1 Introduction

Wild wheat species, such as Triticum dicoccoides and Aegilops sharonensis, are the progenitors of modern cultivated wheat and possess a rich genetic diversity that has been largely untapped in contemporary agriculture. These wild relatives harbor a variety of endophytes - microorganisms that live within plant tissues without causing harm - that can significantly influence plant health and stress resilience. Endophytes, including both bacteria and fungi, have been shown to enhance plant growth, improve resistance to pathogens, and increase tolerance to abiotic stresses such as drought (Sun et al., 2020).

The study of endophyte diversity in wild wheat is crucial for several reasons. Wild wheat species contain a broader and more diverse array of endophytes compared to their domesticated counterparts, which have lost much of this diversity through selective breeding (Herrera et al., 2016; Ofek-Lalzar et al., 2016). This diversity includes unique taxa with potential beneficial effects that are absent in modern wheat varieties. For instance, endophytes from wild wheat have been shown to improve drought tolerance and reduce stress damage in cultivated wheat (Llorens et al., 2019). Additionally, understanding the endophytic communities in wild wheat can lead to the identification of novel biocontrol agents against common wheat pathogens, such as Fusarium graminearum, thereby reducing the reliance on chemical pesticides (Comby et al., 2016; Noel et al., 2021).

The study will characterize the endophytic communities in various wild wheat species and compare them to those in domesticated wheat, evaluate the potential benefits of these endophytes in enhancing stress tolerance, growth, and disease resistance in cultivated wheat, and identify key endophytic taxa that could be harnessed for future wheat improvement programs, with the hope of revealing the potential value of wild wheat endophytes and providing a basis for their utilization in sustainable agricultural practices.

2 Overview of Endophytes

2.1 Definition and types of endophytes

Endophytes are microorganisms, primarily fungi and bacteria, that live inside plant tissues without causing apparent harm to their host. They can be found in various plant parts, including leaves, stems, roots, and seeds. Endophytes are broadly categorized into two main types based on their phylogeny and life history traits: clavicipitaceous (C) and nonclavicipitaceous (NC) endophytes. Clavicipitaceous endophytes are typically found in grasses and are known for their mutualistic relationships, often producing alkaloids that protect the host plant from herbivores and pathogens. Nonclavicipitaceous endophytes, on the other hand, are more diverse and can be found in a wide range of plant species, contributing to plant health through various mechanisms such as stress tolerance and growth promotion (Rodriguez et al., 2009; Caradus and Johnson, 2020).

2.2 Endophyte-host relationships

The relationship between endophytes and their host plants spans a continuum from mutualism to antagonism. Mutualistic endophytes can enhance the fitness of their host plants by improving stress tolerance, promoting growth, and providing protection against pests and pathogens. For instance, Epichloë endophytes in grasses produce alkaloids that deter herbivores and protect the plant from diseases, making them essential for resilient high-performing pastures. Conversely, some endophytes can become pathogenic under certain conditions, highlighting the complexity of these interactions (Khare et al., 2018; Grabka et al., 2022). The endophyte-host relationship is influenced by various factors, including the specific endophyte species, the host plant species, and environmental conditions.

2.3 Role of endophytes in plant health

Endophytes play a crucial role in enhancing plant health by conferring tolerance to abiotic and biotic stresses, promoting growth, and protecting against pathogens. For example, endophytes from wild cereals have been shown to improve wheat performance under drought conditions by altering the plant's physiological responses to water stress, reducing stress damage markers, and modifying metabolite accumulation (Llorens et al., 2019). Additionally, endophytes can produce bioactive compounds that suppress pathogens, solubilize phosphate, and contribute assimilable nitrogen to plants, thereby enhancing plant growth and yield (Ek-Ramos et al., 2019). The diversity of endophytes in wild wheat ancestors, such as Triticum dicoccoides and Aegilops sharonensis, suggests that these plants harbor a wealth of beneficial endophytes that could be harnessed for agricultural improvement (Ofek-Lalzar et al., 2016). Understanding the multifaceted interactions between endophytes and their host plants is essential for developing sustainable agricultural practices that leverage these natural symbionts (Kaul et al., 2016).

3 Endophyte Diversity in Wild Wheat

3.1 Methods for assessing endophyte diversity

The assessment of endophyte diversity in wild wheat involves a combination of cultivation-dependent and cultivation-independent methods. Cultivation-dependent methods include isolating endophytes from plant tissues and analyzing their genetic material. For instance, in the study of endophyte communities in Triticum dicoccoides and Aegilops sharonensis, both cultivation and cultivation-independent methods were used, resulting in the identification of 67 operational taxonomic units (OTUs) from single cultures. Similarly, the diversity of endophytic fungi in wheat and its wild relatives was characterized using next-generation sequencing, which identified a total of 1 666 taxa.

Cultivation-independent methods, such as metabarcoding and next-generation sequencing, are crucial for capturing a broader spectrum of endophytes, including those that are difficult to culture. For example, ITS1 metabarcoding was employed to study the fungal wheat microbiome, revealing significant influences of host genotype, tissue type, and abiotic factors on fungal communities (Latz et al., 2020). Additionally, the use of MiSeq Illumina technology allowed for the identification of endophytic bacteria in different parts of wheat species, providing insights into the stability and changeability of the core microbiome (Kuźniar et al., 2019).

3.2 Geographic and environmental factors

Geographic and environmental factors play a significant role in shaping the diversity and composition of endophytic communities in wild wheat. Environmental heterogeneity, including variations in temperature, humidity, and precipitation, can influence the abundance and diversity of endophytes. For instance, a study on the fungal endophytic microbiome of wheat demonstrated that location-dependent weather conditions largely explained differences in the phyllosphere microbiome, while root communities were less affected by abiotic factors.

Geographic location also contributes to the differentiation of endophytic communities. Research on cereal crops-related wild grasses revealed substantial differences in community composition across host species and locations, with both stochastic and deterministic processes affecting fungal endophyte community (FEC) assembly (Sun et al., 2020). Additionally, the diversity of endophytic fungi in wild and domesticated wheat showed that wild plants from specific sites had greater richness and diversity compared to domesticated wheat from corresponding fields (Sun et al., 2020).

Moreover, the mode of transmission of endophytes, whether vertical (from progenitors) or horizontal (from the environment), influences the composition of endophytic communities. A study on seed fungal endophyte communities in wheat and its wild relatives found that external infection of seeds is the main source for specific taxa, although vertical transmission also plays a role (Sharon et al., 2023). This highlights the importance of both geographic and environmental factors in shaping the endophytic diversity in wild wheat.

4 Molecular Characterization of Endophytes

4.1 DNA sequencing techniques

The molecular characterization of endophytes in wild wheat and its relatives has been significantly advanced by the application of various DNA sequencing techniques. One of the most commonly used methods is the sequencing of the internal transcribed spacer (ITS) regions and 16S ribosomal RNA (rRNA) genes. These regions are highly informative for identifying and classifying fungal and bacterial endophytes, respectively.

For instance, in the study of endophytes in Triticum dicoccoides and Aegilops sharonensis, both cultivation-dependent and cultivation-independent methods were employed. The ITS region sequences from single cultures were analyzed, resulting in the identification of 67 operational taxonomic units (OTUs) at 97% sequence similarity, and found in total more than half of the cOTUs (36 out of 67) were only detected in stems (Figure 1) (Ofek-Lalzar et al., 2016). Similarly, in another study, next-generation sequencing (NGS) technologies, such as MiSeq Illumina, were utilized to identify the endophytic microbiome in Triticum aestivum and Triticum spelta. This approach allowed for a comprehensive analysis of the endophytic communities across different plant organs (Kuźniar et al., 2019).

Figure 1 New ICT based fertility management model in private dairy farm India as well as abroad

The use of 16S rRNA gene sequencing has also been pivotal in characterizing bacterial endophytes. For example, in the analysis of endophytic bacteria in Zea mays, isolates were identified using 16S rRNA gene sequencing, which revealed a diverse community of endophytes belonging to major groups such as α-Proteobacteria, γ-Proteobacteria, and Actinobacteria (Pereira and Castro, 2014). Additionally, a meta-analysis of 148 scientific papers highlighted the importance of 16S rRNA gene sequencing in providing a broad overview of culturable plant endophytic bacteria across various plant species and geographical regions (Riva et al., 2022).

4.2 Phylogenetic analysis

Phylogenetic analysis is a crucial step in understanding the evolutionary relationships and diversity of endophytic communities (Comby et al., 2016). By constructing phylogenetic trees, researchers can infer the genetic relatedness of endophytes and identify novel taxa.

In the study of fungal root endophytes in wild barley (Hordeum murinum), phylogenetic analysis based on ITS sequence similarity revealed representatives from 8 orders, 12 families, and 18 genera. Notably, 21% of the isolates had no significant match in GenBank, indicating a high proportion of novel fungi (Murphy et al., 2015). This underscores the potential of wild relatives of crops as reservoirs of unexplored genetic diversity.

Similarly, phylogenetic analysis of endophytic bacteria in various agricultural crops, including coffee, sugar cane, beans, corn, soybean, tomatoes, and grapes, identified common orders such as Bacillales, Enterobacteriales, and Actinomycetales. The most frequently observed genera were Bacillus, Pseudomonas, and Microbacterium. This analysis demonstrated the reliability of 16S rRNA gene sequencing in accurately grouping endophytic bacteria (Bredow et al., 2015).

In another study, the phylogenetic diversity of endophytic bacteria in wheat was analyzed using 16S rRNA variability. This metagenomic approach revealed changes in bacterial endophytes associated with drought stress, highlighting the dynamic nature of endophytic communities in response to environmental conditions (Žiarovská et al., 2020).

5 Functional Roles of Endophytes in Wild Wheat

5.1 Enhancing stress tolerance

5.1.1 Abiotic stress tolerance

Endophytes play a crucial role in enhancing the abiotic stress tolerance of wild wheat. These microorganisms help plants cope with various environmental stresses such as drought, salinity, and extreme temperatures. For instance, endophytes from wild cereals have been shown to protect wheat plants from drought by altering their physiological responses to water stress. This includes reducing stress damage markers and the accumulation of stress-adaptation metabolites, thereby improving plant performance under water-limited conditions. Similarly, the endophytic isolate Priestia aryabhattai BPR-9 has demonstrated significant tolerance to salinity, drought, and heavy metals, enhancing wheat growth and stress resilience through various biochemical mechanisms (Shahid et al., 2022). Additionally, endophytic fungi isolated from wheat have shown high tolerance to heavy metals, salinity, and drought, indicating their potential as biofertilizers or bioagents for sustainable crop production (Ripa et al., 2019).

5.1.2 Biotic stress resistance

Endophytes also contribute to biotic stress resistance in wild wheat by providing protection against various pathogens. For example, endophytic bacteria from halophytes have shown antagonistic activity against economically important phytopathogens such as Verticillium dahliae and Ralstonia solanacearum, thereby enhancing the host plant's resistance to these pathogens (Christakis et al., 2021). Furthermore, endophytic fungi and bacteria have been reported to enhance disease resistance in host plants, reducing the need for synthetic pesticides and contributing to sustainable agricultural practices (Watts et al., 2023). The ability of endophytes to modulate the host plant's immune system and produce antimicrobial compounds plays a significant role in their biotic stress resistance capabilities (Verma et al., 2021).

5.2 Promoting growth and yield

Endophytes are known to promote plant growth and yield by enhancing nutrient uptake, producing growth-promoting hormones, and improving overall plant health. For instance, endophytic bacteria have been shown to increase the germination rate, plant length, and vigor indices of wheat seedlings under high salinity conditions, demonstrating their potential as growth promoters (Figure 2) (Shahid et al., 2022). Additionally, endophytic fungi isolated from wheat have exhibited plant growth-promoting traits such as phosphate solubilization, indole acetic acid production, and siderophore production, which contribute to improved plant growth and yield. The use of endophytes as bio-inoculants has been suggested as a sustainable approach to enhance crop productivity, especially in marginal lands with sub-optimal growing conditions (Watts et al., 2023).

Figure 1 New ICT based fertility management model in private dairy farm India as well as abroad

6 Potential Agricultural Applications

6.1 Endophyte-inoculated biofertilizers

Endophytes have shown significant potential as biofertilizers due to their ability to enhance plant growth and nutrient uptake. For instance, endophytic bacteria isolated from various wheat genotypes have demonstrated multifarious plant growth-promoting attributes, including nitrogen fixation, phosphate solubilization, and production of indole-3-acetic acid (IAA) (Rana et al., 2020). These beneficial traits can be harnessed to develop biofertilizers that improve crop yield and reduce dependency on chemical fertilizers. Additionally, endophytes like Acinetobacter guillouiae have been shown to significantly promote plant growth under greenhouse conditions, indicating their potential for practical agricultural applications.

6.2 Development of endophyte-enhanced crops

6.2.1 Breeding strategies

The integration of endophytes into breeding programs can lead to the development of crops with enhanced stress tolerance and growth performance. Research has shown that endophytes from wild wheat relatives, such as Aegilops sharonensis, can improve the sustainability and performance of bread wheat under water-limited conditions by altering physiological responses to water stress. This suggests that breeding strategies incorporating beneficial endophytes from wild relatives could enhance the resilience of modern crops to abiotic stresses. Furthermore, the diversity of fungal endophytes in wild wheat ancestors like Triticum dicoccoides and Aegilops sharonensis offers a rich reservoir of beneficial microbes that can be utilized in breeding programs to improve modern wheat varieties (Sun et al., 2020).

6.2.2 Field trials and performance evaluation

Field trials are essential to evaluate the performance of endophyte-enhanced crops under real-world conditions. Studies have demonstrated that endophyte-treated wheat plants exhibit reduced levels of stress damage markers and improved physiological status under drought conditions (Llorens et al., 2019). Similarly, endophytic bacteria like Priestia aryabhattai have been shown to enhance salt tolerance in wheat by modulating physio-biochemical mechanisms, leading to improved growth and stress resilience (Shahid et al., 2022). These findings underscore the importance of conducting extensive field trials to assess the efficacy of endophyte-enhanced crops in various environmental conditions. Additionally, the use of endophytes as biocontrol agents has shown promise in managing plant diseases, further supporting their potential in sustainable agriculture (Silva et al., 2019; Chaudhary et al., 2022).

7 Challenges and Limitations

7.1 Technical challenges in endophyte research

Research on endophytes, particularly those associated with wild wheat, faces several technical challenges. One significant issue is the difficulty in isolating and culturing endophytes. Traditional cultivation methods often fail to capture the full diversity of endophytic communities, as many endophytes are not easily culturable under standard laboratory conditions. For instance, cultivation-independent methods have revealed a larger number of operational taxonomic units (OTUs) compared to cultivation methods, highlighting the limitations of traditional techniques. Additionally, the identification and classification of endophytes can be problematic due to the high genetic diversity and the presence of novel taxa that do not match existing sequences in databases like GenBank (Murphy et al., 2015). This genetic diversity complicates the accurate identification and functional characterization of endophytes, which is crucial for their potential agricultural application.

Another technical challenge is the need for advanced molecular techniques and bioinformatics tools to analyze endophytic communities. Next-generation sequencing (NGS) technologies, such as Illumina MiSeq, have been employed to identify endophytic microbiomes in wheat, revealing complex and diverse communities (Kuźniar et al., 2019). However, these techniques require significant expertise and resources, including sophisticated bioinformatics software for data analysis, which may not be readily available in all research settings. Moreover, the interpretation of metagenomic data can be challenging due to the presence of low-abundance taxa and the need to distinguish between beneficial endophytes and potential pathogens.

7.2. Ecological and environmental concerns

The ecological and environmental implications of utilizing endophytes from wild wheat in agriculture also present several challenges. One concern is the potential impact on native microbial communities and ecosystem balance. Introducing endophytes from wild relatives into domesticated wheat could disrupt existing microbial interactions and lead to unintended ecological consequences. For example, the introduction of specific endophytes might outcompete native microbial species, altering the microbial community structure and potentially affecting plant health and soil ecology (Sharon et al., 2023).

Another environmental concern is the variability in endophyte effectiveness under different environmental conditions. Endophytes that confer benefits in controlled experimental settings may not perform as well in diverse field conditions. Factors such as soil type, climate, and agricultural practices can influence the establishment and function of endophytic communities. Studies have shown that endophyte communities can vary significantly between different plant species and environmental conditions, suggesting that the benefits observed in one context may not be universally applicable (Žiarovská et al., 2020). This variability poses a challenge for the consistent and reliable use of endophytes in agriculture.

Furthermore, there is a need to understand the long-term effects of endophyte application on plant health and productivity. While some endophytes have shown promise in enhancing drought tolerance and disease resistance in wheat (Noel et al., 2021), the long-term sustainability of these benefits remains uncertain. Continuous monitoring and evaluation are necessary to ensure that the use of endophytes does not lead to negative outcomes, such as the development of resistance in pathogens or adverse effects on plant growth and yield.

8 Future Directions and Research Priorities

8.1 Advances in endophyte research

Recent studies have highlighted the significant potential of endophytes in enhancing the resilience and performance of wheat under various stress conditions. For instance, endophytes from wild cereals have been shown to protect wheat plants from drought by altering their physiological responses to water stress, leading to reduced levels of stress damage markers and improved sustainability under water-limited conditions1. This underscores the importance of further exploring the physiological and biochemical mechanisms through which endophytes confer stress tolerance.

The diversity of fungal endophytes in wild wheat ancestors such as Triticum dicoccoides and Aegilops sharonensis has been found to be significantly higher than in domesticated wheat, with many unique taxa that are not present in modern wheat varieties. This suggests that wild relatives of wheat harbor a wealth of untapped genetic resources that could be harnessed for crop improvement. The identification of these diverse endophytic communities through both cultivation-dependent and independent methods provides a comprehensive understanding of the endophytic landscape and its potential benefits.

The study of endophytic bacterial microbiomes in wheat has revealed that different plant organs host distinct microbial communities, which can influence plant health and stress responses (Žiarovská et al., 2020). This highlights the need for a more detailed investigation into the tissue-specific interactions between endophytes and their host plants, as well as the factors that influence the assembly and succession of these microbial communities (Latz et al., 2020).

8.2 Integration with modern breeding programs

The integration of endophyte research with modern wheat breeding programs presents a promising avenue for developing more resilient and high-performing wheat varieties. The genetic diversity found in wild relatives of wheat, such as Aegilops and Triticum species, offers a valuable gene pool for breeders to tap into (Pour-Aboughadareh et al., 2021). By incorporating beneficial endophytes from these wild relatives into breeding programs, it is possible to enhance the stress tolerance and overall performance of domesticated wheat.

One approach to achieving this integration is through the identification and selection of endophytes that confer specific beneficial traits, such as drought tolerance or disease resistance. For example, certain fungal endophytes have been shown to improve agronomic traits in cultivated barley, suggesting that similar benefits could be achieved in wheat. Additionally, the study of seed transmission modes and the factors influencing endophyte community composition can inform strategies for ensuring the stable inheritance of beneficial endophytes in new wheat varieties (Sharon et al., 2023).

Advances in genetic and biotechnological tools can facilitate the precise manipulation of endophytic communities to enhance their beneficial effects. For instance, next-generation sequencing and bioinformatics analyses can be used to identify core microbiomes and key functional taxa that are associated with improved plant performance (Kuźniar et al., 2019). By leveraging these tools, breeders can develop targeted strategies for incorporating beneficial endophytes into wheat breeding programs, ultimately leading to the development of more resilient and productive wheat varieties.

Acknowledgments

We appreciate Mr.W. Wang's help in collecting literature and participating in discussions during the research process.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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