Diversity of Soil Microbes in Rhizosphere: History
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Neha Sharma
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Gaurav Swaroop Verma
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Mukesh Meena
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Prashant Swapnil

Plant roots aid the growth and functions of several kinds of microorganisms such as plant growth-promoting rhizobacteria, mycorrhizal fungi, endophytic bacteria, actinomycetes, nematodes, protozoans which may impart significant impacts on plant health and growth. Plant soil–microbe interaction is an intricate, continuous, and dynamic process that occurs in a distinct zone known as the rhizosphere.

  • plant growth-promoting bacteria
  • mycorrhizae
  • stress tolerance
  • soil health

1. Plant Growth-Promoting (Rhizo)Bacteria (PGPR or PGPB)

In 1978, Kloepper came to coin the term “plant growth-promoting rhizobacteria” (PGPR) [1]. PGPR or PGPB are a significant group of beneficial, root-colonizing bacteria thriving in the plant rhizosphere. PGPBs are described as symbiotic or free-living bacteria in soil that can effectively inhabit the roots and have advantageous effects on the host plant. Rhizospheric bacteria, which are often found around plant roots, and endophytic bacteria both have been shown to have the ability to act as PGPBs [2]. The key difference is that once established within the tissues of the host plant, endophytic PGPB are no longer susceptible to the whims of shifting soil conditions [2]. Temperature, soil pH, moisture content, and the population of soil bacteria that may compete for binding sites on the host plant’s root surface are among the changing conditions that may hinder the function and growth of rhizospheric PGPB [3].
Rhizobacteria that encourage plant growth can be categorized as extracellular plant growth-promoting rhizobacteria (ePGPR) that reside in the rhizosphere, or in intercellular spaces in the root cortex, and the intracellular plant growth-promoting rhizobacteria (iPGPR) that exist inside the root cells [4]. It is estimated that ~2–5% of rhizobacteria act as PGPR [5]. They are a useful group of rhizosphere microorganisms that can assist plant development through a variety of mechanisms which includes synthesis of ACC (1-aminocyclopropane-1-carboxylate) deaminase, nutrient uptake, increased root volume, phytohormone synthesis, siderophore synthesis, biological N2 fixation, phosphorous solubilization, and the introduction of systemic tolerance genes, accumulation of stress-related metabolites like glycine betaine, poly-sugars, proline, various volatile organic compounds (VOC), upregulation of antioxidants enzymes as catalase (CAT), ascorbate peroxidase (APX), superoxide dismutase (SOD), glutathione (GSH), ascorbic acid (AsA), glutathione reductase (GR) and α-tocopherol [6][7][8][9].
The major taxonomic groups of PGPB belong to Proteobacteria and Firmicutes [10][11]. The most explored genera of Firmicutes and Proteobacteria for promoting plant development are Bacillus and Pseudomonas, respectively. Strains ascribed to the genera Rhizobium, Achromobacter, Azospirillum, Azotobacter, Pseudomonas, Burkholderia, Acinetobacter, Serratia, Enterobacter, Pantoea and Rahnella are the major representative’s genera of the phylum Proteobacteria [12][13][14]. Strains ascribed to the genera Staphylococcus, Oceanobacillus, and Paenibacillus are the major representative genera of the phylum Firmicutes [14]. PGPR also interact with other microorganisms such as arbuscular mycorrhizal fungi, to support plant growth [15]. Bacillus and Pseudomonas species are widely investigated PGPRs [16]. Rhizobacteria from certain genera are the most efficient Arthrobacter, Azospirillum, Alcaligenes, Bacillus, Azotobacter, Bradyrhizobium, Burkholderia, Flavobacterium, Serratia, Enterobacter, Streptomyces, Pseudomonas, Rhodococcus, Mesorhizobium, Klebsiella, etc. [17]. Symbiotic nitrogen-fixing rhizobia are classified into 36 species distributed among seven genera (Allorhizobium, Bradyrhizobium, Azorhizobium, Mesorhizobium, Rhizobium, Methylobacteriu, and Sinorhizobium) [18]. Some important non-symbiotic nitrogen-fixing bacteria include Achromobacter, Alcaligenes, Acetobacter, Arthrobacter, Azospirillum, Azomonas, Azotobacter, Beijerinckia, Bacillus, Clostridium, Derxia, Corynebacterium, Enterobacter, Klebsiella, Herbaspirillum, Rhodopseudomonas, Pseudomonas, Rhodospirillum, and Xanthobacter [19].

2. Fungi

Fungi are eukaryotic, heterotrophic organisms that help in nutrient cycling, decomposition of debris, increase nutrient availability in soil and helps in plant growth [20].

Mycorrhiza

Mycorrhizae are fungi that grow in symbiotic association with plant roots. Mycorrhizal fungi can be found living within the cortex of a plant’s root, on the surface of the root, or surrounding the root’s epidermal cells. These fungi’s roots produce hyphae that spread out into the soil, where they scavenge for minerals that promote plant growth, particularly phosphates and nitrates. On the basis of structure and function, four main mycorrhizal types have been described namely Ectomycorrhizae, Endomycorrhizae, Ericoid and Orchidaceous types [21]. The term “arbuscular mycorrhiza” (AM) refers to a particular kind of mycorrhiza in which the symbiotic fungus enters the cortical cells of the roots of vascular plants to create arbuscules.
A type of symbiotic association known as an ectomycorrhiza develops between the roots of different plant species and a fungal symbiont, or mycobiont. The Hartig net forms when hyphae (typically coming from the inner region of the mantle enclosing it) infiltrate the root of the plant host. In order to create a network connecting the outer cells of the root axis, the hyphae penetrate and develop in a transverse direction to the axis of the root [22]. The area where the fungus and root cells connect is where the exchange of nutrients and carbon takes place [23]. These associations are exceedingly prevalent in the plant kingdom. According to studies, fungus from the Glomeromycota group form AMs with 74% of all plant species, orchid mycorrhizae are present in 9% of plants, 8% of plants are entirely non-mycorrhizal, 7% have inconsistent non-mycorrhizal and mycorrhizal interactions, 2% form EM (Ectomycorrhizas) associations and 1% of plants form ericoid mycorrhizas [24][25]. Ectomycorrhizas associations are the most commonly found in, Pinaceae, Fagaceae, Betulaceae, Salicaceae, Junglandaceae, Myrtaceae, and Ericaceae. The majority of mycorrhizal fungi belong to ascomycetes and basidiomycetes [26].

3. Plant Growth-Promoting Fungi (PGPF) in Soil

Rhizosphere fungi are plant-associated fungi that utilize nutrients produced by a host plant to establish plant rhizospheric fungal interactions that are essential to the growth of healthy ecosystems and the sustainability of the environment [27]. Many PGPF species such as Trichoderma, Fusarium, Talaromyces, Phytophthora and Penicillium, are known to enhance plant growth, their innate immunity and some important secondary metabolites [28]. PGPF can both promote systemic resistance and act as a biocontrol agent against phytopathogens. The mineralization of the major and minor elements necessary to sustain plant development and production is the possible mechanism of action for PGPF. Additionally, PGPF creates defense-related enzymes, induced resistance, and phytohormones to prevent or stop the invasion of harmful bacteria, or in other words, to support plants under stress [29].

4. Endophytes

A group of microorganisms that dwell inside the tissues of plants and have “closer” interactions with them without harming them are known as endophytes. The wide majority of plants include endophytes [30]; in fact, every plant species that has been examined is known to house microbial endophytes. An endophyte-free plant is extremely uncommon in nature [31]. Broadly, the endophytes can be grouped into systemic and non-systemic. Non-systemic endophytes are facultative and transient, and their population size and species richness change with time. Under difficult environmental conditions, they can also switch between mutualism to parasitism. Conversely, mutualist systemic endophytes have closely developed with the plant host [32]. Endophytes perform diverse functions in the host plant including nutrient acquisition, phytohormone and siderophore production, protection from abiotic stresses and biotic [33].

4.1. Fungal Endophytes

Numerous fungi colonize the roots of plants including endophytic and mycorrhizal fungi. The fungal endophytic relationships unlike mycorrhizal symbioses lack specialized structures for nutrient exchange, synchronized development, and substantial advantages for both individuals [34]. The most well-known members of the wide group of fungi that make up root-endophyte interactions are the dark septate endophytes. Endophytes can infiltrate and colonize host plant tissues either through vertical seeding or horizontal transfer. The recognition and attraction of endophytes by the host plant are mediated by chemical signals such as root exudates and signaling molecules. Endophytes employ various strategies such as motility and cell wall degradation to actively colonize plant tissues and also modulate plant physiology and biochemistry to their advantage. Once inside the plant, endophytes can produce compounds that stimulate plant development and aid plants in coping with stress [35]. The influence of fungal root endophyte colonization shows a full spectrum of variation from harmful to beneficial [36]. Numerous host plants have been reported to naturally comprise fungus endophytes [37]. Basidiomycetes groups were found to be the most dominant endophytes among fungi. While some blatantly benefit the host plants, others might impair plant performance [38][39]. The degree to which the roots have been colonized by fungi may differ, indicating the adaptability of both the individual fungi and the endophytes as a whole. Colonization is frequently extensive, inter- or intracellular, and occasionally restricted to the cortex or epidermis [40]. The common genera of endophytic fungi include Aspergillus, Chaetomium, Bipolaris, Cladosporium, Fusarium, Diaporthe, Alternaria, Mucor, etc.

4.2. Bacterial Endophytes

Rhizobacteria are known as endophytic bacteria that colonize their host plant [41]. The most prevalent bacterial endophyte genera include Pseudomonas, Burkholderia, Bacillus, Micrococcus, Stenotrophomonas, Pantoea, and Microbacterium [42]. Taxonomically, they are classified into 16 phyla with more than 200 taxa. The majority of them belong to the three phyla: Actinobacteria, Proteobacteria and Firmicutes [43]. Through interactions with other bacteria, some endophytic bacteria, such as nitrogen-fixing rhizobia, increase the positive effects of other beneficial bacteria. Under both normal and stressful conditions, bacterial endophytes directly benefit plants by aiding them in acquiring nutrients and promoting growth by modulating growth hormones [44]. They can also indirectly promote plant growth by antagonizing phytopathogens or enhancing plant defensive response by producing siderophores, chitinases, and proteases [45][46]. When compared to many rhizospheric bacteria, endophytic bacteria typically have stronger positive effects on host plants as residing inside plant tissues allows them to be in close contact with the host plants to readily exchange nutrients [47].

This entry is adapted from the peer-reviewed paper 10.3390/su151914643

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