake of nutrients and plant biomass) and overcome osmotic and drought stress caused by elevated polyethylene glycol and sodium levels (Waqas et al. 2012). Plants such as tomatoes and rice with useful endophytes could survive in water-deficient conditions, even exhibiting better growth potentials than plants which lack these endophytes (Lata et al. 2018).

Salt and drought stress mitigation is normally concerned with consequent scavenging and accumulation of reactive oxygen species (ROS) (Sekmen et al. 2007). Though reduced levels of ROS to plant may support various antioxidants, e.g. tocopherol and glutathione, the main ROS scavengers include glutathione reductases (GR), monodehydroascorbate reductase (MDHAR), and dehydroascorbate reductase (DHAR) (Rouhier et al. 2008). ROS accumulation in the cells of plants can be toxic, leading towards DNA, lipid and protein oxidative damages. ROS respond signalling cascades while acting as the preliminary plant stress event (Noctor et al. 2017). Pathogen-plant interaction observed the accumulation and production of ROS, similarly, leading salt and drought stress in association with successive scavenging of species of reactive oxygen (Sekmen et al. 2007). Whereas, ROS in low concentration is significant for the signalling and growth of pants, raised accumulation of ROS can create harmful effects. Endophytes residing within the plants benefit their host to manage the accumulation of ROS and, hence, protect them from the harmful effects of ROS. Various endophytic plants like those associated with roots are studied, showing the tolerance of host plant to the toxic level of heavy metals (Choo et al. 2015).

10.5.4 Endophytic-Mediated Response of Plant Defence

Plant growth and development is often compromised by the onset of several environmental stresses as plants prioritize resistance over growth. In this scenario, the endophytes living inside the host plants come in great support in overcoming the challenges. Although endophytes are very short-lived as compared to their host, their shorter life span helps in their rapid evolution in aiding the host toward tackling the diversities. The capacity of different endophytes providing resistance against these environmental stresses are exploited in modern sustainable agriculture (Zamioudis and Pieterse 2012) (Fig. 11.2). Moreover, the endophytic colonization in the plants induces a response to defence strategy while providing higher resistance to other pathogens of plants. Such idea in plants is known to be induced systematic resistance (ISR) which could be normally observed in endophytic association of plant and bacteria (Robert-Seilaniantz et al. 2011). ISR induction and pathogen defence enhanced repeatedly were studied in response to Bacillus spp. and Pseudomonas colonization. Endophytic bacteria can control plant defence manipulation and simulate the effect of primary defence against plant pathogens through ISR (Bae et al. 2011). Contrariwise, the endophytic fungus produces the chemical compound that inhibits growth, and these compounds function against offensive herbivores and invaded pathogens while protecting their host (Brader et al. 2014).

Fig. 11.2
figure 2

Different mechanisms adopted by endophytes in promoting plant growth and mitigating different types of stress

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11 Secondary Metabolite Production: Challenges in Endophytic Research

Although a lot of researches have been done on endophytes showing valuable sources of new metabolites, still, many features of endophytes are not explored. Endophytes have significant importance in the industry producing various enzymes which are helpful to speed up many processes, and also stresses in many plants are also relieved by endophytes. Although many endophytes are forming bacterial and fungal origin and affect many aspects of plant growth (growth, yield and bioactive metabolite production), in-depth understanding of secondary metabolites produced and a chemical released by endophytes in a host plant still needs to be explored. There is a need to investigate the role of endophytes in bioreactors although researches are there where some anticancer metabolites are produced by endophytes (Amna et al. 2006). A classical example of this might be Entrophospora infrequens (an endophytic fungus) that produced some anticancer alkaloid camptothecin in bioreactors. Nowadays, “omics” tools are used to better understand the host-endophyte niche. These omics tools consist of genome sequencing, next-generation sequencing, comparative genomics, microarray, metagenomics and metatranscriptome which help to recognize metabolic diversity and genetics of similar or related microbes. There is a lack of knowledge in the production of endophytes on a large scale for bioreactors to know the pathway shared by hosts and endophytes, an area of research for many scientists to explore and focus on.

12 Recent Developments in the Field of Microbiome Research

Studies regarding the use of microbiome have improved radically in recent years, due to the cost of analysis reduction and technological advancement. These researches have opened a gateway of data which has increased a significant amount of intuition to the scope of microbial populations consisting of interaction and their effect inside or outside of host as a particular portion of the ecological community. Keeping in view the significant role of microbiome including their combination with the host and other microbes provides a base for studying the engineering of new diagnostic techniques and strategies, which can be used in a diverse array of fields starting from ecology and agriculture to agriculture to medicine and from forensics to exobiology. The microbiome refers to a set of highly interactive microbial species that is shaped by the environment in which it exists, which includes hosts, and exogenous natural and human factors.

12.1 Interaction of Host with Microorganisms

The host along with its entire related microorganism is collectively called as “holobiont”, while the study of host and microorganism genome is called “hologenome”. According to researchers, the unit for natural selection is holobiont (Davenport et al. 2017). Every host can adopt two ways to procure microorganisms which are inherited from the parents (vertical) and taken from the environment (horizontal). A correlation of similar microbiome and host phylogeny is due to vertical transmission hence known as “phylosymbiosis”—however, it is important to bear in mind that the emergence of phylosymbiosis is irrespective of vertical transmission, e.g. contact of host species to other members (Groussin et al. 2017). Co-diversification (similar selective pressure or co-speciation results in microorganism with similar evolutionary histories) and co-speciation (host speciation results in microorganism speciation) are also the outcomes of vertical transmission (Davenport et al. 2017). In contrast to vertical transmission, horizontal transmission causes breakage of association with evolutionary histories, so mix them up. Hence, erode phylosymbiosis.

12.2 Interaction of Host and Microbiome with the Environment

12.2.1 Relationship of Microbiome with Environment and Ecology

Recent studies show the effect of microbiome on the different features of human health (Martí et al. 2017). However, generally speaking, interaction of microbiota with environment gives a clear picture of a healthy ecosystem and mankind. A healthy microbiome and environment results in healthy human microbiome and vice versa (Lloyd-Price et al. 2016). Therefore, it is very much important to study microbiome in ecosystem. The functional and structural richness of ecosystem communities determines the individual and populations of microbiome at various sides of biological organization (Rees et al. 2017).

12.2.2 Microbiome Ecology in a Population

There is a deep, empirical, computational and theoretical understanding of community ecology (a sub-branch of ecology) nowadays. Diversity determines a stable microbiome-related population health and microbiome itself (Coyte et al. 2015). The state of microbiome is determined by functional diversity (a more meaningful and fundamental feature) rather than taxonomic diversity (Li and Convertino 2019). Metacommunity approach (a useful tool to predict biodiversity assemblage) of microbiome is determined by alpha (diversity within), beta (diversity between) and gamma diversity (total diversity of microorganisms) that consists of multiple interacting communities. The scale for sharing fluctuation of information representing microorganism interdependencies greatly varies with biology, space and time (Leibold et al. 2004).

12.2.3 Nexus of Human, Microbiome and Environment

On a long and short timescale, microbiome research helps in making a positive relationship between human health and the environment. Efforts have been made to map microbiome of the globe for various habitats but the information regarding environment and microbiome population interaction is still lacking. Hence, a steady struggle for alternations in symptom-specific or disease analysis of microbiome to an outside environmental agent is the need of the day (Karkman et al. 2017; Mitmesser and Combs 2017). The noteworthy that targeted monitoring, models, and theory guides this ecological examination need no in-depth health analysis of microbiomes but time, space pattern establishing an ecological state of the co-evolving microbiomes Parfrey and Knight (2012) such as the pattern in biodiversity (Ochman 2016) and other services relating to the socio-ecological ecosystem.

13 Conclusion

Bioactive compounds, normally, can be used in controlling various diseases of plants biologically. The biological production of such antimicrobial bioactive compounds depends specifically on the resources and space competition. As a natural derivative metabolite, bioactive compounds played a havoc role in the world of pharmaceuticals and agrochemicals to combat against various diseases in plants and play a key role in human welfare. A huge number of biological antimicrobials are formed as a result of biological secondary metabolism providing benefits to the plants. Such bioactive metabolites have great potential use in the agriculture industry, specifically in controlling pathogens, and concerning the sustainability of the environment. Where the endophytes are known as biological endosymbiotic microbes found almost everywhere in the ecosystem, specifically distributed in a wide range in many plants, possess a long-term beneficial association with the host plant, combat against biotic and abiotic stresses and help in metabolism and stimulate immunity responses. Further, distributed in endophytic bacteria, fungi and actinomycetes in association with plants produce bioactive compounds. Actinobacteria , Beta- and Gammaproteobacteria function differently, i.e. Actinobacteria found abundantly in soil and other natural spaces act as a biological controlling agent against pathogens, Betaproteobacteria function as pH moderator and Gammaproteobacteria containing DAP work in the growth phase of cells. Where volatile organic compounds (VOCs) play a significant role in carbon sources, defence metabolites and chemical attractants, various endophytes can produce bioactive compounds/metabolites that can be used against many diseases either directly or indirectly. Studies regarding the use of microbiome have improved radically in recent years, due to the cost of analysis reduction and technological advancement. There is a great need for new bioactive compound production to replace agrochemicals used in controlling plant diseases, and a vast research study is needed to be carried out globally.