Genome Editing in Bacteria (Part 2) E-Book
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- Herausgeber: Bentham Science Publishers
- Kategorie: Lebensstil
- Sprache: Englisch
- Veröffentlichungsjahr: 2024
This reference is a comprehensive review of genome editing in bacteria. The multi-part book meticulously consolidates research findings and insights on the applications of bacteria across several industries, including food processing and pharmaceutical development. The book covers four overarching themes for readers: a historical perspective of genome editing, genome editing in probiotics, applications of genome editing in agricultural microbiology and genetic engineering in environmental microbiology. The editors have also compiled chapters that provide an in-depth analysis of gene regulation and metabolic engineering through genome editing tools for specific bacteria.
Key topics in part 2:
- Targeting pathogenic microbes for plants and animals using CRISPR-CAS
- Genome editing microbes to improve crop yield plant growth for sustainable agriculture
- Applications of genome editing for bioremediation
- Microbial genome editing for environmental bioprocessing
- Genetic engineering for methanotrophs
- Genome engineering in Cyanobacteria
- Genome editing in Streptomyces
Genome Editing in Bacteria is a definitive reference for scholars, researchers and industry professionals navigating the forefront of bacterial genomics.
Readership
Scholars and professionals interested in bacterial genomics.
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PREFACE
In the vast landscape of scientific exploration, genetic engineering stands as a beacon illuminating pathways in both basic research and industrial biotechnology. At its heart lie metabolic and genomic manipulations that coax microorganisms to yield invaluable products, sparking innovations that redefine possibilities.
The saga of genetic inquiry into microorganisms hinges upon accessibility to their genomes and the arsenal of molecular tools at our disposal. Early genetic methods for genome editing in bacterial species, rooted in culture and transformation, were painstakingly laborious, often reliant on introducing resistance markers that hindered the pursuit of precise edits such as single amino acid mutations.
Yet, the tide turned with the groundbreaking discovery of CRISPR-Cas technology, unraveling the adaptive immune system of prokaryotes and unfurling vistas of targeted genetic engineering in these organisms. In this tome, we delve into the cutting edge gene editing, exploring diverse strategies employed in prokaryotic genetic manipulation.
This book embarks on a journey that traverses historical perspectives of genome editing, its application in probiotics, and its relevance in agricultural and environmental microbiology. It endeavors to consolidate and update the compendium of knowledge and research in bacterial applications across industries like food and pharmaceuticals, illuminating gene regulation for metabolic engineering through genome editing tools.
Our heartfelt gratitude extends to the esteemed contributing authors who embraced our call to enrich this compendium. Each chapter bears the mark of dedication and expertise, a testament to their profound contributions to bacteriology and molecular biology.
The Bentham Science Group's commitment to publication has facilitated the realization of this comprehensive endeavor, offering a resource intended for researchers, students, teachers, scientists, and enterprising minds intrigued by bacterial metabolic engineering.
In the vast ocean of scientific literature, this book, "Gene Editing in Bacteria," stands as a pioneering compilation, weaving together diverse applications of bacteria across the tapestry of biotechnology.
I dedicate this book to the pioneers of indigenous knowledge in molecular biology and genetic engineering. They not only laid the foundation for an ocean of knowledge but also kindled the flame that propels our relentless pursuit of understanding genome editing techniques in bacteria.
List of Contributors
Advances in Microbial Study for Crop Improvement
Vinay Sharma1,2,Neelam Mishra3, ǂ,Sherin Thomas4, ǂ,Rahul Narasanna5,Kalant Jambaladinni5,Priscilla Kagolla5,Ashish Gautam5,Anamika Thakur6,Abhaypratap Vishwakarma7,Dayanand Agsar3,Manish K. Pandey1,Rakesh Kumar5,*Abstract
Now and in the future, meeting the global demand for healthy food for the ever-increasing population is a crucial challenge. In the last seven decades, agricultural practices have shifted to the use of synthetic fertilizers and pesticides to achieve higher yields. Despite the huge contribution of synthetic fertilizers in agronomy, their adverse effects on the environment, natural microbial habitat, and human health cannot be underrated. Besides, synthetic fertilizers are manufactured from non-renewable sources such as earth mining or rock exploitation. In this context, understanding and exploiting soil microbiota appears promising to enhance crop production without jeopardizing the environment and human health. This chapter reviews the historical as well as current research efforts made in identifying the interaction between soil microbes and root exudates for crop improvement. First, microbial consortium viz. bacteria, algae, fungi, and protozoa are briefly discussed. Then, the application of bio-stimulants followed by genome editing of microbes for crop improvement is summarized. Finally, the perspectives and opportunities to produce bioenergy and bio-fertilizers are analyzed.
INTRODUCTION
The world population is constantly increasing and is projected to be 10 billion by 2050. Barea [1] estimated that by 2050, food demand is supposed to increase by 70% in the agricultural area. Although conventional farming (high-yield varieties, irrigation, synthetic pesticides and fertilizers) has shown an increase in food production by 70% from 1970 to 1995 in developing countries, its adverse effects on the environment, plants, humans, and aquatic ecosystem cannot be overlooked [2, 3]. Therefore, it is time to change our trajectory towards advanced microbial agricultural practices to combat pests and provide natural nutrition resources to plants without compromising the sustainable environment [4]. A microbial consortium is set of microorganisms, including bacteria, Cyanobacteria, algae, protozoa, yeast, and fungi, that works synergistically for hydrolyzing biomass, there by increasing soil fertility [5]. Soil bacteria are very important for biogeochemical cycle and agriculture. Plant-soil bacteria interaction plays a key role in determining the plants’ health and growth. Usually, such beneficial bacteria are termed plant growth promoting Rhizobacteria (PGPR), which colonize in rhizosphere [6]. Species of Rhizobium (Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium, and Sinorhizobium) form symbiotic relationship with legume plants, through flavonoids signals produced by plants. Flavonoids lead to nodule formation by inducing nodulation (nod) genes in Rhizobia [7]. PGPR is being used worldwide to increase crop production [8-10]. On the other hand, non-symbiotic PGPR such as Azospirillum enhances plant's resistance and ion uptake by producing antibacterial and antifungal compounds, growth regulators and siderophores [11]. Further, Cyanobacteria play an important role in raising the oxygen level in the atmosphere and ocean. Oxygenic photosynthesis enabled aquatic and terrestrial environments to undergo diversification and form complex life [12, 13]. Cyanobacteria Anabaena, Calothrix, Scytonema, and Nostoc have been widely used in rice cultivation. These Cyanobacteria develop specialized cells heterocysts to fix the aerobic nitrogen, particularly when nitrate and ammonia are limited in soil [14]. Recently, a pot experiment study has demonstrated that inoculation of Nostoc caused significant increase in root length. However, half dose of recommended chemical fertilizer with Nostoc improved the growth and production of rice. Pathum Thani [15]. Rice sheath blight is a serious disease in Asian countries caused by pathogenic fungi Rhizoctonia solani. Application of Nostoc piscinale (SCAU04) and Anabaena variabilis (SCAU26) found to produce bioactive substances to inhibit R. solani by 90%, and secrete phytohormones to promote plant growth and development, and induce resistance against disease. Fungi are mostly considered harmful pathogens for both plants and animals, because they produce mycotoxins as secondary metabolites. The major mycotoxins are aflatoxin, ochratoxins, trichothecenes, fumonisins, zearalenone, cyclopiazonic acid, and putulin [16]. In contrast, Trichoderma, Aspergillus, and Clonostachys rosea are beneficial fungi, found to be very effective against mycotoxin producing Fusarium and Aspergillus [17, 18]. These fungi have special characteristics such as promoting plant growth, producing antibiotics, and parasitizes other fungi (hyperparasitism) [19]. Seed coating with PGPR, rhizobia, arbuscular mycorrhizal fungi, and Trichoderma resulted in higher yield and resistance against pathogens in several plant species, thus can be used as an ideal biocontrol agent instead of chemical fungicide [20, 21]. In addition to nitrogen fixation, ion uptake, growth promotion, and protection from toxins, microbes are being explored for wastewater treatment, biodiesel production, bioelectricity, and biosensing [22-24]. In this regard, Saccharomyces cerevisiae, Pichia stipitis, and Kluyveromyces fagilis have been used extensively for ethanol production [25]. Metabolic engineering of Clostridium acetobutylicum enhanced butanol yield of 0.71 mol butanol/mol glucose, which was 245% higher compared to wild-type strains [26]. Some Oleaginous yeasts like Cryptococcus psychrotolerans (IITRFD) and Rhodosporidiobolus fluvialis (DMKU-SP314) are used for the production of biodiesel [27, 28]. Here, we have diSome Oleaginous yeasts likscussed the current scenario of microbial uses in crop improvement by biochemical and genetic engineering approaches.
MICROBIAL CONSORTIA
Rhizosphere microorganism plays an essential role in sustainable agriculture, influencing natural plant communities' composition and productivity (Fig. 1). Bacteria, archaea, fungi, algae, viruses, protozoa, oomycetes and microarthropods are the microbial groups residing in the rhizosphere [29]. The leading population of microbes in the rhizosphere is bacteria, trailed by fungi, actinomycetes and other groups. Bacteria, fungi, algae and protozoa coexist in the rhizosphere and exert multiple strategies to utilize minerals and organic wastes. They act as metal sequestering and growth-promoting bioinoculants for plants in metal-stressed soils [29].
Bacteria
Azospirillum, Azotobacter, Bacillus, Enterobacter, Pseudomonas and Serratia are successfully used along with Rhizobium for microbial consortia for crop improvement [30]. Microbial consortia under extreme environmental conditions enhance crop production. The production of plant growth hormones and vitamins are significantly increased with the application of Rhizobium along with Azotobacter as consortia [31]. Rhizobium's microbial consortia with G. intraradices and P. striata show enhanced plant growth in chickpeas root rot along with improved chlorophyll content [32]. Consortia of Mezorhizobium sp. and P.aeruginosa increased dry weight and nodule formation in chickpeas [33]. Fox et al. [34] co-inoculated Pseudomonas fluorescens WSM3457 and Ensifer (Sinorhizobium) medicae WSM419, increasing nodule numbers in green gram. A physiological defence response was activated against Sclerotium rolfsii, a collar rot pathogen using P. fluorescens, Trichoderma and Rhizobium consortium [35]. Similarly, improved yield with disease resistance was observed with consortia of B. subtilis, T. harzianum and P. aeruginosa [36].
Fig. (1)) Schematic representation for rhizosphere microbial diversity and plant strategies to use minerals and organic wastes.Root length of Arabidopsis was significantly enhanced using consortia of Bacillus, Burkholderia, Pseudomonas, Ralstonia and Variovorax in response to abiotic stress [37]. Jha and Subramanium [38] reported an increase in NPK concentration and reduction in Na and Ca concentration in response to salinity stress in paddy using a consortium of P. pseudoalcaligenes with B. pumilus. Increased production of flavonoids and lipochitooligosaccharide, along with enhanced nodulation was observed using a combination of A. brasilense and Rhizobium [39]. Cyanobacterial consortia of Anabaena – Azotobacter biofilms and Anabaena sp.-Providencia sp. elicited plant defense response in maize hybrids [40].
Fungi
Arbuscular Mycorrhizal fungi (AMF) in combination with plant growth-promoting Rhizobacteria (PGPR), such as nitrogen fixing rhizobia, phosphate solubilizing rhizobia and free living bacteria such as Azospirillum., Bacillus sp., and Pseudomonas sp. shows synergistic interaction enhancing growth and productivity in various crops [41, 42]. Sharma et al. [43], emphasized that Mycorrhizal fungi and PGPR consortia act as biostimulators, biofertilizers and bioprotectants on plant growth and health. The phosphorus use efficiency was increased in common bean (Phaseolus vulgaris L.) for symbiotic nitrogen fixation using consortia of Glomus intraradices, a phosphate solubilizer and R. tropici CIAT899, a nitrogen fixer [44]. Gao et al. [45] evaluated the impact of consortia of Bradyrhizobium sp. BXYD3 and G. mossae in soybean show alteration of pathogen defence-related genes reducing the severity of Cylindrocladium parasiticum incidence. Draught resistance was observed in the finger millet plant using consortia of Pseudomonas fluorescens (KB-7), Pseudomonas poae (KA-5), Streptomyces flavofuscus (SA-11) and Streptomyces labedae (SB-9), thus increasing plant growth [46]. Several studies were performed using microbial consortia to grow and develop plants (Table 1).
Algae
Algae are essential microbes in soil which affect various crops' growth and yield through different mechanisms [89]. A consortium of Codium tomentosum, Gracilaria gracilis and Cystoseira barbata positively influenced seed germination for tomato, pepper and aubergine [90]. Similarly, salinity stress was alleviated in Capsicum annuum var. using algal extracts of Jania rubens and Padina pavonica [91]. Nostoc muscorum and Ulva lactua, along with Rhizobium leguminosarum, influence the overall growth of faba beans in terms of improved root and shoot length, dry weight of nodules, pods and other growth parameters along with nutritional status of the plant [92]. Enhanced growth parameters, carbohydrate content and seed germination reported for wheat using algal fertilizer of Gracilaria corticata, Nizimuddinia zunardini and Ulva fasciata [93]. Similarly, consortia of Stephanoystis crassipes, Neohodamela larix and Ahnfeltiopsis flabelliformis acts as a biofertilizer enhancing the growth of buckwheat [94]. The photosynthetic performance and growth of willow (Salix viminalis L.) enhanced using consortium of Anabaena sp. PCC 7120, Microcystis aeruginosa MKR 0105 and Chlorella sp., under limited fertilizer content [95].
Thus, the combined effect of plant growth-promoting bacteria (PGPR) with other microbe’s increases plant/crop biomass and yield, provides abiotic stress resistance, improves nutrient uptake, act as a biocontrol agent and therefore, these consortia needs to be employed commercially for complete benefits package [96].
BIO-STIMULANTS: INTERACTION OF ROOT EXTRACT WITH SOIL MICROBES
Agriculture is facing simultaneous challenges of increasing productivity to feed the growing world population while at the same time reducing the environmental effects on ecosystems and human health. Several groundbreaking technological ideas have been suggested to aid sustainability in agricultural production systems by using a decreased usage of synthetic pesticides and fertilizers. An eco-sustainable and promising innovation is the use of plant biostimulants (PB) that boost the growth of plants, flowering, fruit development, crop yields, and enhance nutrition efficiency, as well as enhance the tolerance to stresses (Biotic & abiotic) [97]. Plant-microbial interaction is one of the primary form of communication that defines the zone below ground (Fig. 2). Certain substances identified in root exudates play a vital role in root-microbe interactions, including flavonoids found in legume root exudates, which trigger the Rhizobium meliloti genes required for nodulation. Microbial interactions promote plant growth in a number of ways, including biological nitrogen fixation by various classes of proteobacteria, stress tolerance provided by the involvement of endophytic microbes, and direct and indirect benefits conferred by plant growth-promoting Rhizobacteria (PGPR) [98]. Additionally, exudation provides a carbon-rich environment, and plant roots also produce signals which initiate cross-talks with the soil microbes (Fig. 2). Nitrogen-fixing interaction has been observed in tree roots and the filamentous, gram-positive actinobacterium Frankia, with 200 angiosperm species belonging to eight families [99]. Various studies have reported nitrogen fixing bacteria can solubilize and mineralize inorganic and organic pools of soil phosphorus, which convert it into plant-available form, resulting in increased uptake of phosphorus in plants [100]. Most fungi have plant growth promoting properties and have possessed the ability to solubilize P and enhance N uptake in host plants [101, 102]. Up to 70–90% of plant P is supplied by arbuscular mycorrhizal fungi (AMF), and their contribution greatly improve plant growth under low P condition [103, 104]. There is also evidence that plant colonization by AMF is related to enhancing N uptake [105] and improving drought tolerance [106].
Fig. (2)) Microbial interaction with the roots of the plant.Many asymbiotic relationships have been drawn between microbes and plant roots, such as Azospirillum with grass family crops like Hordeum vulgare, Sorghum bicolor, and Triticum aestivum, Acetobacter associated with Saccharum officinarum or Ipomoea batatas and Achromobacter with Oryza sativa [107]. Previous study reported [108] the presence of tryptophan found in the root tip region. Tryptophan is the precursor for indole acetic acid, which suggest that PGPR have been utilizing root exudate pools as a source for promoting plant growth. Several soil bacteria are known to synthesize growth hormones, which have an impact on plant growth. Production of gibberellic acid and cytokinin was observed in Arthrobacter [109], Azospirillum [110], and Azotobacter [111]. These approaches may involve the discovery of new PGP microbes in agricultural fields [112], which help to find the existence of an essential root microbiome that will help a crop better cope with abiotic stress [113].
Recently, in sorghum seedlings, Streptomyces isolates showed moderate PGPR activity by enhancing the growth of root [114]. The relative abundance of one sequence variant from the genus Streptomyces is positively associated with drought tolerance in plant species [115]. Several other examples exist, including the ability to tolerate drought through higher photosynthesis, evapotranspiration, and stomatal conductance in Capsicum annuum that has been inoculated with different root bacteria obtained from naturally drought-tolerant plants [116]. Several species of micro-organisms including; Pseudomonas spp., Acinetobacter spp., Azospirillum ssp., and various AMF have been identified which enhance the uptake of Zn [117], Cu, Mn [118], Ca, and Mg [119].
AGRONOMICALLY IMPORTANT SOIL MICROBES
Sustainable agriculture for global food security is an urgent need for future generations, causing minimum deterioration of the ecosystem [120, 121]. Excessive use of chemical fertilizers and pesticides can be detrimental to soil quality [122, 123]. Thus, beneficial plant-associated microbes could be used for crop improvement in terms of nitrogen fixation, phosphate and potash solubilization, siderophore and phytohormone production, and biotic and abiotic stress tolerance for environmental benefits [124, 125].
Nitrogen-Fixing Bacteria
Nitrogen fixation is a pivotal phenomenon to make Nitrogen (N) available for plant growth and development. Nitrogenase, an oxygen-sensitive enzyme complex, converts atmospheric nitrogen into ammonia utilizing ATP as the energy source [23]. Pathania et al. [126] emphasized that the microbial sp. such as Azospirillum, Azotobacter, Bacillus, Burkholderia, Cyanobacteria, Enterobacter, Erwinia, Flavobacterium, Gluconacetobacter diazotrophicus, Pseudomonas, Rhizobium and Stenotrophomonas can fix atmospheric nitrogen (Table 1).
Azotobacter chroocochum
Azotobacter is free-living bacteria causing non-symbiotic nitrogen-fixation, although some fix molecular nitrogen from the atmosphere symbiotically [127]. Ammonium ions and nitrate inhibits nitrogen fixation [128].
Azotobacter vinelandii
Azotobacter is a gram-negative diazotroph causing non-symbiotic nitrogen fixation aerobically. They produce phytohormones, vitamins and pyoverdine pigments [129].
Glucanobacter diazotrophicus
Glucanobacter is a nitrogen-fixing bioinoculant associated with sugar-rich plants and also found with other types of plants [130].
Acetobacter xylinum
Acetobacter oxidizes lactate and acetate into carbon dioxide and water. It belongs to the genus of acetic acid bacteria capable of converting ethanol into acetic acid in the presence of oxygen [131].
Azospirillum lipoferum
It is a gram-negative free-living bacteria affecting the growth and yield of many plants by producing phytohormones [132].
Rhizobium sp.
Rhizobium sp. fix atmospheric nitrogen and lives in a symbiotic relationship with legumes such as Peas, Lathyrus, Vicia, Lentils, Berseem, Kidney beans, Lupinus, Ornithopus, Soybean, Melilotus, Lucerne and Fenugreek [133].
Phosphate Solubilizing Microbes
Phosphorus is an essential element for the growth of plants acquired in the form of phosphate ions from the soil [134]. The most cost-effective and sustainable approach is the use of phosphate solubilizing microbes to make phosphorus available to the plant through mineralization and solubilization of inorganic phosphorus [135], and many genera of bacteria and fungi as phosphate solubilizers (Table 2). They release organic acids such as oxalic acid, succinic acid and malic acid, thus decreasing the surrounding pH and releasing phosphate ions to make them available [136].
Bacillus megaterium
It is a gram-positive, rod-shaped spore-forming bacteria capable of phosphorus solubilization. It is also a cytokinin promoting bacterium capable of plant root overgrowth [137].
Pseudomonas putida
It lives in most soils, associated with plant roots improving plant health through phosphate solubilization. It also produces siderophores, limiting the growth of fungi and other bacteria [123].
Potash Mobilizing Bacteria
Frateuria aurentia
It is a species of proteobacteria that works well in soil with low K content to mobilize available potash near the plant's roots. The availability of potash can be increased by the use of such bacteria in powder form [138].
Plant Growth-Promoting Rhizobacteria (PGPR)
PGPR causes phytostimulation, i.e., production of phytohormones such as auxins, cytokinins, gibberellins, indole 3 acetic acid, abscisic acid and ethylene. Phytohormones enhance plant growth by root initiation, cell enlargement, and cell division [139]. Azotobacter, Azospirillum, Bacillus, Pseudomonas and Rhizobium are the PGPR known to produce phytohormones and may be used with biofertilization [140]. These phytohormones enhance plant growth by altering the endogenous mechanism of the plant (Table 2).
Bacillus sp.
Bacillus sp., such as Bacillus subtilis and Bacillus polymyxa, are gram-positive spore-forming bacteria. Bacillus subtilis protect the plant throughout the growing season by colonizing the developing root system of plants. On the other hand, Bacillus polymyxa produces exopolysaccharides and causes root hairs to undergo physical changes promoting plant growth [141].
Pseudomonas sp.
Pseudomonas fluoroescens is a non-pathogenic saprophyte producing several secondary metabolites that suppress plant diseases and colonize soil, water and plant surface environments. Pseudomonas putida shows mutual interaction with Saccharomyces cerevisiae, regulating plant health [142, 143].
Biological Control Organisms
Biocontrol agents are the rhizospheric microbes playing a role in protecting plants from various pathogens (Table 1). Antagonism, competition and induced resistance are some of the common methods for microbial-based pathogen control. Aeromonas, Alcaligenens, Bacillus, Pseudomonas, Stenotrophomonas maltophilia, Trichoderma and Rhizobium are some of the rhizospheric microbes which release antibiotics, biosurfactants, toxins, chitinase, β-1, 3-glucanase and volatile organic compounds that cause inhibition of growth of plant pathogens [144-146]. These microbes can also create competition for nutrients and trace elements required for growth and development. e.g. Siderophore production by Pseudomonas sp [147]. They are also able to produce ethylene, jasmonic acid and salicylic acid, which helps to defend plants against pathogens by induced systemic resistance [148].
Metarhizium anisopilae
It is an entomopathogenic fungus controlling several insect pests such as Grasshoppers, Termites, Thrips, Caterpillars, Aphids and many more. It causes infection in the insect by attaching to the insect's surface, penetrating the exoskeleton and causing the insect's death by proliferating inside [123].
Beauveria bassiana
It is a naturally occurring entomopathogenic fungus, functioning as an insecticide, controlling termites, whiteflies and many other insects. The spores are sprayed on affected crops causing the killing of an insect in 48-72h [123]. Its use as a mosquito control agent is still under investigation [149].
Verticillium lecanii
It is a biological pesticide producing insecticidal toxins such as bassainolide, dipicolinic acid controlling aphids, whiteflies, rust fungi, thrips, and scale insects [123].
Paecilomyces lilacinus
It is a naturally occurring fungus controlling nematodes attacking plant roots. The mechanism of action as nematicide is by infecting eggs, juvenile and adult females.
Arthrobotrys spp.
Arthobotrys oligospora is a biological indicator of nematodes, potentially used as a nematicide [150].
Trichoderma viride
Trichoderma is an antagonistic fungus acting as a fungicide for different plants preventing various diseases such as root rots, wilts, brown rots and other diseases. Botritis, Fusarium, and Sclerotinia are some of the fungal species suppressed by Trichoderma [151].
Microbes for Stress Tolerance
Rhizobacteria play a vital role in stress tolerance in plants. Drought, salt, salinity, and heavy metal tolerances are some of the stress conditions tolerated by hormonal modification and exopolysaccharide (EPS) secretion in plants [152]. Pseudomonas sp., Trichoderma sp. and Hebeloma sp. are some of the microbes involved in stress tolerance [153-156].
Pseudomonas putida
It is a gram negative bacterium found abundantly in soils. P. putida synthesizes EPS in sunflower roots while maintaining water availability during water stress [155].
Trichoderma harzianum
Trichoderma is a fungus known to combat salinity and drought stress in wheat varieties [156].
Mycorrihizal Fungi
Hebeloma sp., a Mycorrhizal fungus, has shown its benefits in nitrogen and phosphorus limitations in unfavourable soil pH [153]. They can also immobilize metals, thus reducing heavy metal contamination [154].
GENOME EDITING OF MICROBES TO BENEFIT CROP PLANTS
Genetic engineering is commonly seen in bacteria, yeast, and other fungi to develop agriculturally profitable crops. Bacteria are known to generate numerous biochemical and by-products, which assist plant roots in getting nutrients from the soil. By altering the genetic makeup of microbes, the biosynthetic pathway of these biochemicals or bioproducts have been regulated. Previously, for the modification of the genome in microorganisms, various approaches like homologous recombination, Group II retrohoming, and automated multiplex genome engineering has been used [183, 184]. But all of these methods proved to be laborious and time-consuming. In 2013, CRISPR/Cas was explored as a potential genome modification approach in E. coli [185]. Afterward, in other Saccharomyces cerevisiae and Streptomyces species, it was effectively applied [186, 187]. In agriculturally important microbes, genome editing approaches have been extended, i.e., B. subtilis and B. mycoides, and fungal pathogens, i.e., Neurospora crassa, Myceliopthora heterotalica, Aspergillus niger, and Aspergillus oryzae, etc [188].
Plant growth associated bacterial species are usually colonized near roots and release siderophore or related biochemical by-products. Potato endospore and rhizophore of grasses are associated with soil-borne bacteria such as B. mycoides EC18 and B. subtilis HS3. Both of these bacteria have shown antifungal, endophytic, and plant growth promoting function. Traditional methodology of genome editing, on the other hand, makes genetic modification complicated inside the genome. Recent advances in CRISPR/Cas9 based genome editing have been utilized to develop three B. subtilis HS3 mutants and two B. mycoides EC18 mutants, respectively [189]. B. subtilis HS3 release a volatile organic compound 2, 3-Butanediol, which is known to promote growth and development in grass [190]. Through modifying two genes in B. mycoides, Yi et al. [189] demonstrated that petrobactin is crucial for growth of plants via root colonization, respectively. Recently, several studies have reported use of advanced approaches of genome editing enables to modify E. coli genome as to our convenience. Heo et al. [191], demonstrated CRISPR-Cas9-directed citrate synthase gene modification in the genome of E.coli led to an enhancement in the production of n-butanol. In another study, through CRISPR/Cas9, the β-carotene pathway has been integrated into the E. coli genome. They modified the methylerythritol-phosphate and metabolic pathways to enhance the production of β-carotene [192]. In the current scenario, the numerous pathogenic fungal species, such as Puccinia, Fusarium, and others like Blumeria, cause severe damage in several crops such as Triticum aestivum, Oryza sativa, Zea mays, and Sorghum bicolor. Several techniques have been utilized for controlling losses due to these diseases, such as the use of non-pathogenic fungal antagonists, conventional breeding, and genetic manipulation. In this concern, the most promising approach for developing fungal-resistance crops is genetic engineering. Fungal disease in plants can be managed by inhibiting infection, growth and reproduction using a competing fungal species [193]. Mutant non-pathogenic fungi could be developed by utilizing CRISPR/Cas9 approach, which could be used to form new competitors for the wild type existing pathogen. Only a small number of fungi serve as cell factories, which could be utilized for the biosynthesis of secondary metabolites [188]. Qin et al. [194] demonstrated the knockout of the ura3 gene in Ganoderma lucidum 260125 and Ganoderma lingzhi using CRISPR/Cas9 approach. These fungi produce anti-tumor and anti-metastatic ganoderic acids. Another study in durum wheat reported a reduction in crown and foot rot disease percentage range from 40 to 80% by altering trichothecene biosynthesis [195]. The genome modification approach provide a toolkit for pathway engineering in microbes and also ways to modify putative genes involved in pathogenicity, which will help to develop disease resistant agriculturally important crops.
TRANSFER OF MICROBIAL GENE INTO PLANT SPECIES
Genetic engineering facilitates the easy transfer of genes, paving the way for crop improvement through enhanced yield, and resistance to abiotic stress, disease, pest and herbicide. To date, many direct and indirect methods have been developed (Table 3), but gene transfer through Agrobacterium is the most efficiently utilized method for crop improvement. Tobacco leaf tissues were used to produce the first genetically modified plant with Agrobacterium tumefaciens in 1982 [196]. Nearly 120 crop species, such as rice, wheat, maize, soybean, tobacco and cotton, were genetically modified in plant breeding experiments through this method [197-200]. Every technique of gene transfer has its pros and cons (Table 1), but there is a continuous improvement in gene transformation approaches in the last three decades, leading to significant improvement in agricultural production, crop production, and crop improvement [201].
The most extensively used herbicide used for killing weeds by non-selective mode of action is glyphosate and glufosinate. Glyphosate inhibits explicitly 5–enolpyruvyl shikimate-3 phosphate synthase (EPSPS) required for the biosynthesis of amino acid, playing a pivotal role in the shikimate pathway. Globally, the most widely grown herbicide-tolerant plant is Glyphosate-resistant soybean [217]. Glufosinate (also known as phosphinothricin) inhibits glutamine synthetase enzymes competitively [218]. Various herbicide-tolerant transgenic plants were engineered by transferring specific herbicidal genes from microbes into the plant cell (Table 1). Transgenic plants have been obtained for many crop varieties such as sorghum, soybean, grapes, apricot and many more in the last three decades [219-224]. The cultivation of herbicide-resistant crops leads to increased yield and reduced cost due to simplified weed management strategies [225, 226].
Baloglu et al. [227] emphasized that agricultural productivity is drastically affected by the pest, providing the basis for developing insect resistance crops through genetic engineering approaches. Transfer of gene coding for crystal toxin (cry) and vegetative insecticidal protein (vip) from Bacillus thuringiensis and Bacillus cereus in plant cells provides resistance against various insects, as shown in Table 2 [228-230]. Cry toxin works by binding specifically to the receptor, inserts into the cell membrane of the insects midgut and forms pores, causing paralysis followed by death. All the functions are carried out by three domains of Cry protein [231]. The first commercially available insect-resistant crop was cotton, showing the incorporation of cry protein and resistance to Lepidopteron pest [232]. Alternatively, insecticidal genes from other sources, including plants and mammals, would be introduced into the plant cell to provide insect resistance [227].
Agricultural production worldwide is decreased due to various abiotic stress factors such as drought, heat, cold, flood and salinity [233, 234]. Plants alter their metabolism (activating signalling cascade and regulatory factors such as transcription and heat shock factors) to withstand abiotic stress [235]. Wani et al. [236] suggested the utilization of plant biotechnology, genetics and breeding approaches to develop climate resilient crops to overcome the effect of environ- mental stress. Various microbial genes have been transferred into different plant varieties to mitigate drought, salt and osmotic stress (Table 4).
Engineering crops for nutritional improvement, such as increasing vitamin content and modified amino and fatty acids, are of utmost importance because of different deficiency and health diseases (Table 2). The golden rice engineered for carotenoid biosynthesis was a breakthrough study to combat vitamin A deficiency (VAD). There were different golden rice versions to enhance carotenoid accumulation [266-269]. Oleic acid, linoleic acid and alpha-linolenic acid are essential amino acids derived from oils. According to WHO, a high proportion of polyunsaturated fatty acid (PUFAs) and low saturated fatty acid content is considered superior for human consumption [270]. Transgenic crop with modified lipid content was engineered, as shown in Table 2. High levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were produced by engineering Camelina sativa with the genes from marine microbes [271, 272]. Similarly, a few transgenic approaches targeted altering the amino acid composition to enhance nutritional value by increasing the amino acid concentration by engineering essential amino acid metabolic pathways [231]. Thus, crop varieties with improved yield, food quality and resistance to abiotic and biotic stresses were contributed through transgenic technology.
USE OF MICROBES FOR THE PRODUCTION OF BIOENERGY FROM AGRICULTURE WASTE
Agricultural crops biomass residue is a good source of bioenergy which is economically feasible and environmentally safe. It helps to meet the rising energy demand in the future and present while curbing greenhouse gas emissions. As demonstrated in various case studies, genetic and metabolic pathway engineering approaches have proven to be important in developing efficient microbial communities which are capable of contributing to bioenergy production [273]. A previous study reported for the production of ethanol, potato wastewater was utilized as a substrate with recombinant Escherichia coli strains [274]. Recombinant E. coli enables biodiesel production by transferring two enzymes required for the production of ethanol and one enzyme which encodes acyltransferase. Because ethanol was produced indirectly from sugar glycolysis, In future, it is necessary to search for more affordable and cheaper sugar sources necessary for further developments [275]. Similarly, in another study, S. cerevisiae, Fusarium oxysporum, and Aspergillus foetidus have been used in the production of ethanol, and Malus domestica pomace has been used as a substrate [276]. Another study on Malus domestica reported consistent alcohol production using a psychrophilic S. cerevesiae AX1 strain [277]. Wasted rice bran has been found to be a suitable feedstock for bioethanol production due to the presence of low lignin content. But in the case of sugarcane bagasse, prior pre-treatment need to remove high lignin content [278]. Ingale et al. [279] reported banana pseudo stem has been a potential substrate for bioethanol production. Various microorganisms such as, Aspergillus ellipticus, Aspergillus fumigatus and S. cerevisiae have been used for biological pre-treatments. In a recent study [280], lignin from barley straw has been utilized as a carbon source for the production of biodiesel using Rhodococcus sp. YHY01. The energy density of biodiesel is greater than that of bioethanol, so it can be used in diesel engines. Biodiesel production utilizing oleaginous microbes is a rapidly expanding research field, and several microbes have been identified in the production of biodiesel from distinct carbon sources such as Cryptococcus curvatus, Yarrowia lipolytica, Chlorella sp., Rhodococcu ssp., etc [280]. Similarly, rice straw hydrolysate has been used as substrate for biodiesel production with recombinant Escherichia coli strains [281]. Various biotechnological applications utilized rice straw hydrolysate as feedstock for the production of bioethanol and lipid using yeast [282, 283]. Utilizing agricultural waste as a sugar source in E. coli mediated production for biodiesel is a promising approach.
