Reza Sharafi’s research while affiliated with Agricultural Research, Education and Extension Organization and other places

This review explores the diverse applications of Bacillus thuringiensis (Bt) beyond its traditional role as a bioinsecticide. Bt produces a variety of compounds with distinct chemical structures and biological activities. These include antimicrobial agents effective against plant pathogens and bioactive compounds that promote plant growth through the production of siderophores, hormones, and enzymes. Additionally, Bt’s industrial potential is highlighted, encompassing biofuel production, bioplastics, nanoparticle synthesis, food preservation, anticancer therapies, and heavy metal bioremediation. This critical analysis emphasizes recent advancements and applications, providing insights into Bt’s role in sustainable agriculture, biotechnology, and environmental management.

Bacillus cereus group produces diverse antimicrobial compounds through different metabolic pathways, including amino acid‐based compounds, sugar derivatives, volatile and miscellaneous compounds. These antimicrobial compounds exhibit antibacterial and antifungal activities against various plant pathogens, promoting plant growth and enhancing tolerance to abiotic stresses. They also exhibit nematicidal activities against plant nematodes and antagonistic effects against pathogens in aquatic animals, promoting growth and inducing immune responses. Moreover, B. cereus group bacteria play a significant role in bioremediation by breaking down or neutralizing environmental pollutants, such as plastics, petroleum products, heavy metals, and insecticides. They produce enzymes like laccases, lipases, proteases, and various oxidases, contributing to the degradation of these pollutants. In the food industry, they can cause food poisoning due to their production of enterotoxins. However, they are also utilized in various industrial applications, such as producing environmentally friendly bio‐based materials, biofertilizers, and nanoparticles. Notably, B. cereus transforms selenite into selenium nanoparticles, which have health benefits, including cancer prevention. In summary, B. cereus group bacteria have diverse applications in agriculture, bioremediation, industry, and medicine, contributing to sustainable and eco‐friendly solutions across multiple fields. In this review, we have revised B. cereus group and the characteristics of every species; we have also highlighted the more important compounds secreted by the species of B. cereus group and the applications of these compounds. The aim is to explain the available secondary metabolites to classify the species from this group, increasing the knowledge about taxonomy of this group.

Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg⁻¹ and in pilot level 65 °C, 72.11%, 310 g kg⁻¹) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.

Management of agricultural waste like rice straw is essential in reducing environmental pollution and also creating added value. For this purpose, microorganisms with high hydrolytic activities were isolated from a simulated composting process. The effects of different materials, including rice straw, chicken manure, urea, olive pomace, and two groups of microbial boosters were assayed at lab-scale and pilot-scale for 60 days. The lab-scale results showed that two treatments containing chicken manure and microbial cocktails (E and F) improved the composting process significantly better than others. They had maximum temperature (59°C), C/N reduction rate (76.7%), and macro/microelements contents. Treatment E showed maximum wheat growth indexes, including dry (1.1 g) and wet (4.7 g) weight of aerial parts, plant height (47 cm), leaf area index (18.9 cm ² ), and leaf specific area index (45 cm ² /g) compared to the control. The pilot-scale results showed that E treatment could reduce C/N (73.48%) better than F (58.32%) and control (13.03%) and it also caused most of the temperature changes up to 69°C. Finally, considering the highest germination index (96%) and lack of phytotoxicity, and also the greatest impact on wheat growth indexes, treatment E was selected for industrial production of compost.

Every year, many agricultural wastes such as rice straw are produced in different countries that need to be managed and converted into valuable materials. The present study was planned to design a bioprocess for fast production of enriched biocompost from rice straw (RS) as an available lignocellulosic biomass. Three native bacterial strains (MC: 10⁷ cells/gram RS), chicken manure (CM), and vinasse were used as starter cultures and accelerators, respectively. The research was conducted in a completely randomized design with five treatments (each 18 kg) in insulated composters. The treatments included RS as control; RS and chicken manure (CM) (T1); RS, CM, and microbial cocktail (MC) (T2); RS, CM, vinasse, and MC (T3); and RS, vinasse, and MC (T4). Treatment T2 showed maximum changes in bulk density, color, odor, pH, EC, and temperature increase (55 °C). Significant reduction of C/N and NH4⁺/NO3⁻ (36%) ratios and a maximum increase of nutrient content were observed for T2. In the supplementary experiment that followed, application of T2 (5% w/w) showed significant effects on wheat growth factors, including plant height (47.11 cm), leaf area (15.35 cm²), fresh weight (3.18 g), dry weight (0.57 g), and special leaf area. The use of native effective microorganisms and chicken manure enhanced efficient lignocellulose degradation, reduced the composting process time, and increased the quality of the compost from RS.

Currently, the modern world is facing with a major challenge regarding the production of renewable energy for phasing out fossil fuels. Lignocellulosic biomass can potentially be used as a substrate for the production of a diverse range of different biofuels such as bioethanol while not triggering food vs. fuel debate. Generally, the bioethanol production from lignocellulosic biomass involves four major steps including lignocellulose delignification/pretreatment, hydrolysis (i.e., chemical or enzymatic), hydrolyzate sugar fermentation, and distillation. The economic and environmental feasibilities of the mentioned process could significantly be enhanced through the application of phytopathogenic fungi or their enzyme cocktails. Typically, necrotrophic pathogenic fungi have exceptionally high capabilities for a copious production of various hydrolytic enzymes with activity on wide range of plant biomass, compared to biotrophic or hemibiotrophic ones. In this chapter, ten filamentous plant-pathogenic fungi species belonging to six genera, including Fusarium, Aspergillus, Phoma, Cryphonectria, Ustilago, and Colletotrichum, have comprehensively been discussed in respect to hydrolytic enzyme capabilities from bioethanol industry viewpoint. On this basis, their potential for application in simultaneous saccharification and fermentation (or co-fermentation), separate hydrolysis and fermentation, and consolidated bioprocessing process has been investigated. Eventually, their genome richness in respect to the construction of lignocellulose-degrading microorganisms or ethanologens with astonishing hydrolysis production ability from these fungi has also been scrutinized.Keywords Aspergillus Colletotrichum Fusarium Lignocellulose Phoma Ustilago SaccharificationHydrolysisHydrolytic enzymeRecombinant technologyBiofuel

The Egyptian cotton leafworm is a polyphagous pest with a broad range of hosts causing annually significant damage to agricultural crops. It has been found that no all strain of Bacillus thuringiesis are effective on this pest and small numbers of the isolates are effective due to the contents of their crystalline proteins. The aim of the present study was to obtain native isolates of Bt that were capable of controlling and investigate the effect of growth medium of Bt on the insecticidal ability of selected isolates. Hence, the pathogenicity of 118 native isolates of B. thuringiesis cultivated in R2NB medium were determined on five–day–old larvae of Spodptera.littoralis at 27 °C on artificial diet. The mortality rate of 118 native isolates of Bt with a concentration of 103 spore ml–1 illustrated that the highest mortality rates belong to four isolates GON–9, QM–2, GN–13 and QM–1 with 93.33, 70, 46.67 and 43.43, respectively. In addition, GN–12, EN–2, GON–7, CHI–2, AGI–7, AGI– 3 and AGI–2 isolates were ineffective on S. littoralis larvae. Then, the effective isolates grown in nutrient broth and R2NB medium were evaluated on mentioned pest. The results showed that the four selected isolates were more lethal on R2NB medium than NB on larvae of Egyptian cotton leafworm and their differences were significant. Also, the content of cry genes particularly cry 2Ab in effective isolates were examined and traced. The outcomes of polymerase chain reaction demonstrated QM–1, QM–2 and GON–9 have cry 2Ab.

Biodiesel is being considered as a renewable fuel candidate to completely or partially replace fossil diesel. The most important challenge in development of different generations of biodiesel is input cost, low oil yield in the sources, and lack of efficient technologies for biodiesel production. Recent developments in next-generation sequencing technologies (NGS) and new “omics” methodologies have provided excellent opportunities for high-throughput functional genomic surveys in different organisms. In this context, different “Omics” technologies have been widely used to enhance the oil yield in oil-producing plants and microorganisms. This chapter reviews the existing studies revolving around new “Omics” technologies used to enhance the oil and biodiesel production in the promising plant for biodiesel production, Jatropha, as a sample.

Biodiesel has huge potentials as a green and technologically feasible alternative to fossil diesel. However, biodiesel production from edible oil crops has been widely criticized while nonedible oil plants are associated with some serious disadvantages, such as high cost, low oil yield, and unsuitable oil composition. The next generation sequencing (NGS), omics technologies, and genetic engineering have opened new paths toward achieving high performance-oil plants varieties for commercial biodiesel production. The intent of the present review paper is to review and critically discuss the recent genetic and metabolic engineering strategies developed to overcome the shortcoming faced in nonedible plants, including Jatropha curcas and Camelina sativa, as emerging platforms for biodiesel production. These strategies have been looked into three different categories. Through the first strategy aimed at enhancing oil content, the key genes involved in triacylglycerols (TAGs) biosynthesis pathway (e.g., diacylglycerol acyltransferase (DGAT), acetyl-CoA carboxylase (ACCase), and glycerol-3-phosphate dehydrogenase (GPD1)), genes affecting seed size and plant growth (e.g., transcription factors (WRI1), auxin response factor 19 (ARF19), leafy cotyledon1 (LEC1), purple acid phosphatase 2 (PAP2), G-protein c subunit 3 (AGG3), and flowering locus T (FT)), as well as genes involved in TAGs degradation (e.g., sugar-dependent protein 1 triacylglycerol lipase (SDP1)) have been deliberated. While through the second strategy targeting enhanced oil composition, suppression of the genes involved in the biosynthesis of linoleic acids (e.g., fatty acid desaturase (FAD2), fatty acid elongase (FAE1), acyl-ACP thioesterase (FATB), and ketoacyl-ACP synthase II (KASII)), suppression of the genes encoding toxic metabolites (curcin precursor and casbene synthase (JcCASA)), and finally, engineering the genes responsible for the production of unusual TAGs (e.g., Acetyl-TAGs and hydroxylated fatty acids (HFA)) have been debated. In addition to those, enhancing tolerance to biotic (pest and disease) and abiotic (drought, salinity, freezing, and heavy metals) stresses as another important genetic engineering strategy to facilitate the cultivation of nonedible oil plants under conditions unsuitable for food crops has been addressed. Finally, the challenges faced prior to successful commercialization of the resultant GM oil plants such have been presented .

Biogas production from wastes and residues is classified among the versatile, energy-efficient, and environmentally beneficial strategies considered to gradually replace fossil fuels in the future. Nevertheless, biogas production from different resources is faced with many technical, efficiency, and cost challenges, and therefore, optimization of the various aspects of the process, including feeding, mixing, microbial community, as well as process monitoring and control are vital to enhance process efficiency. The microbial community structure and functions exert vital effects on the process stability and biogas yield. However, due to the lack of optimized culture media and conditions for most of the organisms involved in biogas production, the majority of the participating microbes as well as their genes and metabolic pathways during the process are yet to be well known. Recent developments in culture independent “omics” and next generation sequencing technologies (NGS) have provided excellent opportunities for exploring microbial communities and their factions during the anaerobic digestion process. Therefore, this chapter has focused on recent applications of new “omics”, including NGS-based whole genome sequencing, metagenomics, meta-transcriptomics, meta-proteomics, and met-metabolomics in characterization of microbial flora, their genes and encoded transcripts, proteins, and metabolites, as well as the metabolic pathways contributing to the anaerobic digestion process. Recent findings have confirmed that the revolutionary innovations and developments in these domains will help to enhance the efficiency of biogas production from a diverse range of organic matters with complex structures in the near future.