Future Microbial Applications for Bioenergy Production: A Perspective

Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy

Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.

Conventional and microwave-assisted acid pretreatment of tea waste powder: analysis of functional groups using FTIR

Tea waste powder (TWP) is one of the potential biomass waste to recover valuable chemicals and materials. The prime objective of this work is to investigate the role of acid pretreatment on TWP. Diluted acids (HCl, H₃PO₄, CH₃COOH, and H₂SO₄) were used to soak the TWP to understand the role of acids on bond cleavage and chemicals formation. One gram of TWP was soaked in 100 mL of diluted acids for 24 h. The soaked samples were further subjected to a hot air oven (temperature: 80 °C, duration: 6 h), orbital shaking (shaking speed: 80-100 rpm, duration: 6 h), and microwave irradiation (microwave power: 100 W, duration: 10 min) to understand the synergistic effects of acids and mode of exposure. The pretreated solid samples and liquid samples were analyzed using FTIR to understand the presence of functional groups. The mass loss of TWP after treatment significantly varied with the type of acid and exposure mode used. In the orbital shaker, the mass loss was varied in the following order: H₂SO₄ (36%) > CH₃COOH (32%) > H₃PO₄ (22%) > HCl (15%). In hot air oven, high mass loss was observed compared to orbital shaking [HCl (48%) > CH₃COOH (37%) > H₂SO₄ (35%) > H₃PO₄ (33%)]. The mass loss in microwave irradiation is lower (19 to 25%) with all acids compared to orbital shaking. In the solid samples, O-H stretching, C-H stretching, C=O stretching, C=C stretching, -C-O-, and -C-OH- functional groups were noticed. Similarly, C=O and C=C peaks and C-O and -C-OH peaks were noticed in liquid samples. Interestingly, microwave irradiation showed promising results in 10 min of pretreatment, whereas orbital shaking and hot air oven pretreatments require 6 h to achieve the same result.

Single-cell transcriptomics and data analyses for prokaryotes-Past, present and future concepts

Transcriptomics, or more specifically mRNA sequencing, is a powerful tool to study gene expression at the single-cell level (scRNA-seq) which enables new insights into a plethora of biological processes. While methods for single-cell RNA-seq in eukaryotes are well established, application to prokaryotes is still challenging. Reasons for that are rigid and diverse cell wall structures hampering lysis, the lack of polyadenylated transcripts impeding mRNA enrichment, and minute amounts of RNA requiring amplification steps before sequencing. Despite those obstacles, several promising scRNA-seq approaches for bacteria have been published recently, albeit difficulties in the experimental workflow and data processing and analysis remain. In particular, bias is often introduced by amplification which makes it difficult to distinguish between technical noise and biological variation. Future optimization of experimental procedures and data analysis algorithms are needed for the improvement of scRNA-seq but also to aid in the emergence of prokaryotic single-cell multi-omics. to help address 21st century challenges in the biotechnology and health sector.

Isolation and Characterization of Bacteria with High Electroactive Potential from Poultry Wastewater

Natural resources are in short supply, and the ecosystem is being damaged as a result of the overuse of fossil fuels. The creation of novel technology is greatly desired for investigating renewable and sustainable energy sources. Microorganisms have received a lot of interest recently for their potential to transform organic waste into sustainable energy and high-value goods. New exoelectrogens that can transmit electrons to electrodes and remove specific wastewater contaminants are expected to be studied. In this study, we examined three distinct samples (as determined by chemical oxygen demand and pH) that can be used as anolytes to generate power in single-chamber and double-chamber microbial fuel cells using graphite electrodes. Wastewater from poultry farms was studied as an exoelectrogenic anolyte for microbial fuel cell power generation. The study examined 10 different bacterial strains, numbered A1 through A10. Due to their highly anticipated capacity to metabolize organic/inorganic chemicals, the diverse range of microorganisms found in poultry wastewater inspired us to investigate the viability of generating electricity using microbial fuel cells. From the investigated bacterial strains, the highest voltage outputs were produced by strains A1 (Lysinibacillus sphaericus) and A2 (Bacillus cereus), respectively, at 402 mV and 350 mV. Among the 10 different bacterial strains, strain A6 generated the least amount of electricity, measuring 35.03 mV. Furthermore, a maximum power density of 16.16 1.02 mW/m² was achieved by the microbial fuel cell using strain A1, significantly outperforming the microbial fuel cell using a sterile medium. The strain A2 showed significant current and power densities of 35 1.12 mA/m² and 12.25 1.05 mW/m², respectively. Moreover, in the two representative strains, chemical oxygen demand removal and Coulombic efficiency were noted. Samples from the effluent anode chamber were taken in order to gauge the effectiveness of chemical oxygen demand removal. Wastewater had an initial chemical oxygen demand content of 350 mg/L on average. Strains A1 and A2 decomposed 94.28% and 91.71%, respectively, of the organic substrate, according to the chemical oxygen demand removal efficiency values after 72 h. Strains A1 and A2 had electron donor oxidation efficiencies for 72 h of 54.1% and 60.67%, respectively. The Coulombic efficiency increased as the chemical oxygen demand decreased, indicating greater microbial electroactivity. With representative strains A1 and A2, Coulombic efficiencies of 10% and 3.5%, respectively, were obtained in the microbial fuel cell. The findings of this study greatly advance the field as a viable source of power technology for alternative energy in the future, which is important given the depletion of natural resources.

Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics

Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.

Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes

Plant-microbe interactions are critical for ecosystem functioning and driving rhizosphere processes. To fully understand the communication pathways between plants and rhizosphere microbes, it is crucial to measure the numerous processes that occur in the plant and the rhizosphere. The present review first provides an overview of how plants interact with their surrounding microbial communities, and in turn, are affected by them. Next, different optical biosensing technologies that elucidate the plant-microbe interactions and provide pathogenic detection are summarized. Currently, most of the biosensors used for detecting plant parameters or microbial communities in soil are centered around genetically encoded optical and electrochemical biosensors that are often not suitable for field applications. Such sensors require substantial effort and cost to develop and have their limitations. With a particular focus on the detection of root exudates and phytohormones under biotic and abiotic stress conditions, novel low-cost and in-situ biosensors must become available to plant scientists.

The BioExperience Research and Entrepreneurship Challenge: An iGEM-inspired applied research program for BIOSTEM talent and skills development

Post-secondary education is falling behind in delivering the talent and skills development needed to support the growth of biology-based economies and the demands of professional and research-based graduate degree programs. Here, we describe an applied research program, the BioExperience Research and Entrepreneurship Challenge, launched in May 2020 to mitigate the impact of the COVID-19 pandemic on undergraduate experiential learning programs at the University of Ottawa, Ontario, Canada. The program provided undergraduates with meaningful talent and skills development opportunities by implementing a student-centred, project-based learning approach inspired by the International Genetically Engineered Machine (iGEM) competition. We present evidence from participant exit surveys suggesting that the program delivers a high-quality learning environment and improves learning outcomes compared to traditional work-integrated learning. Notably, 84% of respondents reported an excellent or exceptional learning experience and significant or profound improvements in skills, such as leadership (72% of respondents), problem-solving (42% of respondents) and research preparedness (52%) that are difficult to develop in conventional academic programs. Remarkably, 60% of respondents report that the job-readiness training provided by the program is better or much better than traditional work-integrated learning. Our study demonstrates that a cost-effective and scalable alternative to the iGEM competition can improve talent and skills development in BIOSTEM fields.

A review on the conversion of cassava wastes into value-added products towards a sustainable environment

The solid and liquid wastes generated from cassava-based industries are organic and acidic in nature, which leads to various global concerns-primarily global warming and biodiversity loss. But the conversion of these wastes into value-added products associated with environmental pollution control contributes to sustainable development. Generally, the thermochemical process such as pyrolysis and gasification and biochemical processes such as anaerobic digestion have been applied for the conversion of cassava waste into value-added products. This review addresses the valorization of cassava wastes, which fulfill almost all needs of the hour, such as energy (biofuel), wastewater treatment (adsorbents), bioplastics, starch nanoparticles, organic acid production, and antimicrobial agents. The major aim of this paper is to analyze and provide the disclosure of the efficiency of cassava-based industrial waste as a source to minimize the problem associated with conventional fossil fuels and through which mitigate the impact of global warming and climate change. Furthermore, recent research and achievements in the valorization of cassava waste have been highlighted.

Microorganisms as New Sources of Energy

The use of fossil energy sources has a negative impact on the economic and socio-political stability of specific regions and countries, causing environmental changes due to the emission of greenhouse gases. Moreover, the stocks of mineral energy are limited, causing the demand for new types and forms of energy. Biomass is a renewable energy source and represents an alternative to fossil energy sources. Microorganisms produce energy from the substrate and biomass, i.e., from substances in the microenvironment, to maintain their metabolism and life. However, specialized microorganisms also produce specific metabolites under almost abiotic circumstances that often do not have the immediate task of sustaining their own lives. This paper presents the action of biogenic and biogenic–thermogenic microorganisms, which produce methane, alcohols, lipids, triglycerides, and hydrogen, thus often creating renewable energy from waste biomass. Furthermore, some microorganisms acquire new or improved properties through genetic interventions for producing significant amounts of energy. In this way, they clean the environment and can consume greenhouse gases. Particularly suitable are blue-green algae or cyanobacteria but also some otherwise pathogenic microorganisms (E. coli, Klebsiella, and others), as well as many other specialized microorganisms that show an incredible ability to adapt. Microorganisms can change the current paradigm, energy–environment, and open up countless opportunities for producing new energy sources, especially hydrogen, which is an ideal energy source for all systems (biological, physical, technological). Developing such energy production technologies can significantly change the already achieved critical level of greenhouse gases that significantly affect the climate.

A Kinetic Framework for Modeling Oleochemical Biosynthesis in E. coli

Microorganisms build fatty acids with biocatalytic assembly lines, or fatty acid synthases (FASs), that can be repurposed to produce a broad set of fuels and chemicals. Despite their versatility, the product profiles of FAS-based pathways are challenging to adjust without experimental iteration, and off-target products are common. This study uses a detailed kinetic model of the E. coli FAS as a foundation to model nine oleochemical pathways. These models provide good fits to experimental data and help explain unexpected results from in vivo studies. An analysis of pathways for alkanes and fatty acid ethyl esters, for example, suggests that reductions in titer caused by enzyme overexpression-an experimentally consistent phenomenon-can result from shifts in metabolite pools that are incompatible with the substrate specificities of downstream enzymes, and a focused examination of multiple alcohol pathways indicates that coordinated shifts in enzyme concentrations provide a general means of tuning the product profiles of pathways with promiscuous components. The study concludes by integrating all models into a graphical user interface. The models supplied by this work provide a versatile kinetic framework for studying oleochemical pathways in different biochemical contexts. This article is protected by copyright. All rights reserved.

Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions

The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.

Recent advances in metabolic engineering of microorganisms for advancing lignocellulose-derived biofuels

Combating climate change and ensuring energy supply to a rapidly growing global population has highlighted the need to replace petroleum fuels with clean, and sustainable renewable fuels. Biofuels offer a solution to safeguard energy security with reduced ecological footprint and process economics. Over the past years, lignocellulosic biomass has become the most preferred raw material for the production of biofuels, such as fuel, alcohol, biodiesel, and biohydrogen. However, the cost-effective conversion of lignocellulose into biofuels remains an unsolved challenge at the industrial scale. Recently, intensive efforts have been made in lignocellulose feedstock and microbial engineering to address this problem. By improving the biological pathways leading to the polysaccharide, lignin, and lipid biosynthesis, limited success has been achieved, and still needs to improve sustainable biofuel production. Impressive success is being achieved by the retouring metabolic pathways of different microbial hosts. Several robust phenotypes, mostly from bacteria and yeast domains, have been successfully constructed with improved substrate spectrum, product yield and sturdiness against hydrolysate toxins. Cyanobacteria is also being explored for metabolic advancement in recent years, however, it also remained underdeveloped to generate commercialized biofuels. The bacterium Escherichia coli and yeast Saccharomyces cerevisiae strains are also being engineered to have cell surfaces displaying hydrolytic enzymes, which holds much promise for near-term scale-up and biorefinery use. Looking forward, future advances to achieve economically feasible production of lignocellulosic-based biofuels with special focus on designing more efficient metabolic pathways coupled with screening, and engineering of novel enzymes.

Unveiling lignocellulolytic trait of a goat omasum inhabitant Klebsiella variicola strain HSTU-AAM51 in light of biochemical and genome analyses

Klebsiella variicola is generally known as endophyte as well as lignocellulose-degrading strain. However, their roles in goat omasum along with lignocellulolytic genetic repertoire are not yet explored. In this study, five different pectin-degrading bacteria were isolated from a healthy goat omasum. Among them, a new Klebsiella variicola strain HSTU-AAM51 was identified to degrade lignocellulose. The genome of the HSTU-AAM51 strain comprised 5,564,045 bp with a GC content of 57.2% and 5312 coding sequences. The comparison of housekeeping genes (16S rRNA, TonB, gyrase B, RecA) and whole-genome sequence (ANI, pangenome, synteny, DNA-DNA hybridization) revealed that the strain HSTU-AAM51 was clustered with Klebsiella variicola strains, but the HSTU-AAM51 strain was markedly deviated. It consisted of seventeen cellulases (GH1, GH3, GH4, GH5, GH13), fourteen beta-glucosidase (2GH3, 7GH4, 4GH1), two glucosidase, and one pullulanase genes. The strain secreted cellulase, pectinase, and xylanase, lignin peroxidase approximately 76-78 U/mL and 57-60 U/mL, respectively, when it was cultured on banana pseudostem for 96 h. The catalytically important residues of extracellular cellulase, xylanase, mannanase, pectinase, chitinase, and tannase proteins (validated 3D model) were bound to their specific ligands. Besides, genes involved in the benzoate and phenylacetate catabolic pathways as well as laccase and DiP-type peroxidase were annotated, which indicated the strain lignin-degrading potentiality. This study revealed a new K. variicola bacterium from goat omasum which harbored lignin and cellulolytic enzymes that could be utilized for the production of bioethanol from lignocelluloses.

Microbial biotechnological approaches: renewable bioprocessing for the future energy systems

The accelerating energy demands of the increasing global population and industrialization has become a matter of great concern all over the globe. In the present scenario, the world is witnessing a considerably huge energy crisis owing to the limited availability of conventional energy resources and rapid depletion of non-renewable fossil fuels. Therefore, there is a dire need to explore the alternative renewable fuels that can fulfil the energy requirements of the growing population and overcome the intimidating environmental issues like greenhouse gas emissions, global warming, air pollution etc. The use of microorganisms such as bacteria has captured significant interest in the recent era for the conversion of the chemical energy reserved in organic compounds into electrical energy. The versatility of the microorganisms to generate renewable energy fuels from multifarious biological and biomass substrates can abate these ominous concerns to a great extent. For instance, most of the microorganisms can easily transform the carbohydrates into alcohol. Establishing the microbial fuel technology as an alternative source for the generation of renewable energy sources can be a state of art technology owing to its reliability, high efficiency, cleanliness and production of minimally toxic or inclusively non-toxic byproducts. This review paper aims to highlight the key points and techniques used for the employment of bacteria to generate, biofuels and bioenergy, and their foremost benefits.

Optimization of growth conditions for enhancing the production of microbial laccase and its application in treating antibiotic contamination in wastewater

In this work, seven indigenous macrofungal isolates were selected to screen for their laccase production capability. Among them, isolates viz., Pleurotus eryngii, Pleurotus florida, Pleurotus sajor caju and Gandoderma lucidum were found to exhibit high laccase activity in the preliminary studies and were thus selected for the optimization studies with an aim to enhance laccase production. The pH optimization studies were carried out between pH range of 4-6. The laccase activity and biomass were found to be optimum at pH 4, 4.5, 4.5 and 5 for P. eryngii, P. florida, P. sajor caju and G. lucidum, respectively. Optimization studies with chemical inducers namely, tannic acid, 2,6 dimethoxyphenol and copper sulphate at three different concentration levels were conducted and tannic acid at 2 mM concentration was found to increase the laccase activity to about 45% followed by 2,6 dimethoxyphenol (2 mM) with an increase of about 43% and copper sulphate (0.1 mM) showing 21% increase in the yield. Biodegradation studies utilizing laccase isolated from P. eryngii, P. florida and P. sajor caju was carried out for a commonly detected fluoroquinolone antibiotic, levofloxacin, in water and pharmaceutical wastewater. The results indicated that the degradation efficiency of levofloxacin using laccase isolated from P. eryngii (88.9%) was comparable to commercial laccase (89%). When the cost economics of using crude laccase was evaluated against commercial laccase it was evident that the total cost of the treatment could be reduced by 71.7% if commercial grade laccase was replaced by crude enzyme extracted from indigenous macrofungi such Pleurotus eryngii, Pleurotus florida, and Pleurotus sajor caju indicating a promising and cost-effective alternative for wastewater treatment.

Microbial single-cell omics: the crux of the matter

Abstract

Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies.

Key points

• Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways.

• Disadvantages of metagenome-assembled genomes are overcome by single-cell omics.

• Functional analysis of single cells explores the heterogeneity of gene expression.

• Technical challenges still limit this field, thus prompting new method developments.

Accelerating the sustainable development goals through microbiology: some efforts and opportunities

Modernization has thrown humanity and other forms of life on our planet into a ditch of problems. Poverty, climate change, injustice and environmental degradation are a few of the shared global problems. The United Nations Sustainable Development Goals (SDGs) are the blueprint to achieve a better and more sustainable future for all. The SDGs are well structured to address the global challenges we face including poverty, inequalities, hunger, climate change, environmental degradation, peace and justice. Five years into the implementation, the SDGs have been driven mainly by international donors and 'professional' international development organizations. The world is left with 10 years to achieve these ambitious goals and targets. Various reviews show that little has been achieved overall, and the SDGs will not be a reality if a new strategy is not in place to bring inclusion. Microbiology, the scientific discipline of microbes, their effects and practical uses has insightful influence on our day-to-day living. We present how microbiology and microbiologists could increase the scorecard and accelerate these global goals. Microbiology has a direct link to achieving SDGs addressing food security, health and wellbeing, clean energy, environmental degradation and climate change. A non-classical growing relationship exists between microbiology and other SDGs such as peace, justice, gender equality, decent work and economic growth. The pledge of 'Leave No One Behind' will fast track progress and microbiology is in a better position to make this work.

Synthetic microbial consortia for small molecule production

Microbial consortia were designed for the production of small molecules with 'labor' being divided between two or more microorganisms. Examples of linear designs are substrate conversion preceding target molecule production or subdivision of two consecutive steps of target molecule production. Here, we review synthetic biology design approaches for microbial consortia based on ecological principles and microbial interactions that is, mutualism, and commensalism. Besides highlighting the technical challenges regarding industrial application of synthetic microbial consortia, we forecast the extension of the concept from binary linear to ternary linear and more complex microbial consortia in biotechnological applications. Microbial consortia are here reviewed and proposed as a rational solution toward feedstock accessibility as it has been shown for production of l-lysine, l-pipecolic acid and cadaverine from starch or production of fumarate from microcrystalline cellulose and alkaline pre-treated corn, or alternatively to establish new multi-step pathway for the production of rosmarinic acid from xylose and glucose.

Molecular parts and genetic circuits for metabolic engineering of microorganisms

Microbial conversion of biomass into value-added biochemicals is a highly sustainable process compared to petroleum-based production. In this regard, microorganisms have been engineered via simple overexpression or deletion of metabolic genes to facilitate the production. However, the producer microorganisms require complex regulatory circuits to maximize productivity and performance. To address this issue, diverse genetic circuits have been developed that allow cells to minimize their metabolic burden, overcome metabolic imbalances and respond to a dynamically changing environment. In this review, we briefly explain the basic strategy for constructing genetic circuits by assembling molecular parts such as input, operation and output modules. Next, we describe recent applications of the circuits in the metabolic engineering of microorganisms to improve biochemical production. Beyond those achievements, genetic circuits will facilitate more innovative approaches to future strain development through mining and engineering new genetic elements and improving the complexity of genetic circuit design.