Role and Mechanism of Action of Extremophilic Marine Actinobacteria in Plant Growth Promotion

Abstract

Food is an essential component of life for all humans and animals present on this planet, and food security is becoming more challenging across countries due to reduced food production, increased population, and climatic changes. Most of the nations are hastening to increase their food productivity to counteract food scarcity and undernourishment. The agriculture industry is the primary reservoir for food production and aids in reducing hunger, poverty, and food security. Recent trends in the usage of chemical fertilizers, pesticides, and herbicides to enhance crop productivity may provide better yields for shorter duration. Still, in the long run, this causes severe issues in soil fertility and affects soil ecosystems. Sustainable, eco-friendly agricultural practices are the future ventures of agriculture using microbe-based plant growth stimulants, fungicides, and pesticides. The genus Actinobacteria is renowned for its therapeutic and industrial values. However, their agricultural applications are merely overlooked. In addition, actinobacteria from terrestrial and coastal ecosystems have been widely explored, leaving the extreme marine environmental sites untouched. This book chapter focuses on uncovering the functional properties of polyextremophilic marine actinobacteria and their role and mechanism of action in plant growth promotion.

1. Introduction

Agriculture is an essential contributor to economic growth, accounting for nearly 4–25% of the country’s GDP, and is a powerful tool to enhance food security to feed ∼8.2 billion people, reduce poverty, and increase people’s prosperity [1, 2] Several developed and developing countries are focusing on increasing agriculture yield to develop immunity against food scarcity and malnutrition [3]. Such schemes were shocked due to changes in geopolitics impacting agriculture, such as increased prices of agricultural equipment, reduced crop yield due to climatic changes, pollution, and harsh chemical fertilizers and pesticides, causing soil infertility [4, 5]. In contrast to the issues in food production, it was also noticed that nearly 17% of the food produced is being wasted at various stages: production, transportation, processing, storage, and shelf life [6]. This is a severe concern, causing grievous damage to society by reducing food availability, creating malnutrition, and inflating food products. In addition, food waste management requires massive funding to process food waste [7, 8]. Meanwhile, underdeveloped countries dump food and agriculture waste and allow the waste to compost naturally, which is highly ineffective and can generate lethal effects on the environment, such as foul odor, leaching of toxins, burning causing reduced air quality, rearing of pests, and promotes the growth of pathogenic microbes [9].

Despite such issues on food scarcity and availability, global countries are increasing their food reserve by using higher volumes of chemical fertilizers, pesticides, and herbicides to promote plant growth and yield to reserve food and feed the increasing global population [10, 11]. This strategy has ripe sufficient results and increased food availability. Several decades away now, the butterfly effect on the usage of chemical fertilizers, pesticides, and herbicides is causing severe issues in soil health, such as disruption of the soil ecosystem, eutrophication, groundwater contamination, soil infertility, and inducing carcinomas and other health ailments to humans [12, 13, 14]. To counteract such issues, sustainable and eco-friendly approaches are required in agricultural practices. One such advancement is the use of biofertilizers, biofungicides, pesticides, and herbicides to enhance plant growth and control pathogens, pests, and herbs, respectively [15]. Globally, biofertilizers are gaining serious momentum, and their usage is constantly increasing due to their lower price, higher yield, and longer shelf life. It has been projected to reach nearly 5.2 billion USD by 2025. Finally, the usage of biofertilizers aids in rejuvenating the soil ecosystem and protects the plants from biotic and abiotic stress [16].

2. Actinobacteria

The genus Actinobacteria is a gram-positive, aerobic bacteria with a high G-C content of up to 70% in their DNA [17]. Actinobacteria are unicellular bacteria that have non-distinct cell wall morphology (nonseptate) resembling fungi, which are also called higher-order bacteria. Furthermore, they also produce pigments, substrate, aerial mycelium, hyphae, and conidia, which gives the bacterial colonies their signature powdery nature [18]. Actinobacteria are well-known as omnipresent microbes that are present almost everywhere and commonly found across all types of soils, freshwater, and marine resources [19, 20]. In addition, actinobacteria are micro waste-processing bio-factories that decompose most of the organic matter present in the soil, such as proteins, fats, polysaccharides, humus, cellulose, and other organic compounds; without them, the earth will be filled with waste matter [21].

The emergence of diseases has made researchers explore microbial secondary metabolites, which has led to the discovery of nearly 23,000 metabolites, from which over 10,000 metabolites were extracted from the genus Actinobacteria. Antibiotic discoveries over the last decades have identified 12,000 antibiotic lead molecules, 70% of which were from actinobacteria. Meanwhile, the genus Streptomycetes has a distinctive contribution, and so far, 7600 compounds have been identified. In addition, the actinobacteria also produce several unique enzymes that have therapeutic, industrial, and bio-remediation values. Such properties make the actinobacteria worthy of further exploration, where the genus actinobacteria has been classified into 18 major lineages, with 6 classes, 5 subclasses, 6 orders, and 14 suborders. All the existing studies on actinobacteria with respect to the secondary metabolites and enzymes were only focused on the terrestrial and aquatic ecosystems, leaving the microbes from the extreme environmental sites untouched.

2.1 Extremophilic actinobacteria

Apart from the typical aquatic and terrestrial environments, the actinobacteria also thrive at extreme environmental sites such as hypersaline lagoons, salt pans, deep sea, acidic and alkaline environments, deserts, hydrothermal vents, radioactive sites, icebergs and glaciers. Such microbes present under extreme environmental conditions are generally addressed as extremophilic bacteria. Microbes that survive/tolerate multiple extreme environmental conditions are denoted as polyextremophilic bacteria. Due to their fungi-like resemblance, vegetative spore production, and unique metabolism, the actinobacteria can tolerate polyextremophilic abiotic stress present in the environment. Over the years, normal terrestrial and aquatic actinobacteria were considered for extracting antibiotics and natural compounds, leaving the actinobacteria present in extreme environmental conditions. Microbes surviving in extreme conditions have unique metabolic potential to efflux ions more effectively to survive in acidic and alkaline pH.

Furthermore, it also has unique enzymes which effectively function at wider temperatures, pH, and salinity. Finally, the presence of cryptic gene clusters of the microbes from the extreme environment has unique combinations to produce new secondary metabolites, which have not been identified so far. All such wonders from the actinobacteria make them more attractive to study and expose further properties of their extremophilic nature.

2.1.1 Halophilic actinobacteria

The earth is covered with ∼70% sea, which makes it the most prominent geographic location hard to access, which also contains a plethora of microbes waiting to be explored. So far, we have only identified less than 1% of microbes, and the rest are unexplored. The marine environment holds diverse extreme ecological niches such as coastal, deep sea, salt lakes, and mangroves. In general, the halophiles were broadly classified based on their salt tolerance levels as mild (0.5–2.5 M NaCl), moderate (1.5-4 M NaCl), and extreme-halophiles (2.5–5.5 M NaCl). In general, the actinobacteria thrive well in the typical coastal regions, with a copious amount of actinobacteria dominated by Streptomyces sp., Micromonospora sp., Rhodococcus sp., and Nocardia sp., as major genera commonly identified, followed by Nocardiopsis sp., Saccharothrix sp., Nonomuraea sp., Actinomadura sp., Saccharomonospora sp., and Promicromonospora sp., as least identified microbes from the coastal ecosystems (Table 1) [45, 46].

Extreme condition	Strain	Sampling site	Natural Compounds	PGP Properties	Reference
a. Salt Desert
	Streptomyces sp. DB634	Salar de Tara of the Atacama Desert, Chile	Abenquines A and D	—	[22]
	Streptomyces sp. C3		ChaxamycinD Chaxmycins A–D	—	[23]
	Streptomyces sp. DA3-7		Lentzeosides A–F	—	[24]
	Lentzea sp. H45	Saudi Arabia	Pyridine-2,5-diacetamide	—	[25]
	Streptomyces sp.	Morocco	—	—	[26]
	Streptomyces mutabilis IA1	Saharan soil	—	IAA, GA	[27]
	Nocardiopsis dassonvillei MB22	Algerian Sahara soil	—	IAA, siderophore, HCN	[28]
b. Halophiles
	Saccharomonospora azurea NA-128	Morocco	—	N2 and K solubilization	[26]
	Georgenia halophila	Salt Lake in Xinjiang Province, China	—	—
	Streptomyces sp. KLBMP S0051	Salt Marsh, Jiangsu Province, China	—	IAA, siderophore, ACCD, P-solubilization	[29]
	Micromonospora sp. KLBMP S0019		—
	Nocardiopsis sp.	Deep Sea, Antarctica	—		[30]
c. Acidophilic
	Acidimicrobium sp.		—	—	[31]
	Actinospica sp.	Salerno, Italy	—	—	[32]
	Acidothermus sp.		—	—	[33]
	Catenulispora sp.	Salerno, Italy	—	—	[32]
	Ferrimicrobium sp.	Sulfur mine, UK	—	Iron chelation	[34]
	Ferrithrix sp.		—
	Rubrobacter sp.	Hotsprings, Taiwan	—	—	[35]
	Amycolatopsis sp.; Streptomyces sp.	Thailand	—	P-solubilization, siderophore, antifungal properties	[36]
d. Alkaliphilies
	Microcella sp.	Cabeço de Vide in Southern Portugal	—	—	[37]
	Nesterenkonia sp.	Wuhan, China	—	—	[38]
	Nitriliruptor sp.	Soda Lake, Russia	—	—	[39]
	Yaniella sp.	Salt mine, Pakistan	—	—	[40]
e. Thermophilic
	Microbispora siamensis DMKUA 245 T	Soil sample, Thailand	—	—	[41]
	Actinokineospora soli YIM 75948 T	Yunnan province, China	—	—	[42]
	Saccharomonospora viridis SJ-21	Hotspring, Gujarat	—	—	[43]
	Ferrithrix thermotolerans Y005T	Geothermal site in Yellowstone National Park, Wyoming, USA	—	—	[34]
	Streptomyces Calidiresistens YIM 7808 T	Hotspring, Tengchong, Yunnan province, southwest China	—	—
	Actinomadura miaoliensis BC 44–5 T	Miaoli County, Taiwan	—	—	[44]

Table 1.

Various extremophilic actinobacteria strains have been identified so far.

2.1.1.1 Deep sea

The marine ecosystem has a wide range of zones and geographic variations based on which several ecosystems are thriving; one such is the deep sea ecosystem. The deep sea is one of the enigmatic sites that stayed unnoticed till the challenger deep sea mission was carried out using the Mariana Trench, which is below 10,916 metres from the surface. The diversity analysis carried out using advanced high throughput sequence (HTS) analysis revealed the presence of Chloroflexi (SAR202 and other lineages), Planctomycetes sp., Bacteroidetes sp., “Ca. Marinimicrobia” (Marine group A and SAR406), Thaumarchaeota, “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6), and Gemmatimonadetes (archaeal α subgroup) [47]. Similarly, the deep sediment analysis performed from the south Colombian Caribbean Sea at a depth of 1681–2409 metres results highlighted the presence of 36 phyla, 89 classes, 93 orders, 104 families, 90 genera, and 53 species, among them Proteobacteria sp., Bacteroidetes sp., Firmicutes sp., Actinobacteria sp., and Chloroflexi sp., were the top 5 phyla identified from the selected deep-sea sediments [48]. Such studies indicate the presence and abundance of richer polyextremophilic microbial diversity of microbes tolerating higher pressure, lower temperature, and anoxic conditions from the deep sea regions. Such conditions cause microbes to produce various unique metabolites and enzymes for their survival to avoid competition, nutrient depletion, and effective adaptation to harsh environmental conditions.

2.1.1.2 Salt lakes and salt pans

Salt lakes are one of the harshest ecological niches developed due to the natural process of constant fluctuation and evaporation of water levels, precipitation, increased salt concentration, and intense UV radiation, which allow the formation of arid crystalline salt sedimentation over the soil. In addition, the salt deserts contain higher concentrations of Na, Ca, K, SO4, Mg, HCO3, and Cl⁻ ions [49]. Most of the halotolerant and halophilic microbes flourish in such environmental conditions. Diversity studies conducted on salt flats from UAE at various zones reveal the ample abundance of Bacteroidetes, followed by Euryarchaeota sp., unclassified bacteria, Actinobacteria sp., and Cyanobacteria sp., from the core salt flat samples and an abundance of Proteobacteria and Parcubacteria species from the samples collected away from the salt flats. In continuation, diversity analysis conducted from the salt pans from Goa, India, showcased the dominant phyla as Pseudomonadota sp., Bacillota sp., and Candidatus Patescibacteria. Finally, studies in Qaidam and Qinghai Lake, from China, highlighted the actinobacteria diversity and revealed the presence of 19 generas, such as Actinotalea sp., Corynebacterium sp., Tsukamurella sp., Gaiella sp., Rhodococcus sp., and Tetrasphaera sp., from Qaidam Lake and 69 generas such as Ilumatobacter sp., Actinotalea sp., Aquihabitans sp., Marmoricola sp., Arthrobacter sp., and Demequina sp., from Qinghai Lake. Such actinobacteria are exceptionally rare and require further analysis by cultivable approach to unlock the mystery of their cryptic gene clusters and the mode of action [50]. As mentioned earlier, the salt pans and flats ecosystems are constantly exposed to UV radiation. Research studies have identified that such strains have genes encoding for HQ443199 of Ver 3 (class-I photolyase), which is responsible for repairing the UV-induced DNA lesions at the pyrimidine (6–4) pyrimidone photoproducts (6-4PPs) and cis-syn cyclobutane pyrimidine dimer (CDP). Such gene regulatory mechanisms can do wonders in genetic engineering and have a significant impact on scientific advancements [51].

2.1.2 Alakiphilic and acidophilic actinobacteria

The Industrial Revolution paved the way for higher emissions of pollutants in the soil and air. Also, the higher use of nitrogenous fertilizers has led to the occurrence of acid rain and soil acidification and a reduction in the soil pH of 4–6.5. Such acidic environments are commonly found in mines, where minerals are extracted using chemical techniques, higher crop cultivation without crop rotation, nitrification using fertilizers, and waste dumping yards. Similarly, the alkaliphiles are microbes surviving at alkaline soil conditions ranging from pH 8–11.5. The primary alkaline environments are soda-salt lakes and arid saline mineral-rich soil, which are the primary sources of alkaline environments. The alkaline environment is commonly found with reduced Mg²⁺ and Ca²⁺ ions, which is due to the weathering of calcium and magnesium ions by CO₂, which releases OH⁻ and increases the soil pH to 11.5 [52]. The marine actinobacteria mainly withstand acidic environmental conditions due to their H⁺ antiport systems, like H⁺ATPase activity, which efflux acidic products out of the cells and reduce the proton concentrations in the cells, using the which regulate the intracellular cytosol pH [53]. Previous reports on commonly identified acidophilic actinobacteria are Streptomyces sp., Nocardia sp., Amycolatopsis sp., Mycobacterium sp., Nonomuraea sp., Verrucosispora sp., Micromonosporas sp., and Saccharopolyspora sp. [36]. Similarly, studies on alkaliphilic microbes state that alkaliphiles are mostly polyextremophilic in nature, such as alkali thermophiles, alkali-halophiles, and alkali-psychrophiles. The most identified alkaliphilic bacterial genera are Streptomyces sp., Micromonospora sp., Nocardioides sp., Nesterenkonia sp., Isoptericola sp., Microcella sp., Streptosporangium sp., Georgenia sp., Corynebacterium sp., Nocardiopsis sp., Cellulomonas sp., Saccharothrix sp., Arthrobacter sp., and Saccharomonospora sp. [37, 54, 55, 56, 57].

2.1.3 Thermophilic actinobacteria

The thermophilic actinobacteria are chemoorganotrophs that can prosper beyond 28 to 80°C and are predominantly found in hot springs, hydrothermal vents, salt pans, deserts, and decaying matter. Where the thermotolerant strains can tolerate and survive till 45–50°C. At the same time, the thermophilic microbes can only thrive at higher temperatures, 45–55°C being the optimum temperature. The thermophilic bacteria can tolerate and survive at much higher temperatures due to their unique adaptation on the DNA levels. These strains mainly contain higher GC content, which makes them more stable at higher temperatures. In addition, the amino acid analysis reveals that mesophilic and thermophilic strains contain a higher percentage of charged amino acid residues on the proteins (Glu, Asp, Lys, and Arg) than polar amino acids [58]. Finally, the chemotaxonomic analysis on the cell wall composition states that the thermophilic and thermotolerant strains mainly contain type-III (meso-DAP with the presence or absence of madurose) and type-IV (meso-DAP with galactose and arabinose) cell wall composition. The most identified class of actinobacteria strains are Streptomyces sp., Thermophilia sp., Actinobacteria sp., Rubrobacteria sp., and Acidimicrobiia sp., which includes Thermomonospora sp., Thermopolyspora sp., Thermocatellispora sp., Thermobispora sp., Thermotunica sp., Thermoleophilum sp., Acidimicrobium sp., and Acidothermus sp., including only thermophilic species of actinobacteria [59].

3. Plant growth-promoting actinobacteria (PGPA)

Despite the negative echoes of the usage of chemical fertilizers, pesticides, and herbicides, inducing abiotic stress, it has left us to search for substitutes and allowed us to explore other non-conventional ventures. Microbe-based plant growth promotion is gaining substantial attention due to its availability, low cost, ease of administration, better yield rates, and new opportunities for biofertilizer development. The microbes near and around the plant rhizosphere region contribute greatly to plant growth promotion. In general, the bacterial genera Pseudomonas sp., Bacillus sp., Actinobacteria sp., Cellulosimicrobium sp., Klebsiella terrigena, Acetobacter sp., and Enterobacter sp., were known to have plant-growth-promoting properties [60]. Similarly, in the fungal kingdom, the Trichoderma, Aspergillus, Fusarium, and Penicillium genera are studied and commercially available as plant growth-promoting fungi [61, 62]. Among these existing plant growth-promoting microbes (PGPM), the marine polyextremophilic actinobacteria have not been extensively studied for their plant growth-promoting properties. Despite their extremophilic and extremely tolerant nature, marine actinobacteria can be suitable for application as plant growth-promoting actinobacteria (PGPA) and exploring their mechanism of direct and indirect plant growth promoting can lead us to the development and commercialization of eco-friendly, cost-effective biofertilizers (Figure 1).

Figure 1.

Direct and indirect plant growth promotion of the marine actinobacteria.

4. Direct mechanism

4.1 Nitrogen fixation

Nitrogen is an essential component for all living beings, including plants, to support their growth. Nitrogen is the critical component for photosynthesis, amino acid production, and DNA replication mechanism. The nitrogen is mainly available as atmospheric nitrogen (N₂) and is naturally converted into ammonia. Which only contributes to the niche percentage of the ammonia present in the soil. The primary mode for nitrogen fixation is where nearly 70% of the atmospheric nitrogen is fixed through biological nitrogen fixation (BNF) using soil microorganisms or rhizosphere bacteria. The nitrogen fixation mechanism occurs based on two different types of microbes: associative method (synbiotic) and free-living (Figure 2).

Figure 2.

Biological nitrogen fixation process in soil.

4.1.1 Symbiotic nitrogen fixation

In the associative nitrogen fixation process, the microbes fix the atmospheric nitrogen for the plants, where the plants produce a flavonoid substance from their roots, which attracts bacteria and triggers the nod gene present in the bacteria to produce nod factor and cause root infection and form the nodule primordia [63]. Further, the leguminous hemoglobin (LegHb) present in the root nodule scavenges the oxygen present in the root nodule. It makes the nodule anoxic, which facilitates the nitrogenase enzyme, which is a complex metalloenzyme dinitrogenase (molybdenum nitrogenase, vanadium nitrogenase, and iron-only nitrogenase) containing two-alpha subunits synthesized by NifDK genes. Paired with dinitrogenase reductase (Fe protein) containing two-beta subunits synthesized using NifH genes. Two nitrogen atoms form the atmospheric nitrogen (N2) fused using triple covalent bonds, making the molecule unreactive [64]. The nitrogenase enzyme, in the absence of oxygen, breaks the covalently bonded nitrogen atoms and replaces the H ions, resulting with the aid of ATP molecules scavenging from the host plant or produced by its own (Cyanobacteria) and producing two molecules of ammonia and 16 molecules of inorganic phosphate are produced. Finally, the produced ammonia is converted into ammonium ions and further oxidized to form nitrate and nitrite salts using Nitrococcus and Nitrosomonas soil bacteria, which the plants can uptake through roots. There are several known bacterial genera for fixing atmospheric nitrogen, such as Azotobacter sp., Clostridium sp., Cyanobacteria sp., and Beijerinckia sp. Meanwhile, in actinobacteria, the genus Frankia is well-known for nitrogen fixation on leguminous plants.

$$N2+8e^{-}+8H^{+}+16\mathit{ATP}\to 2N{H}_3+H_2+16\mathit{ADP}+16\mathit{Pi}$$E1

4.1.2 Asymbiotic nitrogen fixation

Apart from host-assisted nitrogen fixation, ammonia is also produced by non-symbiotic microbes such as Klebsiella sp., Bacillus sp., and Clostridium sp., and actinobacteria genera include Arthrobacter sp., Agromyces sp., Corynebacterium sp., Mycobacterium sp., Micromonospora sp., Propionibacteria sp., and Streptomyces sp., can fix atmospheric nitrogen as free-living microbes. The genus Frankia can function as a symbiotic and free-living nitrogen-fixing microbe [65, 66].

4.2 Nutrient solubilization

4.2.1 Phosphate solubilization

Phosphate is one of the essential factors required for plant growth; in general, phosphate is available in an insoluble form, which limits plant growth, and the phosphate-solubilizing microbes are essential for converting the insoluble phosphate to plant-soluble form. The soil phosphate is available in the form of aluminum phosphate, tricalcium phosphate, and iron phosphate. In addition, organophosphates are available in the form of phytin, sugar phosphates, inositol phosphates, phosphonates, nucleotides, phospholipids, and phosphoproteins. Typically, the phosphate in the soil can be solubilized using the acidification process by replacing the H⁺ ions in substitution with cations to the phosphate. Soil microbes convert the phosphate by producing organic acids as a result of metabolizing the carbon sources. In contrast, actinobacteria have not been well studied for their organic acid production. Studies have reported that the actinobacteria produces citric acid, lactic acid, malic acid, oxalic acid, and gluconic acid. At the same time, the actinobacteria are reported to produce phosphatases and phytase enzymes, which convert the organophosphates to plant-soluble phosphates. Studies have reported that Pseudomonas sp., Bacillus sp., and Actinobacteria sp., are well-known for their phosphate solubilization, from which Streptomyces sp., and Norcardiopsis sp., are well-studied for their phosphate solubilization activity (Figure 3) [67, 68].

Figure 3.

Microbial phosphate solubilization process.

4.2.2 Potassium solubilization

Similar to phosphate, potassium (K⁺) is also an essential macronutrient for plants. By nature, in soil, the K⁺ is available as rock potassium and potassium aluminosilicate, from which only 2% of the K⁺ is available in the plant uptake form. The K⁺ is biologically converted using the microbes by producing siderophores and producing organic acids, and chelating the metal ions (Ca⁺², Fe⁺², Si⁺⁴, and Al⁺³), which liberates K⁺ and converting them into potassium silicate or aluminum silicate ions. In addition, the potassium can also be solubilized using the extracellular polymers, which assimilate the K⁺ ions. The well-known microbes with K⁺ solubilization are Acidothiobacillus sp., Azospirillum sp., Azotobacter sp., Bacillus sp., Enterobacter sp., Erwinia sp., Paenibacillus sp., Pantoea sp., Pseudomonas sp., Streptomyces sp., Marinococcus sp., and Serratia sp. (Figure 4).

Figure 4.

Microbial potassium solubilization process.

4.3 Phytohormones

4.3.1 Auxins

Plant hormones are vital resources that contribute to plant growth, metabolic regulation, and tolerating biotic and abiotic stress. The auxin is synonymously known as IAA (indole 3-acetic acid) and is produced through six various pathways; one such is the IPA (indole-3-pyruvate) pathway. Most of the pathways use the L-tryptophan as the precursor molecule (Figure 5). The IAA is essential for adventitious and lateral plant root development, by which plants can take up better nutrients and minerals. The endogenous production of auxin levels in plants is affected mainly due to abiotic stress factors such as pH, environmental stress, and root exudates. So, supplementing the exogenous auxin can be an alternative technique to promote plant growth. Biochemical studies have identified microbes that also produce IAA, which can be used to facilitate better plant growth. The bacterial genera Azospirillum sp., Bacillus sp., Pseudomonas sp., and Actinobacteria sp. are well-known genera that produce the IAA. Constant application of the IAA hormone through biofertilizers can provide sustained plant growth without having any adverse effect on the plants [69, 70].

Figure 5.

Structure of auxin.

4.3.2 Cytokinins

Cytokinins are one of the critical growth regulators that play a crucial role in root cell development, division, and differentiation. In addition, it also reduces leaf senescence, increases chlorophyll production, enhances protein production for mitosis, and increases apical dominance in plants. So far, nearly 200 different types of cytokinins have been identified from plants, mosses, bacteria, and fungi. In the bacteria, the cytokinins were first identified on the Agrobacterium tumefaciens and subsequently identified on Azospirillum sp., Azotobacter sp., Bacillus sp., Rhizobium sp., Pseudomonas sp., and Actinobacteria sp. The seed treated with cytokinins showed higher seed germination and shoot propagation (Figure 6).

Figure 6.

Structure of cytokinin.

4.3.3 Gibberellins

The gibberellins (GA) are part of the plant growth-regulating hormones known for plant shoot promotion. Nearly 136 different varieties of GA have been identified in plants, fungi, and bacteria [71]. Structurally, the GA are tetracyclic diterpenoid carboxylic acids containing ent-20-norgibberellane (C₁₉) carbon skeletons or ent-gibberellin (C₂₀) among the existing GA. The GA₃ is most widely seen in microbes, followed by GA₁, GA₄, and GA₇, which are known to promote shoot development. The GA is commonly applied for promoting seed germination under low light conditions, elongation of internodes, treatment of plant dwarfism, reducing dormancy in buds, and trait selection. The Gibberella fujikuroi and Trichoderma are the fungal species well studied for GA production and the bacterial communities [72]: Actinobacteria sp., Azotobacter sp., Acetobacter sp., Azospirillum sp., Bacillus sp., Herbospirillum sp., Rhizobium sp., and Pseudomonas sp., are the commonly explored bacterial species with gibberellin production [73]. Among the actinobacteria genus, Streptomyces sp. and Nocardiosis sp. have been frequently identified for gibberellin production so far. The mode of action and gibberellin production is not yet understood (Figure 7) [74, 75].

Figure 7.

Structure of various types of gibberellins found in the microbes.

4.3.4 ACC deaminase

Plants present under various abiotic stress (increased pH, temperature, salinity, and nutrient availability) and biotic stress (infection and weeds) cause the plants to produce ethylene. Ethylene is a stress hormone that causes stunting of growth, leaf abscission, flower wilting, and ripening of fruits. The 1-aminocyclopropane-1-carboxylic acid (ACC) is the precursor for the ethylene production. Administration of the PGPB, which produces ACC deaminase, will convert the ACC into ammonia and α-ketobutyrate. This mechanism of action reduces the adverse effects caused by ethylene and can attain better growth promotion for plants growing in unfavorable conditions. The actinobacteria producing ACC deaminase are Streptomyces sp., Arthrobacter sp., Actinoplanes sp., Brevibacterium sp., Nocardioidaceae sp., and Rhodococcus sp. In addition, the halophilic actinobacteria, such as Micrococcus sp., Corynebacterium sp., and Arthrobacter sp., can promote plant growth at higher salinity (Figure 8) [75, 76].

Figure 8.

Mechanism of action of the ACC deaminase by the PGPB.

4.4 Siderophore production

The siderophores are low molecular weight iron chelating compounds with greater affinity for iron molecules. The plant grows in iron-depleted regions such as soil with high CaCO₃ contents, higher pH, and salinity. In such regions, the soil iron content will be very minimal and, in complex form (Fe³⁺), which plants cannot uptake. So far, 500 different siderophores have been detected, among which 270 have been structurally classified. The siderophore from the plants, bacterial, and fungal sources converts and mobilizes the complex iron (Fe³⁺) to (Fe²⁺) irons. Moreover, iron is required and part of enzymes such as cytochromes, photosystem I and II, ferredoxin, chlorophyll synthesis, and other metabolic processes. Generally, the siderophores are synthesized by Azotobacter sp., Azospirillum sp., Bacillus sp., Klebsiella sp., Methylobacterium sp., Nocardia sp., Pseudomonas sp., Rhodococcus sp., and Streptomyces sp. The most emphasized actinobacteria genera producing siderophore are Actinomadura sp., Arthrobacter sp., Brevibacterium sp., Streptomyces sp., Micromonospora sp., Nocardiopsis sp., Pseudarthrobacter sp., Pseudonocardia sp., and Rhodococcus sp.

4.5 Systemic resistance

Systemic resistance in plants is the profound defense mechanism found among all plants. Which is the underlying mechanism and can be classified into induced systemic resistance (ISR) and systemic acquired resistance (SAR).

4.5.1 Induced systemic resistance

The first stage in the ISR reaction is the detection of the microbe-associated molecular pattern (MAMP), which can be further coined as the pathogen-associated molecular pattern (PAMP). Along with it, the ISR mechanism is triggered by various chemical and hormonal elicitors such as volatile organic compounds (VOC) (alcohols, ketones, esters, sulfides, alkanes, terpenoids, and sesquiterpenes), siderophores, auxin, cytokinins, flagellin, chitin, nitrous oxide, and other stimulating agents produced by the pathogenic microbes. The plants can distinguish and process information about the type of microbes, either beneficial or pathogenic, using the pattern recognition receptor (PRR). In contrast, other chemical and hormonal elicitor trigger their defense mechanism using the receptors (Rs) or hormonal receptors (HRs). When the pathogenic microbes come in contact with the plants and express PAMP, the plant’s roots undergo conformational changes mediated by the elicitors and trigger the ISR mechanism, which causes increased jasmonic acid (JA) levels, which cascades in elevated ethylene (ET) levels, followed activation of non-expressor of pathogenesis-related genes and production of defensive compounds. Researchers have identified a strong correlation between the levels of iron (Fe²⁺) in the soil and the ISR mechanism. Studies have also reported that a reduction in the soil iron levels can facilitate the defense mechanism by elevating the JA and salicylic acid (SA) followed by ET and NPR1, leading to the response for iron deficiency response by the plants. The beneficial microbe present at 10⁻⁵ to 10⁻⁷ levels in the plant rhizosphere regions can suppress the plant’s ISR mechanism by priming to the host plant roots, creating a symbiotic relationship between the plants and beneficiary microbes. The symbiotic microbes reduce the ET levels caused by the ISR mechanism by producing ACC deaminase and reducing the stress in the plants. In addition, it also produces siderophores and creates a Fe⁻ environment, which reduces the iron availability for the pathogens and eliminates them. Such approaches pave the way for plant growth promotion (Figure 3) [77, 78].

4.5.2 Systemic acquired resistance

The SAR in plants is analogous to non-specific immunity or innate immunity found in the eukaryotes and fungi. The primary mechanism is similar to the ISR, where in SAR, the infection can be site-specific near the roots or general infection caused by viruses, bacteria, and fungi. When the pathogen induces infection, the PAMP is recognized by the plants and induces PAMP-triggered immunity (PTI), where the plants induce a hypersensitivity reaction followed by increasing the salicylic acid (SA), which induces the NPR-1 gene by positive regulation and further cascades and interacts with the TGA transcription factors and leads to the expression of PR genes which produces various metabolites inhibiting the infection and growth of pathogens [79]. The detailed mechanism of action is illustrated in Figure 9.

Figure 9.

Systemic resistance inducing ISR and SAR mechanism in plants.

5. Indirect mechanism

5.1 Biocontrol of pathogens

Apart from the direction, PGP contribution is through various phytohormones, degradative enzymes, nutrient assimilation, and volatile organic compounds. Plant growth promotion is also achieved indirectly by controlling the phytopathogens such as fungal, bacterial, and viruses present in the environment. Over the decades, research on beneficiary microbes has been conducted, and conclusive results have been obtained for the Bacillus sp., Pseudomonas sp., Trichoderma sp., and nuclear polyhedrosis virus are used commercially for controlling the phytopathogens present in the soil ecosystems [80]. Meanwhile, the actinobacteria, except the genus Frankia sp., have not been thoroughly studied for their PGP properties. In addition, actinobacteria are known for their antibiotic biosynthesis and are a dominant contributor to nearly 80% of the antibiotics produced, especially the genus Streptomycetes sp. Having such broad natural product biosynthesis properties, the marine actinobacterium is an excellent microbe to be used as a PGPA. The production of VOC from the marine actinobacteria plays a crucial role in the soil ecosystem protecting the plants from pathogens such as the siderophores and hydrogen cyanide nitrogen (HCN) aids in Fe-scavenging from the soils leads to the inhibition of the cytochrome c oxidase due to termination of the enzyme activity especially from the genus Streptomycetes sp., Actinomadura sp., Nocardia sp., Micromonospora sp., and Microbispora sp. Furthermore, the VOC, such as nitric oxide, alcohols, ketones, aldehydes, and other cyclic compounds, aids in the suppression of pathogenic microbes and fungi [81, 82].

In continuation, the microbes with the properties to produce various hydrolytic enzymes such as protease, chitinase, phospholipase, glucanase, and cellulase destroy the bacterial and fungal cell walls and inactivate the pathogens. Most of the actinobacteria genera mentioned earlier have the ability to produce various enzymes, especially the extremophiles, which can produce enzymes with their activity in extreme environmental conditions. Finally, microbial quorum sensing is a prominent phenomenon in the bacterial ecosystem, specifically the rhizosphere areas. Detection of the pathogenic microbes instantly triggers the actinobacteria to act against the pathogens (Table 2).

Strains	Target fungi	Fungal Disease Prevention	Reference
Streptomyces sp.	Fusarium oxysporum; F. cucumerinum; F. moniliforme; Botrytis cinerea; Ceratocystis fimbriata; Colletotrichum capsica; Xanthomonas oryzae pv. oryzae	Wilting, leaf curls, spots, stunting, and blight	[83, 84, 85, 86]
Streptomyces sampsonii; Streptomyces flavovariabilis	Aspergillus niger; Alternaria tenuissima; Rhizoctonia solani; Penicillium expansum	Wilting	[87]
Nocardiopsis dassonvillei	Bipolaris sorokiniana	Root rot	[88]
Amycolatopsis sp.	F. graminearum	Blight	[89]
Arthrobacter humicola	A. alternata	Leaf spot, blight, and rot	[90]

Table 2.

Actinobacteria strains tested for their phytopathogen activity on plants.

5.2 Biocontrol of weeds

Weeds are an unavoidable threat to the agriculture industry, and they have a profound impact on plant cultivation. In general, weeds are unwanted plant growth present in the field, which scavenge all the necessary nutrients in the soil, leading to nutrient depletion in the soil and undernourishment of the desired plants. Over the years, manual removal of the weeds has predominantly been practised, which is laborious and time-consuming and cannot cope with the weed growth. Further, the chemical weedicides were identified, such as Pendimethalin, S-Ethyl dipropyl thiocarbamate, Metolachlor, Glyphosate, Isoproturon, Ethyl ester, Pendimethalin, Neem extract, and Pretilachlor. Moreover, higher usage to suppress the weeds is reported to cause severe issues to the soil, plants, humans, and livestock [91]. Microbe-based biopesticides are being developed to avoid the lethal effects of chemical pesticides. Studies have identified the genus Streptomycetes sp. as the potential candidate, which illustrates higher weedicide activity based on its reputation in secondary metabolite production. In addition, studies were conducted on the endophytic actinobacteria such as Actinomadura sp., Nocardiodes sp., Microbispora sp., Saccharopolyspora sp. and Streptomyces sp., tested against Ageratum conyzoides, Parthenium hysterophorus, and Bidens biternate (Lour.) showcased significant plant inhibition by wilting, leaf curls, and burning effects on the plants [92]. Although it is well-known, advanced research on microbe-based bio-weedicides has not been carried out, and future focus should also target weed management instead of only focusing on plant growth promotion and pest management (Table 3).

Strains	Target weeds	Reference
Actinomadura sp.; Nocardiodes sp.; Microbispora sp.; Saccharopolyspora sp.; Streptomyces sp	Parthenium hysterophorus; Ageratum conyzoides; Bidens biternata	[92]
Micrococcus sp.	Chloris barbata Sw	[93]
Streptomyces sp. strain KR0005	Digitaria ciliaris	[94]

Table 3.

Actinobacteria strains and their weedicide activity.

6. Conclusion

Research studies in the field of agriculture, especially the development of biofertilizers/biostimulants, biofungicides, biopesticides, and bio-weedicides, have not been explored to a greater extent. This facilitates the reliance on synthetic agrochemicals, and the usage of such chemicals is causing a severe impact on the ecosystem. In addition, the agricultural output is saturating, which is insufficient to feed the infinite human population. Also, the prolonged usage of chemical fungicides and pesticides causes increased resistance, which is lethal for controlling pathogens and reduces agricultural yield. The marine actinobacteria are the least studied microbes for their PGP properties, whereas the polyextremophilies are not explored with respect to agricultural applications. The implementation of the extremophilic actinobacteria is the future for sustainable agricultural practices. Due to their high tolerance towards salinity, pH, and temperatures, they can be applied in a variety of environments. In addition, their unexplored nature makes them unique microbes whose functions are yet to be deciphered. To develop alternative biofertilizers, fungicides, and weedicides, we need to have sound knowledge of the PGP microbes. This chapter illustrates and highlights the importance, applications, and future implications of the polyextremophilic marine actinobacteria.

Acknowledgments

The authors of this study wish to thank the Department of Biotechnology, Govt. of India, under the Aquaculture and Marine Biotechnology scheme (Grant No: BT/PR9733/AAQ/3/649/2013) and Vellore Institute of Technology, Vellore, for providing us with all the necessary financial and infrastructure support.

Conflict of interest

The authors declare no conflict of interest.