2024

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Cyanobacteria as a Biocatalyst for Sustainable Production of Biofuels and Chemicals
(Multidisciplinary Digital Publishing Institute (MDPI), 2024) Varsha K. Singh; Sapana Jha; Palak Rana; Renu Soni; Rowland Lalnunpuii; Prashant K. Singh; Rajeshwar P. Sinha; Garvita Singh
The combustion of fossil fuels constitutes a significant catalyst for climate change, resulting in the annual release of about two billion tonnes of carbon dioxide (CO2). The increase in CO2 emission is directly linked to a heightened occurrence of natural calamities and health-related issues. The substitution of fossil fuels with renewable energy sources is a fundamental approach to reduce the negative impacts caused by consumption of these nonrenewable energy resources. The utilisation of biological methodologies to produce environmentally friendly energy from renewable sources holds significant potential for the sustainable production of fuel. However, the cultivation of first- and second-generation biofuel crops presents a challenge, since they compete for limited cropland, hence constraining their overall viability. In contrast, photosynthetic microorganisms such as algae and cyanobacteria exhibit significant potential as third-generation biofuel catalysts, devoid of the limitations associated with contemporary biofuels. Cyanobacteria, a type of photosynthetic prokaryotes, exhibit significant potential for the direct conversion of carbon dioxide (CO2) into biofuels, chemicals, and various other valuable compounds. There has been a growing interest in the concept of utilising biological processes to convert carbon dioxide into fuels and chemicals. The introduction of a limited number of heterologous genes has the potential to confer upon cyanobacteria the capability to convert particular central metabolites into a diverse range of end products. The progress in the field of synthetic biology and genetic manipulation has enabled the manipulation of cyanobacteria to synthesise compounds that are not generally produced by these organisms in their natural environment. This study focuses on recent papers that employ various methodologies to engineer cyanobacteria for the purpose of producing high-value compounds, such as biofuels. © 2024 by the authors.
Ecology and environmental omics
(Elsevier, 2024) Minu Kesheri; Swarna Kanchan; Upasna Srivastava; Bhaskar Chittoori; Ratnaprabha Ratna-Raj; Rajeshwar P. Sinha; Akhouri Vaishampayan; Rajesh P. Rastogi; Donald A. Primerano
Advancements in high-throughput omics technologies enabling rapid profiling of genes, mRNA, proteins, metabolites, metagenomes, etc. have accelerated the research in ecological and environmental omics. Ecological and environmental omics focus on a better understanding of the environmental and genetic factors, chemical toxicity mechanisms/pathways, biomarkers, and modes of action in response to exposure to a single or mixture of chemicals that result in the development of environmental diseases as long-term effects. Environmental omics also aims to investigate the identification of unknown environmental target organisms, environmental monitoring enabling risk assessment, diverse human health outcomes, environmental impacts, ecological functions, and environmental adaptation. Environmental and ecological omics explore acceptable levels and potential impacts of environmental toxicants on environmental target species and ecosystems. Multiomics technologies are also being used in accessing the environment to revise the existing law related to environmental protection. To date, single omics such as transcriptomics (∼43%) are being used frequently compared with multiomics (∼13%) in environmental research, showing the urgent need for multiomics technologies in environmental research. This chapter focuses on the use of various multiomics studies in accessing the environment, exploring the toxicity mechanisms due to exposure to single and mixture of chemicals to the target organisms. This chapter also focuses on the effect of exploring dietary and environmental factors on an organism's genome, environmental monitoring of health risks assessment, etc. © 2024 Elsevier Inc. All rights reserved.
Application of nanoparticles in agriculture: nano-based fertilizers, pesticides, herbicides, and nanobiosensors
(Elsevier, 2024) Jainendra Pathak; Deepak K. Singh; Prashant R. Singh; Neha Kumari; Jyoti Jaiswal; Amit Gupta; Rajeshwar P. Sinha
Climate change has posed unprecedented challenges to the existing global agricultural systems and practices. Advanced nano-engineering technology can boost crop production and assure agriculture sustainability, hence, could help in achieving food security. Nanotechnology has emerged as an important field of interdisciplinary research by controlling crucial agricultural processes owing to its miniature-sized nanomaterials. The ever-increasing global population especially in developing countries faces food shortages because of environmental impacts and political instability. The crucial challenge is development of pest- and drought-resistant crops which would maximize the agricultural yield, and nanotechnology has the potential to improve the agriculture and food industry with novel nanomaterials which enhance the capacity of plants to absorb nutrients and help in rapid disease diagnosis. These nanomaterials have potential applications in agriculture as nanofertilizers and nanopesticides to trail products and nutrients levels and hence increase the productivity without decontamination of soils, and waters. It also provide protection against several microbial diseases and insect pests. Hence, researches in agriculture and food nanotechnologies are increasing because of improved food quality and safety, improved processing and nutrition and reduced agricultural inputs. Nanomaterials could reduce the amount of chemicals used in agriculture, minimize nutrient losses in fertilization, and could increase yields through pest and nutrient management. Nanomaterials could also act as sensors for monitoring soil quality of agricultural field and thus help in maintaining the optimum yield of the crops. The present chapter deals with the potential applications of novel nanomaterials in maintaining the sustainability of agriculture and challenges related with such approach. © 2024 Elsevier Inc. All rights reserved.
Integrative omics data mining: Challenges and opportunities
(Elsevier, 2024) Swarna Kanchan; Minu Kesheri; Upasna Srivastava; Hiren Karathia; Ratnaprabha Ratna-Raj; Bhaskar Chittoori; Lydia Bogomolnaya; Rajeshwar P. Sinha; James Denvir
Next-generation sequencing-based high-throughput data has opened novel opportunities to analyze and describe biological processes at a higher resolution. Nowadays, multiomics technologies are generating large amounts of heterogeneous genomics, proteomics, and metabolomics datasets. Integrative approaches enable us to study complex biological processes that combine the analysis of multiple omics datasets to highlight the interplay of the involved genes, transcripts, proteins, metabolites, etc., and their functions. Thus, data integration and data mining are imperative to exploring the mysteries of life and complex diseases in life sciences research. In the present scenario, integrating heterogeneous and huge amounts of genomics, proteomics, and metabolomics data poses conceptual and practical challenges, and encourages researchers to develop novel data integration methodologies, tools, and virtualization platforms. This chapter reviews the current efforts and state of the art about data integration and its mining in life sciences research. This chapter describes various tools and methods in detail that adopt an integrative approach to analyze multiomics data and data mining methods to address phenotype prediction, disease subtyping, a novel biomarker, novel pathways discovery, etc. This chapter provides an extensive overview in lucid style illustrating the methodologies, limitations of these tools, multiomics data repositories, and visualization platforms along with enumerating the challenges associated with multiomics data integration and mining making this chapter informative and reader friendly. © 2024 Elsevier Inc. All rights reserved.
Health risk assessment of enzymes in different sectors
(Elsevier, 2024) Sonal Mishra; Rajeshwar P. Sinha
Microbial enzymes that perform optimally under harsh conditions are currently in high demand as they have found a lot of applications in various fields such as industrial, environmental, and biomedical sectors. Enzymes used in these sectors have an exceptional safety profile, with a low potential to cause harmful reactions in humans. It is a reasonable assumption that most enzymes have the potential to pose a health risk due to exposure to enzymes through oral, inhalation, skin, and eye contact. Some enzymes have the potential to cause reproductive toxicity, genotoxicity, and allergic and irritating effects at high concentrations. Bacterial and fungal enzymes have the intrinsic ability to act as respiratory and immune sensitizers. This chapter discusses the health risk assessment of enzymes in different sectors that are essential due to their wide application in various fields. © 2024 Elsevier Inc. All rights reserved.
Using systems biology to exploit the resources/natural reservoirs for biofuel production
(Elsevier, 2024) Varsha K. Singh; Niharika Sahu; Sapana Jha; Amit Gupta; Ashish P. Singh; Palak Rana; Jyoti Jaiswal; Neha Kumari; Rajeshwar P. Sinha
Energy carriers such as lipids, starch, and hydrogen found in algae can be converted into biofuels, making them a promising sustainable substitute for fossil fuels. Systems biology, which comprises several types of omics techniques, might aid in the development of algal strains for biotechnological applications by providing important insights. A variety of natural products, including those used in pharmaceuticals, commodity chemicals, polymers, and fuels, have been produced by microorganisms. Increasing interest in producing transport fuels from renewable resources has sparked a number of research efforts that aim to modify microbial systems for the enhanced production of desired products. The development of resilient and productive production hosts depends on removing the limiting factors in microbial metabolic pathways and reducing stressors brought on by the production of these compounds. Research in systems biology provides a thorough understanding of the effects of pathway engineering on the host metabolism as a whole, the detection of stressors resulting from product synthesis, and the justification for designing industrial microbes that are both optimal and economical. The genes and metabolic networks involved can be identified through genomic and transcriptomic analyses, respectively. Proteomic estimations disclose protein quantities and posttranslational modifications (PTMs), which include glycosylation, phosphorylation, ubiquitination and acetylation, whereas metabolomics studies show metabolites, intermediates, and the products of the metabolism. This chapter details the applications of systems biology to better understand metabolic networks in algae and cyanobacteria, along with their role in bioenergy carrier accumulation. © 2025 Elsevier Ltd. All rights reserved.
Biodegradation of various edible oils and fat by Staphylococcus petrasii sub sp. jettensis VSJK R1 for application in bioremediation of lipid rich restaurant wastewater
(Springer Nature, 2024) Vinayak P. Sutar; Varsha K. Singh; Rajeshwar P. Sinha
The disposal of fat, oil, and grease (FOG) pollutants from various sources, including restaurants, food processing facilities, and domestic kitchens, poses significant challenges to wastewater treatment systems. In this study, we isolated and characterized a novel bacterial strain. The result of 16 S rRNA gene and phylogenetic analysis showed that the isolate was Staphylococcus petrasii sub sp. jettensis and named as VSJK R1 (Fig. S1). It was tested for its biodegradation potential of FOG contaminants. Our investigation revealed that Staphylococcus petrasii sub sp. jettensis VSJK R1 effectively degraded a variety of edible oils, including soybean, sunflower, cottonseed, palm, groundnut, and butter, with notable efficiency. Optimization studies were conducted to determine the optimal conditions for biodegradation, including the effects of nitrogen, carbon, phosphorus, pH, temperature, and salt concentration. Results indicated that organic nitrogen sources and glucose as carbon source significantly enhanced biodegradation rates, while the addition of phosphorus further improved degradation efficiency within specific concentration ranges. Moreover, the optimal pH for biodegradation was found to be neutral, with temperature ranging between 22°C and 45°C favoring microbial activity. Remarkably, Staphylococcus petrasii sub sp. jettensis VSJK R1 exhibited resilience to high salt concentrations, making it suitable for treatment of wastewater with elevated salt content. Additionally, comparative studies with other microbial strains underscored the unique biodegradation capabilities of Staphylococcus petrasii sub sp. jettensis VSJK R1, particularly in degrading various edible oils. The results suggest promising applications of this novel isolate in bioremediation efforts targeting FOG pollutants in wastewater treatment plants and grease traps. Future research may focus on scaling up the bioremediation process and field testing the efficacy of Staphylococcus petrasii sub sp. jettensis VSJK R1 in real-world wastewater treatment scenarios. © The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia 2024.
Influence of microorganisms on thermal conductivity of soils and its potential impact on soil aggregation
(Springer, 2024) Manish V. Shah; Payal Tandel; Avadhi Patel; Ajay Chavda; Shalini Singh; Rakesh K. Panchal; Vijay Upadhye; Varsha K. Singh; Rajeshwar P. Sinha
The significance of soil thermal conductivity in designing energy geo structures lies in its role in determining the heat transfer rate through materials. This study delves into the impact of bacterial presence on soil thermal conductivity, utilizing soil samples from six distinct regions in Gujarat—Surat, Madhavpur, Bhadbhut, Navsari, Dholera, and Bhuj. Employing a laboratory-scale experimental setup based on guarded hot plate method, thermal conductivity of soil samples was measured. Microorganisms were isolated from the soil samples using serial dilution and spread plate method, with two types of microorganisms selected from each soil sample. Measurements were conducted at curing periods of 7, 14, and 28 days, and comparative analysis of thermal conductivity values before and after treatment were performed. The findings revealed that E. coli led to reduction in thermal conductivity values in sandy soil, while S. aureus exhibited favorable outcomes in sandy soil compared to clayey soil. The study reveals significance of natural microbes present in raw soil and its potential use to enhance thermal conductivity of soils. © The Author(s) under exclusive licence to Society for Plant Research 2024.
Peculiar Endosymbiosis in the Cyanobiont Nostoc azollae 0708: An In Silico Approach
(Springer Nature, 2024) Minu Kesheri; Swarna Kanchan; Amit Kumar; Upasna Srivastava; Shivani Sharda; Bhagwan Malik; Tarun Mishra; Poonam Kaithal; Jitendra Narayan; Prashant Kumar; Prerna Priya; Rajeshwar P. Sinha
Nostoc azollae 0708 exhibits peculiar endosymbiosis owing to the unique commitment of cyanobiont’s association with fern throughout its life cycle. This chapter elaborates various in silico approaches adopted for intriguing proteomics aspects of Fe and Mn superoxide dismutase in the cyanobiont Nostoc azollae 0708. Prediction of physicochemical parameters elucidating molecular weight, isoelectric point (pI), instability index, aliphatic index, total no. of negatively charged residues (Asp + Glu), total no. of positively charged residues (Arg + Lys), extinction coefficient, and GRAVY are discussed in detail. Generating good quality 3D structural models for Fe-SOD and Mn-SOD by homology modeling and validation by Prosa-web, verify-3D, and PROCHECK is elaborately explained. Conservation of metal binding positions, domains, and motifs suggesting functional conservation, highly conserved exposed as well as buried amino acid residues advocating their structural and functional importance is also discussed. Generation of protein–protein interaction network using STRING illustrating the physical and functional interaction of superoxide dismutase with other proteins and biological cascade of these proteins in Nostoc azollae has been described. The NJ phylogenetic tree for Fe-SOD depicts Nostoc sp. PCC 7524 as the nearest evolutionary homolog, whereas Nostoc sp. PCC 7107 and Nostoc piscinale CENA 21 as evolutionary close homologs of Mn-SOD in Nostoc azollae. The present in silico methodologies discussed in this chapter may pave the way for further experimental validation aiding in exploring the biochemical, biotechnological, and biofertilizer potential of the cyanobiont recruited by the fern Azolla. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.
Microbial Multispecies Symbiosis: A Panomics View
(Springer Nature, 2024) Amit Gupta; Ashish P. Singh; Palak Rana; Varsha K. Singh; Neha Kumari; Sapana Jha; Rajeshwar P. Sinha
Symbiosis offers a technique to overcome the constraints placed on individual microbes. This is demonstrated in natural communities by symbioses like lichens and biofilms resilient to disturbances, an essential characteristic in changing environments. At the same time, microalgae undertake an array of mutualistic interactions with bacteria. Here, we discuss how the addition of microbiological and biochemical investigations to transcriptomic, metagenomic, and metabolomic techniques has helped us better understand the algal–bacterial interactions. In synthetic consortia, microorganisms adapted from the natural world or created through synthetic biology to interact are controlled by external factors. The traditional theory of dual symbiosis, which showed host-specific bacterial microbiomes, has been questioned by recent microbiome research. Recent findings about bacterial associations with lichen symbioses support the idea that they are multispecies symbioses. While numerous abiotic and biotic variables can also affect the bacterial community structure, panomics techniques have demonstrated the functional relevance of the bacterial microbiome to the whole lichen meta-organism. It has recently come to light that several photobionts and bacteria connected to lichens produce a variety of potentially valuable compounds. The abundance of biological and chemical variety within the lichen holobiome is becoming clearer due to the application of multi-omics techniques, genomics, mass spectrometry, and other analytical technologies. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

2024

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