Hydrogen (H₂) is a highly efficient and clean energy source with the potential for renewable energy. The production of H₂ from biological routes such as biophotolysis, photofermentation, dark fermentation, and bioelectrochemical production is characterized as a renewable alternative to current production, which is mainly based on energy-intensive electrochemical and thermochemical processes and responsible for the emission of high amounts of environmentally harmful compounds. Dark fermentation is the most efficient and cost-effective method for producing biohydrogen, making it a key research focus. This article offers a comprehensive overview of the dark fermentation process with the aim of enhancing hydrogen productivity and yields. Aspects related to the main substrates used, the inoculum sources and their pretreatment, and physical-chemical parameters of the process are covered. Furthermore, this manuscript addresses topics such as process integration, genetic and metabolic engineering of fermentative microorganisms, and the main types of bioreactors aimed at greater yields and productivity of biohydrogen to enable its production through dark fermentation on a larger scale.

Agriculture is essential for nutrition and the global economy, becoming increasingly important due to population growth and higher food demand. This situation boosts interest in creating bioproducts that enhance productivity sustainably while reducing environmental issues and strain on natural resources. Bioinoculants are important innovations that use beneficial microorganisms to boost crop growth and resilience. They enhance the interaction between soil and plants by solubilizing essential nutrients and producing phytohormones. This not only boosts agricultural productivity but also promotes environmentally sustainable practices by decreasing reliance on chemical fertilizers. Considering the relevance of this subject to advances in agro-industrial biotechnology, this review analyzes recent studies and patent advances on the production and use of bioinoculants, as well as their integration into agricultural practices and plant development. It also explores the dynamics of production and downstream processes on an industrial scale, regulations in different countries, and growing market demands, which is an important feature of this review. Furthermore, future perspectives for the application of bioinoculants in agro-industrial biotechnology are discussed, emphasizing the critical role that these biological agents play in advancing agricultural sustainability.

Sugarcane ethanol production generates about 360 billion liters of vinasse, a liquid effluent with an average chemical oxygen demand of 46,000 mg/L. Vinasse still contains about 11% of the original energy from sugarcane juice, but this chemical energy is diluted. This residue, usually discarded or applied in fertigation, is a suitable substrate for anaerobic digestion (AD). Although the technology is not yet widespread—only 3% of bioethanol plants used it in Brazil in the past, most discontinuing the process—the research continues. With a biomethane potential ranging from 215 to 324 L of methane produced by kilogram of organic matter in vinasse, AD could improve the energy output of sugarcane biorefineries. At the same time, the residual digestate could still be used as an agricultural amendment or for microalgal production for further stream valorization. This review presents the current technology for ethanol production from sugarcane and describes the state of the art in vinasse AD, including technological trends, through a recent patent evaluation. It also appraises the integration of vinasse AD in an ideal sugarcane biorefinery approach. It finally discusses bottlenecks and presents possible directions for technology development and widespread adoption of this simple yet powerful approach for bioresource recovery.

Recycling bioresources is the only way to sustainably meet a growing world population’s food and energy needs. One of the ways to do so is by using agro-industry wastewater to cultivate microalgae. While the industrial production of microalgae requires large volumes of water, existing agro-industry processes generate large volumes of wastewater with eutrophicating nutrients and organic carbon that must be removed before recycling the water back into the environment. Coupling these two processes can benefit the flourishing microalgal industry, which requires water, and the agro-industry, which could gain extra revenue by converting a waste stream into a bioproduct. Microalgal biomass can be used to produce energy, nutritional biomass, and specialty products. However, there are challenges to establishing stable and circular processes, from microalgae selection and adaptation to pretreating and reclaiming energy from residues. This review discusses the potential of agro-industry residues for microalgal production, with a particular interest in the composition and the use of important primary (raw) and secondary (digestate) effluents generated in large volumes: sugarcane vinasse, palm oil mill effluent, cassava processing waster, abattoir wastewater, dairy processing wastewater, and aquaculture wastewater. It also overviews recent examples of microalgae production in residues and aspects of process integration and possible products, avoiding xenobiotics and heavy metal recycling. As virtually all agro-industries have boilers emitting CO₂ that microalgae can use, and many industries could benefit from anaerobic digestion to reclaim energy from the effluents before microalgal cultivation, the use of gaseous effluents is also discussed in the text.

Biotechnology is increasingly being used as a tool to replace traditional production methods due to concerns about the increasing damage caused by global warming. Bacteria, yeasts, fungi, and microalgae are microorganisms able to transform residues into value-added bioproducts. They produce microbial biomass that can result in the production of several products, such as biofuels, microbial proteins, fatty acids, bioactive polysaccharides, carotenoids, industrial enzymes, polyhydroxyalkanoates, and biofertilizers, among others. To improve microbial biomass and lipid yield, modern genetic engineering techniques can be applied as a way of optimizing processes and conditions. This review aims to explore the latest trends and technological advances in microbial biomass and lipid production, including optimization strategies for cultivation conditions and the use of genetic engineering to enhance yields and efficiency. It also discusses the challenges and future prospects for scaling up production for industrial applications. The potential of microbial lipids to contribute to a sustainable bioeconomy, as well as their applications in renewable energy and food industries, underscores their importance in a world increasingly seeking alternatives to fossil fuel dependence and unsustainable agricultural practices.

Cocoa fermentation is a critical step in chocolate production, influencing the flavor, aroma, and overall quality of the final product. This review focuses on the microbial dynamics of cocoa fermentation, emphasizing the roles of yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). These microorganisms interact in a well-defined succession, producing organoleptic compounds such as alcohols, organic acids, and esters, which are key to the sensory profile of cocoa. This article examines the impact of different fermentation methods, including spontaneous fermentation and the use of starter cultures, on microbial communities and flavor development. Advances in starter culture technology are highlighted, demonstrating how microbial control can enhance fermentation efficiency, reduce fermentation time, and improve the consistency of chocolate flavor. Patents related to cocoa fermentation further emphasize the growing interest in microbial management to meet market demands for high-quality, distinct chocolate. This review also outlines future research directions, including the identification of new microbial strains, optimization of fermentation conditions, and the potential of biotechnological advancements to improve the fermentation process. Understanding microbial dynamics in cocoa fermentation offers significant potential for enhancing chocolate quality, sustainability, and the development of new, region-specific flavor profiles.