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Kassem A, Abbas L, Coutinho O, Opara S, Najaf H, Kasperek D, Pokhrel K, Li X, Tiquia-Arashiro S. Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives. Front Microbiol 2023; 14:1304081. [PMID: 38075889 PMCID: PMC10703385 DOI: 10.3389/fmicb.2023.1304081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/03/2023] [Indexed: 01/02/2024] Open
Abstract
Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.
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Affiliation(s)
- Amin Kassem
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Lana Abbas
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Oliver Coutinho
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Somie Opara
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Hawraa Najaf
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Diana Kasperek
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Keshav Pokhrel
- Department of Mathematics and Statistics, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Xiaohua Li
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Sonia Tiquia-Arashiro
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
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Sobieraj K, Stegenta-Dąbrowska S, Luo G, Koziel JA, Białowiec A. Biological treatment of biowaste as an innovative source of CO-The role of composting process. Front Bioeng Biotechnol 2023; 11:1126737. [PMID: 36845185 PMCID: PMC9947533 DOI: 10.3389/fbioe.2023.1126737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Carbon monoxide (CO) is an essential "building block" for producing everyday chemicals on industrial scale. Carbon monoxide can also be generated though a lesser-known and sometimes forgotten biorenewable pathways that could be explored to advance biobased production from large and more sustainable sources such as bio-waste treatment. Organic matter decomposition can generate carbon monoxide both under aerobic and anaerobic conditions. While anaerobic carbon monoxide generation is relatively well understood, the aerobic is not. Yet many industrial-scale bioprocesses involve both conditions. This review summarizes the necessary basic biochemistry knowledge needed for realization of initial steps towards biobased carbon monoxide production. We analyzed for the first time, the complex information about carbon monoxide production during aerobic, anaerobic bio-waste treatment and storage, carbon monoxide-metabolizing microorganisms, pathways, and enzymes with bibliometric analysis of trends. The future directions recognizing limitations of combined composting and carbon monoxide production have been discussed in greater detail.
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Affiliation(s)
- Karolina Sobieraj
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sylwia Stegenta-Dąbrowska
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China,Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Jacek A. Koziel
- USDA-ARS Conservation and Production Research Laboratory, Bushland, TX, United States,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Andrzej Białowiec
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States,*Correspondence: Andrzej Białowiec,
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Pushparaj K, Meyyazhagan A, Bhotla HK, Arumugam VA, Pappuswamy M, Vadivalagan C, Hakeem KR, Balasubramanian B, Liu W, Mousavi Khaneghah A. The crux of bioactive metabolites in endophytic and thermophilic fungi and their proximal prospects in biotechnological and industrial domains. Toxicon 2023; 223:107007. [PMID: 36563862 DOI: 10.1016/j.toxicon.2022.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Fungi are ubiquitous in distribution and are found in grasses to hot springs. Their mode of nutrition provides sustenance for living and propagation. Ironically, varied fungal species have developed customized strategies for protection and survival by producing diverse secondary metabolites. The review aimed to project the contrasting potential features of the endophytic and thermophilic fungi groups. The metabolites and the enzymes of endophytic and thermophilic fungi served as the backbone to thrive and adapt within-host and in extreme conditions like higher pH, heat, and salinity, respectively. Identification, knowledge of their biochemistry and pathway, exploration, production, and utilization of these bioactive molecules in various commercial, industrial, and pharmaceutical domains were briefly discussed. The uniqueness of endophytes includes stress management and improved biomass production of the host, green fuel production, omnipresence, selected triple-symbiosis with the virus, synthesis of polyketides, and other active metabolites are widely used in biomedical applications and agriculture management. This review attempted to limelight the specific applications of thermophilic fungal metabolites and the roles of thermo-stable enzymes in bioprospecting. Moreover, probing the metabolites of thermophiles rendered novel antibiotic compounds, which were proven effective against multi-drug resistant bacteria and harboured the potential to curtail infectious diseases.
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Affiliation(s)
- Karthika Pushparaj
- Department of Zoology, School of Biosciences, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641 043, Tamil Nadu, India
| | - Arun Meyyazhagan
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Haripriya Kuchi Bhotla
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Vijaya Anand Arumugam
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
| | - Manikantan Pappuswamy
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | | | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | | | - Wenchao Liu
- Department of Animal Science, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China.
| | - Amin Mousavi Khaneghah
- Department of Fruit and Vegetable Product Technology, Prof. WacławDąbrowski Institute of Agricultural and Food Biotechnology - State Research Institute, 36 Rakowiecka St., 02-532, Warsaw, Poland; Department of Technology of Chemistry, Azerbaijan State Oil and Industry University, Baku, Azerbaijan.
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Adebayo EA, Azeez MA, Alao MB, Oke AM, Aina DA. Fungi as veritable tool in current advances in nanobiotechnology. Heliyon 2021; 7:e08480. [PMID: 34901509 PMCID: PMC8640478 DOI: 10.1016/j.heliyon.2021.e08480] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
Fungi have great prospects for synthesis, applications and developing new products in nanotechnology. In recent times, fungi use in nanotechnology is gaining more attention because of the ecological friendly state of their metabolite-mediated nanoparticles, their safety, amenability and applications in diverse fields. The diversity of the metabolites such as enzymes, polysaccharide, polypeptide, protein and other macro-molecules has made fungi a veritable tool for nanoparticles synthesis. Mechanism of fungal nano-biosynthesis from the molecular perspective has been extensively studied through various investigations on its green synthesized metal nanoparticles. Fungal nanobiotechnology has been applied in agricultural, medical and industrial sectors for goods and services improvement and delivery to mankind. Agriculturally, it has found applications in plant disease management and production of environmentally friendly, non-toxic insecticides, fungicides to enhance agricultural production in general. Medically, diagnosis and treatment of diseases, especially of microbial origin have been improved with fungal nanoparticles through more efficient drug delivery systems with great benefits to pharmaceutical industries. This review therefore explored fungal nanobiotechnology; mechanism of synthesis, characterization and potential applications in various fields of human endeavours for goods and services delivery.
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Affiliation(s)
- Elijah A. Adebayo
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
- LAUTECH Nanotechnology Research Group, Nigeria
| | - Musibau A. Azeez
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
- LAUTECH Nanotechnology Research Group, Nigeria
| | - Micheal B. Alao
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
| | - Abel M. Oke
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
| | - Daniel A. Aina
- Department of Microbiology, Babcock University, Ilishan-Remo, Ogun State, Nigeria
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How to outwit nature: Omics insight into butanol tolerance. Biotechnol Adv 2020; 46:107658. [PMID: 33220435 DOI: 10.1016/j.biotechadv.2020.107658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
The energy crisis, depletion of oil reserves, and global climate changes are pressing problems of developed societies. One possibility to counteract that is microbial production of butanol, a promising new fuel and alternative to many petrochemical reagents. However, the high butanol toxicity to all known microbial species is the main obstacle to its industrial implementation. The present state of the art review aims to expound the recent advances in modern omics approaches to resolving this insurmountable to date problem of low butanol tolerance. Genomics, transcriptomics, and proteomics show that butanol tolerance is a complex phenomenon affecting multiple genes and their expression. Efflux pumps, stress and multidrug response, membrane transport, and redox-related genes are indicated as being most important during butanol challenge, in addition to fine-tuning of global regulators of transcription (Spo0A, GntR), which may further improve tolerance. Lipidomics shows that the alterations in membrane composition (saturated lipids and plasmalogen increase) are very much species-specific and butanol-related. Glycomics discloses the pleiotropic effect of CcpA, the role of alternative sugar transport, and the production of exopolysaccharides as alternative routes to overcoming butanol stress. Unfortunately, the strain that simultaneously syntheses and tolerates butanol in concentrations that allow its commercialization has not yet been discovered or produced. Omics insight will allow the purposeful increase of butanol tolerance in natural and engineered producers and the effective heterologous expression of synthetic butanol pathways in strains hereditary butanol-resistant up to 3.2 - 4.9% (w/v). Future breakthrough can be achieved by a detailed study of the membrane proteome, of which 21% are proteins with unknown functions.
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Stegenta-Dąbrowska S, Drabczyński G, Sobieraj K, Koziel JA, Białowiec A. The Biotic and Abiotic Carbon Monoxide Formation During Aerobic Co-digestion of Dairy Cattle Manure With Green Waste and Sawdust. Front Bioeng Biotechnol 2019; 7:283. [PMID: 31737615 PMCID: PMC6828980 DOI: 10.3389/fbioe.2019.00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/04/2019] [Indexed: 11/24/2022] Open
Abstract
Carbon monoxide (CO), an air pollutant and a toxic gas to humans, can be generated during aerobic digestion of organic waste. CO is produced due to thermochemical processes, and also produced or consumed by cohorts of methanogenic, acetogenic, or sulfate-reducing bacteria. The exact mechanisms of biotic and abiotic formation of CO in aerobic digestion (particularly the effects of process temperature) are still not known. This study aimed to determine the temporal variation in CO concentrations during the aerobic digestion as a function of process temperature and activity of microorganisms. All experiments were conducted in controlled temperature reactors using homogeneous materials. The lab-scale tests with sterilized and non-sterilized mix of green waste, dairy cattle manure, sawdust (1:1:1 mass ratio) were carried out for 1 week at 10, 25, 30, 37, 40, 50, 60, 70°C to elucidate the biotic vs. abiotic effect. Gas concentrations of CO, O2, and CO2 inside the reactor were measured every 12 h. The CO concentrations observed for up to 30°C did not exceed 100 ppm v/v. For 50 and 60°C, significantly (p < 0.05) higher CO concentrations, reaching almost 600 ppm v/v, were observed. The regression analyses showed in both cases (sterile and non-sterile) a statistically significant effect (p < 0.05) of temperature on CO concentration, confirming that the increase in temperature causes an increase in CO concentration. The remaining factors (time, O2, and CO2 content) were not statistically significant (p > 0.05). A new polynomial model describing the effect of temperature, O2, and CO2 concentration on CO production during aerobic digestion of organic waste was formulated. It has been found that the proposed model for sterile variant had a better fit (R2 = 0.86) compared with non-sterile (R2 = 0.71). The model predicts CO emissions and could be considered for composting process optimization. The developed model could be further developed and useful for ambient air quality and occupational exposure to CO.
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Affiliation(s)
- Sylwia Stegenta-Dąbrowska
- Faculty of Life Sciences and Technology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Grzegorz Drabczyński
- Faculty of Life Sciences and Technology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Sobieraj
- Faculty of Life Sciences and Technology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek A Koziel
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Andrzej Białowiec
- Faculty of Life Sciences and Technology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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Petrova P, Tsvetanova F, Petrov K. Low cell surface hydrophobicity is one of the key factors for high butanol tolerance of Lactic acid bacteria. Eng Life Sci 2018; 19:133-142. [PMID: 32624995 DOI: 10.1002/elsc.201800141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022] Open
Abstract
Highly butanol-tolerant strains have always been attractive because of their potential as microbial hosts for butanol production. However, due to the amphiphilic nature of 1-butanol as a solvent, the relationship between the cell surface hydrophobicity and butanol resistance remained ambiguous to date. In this work, the quantitatively estimated cell surface hydrophobicity of 74 Lactic acid bacteria strains were juxtaposed to their tolerance to various butanol concentrations. The obtained results revealed that the strains' hydrophobicity was inversely proportional to their butanol tolerance. All highly butanol-resistant strains were hydrophilic (cell surface hydrophobicity<1%), whereas the more hydrophobic the strains were, the more sensitive to butanol they were. Furthermore, cultivation at increasing butanol concentrations showed a clear tendency to decrease the level of hydrophobicity in all tested organisms, thus suggesting possible adaptation mechanisms. Purposeful reduction of cell surface hydrophobicity (by removal of S-layer proteins from the cell envelope) also led to an increase of butanol resistance. Since the results covered 23 different Lactic acid bacteria species of seven genera, it could be concluded that regardless of the species, the lower degree of cells' hydrophobicity clearly correlates with the higher level of butanol tolerance.
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Affiliation(s)
- Penka Petrova
- Institute of Microbiology Bulgarian Academy of Sciences Sofia Bulgaria
| | - Flora Tsvetanova
- Institute of Chemical Engineering Bulgarian Academy of Sciences Sofia Bulgaria
| | - Kaloyan Petrov
- Institute of Chemical Engineering Bulgarian Academy of Sciences Sofia Bulgaria
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Ramió-Pujol S, Ganigué R, Bañeras L, Colprim J. Effect of ethanol and butanol on autotrophic growth of model homoacetogens. FEMS Microbiol Lett 2018; 365:4956523. [DOI: 10.1093/femsle/fny084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/28/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Sara Ramió-Pujol
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Ma Aurèlia Capmany, 40, E-17003 Girona, Catalonia, Spain
- LEQUIA, Institute of the Environment, University of Girona, Ma Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Ramon Ganigué
- Center for Microbiology Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Lluís Bañeras
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Ma Aurèlia Capmany, 40, E-17003 Girona, Catalonia, Spain
| | - Jesús Colprim
- LEQUIA, Institute of the Environment, University of Girona, Ma Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
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