Valorisation of Agro-industrial Residues – Volume I: Biological Approaches

The global rise in demand for fats and oil has made the palm oil industry grown tremendously over the last decades in countries like Indonesia, Malaysia, and Thailand. Malaysian agro-industrial sector alone accounts for about 51% of the world’s palm oil production and 62% of the world’s export. The sector has generated billions of dollars in revenues, and tonnes of wastes too. Palm oil mill effluent (POME) is the most abundant waste generated during the crude oil extraction process. Efficient and effective POME treatment technologies are still being actively investigated. POME has great potential as a substrate for biohydrogen production due to the high content of degradable organic matter. Dark fermentation, among the various biological processes for biohydrogen production, is highly favored due to the lower cost and low energy requirement. However, achieving a high biohydrogen yield is the main challenge, due to the co-production of organic acids. Additional treatment steps using bioelectrochemical systems (BES), such as microbial electrolysis cell (MEC), can provide the much-needed solution. Enhanced biohydrogen production can potentially be achieved when dark fermentation is coupled with MEC, with better POME treatment. Microbial fuel cell (MFC) can provide additional treatment step, with simultaneous electricity generation. This chapter reviews the various dark fermentation technologies that have been employed in producing biohydrogen from POME, the methods employed to improve biohydrogen yield, the advancements in BES, and the potential integration with dark fermentation for enhanced biohydrogen production.

In the face of global changes, plants must adapt to a wide range of abiotic and biotic stress combinations such as water stress conditions, soil fertility losses, soil pollutions, drought, pests, and disease that seriously impaired plant growth and development. In addition, the current agriculture practices of worldwide suffering overuse of chemical fertilizers and pesticides since the use of biofertilizer and biocontrol agents produce slow results and expensive. Therefore, there is a need for new biomaterials that are cheap with the characteristics of high bioavailability of nutrients, carriers of biocontrol agents, detoxification, and rehabilitation of toxic materials for an efficient, economical and versatile biofertilizer. Spent mushroom substrate (SMS) is one of the most abundant agricultural wastes produced at the end of mushroom cultivation production. SMS still contains essential nutrients needed for raising a healthy field crop in addition to cultivated mushroom mycelium and large population of heterotropic microbes. Different potential of applying SMS has been discussed nowadays. The application of SMS in agriculture mainly contributes to improveing the soil quality, chemically adsorb the organic and inorganic pollutants, and serves as a good carrier for the Plant Growth Promoting Microbes (PGRM) and shows the best biological efficiency against soil and plant pathogens. This book chapter basically reviews and discusses different scientific research and practical application of SMS especially focusing on the agricultural field to develop a latest insight of SMS as one of the low cost but high productive biomaterials.

Agro-industrial waste is mostly composed of lignocellulosic biomass, which is inexpensive, renewable, and abundant. It provides a unique natural resource for cost-effective bioenergy collection. Agro-industries generate a wide number of waste products either in the form of solid or liquid. The production of agro-industrial waste is growing worldwide and these wastes cannot be disposed of directly on the ground without any treatment, as they will cause serious environmental concerns. The problem of disposal and management of these wastes is a major issue especially in developing countries nowadays. Hence these agro-industrial waste must be treated before discharging or reuse for other purposes by effective methods. The conventional methods require the use of harsh and toxic chemicals with high processing cost and high waste management cost. In serious consideration of the worldwide economic and environmental pollution issues, there has been increasing research interest in the management of the agro-industrial waste proposing value-added green technologies. Biological treatment is seen as one of the promising green biotechnologies that gives less harm to the environment while balance out the ecosystem. The biological treatment utilizes microorganisms mainly from the bacterial and fungal species to cope with the issue raised and also act as bioremediation. This chapter begins with an overview of agro-industrial waste and further describes a number of biological treatments performed together with its advantages and disadvantages. This chapter finally deals with the possibility of creating a sustainable practice in industries processing agricultural products. Several suggestions and recommendations for future considerations are also thoroughly highlighted. The ultimate goal of this biological treatment chapter is to prepare the agricultural waste for a cleaner process toward a better and safer product.

Anaerobic digestion (AD) is a cost-effective treatment for management of lignocellulosic substrates, viz., agricultural wastes and animal manures, which also aids in generation of methane as biofuel. Although the application of AD technology is increasing, one of the major limitations of the process is that the rate of fermentation is higher than the rate of methanogenesis, which significantly affects process stability and methane yield. Normally, the souring of digesters can be observed after 2–4 weeks after the initiation of the volatile fatty acids accumulation, which makes it difficult for early detection and consequently resulting in acidification of digesters. Of late, metagenomic approaches are gaining importance due to their ability to reveal the microbial diversity and their dynamics in a relatively short time. However, their functional nature could not be clearly explained due to the lack of data on their activity. Recent advances in proteomic studies show its potential as a complementary technology to metagenomic studies for efficient management of digesters. Metaproteomic analyses aid in identifying a shift in metabolic paths and in metabolic networks under stress conditions. This provides insights on functionality, microbial interactions, and provides data on spatiotemporal variations and their dynamics of proteins crucial for efficient performance of the digester. Besides, this technique has led to identify novel phylotypes with novel functions among the microbial communities of the anaerobic digesters, which suggest the potential of proteomics in bioprospection of novel enzymes for industrial purposes. How proteomics along with metagenomics and transcriptomics data could aid in early detection of disturbances in the digesters helps in formulating recovery strategies as well as to increase the methane content of biogas will be discussed in this chapter.

Agro-industrial production generates large volumes of effluents with a high content of solids, nutrients, organic matter, and microorganisms. These effluents can negatively modify natural environments that receive them by surface runoff or infiltration through the soil, with possible damage to the population’s health. The objective of the circular economy is to maintain—as long as possible—the materials, products, and resources used in the production system to diminish, in this way, contaminating wastes. The “biologization” of industrial processes using the purification capacity of microalgae to decontaminate wastewaters has emerged in recent years. It offers two benefits, the production of biomass for different uses and the production of cleaner effluents. After microalgal treatments, ecotoxicity tests are used to assess the effectiveness of decontamination processes. In addition, bioassays indicate how long it is necessary to continue the decontamination process, i.e., when the concentration with no toxic effects has been reached, thus reducing unnecessary costs.

Hydrogen gas (H₂) is a clean fuel and contained a relatively high energy density which is about 142 kJ g⁻¹. Recently, increasing attention has been given to the production of H₂ from biological route. The biological H₂ (biohydrogen) process is an H₂ production by microorganisms that utilize renewable energy resources as substrates. Possible biohydrogen production technologies include biophotolysis, photo-fermentation processes, and the dark fermentation route. Among these three production processes, the dark fermentation process is often regarded as the most potential route. It generates H₂ by utilizing carbohydrates as the carbon sources whereby glucose was found to be the most commonly used substrate. A high yield of biohydrogen, i.e., about 4 mol of H₂ per mole of glucose consumed can possibly be achieved through this route. Despite a reasonably high yield, industrial-grade glucose (35–50 USD per kg) is expensive and therefore, rendering the process less economical especially considering market value for H₂ typically ranging only between 3 and 5 USD per kg. Obviously, cheaper substrates are needed if dark fermentation process is ever to strive as the potential route for biohydrogen production. In Malaysia, abundance of agricultural waste is disposed into landfills annually and thus, making it free un-tap resources. This chapter reports the prospect and challenges of utilizing agro-waste as the carbon source for biohydrogen production in Malaysia. The work will provide basis evaluation on the potential of biohydrogen production where agro-waste is capitalized as main substrates for the process.

There is worldwide interest in process development for the production of pigments from natural sources due to a serious safety problem with many artificial synthetic colorants, which have widely been used in foodstuff, cosmetic, and pharmaceutical manufacturing processes. Low-cost by-products and residues of agro-industrial origin have shown their potential in production of different pigments by diverse group microorganisms and to explore the possibility of pigment production by different microbial isolates from numerous sources on various substrates. The main applications of recycled wastes are enzyme production, organic acid isolation, pigment extraction, bioactive compound production, etc. Therefore, more regulatory approval and capital investments are required to bring these value-added products in the commercial market. The conversion of agro-industrial residues to important substances may not only provide future dimension to researchers but also reduce the current environmental hazards.

The eastern subterranean termite (EST) Reticulitermes flavipes is an insect pest in the USA. Like all wood-feeding termites (WFT), EST relies on a complex system of microbes to meet its nutritional requirements. The microbiome of WFT is stable, but the relative abundance of bacteria changes depending on diet. The purpose of this study was to explore the microbial diversity within EST collected in Thibodaux and St. Francisville, LA and detect differences based on diet and location to determine if the microbiome has a strict structure. It was found that taxa did not differ much between nearby colonies, but relative abundance is impacted by the wood in the diet. Half of bacteria from the gut of termites on nuttall oak were Bacteroidales, of which 22.7% were members of the family Porphyromonadaceae. 44% of bacteria from termites on red maple were Spirochaetes. All Spirochaetes were members of the genus Treponema. Elusimicrobia, a phylum found exclusively within termites and wood-feeding cockroaches was not abundant in either St. Francisville colony. Taxa differed more between termite colonies from different locations, but the mircobiome of St. Francisville colonies appeared to begin diverging at the family level. Overall, the microbiome was typical of termites, harboring cellulolytic protozoa, nitrogen-fixing bacteria, acetogenic Spirochaetes, and methanogenic archaeans. This has implications in microbial ecology because the organisms are changing, but the function, digestion of lignocellulose, is not. A bacterium was isolated and identified from termite gut as Acinetobacter tandoii from our previous studies degraded various phenolics, including phenol, nitrophenol, dinitrophenol, trinitrophenol, and toluene.

The term “environmental biotechnology” has been coined to describe the use of biological systems, ranging from bacteria to plants, to achieve environmental remediation, pollution prevention, detection, and monitoring of contaminants, and more recently transforming waste to produce energy, biopolymers, and other benefits. Latin-American countries have a privileged location to develop ingenious and sustainable alternatives in environmental biotechnology. An advantage to do innovation in tropics is their biodiversity. Useful compounds can be produced in laboratory settings and/or full-scale operations. However, waste (solid, liquid, or gaseous) released into natural and confined (end of pipes) environments are normally mixtures of different chemical compounds and often microorganisms are part of this waste. Waste valorization can conduce to obtain more rentable by-products in bioremediation. To conduct the bioremediation join to valorization, many processes need to be implemented. Coupled biological processes can increase the efficiency and value to end products. In this chapter, different alternatives to valorize organic wastes under the anaerobic digestion-based biorefinery concept were reviewed. Advantages and challenges of developing countries to use environmental biotechnology and to solve waste problems were also analyzed.

Ayurvedic medicines are of great importance to the health of individuals. The global market for herbal drugs are growing rapidly due to their less or no side effects, cost-effectiveness, availability, better patient tolerance, and clinical effectiveness. The traditional ayurvedic medicine manufacturing systems combine with the elements of modern technology to improve the production of reasonable drugs for human health care. Globally, ayurvedic pharma industries are among the leading pharmaceutical industries and they generate large volume of biodegradable wastewater, solid waste, and oil waste during processing and production. The waste from herbal pharmaceutical industry is a complex constitute of plant extracts, plant parts, toxic solutes, and heavy metal ions. They also have high BOD and COD concentrations so they can be discharged only after proper treatment otherwise may lead to environmental problems. Integrated microbial-vermifiltration, vermicomposting, and windrow composting are some of the cost-effective methods for the recycling of solid waste from herbal pharmaceutical industry. Microalgae are used for the treatment of waste water due to their potential to reduce the metal contamination and remove toxic substances. The resultant water after the treatment was clean enough to be reused for irrigation process. Biopharmaceutical oil waste and solid waste can be used also as substrate for fermentation process as well as for isolation of beneficial fungal strains for enzyme production.

Humanity has been used microbial biomass for food production and now; for biofuels, drugs, and other useful compounds. Different microorganisms are employed in the production of biomass ranging from bacteria, yeast, fungi, and algae which are used to produce food, bioactive compounds, enzymes, hydrolysates, among others. Due to the accelerated population growth in the world and the need to meet its nutritional requirements, the search for alternatives that help to solve this social problem is one of the most pressing tasks.

Several studies have demonstrated the nutritional value of microbial biomass related to a high protein content, an excellent source of vitamins and minerals necessary for a quality diet. The production of unicellular biomass has been carried out through submerged and solid-state fermentations. For the production of biomass, the design of various culture media has been considered, where different sources of carbon, nitrogen, pH, and aeration level have been some of the evaluated variables that favor the yields of protein production. The use of various agro-industrial waste as carbon source in the biomass production could contribute in solving a problem of accumulation of waste causing soil contamination. This chapter describes the state of the art of unicellular biomass production, microorganisms used, types of fermentation, carbon sources used, agro-industrial residues used as substrate, characteristics of biomass produced and other related topics.

Pesticides are chemicals which are widely used for the protection of crops from the attack of pathogens. Pesticides include fungicides, insecticides, herbicides, and bactericides. Among the different classes of pesticides used, organophosphorus class of pesticides is commonly used for agricultural applications. Indiscriminate use of such chemicals causes many environmental problems. It also poses high risk to other organisms such as birds, fishes, other beneficial insects, and humans. So it is highly desirable to remove these harmful chemicals from the environment in a proper way. Biodegradation is one of the best available methods and is the breakdown of toxic chemicals into nontoxic compounds through the use of microorganisms. It is a cost-effective, eco-friendly, and efficient method for the detoxification of pesticides. Different microorganisms are involved in the biodegradation process such as bacteria, fungi, and cyanobacteria. Among these organisms, cyanobacteria play an important role in the degradation of pesticides. They can be found in a wide variety of habitats. They are photoautotrophic organisms and hence the use of cyanobacteria for degradation process would overcome the need to supply heterotrophs with organic nutrients. Studies have proved the efficiency of cyanobacteria in the degradation of organophosphorus pesticides. The widespread appearance of cyanobacteria in the polluted area is also a contributing factor for making them a better candidate for biodegradation.

The goal of this study was to investigate the species of the abundance microbial in seed sludge and aerobic granular sludge. Experiments were carried out in a sequencing batch reactor with a working volume of 1.6 L. During the start-up period, the reactor was inoculated with 800 mL of sludge from a municipal sewage treatment plant plus 800 mL of rubber processing wastewater. Further investigation by Illumina high-throughput sequencing was performed to analyze the microbial diversity and phylogenetic structures during the granulation of seed sludge to aerobic granules. A diversity of microorganisms was identified from the seed sludge and aerobic granular sludge. Seed sludge consisted of 96.4% bacteria, 1.7% eukaryote, 1.2% archaea, and 0.7% viruses. Aerobic granular sludge consisted of 97.8% bacteria, 1.0% eukaryote, 0.8% archaea, and 0.4% viruses. As the granulation process succeeded in SBR, distinct differences of the microbial community in the seed sludge and aerobic granular sludge were observed, which suggested that there was high microbial selection pressure during granulation in the system. The most abundance species in seed sludge was Dechloromonas aromatica, while Pseudomonas fluorescens was the most abundance species in aerobic granular sludge.

At least 80,000 tonnes of the condiments were produced in Malaysia and estimated to increase in volume by 5% by the following year. In addition, one tonne of soy sauce generates about 7–9 tonnes of high strength wastewater. Aerobic granules are known to be regular, smooth, and nearly round in shape with excellent settling ability. They also have dense and strong microbial structure and high biomass retention with the ability to withstand high organic loading. These advantages encouraged recent development of aerobic granulation technology to treat high strength wastewaters such as soy sauce wastewater. Therefore, an efficient Granular Sequencing Batch Reactor (GSBR) treatment system ought to be in place to treat the high strength wastewater. The metagenome sequencing analysis revealed an abundance of microbial diversity accommodating in aerobic granular sludge cultivated with soy sauce wastewater. Existence of 77.52% exopolysaccharides substances (EPS)-producing bacteria such as Pseudomonas and Bacteroides which had the capability in biodegraded waste in wastewater biological treatment were found in aerobic granular sludge. Thus, the performances of aerobic granular sludge in biodegraded organic and nutrient from soy sauce wastewater were in consequence to the bacterial community that occupied in aerobic granules.