Cave microbiomes, consisting of diverse and often extremophilic microorganisms, represent an underexplored reservoir for bioprospecting, which entails the systematic exploration of biological resources for commercially valuable compounds. These stable and isolated subterranean ecosystems are characterized by distinct microclimates, fostering the evolution of unique microbial consortia. The metabolic versatility of these microorganisms enables survival under oligotrophic and aphotic conditions, and this adaptability is reflected in their production of novel bioactive compounds, including antibiotics, enzymes, and secondary metabolites with significant therapeutic and industrial applications. This review aims to elucidate the distinctive characteristics of cave microbiomes, evaluate their biotechnological, medical, and industrial applications, and address the technical challenges associated with sampling and cultivating these microorganisms. The focus is extended to India’s diverse cave ecosystems, ranging from the historical Ajanta and Ellora caves to the biodiverse Meghalaya caves, which serve as critical reservoirs for microbial exploration. Special emphasis is placed on sustainable and ethical bioprospecting approaches, advocating for the conservation of cave habitats and ensuring equitable benefit-sharing with local communities. By critically analysing the influence of geological formations, climatic conditions, and nutrient availability on microbial diversity, this review highlights the immense potential of cave microbiomes for novel compound discovery. It underscores the need for further research in this promising domain while promoting practices that balance scientific exploration with environmental conservation.
Anaerobic digestion (AD) systems generate biogas from protein-rich waste, with certain anaerobes modulating gene regulatory networks (GRNs) to manage ammonia toxicity. This study reconstructs GRN models for five key anaerobes—a hyper-ammonia-producing anaerobe Acetoanaerobium sticklandii H1, an anaerobic sulfur-reducing bacterium Desulfovibrio vulgaris Hildenborough, a hydrogenotrophic methanogen Methanothermobacter thermautotrophicus ΔH, a heterotrophic methanogen Methanosarcina mazei Gö1, and a methylotrophic methanogen Methanoculleus bourgensis MS2T—using genome-wide data to understand their metabolic regulation in AD processes. These GRNs integrate gene regulatory elements, thereby revealing species-specific adaptations that facilitate ammonia tolerance, substrate metabolism, and methane production. Regulatory elements, such as ExsA, PtxR, and GadW, influence pathways for carbon, nitrogen, and energy metabolism. A. sticklandii and M. mazei were crucial for carbon source utilization, whereas M. bourgensis adapted to ammonium-rich conditions without a typical ammonium uptake system. The results of our study provide insights into the metabolic interactions and regulatory roles within biogas-producing communities. This work proposes a framework for designing synthetic microbial communities to enhance biomethane yield from protein-based substrates, supporting AD efficiency improvements.
Agricultural wastes are characterized by bioactive compounds that can be used to produce different byproducts, including enzymes, which are obtained through solid state fermentation (SSF). The goal of this study was to evaluate the initial pH and moisture conditions of a substrate composed of carrot peels and corn husk residues (tusa) by SSF to obtain cellulase enzymes. Carrot and corn wastes were characterized to determine their physicochemical properties, confirming their suitability for the fermentation process. It was found that endoglucanase enzyme activity increased with time and was favored at a humidity of 75% and a pH of 5.2, reaching values above 300 U/mg protein. However, no significant trends were observed in exocellulase activity related to the study´s factors. Although the use of agro-industrial wastes to obtain high-value molecules has been widely studied, combining carrot and corn wastes as a substrate for cellulase production using Cladosporium sp. _V3 (GenBank No. PP931187) isolated from pineapple wastes has been poorly characterized.
This study aims to augment the D-lactic acid biosynthetic capacity of Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 through random mutagenesis. The mutant strain, Mut_N23, developed through synergistic application of ultraviolet (UV) irradiation and chemical mutagenesis using N-methyl-N′-nitro-N-nitrosoguanidine (NTG), exhibited 97% increase in D-lactic acid production and 37% enhancement in glucose uptake rate at flask level. Mut_N23 consistently produced optically pure D-lactic acid across seven generations, efficiently metabolizing lactose and sucrose to yield 4.47 g L− 1 and 3.38 g L− 1 of D-lactic acid, respectively. Optimal conditions identified through One-Factor-At-a-Time (OFAT), and Response Surface Methodology (RSM) facilitated maximum D-lactic acid concentration of 7.88 g L− 1 (300% increase) from lactose-MRS (deMan Rogosa Sharpe) with specific productivity of 0.110 g g− 1 h− 1. When lactose was replaced with whey permeate as an application, 4.89 g L− 1 (140% increase) of D-lactic acid was obtained, with specific productivity of 0.066 g g− 1 h− 1 in lab-scale bioreactor setups, achieving 99.09% optical purity. Transcriptomics and enzymatic activity analyses substantiated enhanced performance of Mut_N23 signifying beneficial random mutations. Furthermore, characterization of purified D-lactic acid derived from whey permeate using Fourier Transform Infrared (FTIR) spectroscopy and proton Nuclear Magnetic Resonance (NMR) spectroscopy demonstrated parity with commercially available standards. This study highlights Mut_N23’s potential for efficient D-lactic acid production exploiting a spectrum of carbon sources, providing a foundation for future metabolic engineering to enhance biosynthetic productivity.