Soil–Plant–Microbe Interactions Determine Soil Biological Fertility by Altering Rhizospheric Nutrient Cycling and Biocrust Formation

Abstract

Understanding soil–plant–microbe inter- and intra- interactions are essential for ensuring proper soil health, quality, and soil-mediated ecosystem services (e.g., nutrient cycling) required for human–plant–animal life. Intensive and unsustainable farming practices can decrease soil microbial biodiversity, fertility, and quality leading to soil degradation, impaired nutrient cycling, and the incapability of soil to support plant growth. Under such a context, soil biological fertility can appear as a regenerative component that has the potential to harmonize and improve soil’s physical, chemical, and biological parameters. This study defines and discusses the microbiome in the rhizosphere, microbial nutrient cycling, and biological soil crusts as the major components of soil biological fertility, and explores the answers to the following questions: (i) how does the rhizosphere promote plant growth, development, and nutrient cycling through soil microorganisms (e.g., bacteria, fungi)? (ii) How can soil microorganisms regulate macronutrient cycling and facilitate biocrust formation? This review reveals that soil biological fertility is crucial for increasing crop resilience and productivity as well as sustainability in agriculture. Additionally, the reintroduction of plant growth promoting rhizobacteria, a quantitative estimation of the root exudate’s composition, identifying the spatiotemporal dynamics of potassium solubilizing bacteria and establishing biological soil crusts in agricultural lands remain the major tasks for improving soil biological fertility and the transition towards regenerative agriculture.

1. Introduction

Sustainable food production systems, by 2030, require a progressive improvement in soil quality, preventing the desertification and restoration of degraded soil and land (UN, 2015). Intensive agricultural practices can pose multifaceted consequences of the soil health, quality, and soil-mediated ecosystem services. Mounting bodies of evidence show that intensive farming can stimulate soil degradation [1], reduce soil biodiversity [2], decline soil organic matter levels, resulting in soil nutrient deficiencies impacting soil fertility [3], and decrease crop yield and environmental stability [4]. Under such a context, soil microbial communities have the potential to appear as a restorative agent to reinstate soil health and quality attributes as well as soil-mediated ecosystem services deteriorated by intensive farming [5,6]. This biological potential of soil to supply the required amount of nutrients to plants, humans, and animals to complete their lifecycle while preserving and enhancing the physical and chemical attributes of soil is known as soil biological fertility [7]. Soil biological fertility depends on the interplay between soil microbes and the rhizosphere (a confined region of soil where roots, root secretions, and associated soil microbes have an immediate impact).

Some relevant factors associated with soil biological fertility include (i) rhizosphere and nutrient cycling, (ii) rhizosphere and soil microorganisms, and (iii) biocrusts and nutrient cycling.

The rhizosphere regulates microbe-facilitated soil processes (e.g., nutrient fixation and metabolism) and services (e.g., nutrient cycling). Rhizosphere microorganisms are extremely important in the context of sustainable agriculture and environmental sustainability [8,9]. The beneficial effects of PGPR (plant growth-promoting rhizobacteria)/AMF (arbuscular mycorrhizal fungi) on plants led them to be considered as an alternative to chemical fertilizers [10]. Agricultural practices, e.g., crop rotation, fertilization, and tillage, tend to change the microbial community composition by (1) influencing the physical and chemical parameters of soil [11] and (2) changing rhizospheric synergistic/antagonistic interaction between plants and microbes, which eventually impacts plant productivity, functioning, and capacity [12]. Hence, a better understanding of these dynamics is the key to improving ecosystem stability and increasing the resilience of crops.

In the rhizosphere, plant roots-associated secretions play an important role, by influencing the growth of microorganisms [13]. For example, in wheat fields on the North China Plain, bacterial composition differs dramatically in bulk and rhizosphere soils, and bacterial diversity decreases with distance from the roots [13]. Moreover, the rhizosphere may exhibit a strong influence on the nutrient status of soils [14] depending on the rhizosphere ventilation [15]. Finzi et al. [14] showed in a meta-analysis that rhizosphere activities and root priming can increase carbon (C) and nitrogen (N) mineralization rates in temperate forest soils, while Jiang et al. [16] observed a similar effect in paddy soils under maize cultivation. Rhizosphere ventilation may increase available N and P in soils [17]. The extent and magnitude of soil microbial processes are substantially higher in the rhizosphere compared to bulk soil because of the increased and more diverse microbial biomass, soil, and microbial respiration, mineralization potential, and enzymatic activities [18]. Hoo et al. [19] concluded that Sphingomonas yanoikuyae EC-S001 can reinstate the required Mg²⁺ concentrations in the rhizosphere for plant growth and cell development. These studies indicate that PGPR not only contributes to soil fertility but also reduces the harmful chemical footprints on the environment [20,21,22].

Biological soil crusts/biocrusts (BSCs) act as the mediator among soil microbes, nutrient cycling, and rhizosphere [23,24]. Hawkes [23] showed that BSCs increased the soil N retention capacity by increasing the nitrogenase activities of arbuscular mycorrhizal fungi and cyanobacteria. In addition, because of the higher levels of organic and inorganic C and N, BSCs found in deserts may serve as nutrition reservoirs [24,25]. Studies indicate that BSCs are one of the most important indicators of soil biological fertility [26]. Previous reviews considered, for example, mechanisms of PGPR [27], PGPRs as biofertilizers [9], PGPRs as inducers of salinity stress resistance in plants [28], or as environmental remediation agents [29]. Additionally, some authors reviewed biocrusts in the mesic environment [30] or as ecological restorative agents [31]. This study deals with major rhizospheric microorganisms (bacteria, fungi, nematodes), their inter- and intra- interactions with root exudates, macronutrients present in soil, and in the formation of biocrusts. Based on quantitative and qualitative insights from previously published literature, this review synthesizes and suggests answers to the following research questions:

• How does the rhizosphere foster plant growth, development, and nutrient cycling through soil microorganisms (e.g., bacteria, fungi)?
• How can soil microorganisms regulate macronutrient cycling and facilitate biocrust formation?

This knowledge should elevate our understanding of the soil–plants–microbe interactions required for optimum soil biological fertility, improved crop resilience under a changing climate, and facilitating regenerative agriculture. This study should provide an understanding of the main components of soil biological fertility and could be a reference document when considering soil biological fertility for field studies.

2. Rhizosphere: The Substrate for Soil–Plant–Microbial Interactions

The rhizosphere is the part of the soil adjacent to the roots of living plants which is influenced by root secretions, known as root exudates and soil microorganisms [32,33]. Depending on the plant species, the width of the rhizosphere zone can vary from 2 to 80 mm from the root surface [32]. The rhizosphere hosts bacteria, fungi, nematodes, protozoa, algae, and microarthropods which are taxonomically and functionally different from the microorganisms living in the bulk soil [34]. The structure of the rhizosphere microbiome is highly dependent on plant species and soil type [35,36]. For example, the relative abundance of eukaryotes in oat and pea rhizospheres was more than five times higher than that in wheat rhizospheres [34].

Several processes occur in the rhizosphere (Figure 1), e.g., nitrogen fixation, antibiotic production, element cycling, phytohormone production, root secretion, and enzyme production.

2.1. Root Exudates

Plant root exudates are involved in various processes and their composition is variable [40]. Two groups of root exudates have been observed: (1) low molecular weight (including sugars, amino acids, phenols, and organic acids) and (2) high molecular weight (including proteins and complex carbohydrates) [41]. Studies have shown that the composition of root exudates depends on the genotype [42] and the growth stage of the plant [43], as well as on the physicochemical nature of the soil and the microorganisms living in the environment [44]. Metabolites secreted by plant roots have four main functions: (1) the attraction of beneficial microorganisms; (2) the alteration of soil pH to accelerate the transformation of insoluble forms of nutrients; (3) the binding of toxic compounds; (4) protection from pathogens. The chemical composition and quantity of root exudates affect the mobility of nutrients and the diversity and abundance of the microbial population [45,46].

Plants, through root exudates, regulate the microbiome of their rhizosphere. They can do this in two ways: (1) attracting certain species of the microbe and acting as their nutrients, (2) repelling or inhabiting certain species of microbe [47]. Recruitment primarily involves microbes that are beneficial to the plant, with specific properties (

Table 1. Examples of compounds in root exudates responsible for the recruitment of microorganisms in the plant rhizosphere.

Compounds of Root Exudates	Microorganisms	Plant	References
2,4-diacetylphloroglucinol Organic acids	Pseudomonas spp. Azospirillum spp. Arthobacter spp. Devosia spp.	Wheat	[53]
Flavonoids Salicylic acid	Azospirillum spp. Pseudomonas spp.	Rice	[54,55]
Azelaic acid	Bacillus spp.	Tomato	[45]
Amino acids, proline, exopolysaccharides	Bacillus spp.	Maize	[56]
Isoflavonoids	Rhizobium spp.	Soybean	[57]
7,4-Dihydroxyflavone	Acidobacteria	Alfalfa	[58]

). Moreover, some root exudates are even essential for certain microorganisms to live [40]. For example, Vives-Peris and colleagues [40] showed that Pseudomonas putida and Novosphingobium sp. can obtain energy from proline, a major component of the root exudates of citrus. Components of root exudates, i.e., protein, amino acids, lactic acid [48], and jasmonic acid [49] have been shown to influence the rhizosphere microbiome. Recent studies show that the addition of root exudates to cultures of Pseudomonas sp. caused changes in the expression of multiple genes encoding catabolic and anabolic enzymes, predicted transporters, transcriptional regulators, and stress response [50].

Plants can also secrete antimicrobial agents. For example, basil roots have been shown to secrete rosmarinic acid in response to P. aeruginosa infection [51]. Barley roots in the presence of Fusarium graminearum secrete phenolic compounds with antimicrobial activity [52]. Meanwhile, genomic analyses by Bais et al. [37] showed that soybean, rice, and corn can also secrete a wide range of antimicrobial compounds.

Root exudates affect not only microorganisms but also other plants and herbivores. However, knowledge of root interactions is poor because we are still limited by the methodology of identifying signaling molecules [59]. Interactions between plants can be positive or negative. A negative interaction is the allelopathic mechanism of interfering with the growth of other plants by releasing phytotoxins into the rhizosphere [37]. Positive interactions include the induction of increased resistance in neighboring plants. For example, couch grass (Elytrigia repens) root exudates contain carbolin, which repel aphids [60]. This effect is a defense response of couch grass, but also affects neighboring plants.

Root exudates can also act on the soil microbiome indirectly, by changing the physicochemical properties of the soil [61].

Overall, composition of root exudates affects soil-microbe interactions by increasing/decreasing enzymatic activities. For instance, to meet up the N requirement, rhizospheric microorganisms may release more leucine aminopeptidase enzyme [62]. However, the composition of microorganisms in the rhizosphere, the presence of trace elements, nutrient content and physical factors all influence root exudation processes [40]. The plant–rhizosphere relations are therefore not one-sided.

2.2. Rhizobacteria

Rhizobacteria respond to plant root exudates by chemotaxis and adapt their metabolism to the prevailing conditions [63]. However, rhizobacteria–plant interactions require competitions with other rhizosphere microorganisms for both nutrients and space on the root [64]. Studies indicate that Proteobacteria and Actinobacteria form the dominant populations (>1%, usually much more) in the rhizosphere of various plant species [65]. Bacteria of the genera Pseudomonas and Bacillus often dominate the rhizosphere microbiome [66]. Many rhizobacteria are endophytes (Bacillus sp., Pseudomonas sp., Enterobacter sp., Klebsiella sp., Serratia sp., and Streptomyces sp.) that colonize plant roots but are also prevalent in other plant parts (stem, tuber etc.) [67].

Among the rhizosphere bacteria, the so-called PGPR or plant growth-promoting rhizobacteria can facilitate plant growth promotion through different mechanisms:

(1)

Increasing the interaction between available nutrients in the soil and the plants;

(2)

Preventing pathogen growth/activity to protect plants;

(3)

Directly stimulating plant growth, e.g., by producing phytohormones.

Process (1) focuses on increasing the bioavailability of mineral nutrients in the soil [68], e.g., by fixing atmospheric nitrogen, phosphate solubilization, siderophore production, and metal chelation. In terms of processes, (2) while competing for niche spaces with other microorganisms, rhizospheric microbes secrete antimicrobial substances, e.g., antibiotics, lysozymes, and bacteriocins, which can be applied against plant pathogenic agents [69]. Vaughan et al. [70] evidenced that rhizathalenes (semi-volatile diterpenes) secreted by the roots of Arabidopsis thaliana act as an antifeedant agent against the root herbivore fungus gnat (Bradysia spp.). Moreover, root-secreted diterpene phytoalexins (e.g., momilactones, phytocassanes, and oryzalexins), may stimulate resistance against pathogens that infect the roots of rice (Oryza sativa L.). However, in case of process (3), the compounds secreted by bacteria can be classified as auxins (e.g., indole-3-acetic acid, IAA), cytokinins (CK), gibberellins (Gas), abscisic acid (ABA), and ethylene [71,72]. For example, Park et al. [73] revealed that Bacillus aryabhattai strain SRB02, a potential PGPR, can yield a substantial quantity of abscisic acid (ABA), indole acetic acid (IAA), and different forms of gibberellic acids. They can also affect phytohormone production through the secretion of various enzymes, e.g., 1-aminocyclopropane-1-carboxylate deaminase (ACC) can reduce ethylene levels in plants [67]. Additionally, many rhizobacteria are capable of tolerating stress conditions (e.g., salt, drought) and help plants to survive in extreme soil conditions [44,68]. Additionally, studies have shown that Bacillus aryabhattai have the potential to withstand high biotic and abiotic stresses, implying their importance to be included in biofertilizers and as soil remediation agents [73,74]. Likewise, Bacillus pumilus and Pseudomonas pseudoalcaligens can help paddy plants to cope with saline soils [74]. Some selected examples of PGPR are presented in

Table 2. Selected PGPR and their mechanisms of action on plants.

Bacteria	Implications for the Plant	Plant	References
Azospirillum sp.	Fixation of atmospheric Nitrogen Production of phytohormones (auxins)	-	[75]
	Showed higher panicle and seed weight	foxtail millet	[76]
Azotobacter sp.	Increased grain yield 16.5–19.42% over control	wheat	[77]
Bacillus sp.	Produce many potent antifungal metabolites Production of phytohormones	-	[78]
Pseudomonas sp.	Siderophore production Production of phytohormones (e.g., IAA, cytokinins)	-	[79]
Pseudomonas putida	Improving growth and development under moisture stress conditions	maize	[80]
Bradyrhizobium sp.	Increased yield of haulm yield Increased yield of pod yield (13–40%)	groundnut	[81]
	Increasing leaf number, shoot weight and the content of certain bioactive compounds	lettuce	[82]
	Increase in total nitrogen, carbon and phosphorus in the soil	chickpea	[83]
	Accumulation of dry matter, higher yield of pods and straw	peanut	[84]
Stenotrophomonas maltophilia	Higher levels of defence enzymes (including β-1,3 glucanase, peroxidases (PO) and polyphenol oxidases (PPO)) Significantly increased plant growth (increased shoot length/root length (20–39%), fresh weight/dry weight (28–42%)) higher chlorophyll content (24–56%)	wheat	[85]
Streptomyces sp.	Higher chlorophyll and carotenoid content Lower APX and SOD activity lower Na+ content	wheat	[86]
	Growth promotion Inhibiting the growth of virulent strains of B. glumae, as well as a wide range of bacterial and fungal species	rice	[87]
Serratia marcescens	Reduction in plant growth inhibition (15 to 85%) caused by salt stress Increase in the concentration (20 to 75%) of various osmoprotectants (proline, indoleacetic acid) in plants	wheat	[88]
Serratia sp. AL2-16	Increase in shoot length by 95.52%, shoot fresh weight by 602.38%, root fresh weight by 438% and leaf area by 127.2%	Achyranthes aspera L. (prickly chaff flower)	[89]

.

It is worth noting that, according to the additive hypothesis of Bashan and Levanony [90], multiple mechanisms of rhizobacteria act simultaneously or sequentially to promote plant growth [91]. This is a complex network of relationships not only at the bacterial–plant level, but also bacterial–soil, and bacterial–other organisms [72,92]. Improved plant health and access to nutrients affect plant productivity. Studies have shown that inoculation of wheat with Azospirillum brasilense improved plant yield [93], and the application of a co-inoculation of Rhizobium leguminosarum and Agrobacterium tumefaciens significantly increased Vicia faba yield (number of pods) [94].

2.3. Fungi: Special Emphasis on Arbuscular Mycorrhizal Fungi

Several types of fungi e.g., arbuscular mycorrhizal fungi (AMFs), vesicular-arbuscular mycorrhizas (VAMs), and ectomycorrhiza (ECMs) are prevalent in the rhizosphere. Studies have shown that most AMFs belong to the Glomeromycota [95], and ECMs to the Basidiomycota, Ascomycota and Zygomycota [96]. Fungi-colonizing plants affect growth by influencing their metabolism. Among others, fungi belonging to the genera Ampelomyces, Coniothyrium, and Trichoderma have been described as beneficial to host plants [97]. Fungal–plant interactions produce phytohormones such as ethylene, abscisic acid, or jasmonates, which affect both plant growth and mycorrhiza itself [98].

In addition to influencing plant metabolism, AMFs can transport water and nutrients (N, K, Mg, Cu, Zn, Fe, etc.), especially P to the plant, which improves water balance in the plant and affects plant growth and yield [99,100]. Marschner and Dell [101] estimated that about 80% of the phosphorus taken up by a mycorrhized plant is supplied by the fungus. AMFs can also affect CO₂ assimilation by plants. For instance, Glomus mosseae colonization influenced an increase in stomatal apparatus-opening and greater CO₂ assimilation in tomato [102]. Similarly, the inoculation of Vicia faba with AMF improved ear and pod weight [103]. The large-scale field trials conducted on potato crops have shown that inoculation with AMFs (Rhizophagus irregularis) has a statistically significant effect on increasing potato yields [104]. AMFs (Funneliformis mosseae, Rhizophagus irregularis) also caused an increase in grain yield in rice cultivation [105].

AMFs enable plants to withstand stressful conditions, such as drought (water deficit condition). A study by Baslam, Qaddoury, and Goicoechea [99] showed that AMFs (Glomus intraradices, G. mosseae) increased the shoot height and biomass of date palms under water stress conditions. In addition, a study by Aganchich et al. [106] showed that olive plants inoculated with AMFs had significantly better growth rates compared to non-inoculated plants under water deficit conditions. The effects of two AMFs fungi (Funneliformis mosseae and Rhizophagus intraradices) on tomato growth were also tested under water stress conditions and were found to induce stress tolerance in tomato [107].

Studies have shown that the combination of AMF inoculation with PGPR improves plant physiology (photosynthetic pigment content (chlorophyll and carotenoids) and photosynthetic efficiency, and increases sugar, protein concentrations, and antioxidant enzyme activities (polyphenol oxidase and peroxidase) [21], and improves N, P, Ca, K and Na content in shoots [20]. However, the crop species is the main factor shaping AMF diversity and composition under the same environmental conditions, while fertilization treatments have a minor influence [108].

2.4. Nematodes, Rhizospheric Microorgansims and Their Inter- and Intra-Interactions

As plant parasites, nematodes are one of the main factors limiting plant production. However, to parasitize a plant, they need to locate it, and then interact with the plant’s root exudates [36], which can directly affect the interactions between other soil microorganisms and nematodes [109], and also ensure plant protection against some parasites [37]. Plants can be protected against plant parasitic nematodes by specific microbiomes. The rhizosphere microbiome is more effective in preventing nematode e.g., Pratylenchus penetrans and Meloidogyne incognita invasion than bulk soil [110]. Elhady, Topalović, and Heuer [36] showed that the microbiome associated with the nematode Pratylenchus penetrans is controlled by the plant.

The soil type and nematode species influence the soil microorganisms that selectively and specifically attach to nematodes [111]. In addition to acting as nematode antagonists [36], a specific group of microorganisms can also induce a plant defense response against a nematode attack [112]. For example, Bacillus cereus i.24 and L. capsici i.17 were found to antagonize P. penetrans. Metabolites (fervenulin and 6,8-dixydroxy-3-methylisocoumarin) produced by Streptomyces sp. can hinder egg shedding and cause mortality of Meloidogyne incognita [113]. In addition, B. cereus causes the mortality of Caenorhabditis elegans and M. incognita, and induces nematode resistance in the plant [114]. Nematodes, as part of their protection against microorganisms, can change the composition of their surface coat [115], and produce proteins that mimic those produced by the host plant, allowing them to avoid detection by microorganisms [116]. It has been shown that root exudates can also reduce the adhesion of Pasteuria penetrans endospores (a parasite of Meloidogyne spp.) to root-knot nematodes, which is associated with an increased ability to infect roots [117]. These compounds also affect plant–microorganism–nematode interactions [37].

3. Nutrient Cycling and Soil Microbial Community under Different Agronomic Managements

3.1. Carbon and Nitrogen Cycling

The soil microbial community can either increase or decrease the amount of C and N available to plants (Table 2). It depends on (i) their composition and soil physicochemical properties [118,119] (ii) the prevailing differences in the degradation pathways [119] that lead to the bioavailability of C and N. In agricultural soils, soil organic matter (SOM) formation and soil C and N cycling are dependent on litter decomposition and transformation by soil microbes, thereby affecting microbial nutrient (C and N)-use efficiency [120]. Increased microbial C-use efficiency usually derives from (1) changed assimilation efficiency; (2) biomass specific respiration; or (3) respiration costs from enzyme synthesis-reduced soil organic C (SOC) [121]. Metabolic activities of different soil microorganisms determine soil C (C fixation, degradation, metabolism) and N cycling pathways (N fixation, nitrification, denitrification) [122,123], and alteration in these pathways depend on nutrient-input induced changes in the soil microbial community composition [122]. Wang et al. [124] showed that soil moisture plays a crucial role in C and N cycling by affecting the morphology and physiology of soil microbes by fostering favorable or stress conditions. Additionally, soil moisture acts as the determiner of the C:N ratio in both soil organic matter and microbial biomass. Cui et al. [118] reported that vegetation-induced changes in soil moisture and carbon to nutrient stoichiometry regulates microbial metabolic properties, thus impacting soil nutrient availability and microbial biomass in semiarid regions. Waring et al. [125] predicted that modifying soil C:N ratio under C limited conditions may not be a viable option for altering the relative abundance of both fungus and bacteria. However, when N is scarce, increasing the availability of N over C may promote fungal dominance. Fungal–bacterial (F:B) ratios can be affected by variations in microbial biomass turnover rates. For instance, an intermediate C:N ratio in a substrate accelerates bacterial growth because of the fungal N mineralization, thus increasing the total microbial biomass and reducing net N mineralization. Again, Mooshammer et al. [126] showed that when soil N is scarce, microbes immobilize most of the available N, leading to decreased N mineralization.

Studies have shown that different agricultural practices, e.g., fertilization, manure addition, green manuring, tillage, crop rotation, etc., exhibit a significant impact on soil microbial C and N cycling [118,127,128]. Chemical fertilizers’ addition can increase or decrease nutrient availability in soil [127]. Chemical N addition can cause a change in soil N status that either speeds up or slows down soil C turnover [129] by affecting soil microbial biomass [128]. Nemergut et al. [130] showed that under chronic N fertilization, a relative abundance of Bacteroidetes and Gemmatimonadetes may increase but the Verrucomicrobia population may decrease. Additionally, a shift in a fungal population (e.g., Basiodiomycetes) and archaea to bacteria may occur. Soil C turnover under N addition is contingent on the biomass of gram-negative bacteria and saprophytic fungi as well as peroxidase enzymatic activities [128]. When C is limited, biomass turnover rates in the soil can define the soil microbial community composition (e.g., fungal, bacterial ratio) and N mineralization rate [125]. Moreover, changes in atmospheric N deposition rate may alter soil microbial community composition and their inter- and intra- species interaction [131,132]; SOC sequestration [133] and SOM decomposition [134]. For example, persistent N deposition decreases fungal biomass, species richness, and oxidative enzyme potential, but may enable resistant fungal species to withstand environmental stresses which may further counteract their traits that promote SOM decomposition, hydrolysis, and oxidation [134]. However, N enrichment can increase microbial C use efficiency (e.g., glucose) by decreasing respiration, microbial total phospholipid fatty acids (PLFAs), and the fungal to bacterial ratio [133]. Contrarily, a deficiency in soil N leads to decreased microbial C use efficiency, since more C needs to be consumed by soil microbes to acquire N [135,136] which results in the excess release of atmospheric C through increased microbial respiration [135]. Again, in an experiment carried out in a desert ecosystem in China, Sha et al. [131] found that continuous N input at a rate of 6 g m-2 yr-1 positively contributed to increasing SOC content, but that the influence on soil microbial diversity and community structure was non-significant (p > 0.05). Additionally, this sort of N addition does not reduce competition for N between soil microbes and plants (Leymus secalinus).

Manure addition can induce soil microbial community composition, diversity, species richness, and other associated parameters required for C and N cycling [137]. Studies have shown that long-term farmyard manure (FYM) application can ensure efficient C and N cycling within agroecosystems by increasing microbial biomass rather than altering microbial community composition [138,139]. In addition, FYM can increase the activity of soil enzymes e.g., protease and arylosulphatase [139] which suggests that bacterial (Actinobacteria sp., Pseudomonas sp., etc.) species are abundant in the soil. In contrast, the Soonvald et al. [108] study showed that potato roots grown in FYM plots showed a significant reduction in AMF species richness compared to potato, barley, and wheat roots grown in plots without manure (mineral nitrogen fertilization). Metagenomic sequencing of long-term organically managed paddy soils revealed that organic matter addition promotes the relative abundances of functional genes required for accelerated soil C and N cycling, and the substrate preference of the soil microbial community may cause the community to shift towards a copiotrophic lifestyle. Copiotrophic taxa include Proteobacteria and Actinobacteria [137]. An extensive application of manure-based compost significantly enhanced soil microbial functioning and the relative abundances of functional genes of bacteria, archaea, and ammonia oxidizing bacteria, but microbial diversity was greatly reduced. This may be attributed to the fact that intensive compost addition may considerably contribute to the prolific reproduction of particular types of microorganisms that can exhibit a suppressing impact on other microbial species. In addition, heavy metals can be accumulated in soils through manure addition which can inhibit the growth and development of the diversity of soil microorganisms [140]. Elfstrand et al. [139] revealed that long-term application (47 years) of green manure (fresh grass) can increase bacterial, fungal, and total microbial biomass in soil. The co-incorporation of green manure and crop residue can stimulate soil microbial growth (total phospholipid fatty acids) and soil enzymatic activities (β-glucosidase, β-cellobiosidase, N-acetyl-glucosaminidase, L-leucine aminopeptidase, and phosphatase). Soil enzymes retain the crucial part in C and N cycling (

Table 3. Microbial carbon and nitrogen cycling in agricultural/forest/desert soils.

Agronomic Practice(s)/Forest Ecosystem/Desert Ecosystem	Soil Type and Climate	Region	Soil Microbial Activities	Carbon Cycling	Nitrogen Cycling	Reference(s)
Rainforest conversion into rubber-based plantation	Oxisols developed from sandstone and granite; tropical and monsoonal climate.	Baisha, Hainan, China	Relative abundance of Ascomycota and Zygomycota decreased but Basiodiomycota increased. Relative abundance of Actinobacteria and Verrucomicrobia decreased but Acidobacteria and Chloroflexi increased.	Reduced soil C mineralization rate. Microbial biomass C (MBC) increased.	Increased soil available N. Microbial biomass N (MBN) increased.	[142]
Manure addition compared to fertilization	Black soil and temperate continental monsoonal climate.	Northeast China	Manure can increase the functioning and abundances of Proteobacteria and Planctomycetes (C and N cycler) but inhibited growth of Verrucomicrobia.	Manure can reduce the abundance of cooC (reductive acetyl-CoA pathway) and coxS (CO oxidation) genes but enhance the abundance of icd genes.	Manures can boost the abundances of nasA, nasD, napA, and napC genes.	[143]
Organic mulching	Northern subtropical monsoonal climate.	Nanjing, China	N.E.	SOC, dissolved C and MBC increased.	Total N, soil available N, dissolved N and MBN increased.	[141]
Temperate Coniferous Forest	Peat soils, Temperate and harsh climatic conditions.	Central Europe	Dominant abundance of bacteria include Proteobacteria, Acidobacteria and Actinobacteria. Dominant abundance of fungi include Basidiomycota and Ascomycota.	Fungi regulated C cycling through enzyme stoichiometry.	Bacteria regulated N cycling through enzyme stoichiometry.	[144]
Peat Swamp Forest	Waterlogged peat soils, tropical moist climate.	Malaysia	Bacterial taxa e.g., Dyella spp., Paraburkholderia spp., Klebsiella spp. were involved in the dilapidation of lignocellulose, carbohydrates, sugar alcohols, organic acids and aromatic compounds.			[145]
Conversion of desert to croplands (reclamation)	Aeolian silty loam soils.	Northwest China	Increased bacterial (Proteobacteria, Nitrospirae) and archaeal gene (Euryarchaeota, Thaumarchaeota) abundances observed.	Total organic carbon, SOC, dissolved organic carbon, MBC increased.	Total N content and soil available N increased.	[146]

Note: N.E. = Not evaluated.

) [141].

However, different microbial groups may impact soil C and N cycling synergistically or antagonistically. For instance, Nuccio et al. [147] showed that AMF may consume inorganic N, thereby inciting a shift in Actinobacteria and Comamonadaceae populations. In degraded soils, AMF can improve N cycling by increasing the bacterial gene copies e.g., nifH, AOB-amoA, narG, nirK, and nosZ [148]. In addition, AMF may induce changes in plant functional traits which may positively influence denitrification over N mineralization [149]. Moreover, AMF can act as an ecosystem-restorative agent. Qian et al. [150] showed that AMF can store C in reclaimed mine soil by increasing the soil enzymatic activities and total glomalin content.

3.2. Phosphorus and Potassium Cycling

3.2.1. Phosphorus Cycling

Soil microorganisms regulate soil P availability and cycling as well as microbial P turnover [151,152]. Microbial P turnover includes mineralization and immobilization of organic P leading to the modification of different forms of P in soil [152].

Microbial functional profiling through metagenomics revealed that long-term application of P can increase the conversion of inorganic P to organic P resulting in the absorption by the living cells of soil microbes. The process is facilitated by an increase in the phosphate transporter gene (pit) and a decrease in P-starvation response gene (phoR) [151]. This suggests that soil microbes are reluctant to utilize external P sources [153]. Ecological restoration in southern China enhanced the relative abundances of glucose dehydrogenase (gcd) genes, leading to increased soil P solubilization [154].

P input in a typical temperate grassland in northern China aggravated microbial limited access to N, changed their life strategies from K-strategy (dominated by Acidobacteria, Chloroflexi) to r-strategy (dominated by Proteobacteria, Bacteroidetes), and altered their functional traits [155]. Long-term N addition can decrease the relative abundances of P-solubilizing bacteria e.g., Actinobacter, Gammaproteobacteria and Alphaproteobacteria [151].

Long-term application of organic manure in greenhouse vegetable fields can increase soil and bioavailable P, microbial (fungal and bacterial) biomass P and soil phosphatase (alkaline and acid phosphomonoesterase, phosphodiesterase, and phytase) activities [156]. Likewise, Luo et al. [157] showed in a meta-analysis that organic amendments can increase acid and alkaline phosphatase activities by 22% and 53%, respectively, with a corresponding increase in microbial extracellular phosphatase enzyme leading to the increased transformation of organic P to inorganic P as well as phoD- and phoC-harboring species in soils. Reed-biochar can enhance the abundance and diversity of phoD-harboring microbes in paddy soil [158].

3.2.2. K Cycling

Different forms of soil potassium (K) have been identified, such as structural K, exchangeable K, non-exchangeable K, and soil solution K/water-soluble K [159,160]. Studies have shown that different agricultural practices may increase or decrease these different forms of K in soil (

Table 4. Functions of soil enzymes in carbon and nitrogen cycling.

Enzymes	Function(s)	Reference(s)
β-glucosidase	1. Directly controls the quality and quantity of SOM by regulating SOM decomposition. 2. Split cellobiose into glucose molecules.	[168,169]
β-cellobiosidase	1. Regulate C cycling and ecosystem respiration.	[170]
N-acetyl-glucosaminidase	1. N mineralization in soils. 2. Reducing ecosystem respiration.	[170,171]
L-leucine aminopeptidase	1. Helps soil microbes to acquire N.	[172]
Cellobiohydrolase	1. Facilitates microbial breakdown of cellulose and chitin. 2. Regulates the decomposition of SOC.	[173,174]
α-glucosidase	1. Degrades carbohydrates in soils.	[175]
Xylosidase	1. Regulate C cycle. 2. Produce microbes’ accessible simple sugars from compound carbohydrates.	[176,177]
Proteases	1. Regulates N cycle. 2. Converts protein to oligopeptides and amino acids.	[178]
Ureases	1. Hydrolyzes urea into NH3 and CO2.	[179]
Dehydrogenase	1. Regulates soil microbial metabolism.	[141]
Peroxidase	1. Regulates SOM decomposition. 2. Converts phenolics to form carbohydrates and proteins.	[180]

) [161,162] by impacting the abundance, diversity, and growth of K-releasing soil bacterial communities [161,163] (

Table 5. Relationship among agricultural practices, K cycling and soil microorganisms.

Reference	Agricultural Practices/Sampling Sites	Region	Soil Type	Inference	Impact on Soil Microbial Activities	Impact on Soil Enzymatic Activities
[163]	Peanut shell biochar addition	China	K-deficient acidic soil	Increased soil K content.	Enhanced growth and relative abundance of K-dissolving bacteria e.g., Actinomycetes, Chloroflexi, Proteobacteria, Acidobacteriota, Firmicutes.	Improved functionality of urease, dehydrogenases, and extracellular enzymes.
[161]	Peanut shell biochar addition	China	Yellow-brown soil	Improved soil available K.	Relative abundance of Sphingomonas, Gaiella, Elev-16S-1332, Gemmatimonas was improved by 28–377%.	N.E.
[181]	Soil fertilization with rock K and K-dissolving bacteria (Bacillus mucilaginosus and B. subtilis)	Egypt	Calcareous soil	Soil available K increased significantly i.e., bacterial inoculation and rock K+ bacterial inoculation increase K+ 6% and 80%, respectively.	N.E.	N.E.
[182]	Sudan grass (Sorghum vulgare Pers.) var Sudanensis cultivation using waste mica inoculated with Bacillus mucilaginosus	India	Alfisol	B. mucilaginosus led to around 59% increase in soil available K+	N.E.	N.E.

Note: N.E. = Not evaluated.

). For instance, biochar addition can enhance soil exchangeable K and soil solution K by 30% and 11%, respectively [161], by favoring the growth of K-solubilizing bacteria (KSB) [117], while Dong et al. [162] speculated that agricultural activities can decrease the functionality of KSB (e.g., Enterobacter). The KSB in forest soil is more diversified than in plantation (e.g., rubber) soil, implying that K cycling is much more ubiquitous in forest soil, leading to the differences in soluble K contents in these two types of soil [162]. This may be attributed to the fact that KSB can release organic acids (gluconic/acetic acids) or certain extracellular substances to convert insoluble K to soluble K+, which is plant-uptakeable (see

Table 6. Some selected soil bacterial and fungal species that can release K from minerals in soil.

Soil Microorganisms’ Type	Genus/Species	Mineral	References
Bacteria	Bacillus mucilaginosus (strain K02)	Feldspar	[164]
	Paenibacillus sp.	Feldspar, mica	[183,184]
	Bacillus globisporus	Feldspar, muscovite, biotite	[185]
	Pseudomonas sp. (strain S10-3)	Biotite, muscovite	[186]
	Plesiomonas, Bacillus mucilaginosus, Bacillus subtillis	Feldspar	[167]
Fungi	Penicillium purpurogenum, Taromyces radicus, Aspergillus fumigatus, Aureobasidium pullulan	Muscovite	[187]
	Cenococcum geophilum Fr	Nepheline, illite, muscovite, biotite and feldspar	[188]

for a list of K-solubilizing bacterial and fungal species) [164,165,166]. For example, Enterobacter can dissolve feldspar, a K-containing mineral [167]. These studies indicate that KSB can be employed to improve soil biological fertility [162].

4. Biological Soil Crusts (BSCs): An In-Depth Overview of Classification and Types

Biological soil crusts (bio-crusts; BSCs) cover about 12% of the earth’s terrestrial surface [189] and are composed of highly specialized organisms, which contain (i) photoautotrophic microorganisms such as cyanobacteria, algae, lichens, and mosses, and (ii) heterotrophic micoorganisms such as bacteria, actinomycetes, fungi, and microfauna [190,191]. They associate with soil particles to form a living, protective membrane [192]. BSCs have been shown to be common in the upper 0–1 cm of soil [191,193], and are particularly abundant in arid and semi-arid regions [194] (

Table 7. General classification of BSCs [190].

Crust Categories	Occurrence	Characteristics
Smooth	Hot deserts.	Composed mainly of endedaphic cyanobacteria, algae and fungi. Chemical crusting;
Rugose	Temperate regions.	Low surface roughness. Lots of scattered lichen and/or moss clumps. At high humidity, dominated by filamentous algae, which penetrate the soil to ~4 mm.
Pinnacled	Areas where the soil freezes in winter.	Dominated by cyanobacteria. Locally up to 40% moss lichen cover. Height to ~15 cm.
Rolling	Areas where the soil freezes in winter. High rainfall.	Lichen-moss cover. Height to ~5 cm.

), where they can make up to 80% of the area [195]. Cyanobacterial and microfungal filaments, the rhizinae and rhizomorphs of lichens, and the rhizinae and protonemata of bryophytes weave throughout the top few millimeters of soil, gluing loose soil particles together. BSCs can be categorized according to habitat conditions, taxonomic composition, dominant species, physical appearance, or function [196] (Table 7) and their occurrence in the world is variable (

Table 8. Global occurrence of various BSCs types in various regions [189].

BSCs Type	Climate	Examples of Sites
Smooth	Hyper-arid	Negev, Oman, Israel
	Arid	Israel, Egypt, Iran, Negev, Clark Mountain, Gurbantunggut desert, Oman
	Semi-arid	Canyonlands national park, Yanchi Research Station, Colorado, Niger, Burkina Faso, Utah (USA), National Park (Australia), Chihuahuan desert
	No dryland	Gemrany, Hobq Desert, Tenger desert, HIhnerwasser, Neuer Lugteich, Niger
Rugose	Arid	Navajo, Israel, Gurbantunggut Desert, Clark Mountain
	Semi-arid	Negev, Mongolia, North China, Colorado Plateau, Belichon, Idaho, Mojave Desert, Southen Kalahari, New Mexico, Utah
	No dryland	Germany, Hobq Desert, Tenger desert, Iceland, Sweden, Florida, Slovakia
Rolling	Arid	Nizzana, Hidden Valley Area
	Semi-arid	SE Spain, El Cautivo, Aranjuez, Tengger desert, Soebatsfontein, Kane Creek Road, Gurbantunggut Desert
	No dryland	Hochtor, Austria, Germany, Hobq Desert, Tenger desert, Iceland, Germany, Slovakia
Pinnacled	Arid	Gurbantunggut Desert, Clark Mountain
	Semi-arid	Mongolia, North China, Colorado Plateau, Cannonville, Boulder, Big Water, Utah, Gurbantunggut Desert
	No dryland	Dalateqi County, Tenger desert, Germany, Gurbantunggut desert
Hypolithic	No data	Gobabeb, Moerdverloren 208, Baja california
Only lichen	Arid	Nizanna

). However, the composition of BSCs is still poorly understood and its complexity makes an unambiguous classification difficult [197].

BSCs formation may take 10 to 1000 years, depending on soil–climatic–microorganism interactions, microbial metabolic activities, reproduction strategies, and species diversity [198]. The BSC development begins with the development of smooth cyanobacterial–algal crusts under favorable conditions, followed by the formation of short moss-lichen crusts and eventually tall moss-lichen pinnacled crusts [192]. Soil bio-crusts are characterized by a high diversity of microorganisms. Depending on the proportion of organisms present in bio-crusts, three morphotypes of BSCs have been distinguished according to Williams, Buck and Beyene [192] as follow:

(1)

Cyanobacteria-dominated crust: smooth, composed of filamentous cyanobacteria, 1.5 mm thick bio-rich zone;

(2)

Short moss–lichen crust: ≥50% mosses-lichen cover, some cyanobacteria, 11 mm thick bio-rich zone;

(3)

Tall moss–lichen pinnacle crust: ≥50% mosses-lichen cover, some cyanobacteria, 22 mm thick bio-rich zone.

Based on previous studies by Belnap and Lange [190,199] BSCs can also be classified as follows. These type of BSCs are named after their predominant microorganisms’ composition.

(1)

Physical crusts (rain/desiccation)—bacteria, fungi and radicle thrive before cyanobacteria and algae;

(2)

Cyanobacterial/algal crusts—dominated by cyanobacteria (e.g., Microcoleus and Scytonema sp.);

(3)

Lichen crust—composed of lichens, but also various saprotrophic fungi;

(4)

Bryophyte crusts—dominated by bryophytes (e.g., Microcoleus sp.), developing in the presence of large amounts of organic matter deposited by wind and precipitation;

(5)

Mixed biotic crusts—a complex structure of communities: bryophytes, lichens, algae, cyanobacteria, and associated decomposing microorganisms (humicolous, lignicolous fungi).

However, 11,000 species of mosses have been identified that may be part of BSCs, mainly from the families Pottiaceae, Grimmiaceae, and Bryaceae [200]. Prevalent biocrust-forming lichens may include Buellia zoharyi, Diploschistes diacap-sis, Fulgensia subbracteata, Psora decipiens, Squamarina lentigera, and Toninia sedifolia, among others [201]. Among the cyanobacteria forming BSCs, Schizothrix telephoroides, Microcoleus vaginatus, or Chroococcidiopsis sp. are prominent [190].

4.1. Role of Soil Bio-Crusts in Physicochemical Properties of Soils and Nutrient Cycling

• BSCs can alter the physicochemical properties of soil [190,202,203] (Figure 2). Primarily, they stabilize the soil surface and protect against erosive forces [191]. Seitz et al. [204] showed that bryophyte-dominated BSCs strongly reduce soil erosion in forest environments (southeastern China), being more effective than abiotic soil surface cover. Additionally, Bowker et al. [193] showed that extracellular polysaccharides from cyanobacteria increase soil stability and reduce soil erosion. BSCs can affect water availability, stability, and soil fertility in semi-arid areas [205,206]. More silt or clay is typically present in crust-covered soils, which improves plant macronutrient assimilation and increases the soil’s fertility [190]. BSCs under dry (desert) conditions can facilitate the accumulation, morphology, and ecosystem services of silt and increase water availability (bind surface water) [192,205]. Miralles-Mellado, Cantón, and Solé-Benet [207] showed that BSCs also prevent soil desertification by influencing the detachment and transport of soil particles. Studies in cool deserts have shown that BSCs can increase the nutrient content (i.e., N, K, Ca, Mg, P, Fe, Mn) of soil [208], and modify soil pH [209].
• BSCs from arid ecosystems affect N cycling through nitrification and N fixation [211]. Among the organisms that form BSCs are cyanobacteria and cyanolichens (e.g., Collema, Microcoleus, Nostoc), which fix nitrogen that is then released into the soil environment. Up to 70% of the nitrogen bound by these microorganisms ends up in the soil. Studies have shown that the presence of BSCs significantly increases soil N content [208,212]. Elbert et al. [212] estimate nitrogen uptake by cryptogamic covers at about 49 Tg per year, suggesting that nitrogen fixation by covers may be crucial for carbon sequestration by plants. In addition, the polysaccharide and total carbon content of soil increases due to the presence of BSCs [213,214]. This is because crust-forming organisms secrete extracellular carbon within a short time of its acquisition. In the case of cyanobacteria, this can be as high as 50% of the acquired carbon. An increase in soil carbon is associated with an increase in heterotrophic microorganisms, and a faster rate of decomposition. Globally, cryptogamic communities—which form crusts—are estimated to take up about 3.9 Pg of carbon per year, equivalent to about 7% of net primary production by terrestrial vegetation [212].
• Studies have shown that communities of organisms in BSCs play a key role in the biogeochemical cycling of P, especially by converting stable P into labile, readily available P [215,216]. Beraldi-Campesi et al. [208] showed that bio-crusts have higher total P concentrations than adjacent soils. Baumann et al. [217] showed that especially P-containing mineral concentrations decreased, and organic P concentrations increased in BSCs compared to volumetric soil in a temperate forest in Germany. Cyanobacteria (e.g., Anabaea, Anacystis, Lyngbya, Nostoc), but also fungi, lichens and some bacteria can chelate metals [218,219]. These increases availability of Cu, Zn, Ni, Fe etc. to plants [208]. Chelation of metals by microorganisms is particularly important in soils with a pH higher than 7 (e.g., deserts), where some elements form insoluble oxides/hydroxides [220]. In addition, BSCs can take up significant amounts of available metallic nutrients (Cu, Fe, K, Mg, Mn, Na, and Zn) and play an important role in conserving and protecting these nutrients in dry soils from leaching and erosion [221].
• BSCs also provide habitat for soil biota: protozoa, nematodes, tardigrades, rotifers, mites, collembola, arthropods, and molluscs [222,223,224].
• Apart from these, BSCs has the potential to impact plant growth and development. For example, BSCs in a temperate pine barren ecosystem impacted germination and other early stages of the development of plant species including Lespedeza capitata, Lupinus perennis [225]. The development of BSCs also increases the survival of some vascular plant species [226], leading to greater ecosystem diversity. In postglacial areas, BSCs have been shown to colonize the soil first and successionally facilitate piedmont [227]. At the same time, Song, Li and Hui [228] suggest that BSCs can act as natural regulators of vegetation patterns and thus promote the stability and sustainability of ecosystems. A high cover of BSCs can also protect soils from the negative consequences of climate change as evidenced in a dry ecosystem of Spain [229].

4.2. Establishing BSCs on Agricultural Land Warrants More Research

BSCs primarily thrive in deserts, polar/alpine regions, and under harsh conditions with poor vegetation [230]. Research on bio-crusts in agroecosystems is limited [214,231]. This is because agricultural soils are irrigated, or grazed by animals, which may interfere with the BSCs formation. Studies have shown that the soil under bio-crusts has a higher moisture content, higher nutrient concentrations, and a relative abundance of nitrifying bacteria compared to the root zone under bare soil [214,231,232]. Zaady et al. [233] attempted to determine the effect of long-term agricultural practices (16 years) on BSCs in a semi-arid area (Israel). Findings showed that all applied treatments (scraping, car-tracking, mowing, spraying) affected chlorophyll content, polysaccharides, hydraulic conductivity, and overland runoff on soils with BSCs. Mowing and simulating car tracks led to reduced surface run-off and increased hydraulic conductivity. Mowing and spraying significantly reduced total chlorophyll counts. Further, Ferrenberg et al. [234] in a greenhouse experiment showed that the presence of bio-crusts promoted the growth of B. tectorum, probably through a positive effect on soil fertility, which was elevated in mesocosms with bio-crust and interacting with the effect on grass germination. On agricultural soils, cyanobacteria have been observed accumulating on cropland and non-cropland surfaces in the north-eastern United States, especially when soil is exposed to sunlight after harvest [235,236]. They are often accompanied by cyanobacterial green algae and mosses. However, these are not typical BSCs as they form relatively quickly. The researchers proposed the name ‘soil surface consortia’—SSCs—for this layer. Studies have shown that SSCs can influence the amount of N in agricultural soils—they can bind N₂ or immobilize inorganic N [235,236]. However, rainfed agriculture may have a negative impact on BSCs formation and their community composition. The impact of rainfed agriculture and firewood extraction on the taxonomic structure of BSCs in a tropical semiarid region of central Mexico was assessed by Sosa-Quintero et al. [237,238]. The results showed that in soil under rainfed agriculture, BSCs comprised only 14-18 species and were dominated by cyanobacteria with heterocysts; whereas at firewood harvesting sites, BSCs numbered 23-29 species and were dominated by cyanobacteria and bryophytes. Among the factors affecting BSCs, mechanical agricultural operations (ploughing, sowing), livestock grazing, the use of pesticides and chemical fertilizers, hiking, off-road vehicle driving, agricultural vehicles, fires, and mining may cause decreases in biomass and changes in the community structure of organisms in BSCs, which affects soil functions [239]. Overall, the role of BSCs in soil conservation is very important. It is crucial to identify the responses of BSCs under changing climate and for preserving soils.

5. Conclusions and Perspectives

Soil biological fertility has been found to be a key factor in enhancing crop resilience and productivity, as well as agricultural sustainability. This review concludes that the rhizosphere and its microorganisms, associated nutrient cycling, and biocrusts should be considered as major factors when considering soil biological fertility improvement. In addition, the rhizosphere stores and preserves microorganism life, which is highly susceptible to disturbance, and any disruptions to their life cycle can inhibit crop productivity, as evidenced in the literature. Biological activity is not homogenously distributed throughout the soil profile and is higher in the rhizosphere compared to the bulk soil. Based on current understanding, it can be concluded that the rhizospheric microorganisms take up nutrients from root exudates and then produce enzymes specific to the macronutrient metabolism and cycling. Nutrient bioavailability is fully dependent on the microorganisms of the rhizosphere, which also the ensures fertility of the soil referred to as biological fertility. Biological fertility is essential for proper plant growth and development. However, in response to objectives of this study, the following has been demonstrated:

• The interaction between soil, microorganisms, and plants makes the rhizosphere an ideal space for microorganism growth. This is mostly related to the quantity and type of root secretions and their predominant components that attract microorganisms and influence nutrient mobility.
• Rhizospheric microorganisms exhibit a wide array of positive effects through atmospheric nitrogen fixation, decomposition of organic matter, resilience against plant pathogens, immobilization/mineralization of nutrients, production of phytohormones (ABA, IAA, et al.), osmoprotectants, exopolysaccharides, etc., and by reducing the harmful chemical footprint (e.g., salinity) in the environment.
• The introduction of PGPR in agricultural soils may reduce the chemical fertilizer-associated costs of farmers because of their high efficiency in nutrient cycling. Additionally, they can make crop plants more resilient to biotic/abiotic stresses, thus documenting their responses under elevated CO₂ conditions can facilitate future research on climate change mitigation.
• A quantitative estimation of the composition of root exudates is necessary since it maintains synergistic/antagonistic associations among plant, soil, and soil-dwelling microorganisms.

Prospects for future research include:

• The spatiotemporal dynamics of KSB distribution and their role in K cycling in soils should be included in future research.
• Knowledge about the diversity and functionality of the organisms forming BSCs is diverse, and although this topic has been of interest to researchers for a long time, still not all the relationships occurring in BSCs are known. There is still a lack of information on the biological conservation of BSCs species, the possibilities for soil remediation with BSCs. and the impact of climate change on the structure and function of bio-crusts. It is worth noting the lack of broad studies from other than desert/semi-desert/arid areas and the problem of biodiversity assessment due to the use of different methods by researchers. Future research should be based on accurate, molecular methods using DNA analysis. It is estimated that crusts occupy about 12% of the terrestrial land surface, so researchers should try to analyze BSCs from more ecosystems, to assess whether they also affect the soil environment in systems other than forests and deserts.
• Research on the rhizosphere tends to focus on bacteria and fungi, while other organisms are often neglected. Despite the nature of the threat posed by nematodes to plant crops, the topic of their interactions with microorganisms and plants is not fully understood. The network of these interactions is very complex and requires in-depth analyses. Understanding these interactions could make it possible to control nematodes and thus help protect plants against parasites.