Plants recruit a broad array of microbes surviving in different tiers of their habitat viz., rhizosphere, phyllosphere, and endosphere, predominantly represented by bacteria, archaea, fungi, actinomycetes, protists, and other living entities. These microbial communities constitute structural, as well as functional micro-communities, associated with various parts of the plants under natural environment, are collectively coined as plant microbiomes or phytobiome (Busby et al., 2017; de Souza et al., 2020; Pascale et al., 2020). These microbes either live internally known as endophytes or externally known as epiphytic or rhizospheric microbes (Trivedi et al., 2020). Plant microbiomes influence the plant’s functionality in multiple directions, including supply-chain of essential nutrients to plants, determining the soil fertility vis-à-vis plant health, stimulating plant growth, enhancing biotic and abiotic stress tolerance, sustaining plant health by competing against phytopathogens, induction of resistance, driving the emergence of multiple disease resistance systems through long eventful history of co-evolution of plant-microbiome association (Reinhold-Hurek et al., 2015; Vandenkoornhuyse et al., 2015; Lazcano et al., 2021). There are inevitable reasons that the plant microbiome is deliberated as an essential component of host-plant assemblage, known as a holobiont (Zhang et al., 2017).

Rhizosphere microbiome plays an important role in channelizing many essential soil activities such as decomposition, mineralization, aggregate formation, and plant disease biocontrol, all of which are crucial to optimize citrus productivity (Lazcano et al., 2021). A better understanding of citrus associated microbiomes would impart inevitable consequences on microbial biodiversity, nutrients mobilization, supply of nutrients, nature of multi-directional associations, and soil-plant health maintenance defining the total functionality of ecosystems (Mahmud et al., 2021; Zhang et al., 2021) for multi-dimensional outcomes (Figure 1).

Citrus is an important fruit crop, known globally to contribute significantly in economic, nutritional value, and health importance due to the abundance of the vital nutrient, antioxidants, minerals, vitamins, and dietary fibers present in the juice and fresh fruits (Kreitzman et al., 2020). Above all, the distinct flavors of citrus fruits are extensively preferred and recognized throughout the world (Wang et al., 2017; Trivedi et al., 2021). Commercial citrus cultivation encounters many challenges in the field, with regard to the optimum supply of nutrients in the rhizosphere and is often exposed to untimely nutrient shortage on account of various diseases, either soil-borne or nursery plant origin. In this context, HLB is a globally dreaded disease caused by the bacteria belonging to the genus Liberibacter (Das et al., 2021). The causal agent of HLB predominantly, Candidatus Liberibacter asiaticus (CLas) is restricted to grow and colonize within phloem tissues and does not interact with other microbial flora of the citrus microbiome directly, unless they survive in the phloem of citrus (da Graca et al., 2016; Ginnan et al., 2020). Liberibacter is a systemic bacterial pathogen and causes regulatory metabolic changes in their citrus hosts, which disturbs the citrus microbiome in multiple directions. Predominantly, photoassimilates transport is impaired mainly due to phloem malfunction and reducing the release of plant-derived photosynthates at the initial phase of the Huanglongbing (HLB) infection process (Zhang et al., 2017; Trivedi et al., 2020). At the initial phase of HLB invasion, roots of citrus plants expressively decline, impeding with the loss of carbonaceous compounds from root tissues. HLB also affects the plants’ defense system, which in turn disturbs the core microbiota of the citrus rhizosphere (Zhang et al., 2017; Trivedi et al., 2021).

Apart from disturbing the core microbiome, HLB also brings about nutrient imbalances arising from damages affecting the root architecture, directly disturbing the processes associated with absorption, assimilation, transport, and utilization of nutrients and water (Johnson et al., 2014; Wang, 2020). Likewise, pathogen blocks nutrient resources, either inside infected tissues or within the rhizosphere, leading to under-supply of the number of nutrients (Dordas, 2008; da Silva et al., 2020). Elevated micronutrient fertilization is popularly utilized to enhance the growth and development of HLB-infected citrus plants (Dong et al., 2021b). Additionally, micronutrient is reported to elicit systemic acquired resistance in citrus plants acting as elicitors to reduce disease-related injuries and inhibit the development of pathogens, either by knock-down effect or by controlling gene-linked pathogenicity (Dordas, 2008; Spann and Schumann, 2010; Gottwald et al., 2012; Fones and Preston, 2013). Hence, the changes in the composition of phloem sap mainly due to under supply of different micronutrients revealed some useful insights for inactivating the development and sustenance of CLas in the phloem (Hijaz and Killiny, 2014; Hijaz et al., 2016; Killiny, 2016; Dong et al., 2021a). Indeed, researches have shown that zinc (Zn) can reduce bacterial infection, followed by manganese (Mn) playing an important role in the synthesis of non-structural carbohydrates, nitrogen metabolism, phenols, and phytoalexin in citrus (Srivastava et al., 2005; Datnoff et al., 2007; Bargaz et al., 2018; Ray et al., 2020). Moreover, copper (Cu) has also been applied for several years to control the phytosanitary problems triggered by micro-communities (Russell, 2005; Trivedi et al., 2021). Considering all these collectively, it is feasible that enhancing the concentration of micronutrients in plants might reduce the deleterious impact of HLB in citrus plants (Dong et al., 2021b). Despite these facts, the effect of various micronutrients supplies on CLas acquisition by adults and nymphs of citrus psyllids is still in a rudimentary stage of our understanding.

Considering the severity of CLas imparting substantial loss of plants vigor and soil health, several researchers are using microbes mediated remediation technology in the current cultivation scenario (Bora and Bora, 2020, 2021; Dong et al., 2021b). Microorganisms have been used as biocontrol/biopesticides (Mishra et al., 2018; Saikia et al., 2021) as well as biofertilizers biostimulants (Ngullie et al., 2015; Srivastava et al., 2015, 2021). However, the researchers in the current past-HLB scenario have only achieved partial success toward effective control of HLB due to the unculturable nature of CLas in vitro. Recently, the research report published by the Japanese team stated that the putative causal agent of citrus greening (CLas) could be successfully cultured in the system of co-culture with Pseudomonadaceae, Comamonadaceae, Microbacteriaceae, and Flavobacteriaceae in a modified culture medium with the addition of essential vitamins and nutrients (Killiny-Mansour, 2019). Though, it remained a mystery about culturing of HLB pathogen in a monoculture system, restricting researchers to provide sustainable protection against HLB to date. Despite all these fruitful efforts, microbiome-mediated remedies of HLB and soil health management are on a continuous upsurge with serious concerns, however, it still remains unexplored. Nevertheless, modern biotechnological breakthroughs have paved the way for use of microbiomes and their secondary metabolic products addressing soil-plant health-related issues of citrus.

The proposed review outlines and discusses the recent advancements made toward the citrus microbiome, their core taxonomic, and functional traits involved in citrus protection, in addition to the revitalization of citrus plants through soil health. Correspondingly, we attempted to summarize how the knowledge derived from multi-omics technologies has provided a robust understanding of the structure and functions of citrus-associated microbiomes. Various modes and approaches using microbiomes to improve the performance of citrus plants were critically reviewed by the authors.

Numerous high-throughput sequencing (HTS) based studies have suggested that the core microbiome is a cluster of micro-communities that typically reside inside the host’s microbiome (Compant et al., 2019; Simonin et al., 2020; Trivedi et al., 2021). The core and hub microbiome of citrus compartments (rhizosphere, rhizoplane, and phyllosphere) have been systematically investigated from various angles (Blaustein et al., 2017; Xu J. et al., 2018; Trivedi et al., 2021). Surprisingly, significant overlaps were recorded within different members of the core microbiome through several interactions of either the same plant species or phylogenetically different. Such an imperative overlap implies a possibility that certain specific groups of bacteria have a preferential association with plants for a longer period of time (Simonin et al., 2020; Trivedi et al., 2021), while others failed to survive. Several prominent researchers have stated that a group of micro-communities exhibit their stable and strong association with specific hosts across geographically different habitats (Blaustein et al., 2017; Hamonts et al., 2018; Xu L. et al., 2018). These microorganisms are not only persistent and predominant but occur plentifully in nature.

Various members of the core microbiome are hypothesized to perform a crucial role in shaping the assembly of plant-associated microbiota, besides acting as a key regulator of plant growth and development (Toju et al., 2018; Zhang et al., 2021). Different parts of citrus plants comprise distinct members of core microbiomes (Xu J. et al., 2018; Ginnan et al., 2020; Zhang et al., 2021). Precisely, different compartments of citrus encompass various bacterial population in core microbiomes consist of diverse genera including Pseudomonas, Sphingobium, Chittinophaga, Agrobacterium, Steroidobacter, Mesorhizobium, Dokdonella, Cupriavidus, Novosphingobium, Rhizobium, Hylemonella, PhenylobacteriumRoseateles, Niastella, Devosia, Halomonas, Rhodoplanes, Sphingomonas, Streptomyces, and Bacillus. Numerous genera of microbes are associated with these core microbiota, identified as beneficial microorganisms for the plant in other systems. These beneficial microbial members might benefit in regulating root development, upholding hormonal balance, facilitating mobilization and acquisition of nutrients, and suppressing the disease expression in the host plants (Fravel et al., 2003; Verbon and Liberman, 2016; Lemanceau et al., 2017). Till now, the core microbiome is well-defined on the basis of taxonomy as well as functional features that derive microbiome-plant associations such as colonization, signaling, and competition.

As greater importance of functional attributes of plant-associated microbiota, an emphasis is employed on defining the “central functional microbiome” of plants at various scales (Lemanceau et al., 2017; Zhang et al., 2021). Previous research revealed the core functional attributes of the citrus rhizosphere microbiome, leaving endosphere microbiomes due to complications of extracting the DNA and RNA from the microbiota of host plants. The microbiome’s core functional attributes of the citrus rhizosphere are enhanced for microbial features that facilitate microbe-microbe or microbe-plant interactions, resulting in an elevated acquisition of nutrients and plant-soil health (Xu J. et al., 2018; Trivedi et al., 2021; Zhang et al., 2021).

The citrus rhizosphere microbiome contains a large number of transporter genes responsible for phosphotransferase systems, ATP binding, and metabolite movement, which regulate the variety of plant-derived nutrients. These transporters are likely to allow fine-tuning between the microbial growth and root exudates, facilitating selective rhizosphere microbiome requirement from the bulk soil (Trivedi et al., 2020, 2021; Zhang et al., 2021). A positive selection of attributes (bacterial secretion systems and other outer surface proteins), known to interact directly with plant host, suggest that the immune response of plants plays a pivotal role in the composition of various microbial niches (Hacquard et al., 2017). Considering the importance of microbes in maintaining plant and soil health, there is every possibility to realign these microbes targeted to new crop production and management strategies. Hence, their identification, functionalities, and modes of performance in challenging environment are still a must, to be exploited.

Google scholar based bibliometric analysis of subject using four key words (“citrus” and “metagenomics,” “metagenome” and “HLB,” “metagenome” and “soil health,” “nutrients” and “HLB”) during 1900–2021 showed as an upsurge in systematic research on proposal theme, only after 2010. Whereas prior to the year 2000, hardly any research work on these issues could gather any news in the research arena. Of 4,739 publications, a maximum of 2,239 publications dealing with nutrients and HLB followed by 1,135–1,152 publications covering the issues like citrus metagenome or metagenome and soil health, and only 213 publications touching metagenome and HHLB, vividly showcase the temporal shifts in research interest worldwide. The rise in publications after 2010 was accountable for increased access to technology at affordable prices.

The functionality of the citrus microbiome, where different microbial communities keep interacting with plants is now more precisely decoded through HTS sequencing and metagenomics (metatranscriptomics and metaproteomics).

The microbiome plays a significant role as a key driver to sustain fertility as well as the health of soil (Srivastava et al., 2021). The soil micro-communities frequently help the plant to acquire macro and micronutrients by solubilizing and mobilizing them in addition to a breakdown of organic matter through various complex mechanisms to release the immobilized nutrients (Srivastava and Malhotra, 2017). Particularly, micro-communities also use soil C and N for their growth and energy responses (Wild et al., 2014; Tian et al., 2018; Dong et al., 2021a).

Declining rock phosphate deposits, energy-intensive N-fertilizer manufacture, and emerging adverse environmental issues due to unscientific use of inorganic fertilizers have sparked interest in developing alternative strategies for plant nutrition to improve better sustainability (Jacoby et al., 2017; Dong et al., 2021b). Microbes-mediated nutrient conversion is a crucial driver for the growth of the plant, which could be the rate-determining step in the functioning of an agroecosystem (Schimel and Bennett, 2004; Dong et al., 2021a). Microbiome-plant interactions are driven by fine adjustment between the genetic response of the host and activities of related microbiomes to enable uptake of nutrients (Srivastava and Singh, 2006). For instance, plants have adaptive phosphate starvation responses (PSRs) operating in the presence of their linked microbiome to upraise orthophosphate (Pi) use efficiency in the soil environment (Castrillo et al., 2017). The structural composition of plant-associated microbiome is influenced by suppression of microbial-driven plant immune system, predominantly regulated through genetic linkage of PSR signaling system (Castrillo et al., 2017; Finkel et al., 2019). Activation of microbiome-mediated PSR was proven in response to low Pi circumstances with the help of 35-member SynCom. Finkel et al. (2019) applied 185-member SynComs through an extensive array of P concentrations in Pi-stressed situations to establish the selective recruitment of dormant opportunistic competitors impairing P-starvation.

Nitrogen (N) is an essential element for the synthesis of chlorophyll, nucleic acid, amino acids, and the energy transfer molecule adenosine triphosphate (ATP) for the plants (Werner and Newton, 2005). In the soil, one of the main N sources is organic N, utilized (mineralization) by the soil microbiome to make it easily available to plants. Another macronutrient Potassium (K), a critical inorganic cation found in the cytoplasm is involved in photosynthesis, protein synthesis, and a variety of other primary metabolic activities. The microbiome can enhance the availability of K through various modes of action, including solubilization, acidolysis, and chelation for the multiple benefits of host plants (Srivastava, 2013; Srivastava and Singh, 2006).

Micronutrients also play a pivotal role in sustaining soil health and ecosystem functioning (Srivastava and Singh, 2005). Numerous micronutrients comprising Zinc (Zn), Iron (Fe), Manganese (Mn), Molybdenum (Mo), and Boron (B) are essentially required for plant growth and development of citrus as they are significantly involved in photosynthesis, water oxidation, respiration, and protection against a variety of oxidative stress damages (Srivastava and Singh, 2006; Srivastava and Malhotra, 2017). Despite these, the above micronutrients are not easily available to plants as they are by and large observed in immobilized and complex forms, inaccessible to plants directly (Dong et al., 2021a). Soil microbiome performs enormously to solubilize, oxidize, and mobilize these nutrient elements by synthesizing a large number of enzymes, chelators, and organic acids. There are many members of citrus-based bacterial microbiome (Bacillus, Burkholderia, Pseudomonas, Sphingobium, Chittinophaga, Agrobacterium, Steroidobacter, Mesorhizobium, Dokdonella, Cupriavidus, Novosphingobium, Rhizobium, Hylemonella, Phenylobacterium, Roseateles, Niastella, Devosia, Halomonas, Rhodoplanes, Sphingomonas, and Enterobacter), actively involved in the solubilization and availability of micronutrients in the soil (Verbon and Liberman, 2016; Lemanceau et al., 2017; Lee et al., 2019; Zhang et al., 2021). These microbes oxidize different micronutrients by using different modes of action and make them available directly to the citrus plants. The actual and predicted functions of the microbiome in the sustainable maintenance of soil and plant health could be visualized (Figure 3).

Interestingly, recent research stated that the microbiome colonizes the soil and forms biofilm via the synthesis of exopolysaccharides, eDNA, eProteins, and alginate (Ansari and Ahmad, 2019). Rhizosphere colonization by the microbiomes enhances soil aggregation by rearranging primary soil particles around the soil organic carbon, providing the required protection against mechanical hindrances. Microbiome-soil colonization and biofilm formation maintain the microbial diversity richness and soil fertility in an ecofriendly manner (Ansari and Ahmad, 2019; Ansari et al., 2019; Trivedi et al., 2021). However, the actual role and mechanisms of microbiome-soil colonization are yet to be explored to enhance our understanding to improve soil health with a more sustainable impact on plant health.

Soil microbiome biomass either live or dead, also play a crucial role in soil health by balancing the nutrient pool in form of microbial turnover determined by cell death and cell production of microbes (Kastner et al., 2021). Microbial dead cells adhere either to the soil particles and enter the soil organic carbon (SOC) pool or are metabolized by micro-communities (Hagerty et al., 2014; Dong et al., 2021b). Soil microbes mediate the cycling of carbon and other key nutrients, and therefore, a key goal of a microbes-to-ecosystem model is to identify exact relations among biogeochemical cycling and microbial composition or abundance. Subsequently, enhanced microbial turnover can improve respiration per unit of soil microbial biomass carbon (Kivlin and Hawkes, 2020). Yet, in the context of the citrus microbiome, the possible linkages between soil micro-communities turnover and their linked functions pose a greater challenge to researchers in the current era.

In a plant microbiome, microbes interact with the plants and also with each other, synergistically promoting plant growth and protecting them against various diseases. Pathogenic microbes when introduced into the host act according to the host environment, and microbes present in or around the host (Trivedi et al., 2016; Bora et al., 2021). Thus, the plant health and disease severity depend on the level of interactions between the host plant, surrounding microbes, invading pathogens, and the prevalent environmental conditions. The plant microbial community, therefore, plays a crucial role in promoting plant growth, imparting tolerance against abiotic stresses, and lowering the impact of pathogenic invasion into the host plants. In a microbiome, some microbial members may suppress the pathogens, by pathogenicity of competing for the nutrients or by stimulating plant defense mechanisms to neutralize the invading pathogens (Trivedi et al., 2012; Ginnan et al., 2020). While some members of the microbiome may become the targets of pathogen attack (with the production of virulent factors) leading to a change in the structure of the microbiome, eventually causing a rapid decline in the health of the host plants. Consequently, studies have been performed to elucidate the possible interactions between invading pathogens and the residents of the microbiome showing promising results in relation to host fitness (Kwak et al., 2018).

Various pathogens are well known for weakening citrus health by perturbations in the host’s physiology. Citrus crops are attacked by several groups of pathogens including viruses, viroids, bacteria, oomycetes, and fungi, inflicting severe economic loss in all the citrus growing regions around the world (Datnoff et al., 2007; Busby et al., 2017). Since changes in community structure due to pathogenic infection lead to plant health decline, studies on the interaction between pathogen and the native microbiome are attracting renewed interest, of late. A diagrammatic roadmap of the regulatory mechanisms of the host’s microbiome in plant homeostasis and health management at the cellular level is developed (Figure 1) for a better understanding of these issues.

Several research works have been carried out showing the response of pathogen invasion on the status of the citrus microbiome (Table 2). Studies revealed the effect of infection caused by HLB, canker, root rot, melanose, variegated chlorosis, and pathogenic nematode on the citrus microbiome. Resultantly, the microbial communities were realigned due to infection in host leaves, stem, roots, rhizosphere, and rhizoplane (Blaustein et al., 2017; Ginnan et al., 2020). Significant changes were noticed in the endophytic microbial community due to citrus variegated chlorosis (CVC) caused by Xyllelafastidiosa and CVC stimulated by endophytic Mehthylobacteriumextorquens (Table 2). The root-feeding nematode (Tylenchulussemipenetrans) infected the citrus roots causing shifts in the rhizosphere microbiome, leading to an increase in the population of Bacillus megaterium and Burkholderia cepacia having a deleterious effect on the growth of root rot pathogen, Phytophthoranicotianae (El-Borai et al., 2003). Some bacterial genera like Bacillus, Methylobacterium, Halomonas, etc. were observed abundantly in citrus leaves and fruits following the infection with canker and melanosis diseases (Li et al., 2021).

The previous research findings have though contributed a better interpretation about citrus microbiome comprising taxonomic composition and functional traits across different niches, locales, and disease situations. However, the use of citrus microbiome in maintaining soil health and plant disease management is still in an infancy stage of understanding. By exploiting soil and plant health regulations through microbiome engineering, we need to develop a level of comprehension about the citrus microbiome and its total functionality. We streamlined some important gaps needing systematic readdressed including (i) systematic determination of structural makeup, linking citrus plant traits with microbial traits in a mutually beneficial domain and genetic potential of the citrus-associated microbiome to unlock multilateral interspecies interactions and metabolic features; (ii) ensuring efficacy, accuracy, and reproducibility in experimental vs. natural environments to move beyond cause-and-effect relationship; (iii) bioprospecting of novel growth-promoting and antagonistic microorganisms (and/or their biomolecules) isolated from citrus-associated microbiomes; (iv) development and prediction of host genotype, microbiome genotype, associated environment, and controlling interactions to modify microbial formulations; and (v) advancement and implementation of standardized processes for collating consistent and well-annotated metadata analysis through HTS and metagenomics. These suggested gaps are major challenges to be explored to maintain and protect soil and plant health in a cost-effective manner, where the citrus microbiome would be a service provider.

Broader use of multi-omics approaches, network analysis, microbial consortia, genome editing, artificial intelligence, and high throughput culturing would greatly elevate our understanding of the citrus microbiome and further unravel the microbiome’s potential toward improving citrus health via better rhizosphere ecological interventions. The full potential of citrus-associated functional genes and secondary metabolites is barely explored as yet and therefore warrants continued experimentation.

AS, AD, PJ, and PB developed the concept of review. AS, AD, FA, and RB compiled the literature. FA and RB designed the manuscript. AS, AD, PJ, PB, FA, and RB involved in writing and editing the manuscript in its present form. All authors contributed during the preparation of this study.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.