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Dowaidar M. Synthetic biology of metabolic cycles for Enhanced CO 2 capture and Sequestration. Bioorg Chem 2024; 153:107774. [PMID: 39260160 DOI: 10.1016/j.bioorg.2024.107774] [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: 06/03/2024] [Revised: 08/01/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024]
Abstract
In most organisms, the tri-carboxylic acid cycle (TCA cycle) is an essential metabolic system that is involved in both energy generation and carbon metabolism. Its uni-directionality, however, restricts its use in synthetic biology and carbon fixation. Here, it is describing the use of the modified TCA cycle, called the Tri-carboxylic acid Hooked to Ethylene by Enzyme Reactions and Amino acid Synthesis, the reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle, in Escherichia coli for the purposes of carbon fixation and amino acid synthesis. Three modules make up the THETA cycle: (1) pyruvate to succinate transformation, (2) succinate to crotonyl-CoA change, and (3) crotonyl-CoA to acetyl-CoA and pyruvate change. It is presenting each module's viability in vivo and showing how it integrates into the E. coli metabolic network to support growth on minimal medium without the need for outside supplementation. Enzyme optimization, route redesign, and heterologous expression were used to get over metabolic roadblocks and produce functional modules. Furthermore, the THETA cycle may be improved by including components of the Carbon-Efficient Tri-Carboxylic Acid Cycle (CETCH cycle) to improve carbon fixation. THETA cycle's promise as a platform for applications in synthetic biology and carbon fixation.
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Affiliation(s)
- Moataz Dowaidar
- Bioengineering Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia; Biosystems and Machines Research Center, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia.
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2
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024; 17:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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Tyagi S, Singh RK, Kumar A. Lipophilic bioactive compounds from thermophilic cyanobacterium Leptolyngbya sp. HNBGU-004: Implications for countering VRSA resistance. Heliyon 2024; 10:e29754. [PMID: 38681559 PMCID: PMC11046194 DOI: 10.1016/j.heliyon.2024.e29754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
Extremophiles thrive in extreme conditions, showcasing rich and unexplored diversity. This resilience hints at the existence of novel biochemical pathways and unique bioactive compounds. In contrast, the issue of drug resistance and excessive misuse of antibiotics in various settings, such as healthcare, agriculture, and veterinary medicine, has contributed to the emergence and spread of drug-resistant microorganisms. In the present research, Leptolyngbya sp. HNBGU-004, was obtained from an extreme location, a hot water spring in the Garhwal Himalayan region of India. The lipophilic fraction derived from Leptolyngbya sp. HNBGU-004 exhibited significant inhibitory effects against vancomycin-resistant Staphylococcus aureus (VRSA), displaying a bactericidal concentration of 0.5 mg mL-1. Furthermore, gas chromatography-mass spectrometry (GC-MS) analysis of the lipophilic extract unveiled the major constituents. Leptolyngbya sp. HNBGU-004 holds significant promise as a primary source of potent anti-vancomycin-resistant S. aureus components. These findings emphasize the importance of Leptolyngbya sp. HNBGU-004 as a foundational source for use as both a synergistic and alternative agent against VRSA.
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Affiliation(s)
- Sachin Tyagi
- Department of Microbiology, School of Life Sciences and Technology, IIMT University, Meerut, UP, 250001, India
| | - Rahul Kunwar Singh
- Department of Microbiology, H.N.B Garhwal University, Srinagar Garhwal, Uttarakhand, 246174, India
| | - Ashok Kumar
- Department of Biotechnology, School of Life Sciences and Technology, IIMT University, Meerut, UP, 250001, India
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Wani AK, Ahmad S, Américo-Pinheiro JHP, Tizro N, Singh R. Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study. IRANIAN JOURNAL OF MICROBIOLOGY 2023; 15:723-733. [PMID: 38156301 PMCID: PMC10751607 DOI: 10.18502/ijm.v15i6.14132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Background and Objectives Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and Methods In the present study, physiochemical parameters including temperature (65-75°C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis. Results Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs). Conclusion The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.
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Affiliation(s)
- Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Suhail Ahmad
- Department of Remote Sensing and GIS, University of Jammu, Jammu, India
| | - Juliana Heloisa Pinê Américo-Pinheiro
- Department of Forest Science, Soils and Environment, School of Agronomic Sciences, São Paulo State University (UNESP), Botucatu, Brazil
- Department of Environmental Sciences, Graduate Program in Environmental Sciences, Brazil University, São Paulo, Brazil
| | - Nazli Tizro
- Department of the Environment, College of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reena Singh
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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Holt WV, Comizzoli P. Conservation Biology and Reproduction in a Time of Developmental Plasticity. Biomolecules 2022; 12:1297. [PMID: 36139136 PMCID: PMC9496186 DOI: 10.3390/biom12091297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/24/2022] Open
Abstract
The objective of this review is to ask whether, and how, principles in conservation biology may need to be revisited in light of new knowledge about the power of epigenetics to alter developmental pathways. Importantly, conservation breeding programmes, used widely by zoological parks and aquariums, may appear in some cases to reduce fitness by decreasing animals' abilities to cope when confronted with the 'wild side' of their natural habitats. Would less comfortable captive conditions lead to the selection of individuals that, despite being adapted to life in a captive environment, be better able to thrive if relocated to a more natural environment? While threatened populations may benefit from advanced reproductive technologies, these may actually induce undesirable epigenetic changes. Thus, there may be inherent risks to the health and welfare of offspring (as is suspected in humans). Advanced breeding technologies, especially those that aim to regenerate the rarest species using stem cell reprogramming and artificial gametes, may also lead to unwanted epigenetic modifications. Current knowledge is still incomplete, and therefore ethical decisions about novel breeding methods remain controversial and difficult to resolve.
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Affiliation(s)
- William V. Holt
- Department of Oncology & Metabolism, The Medical School Beech Hill Road, Sheffield S10 2RX, UK
| | - Pierre Comizzoli
- Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC 20008, USA
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Sarli DA, Teixeira Gomes G, Reznikov S, Acosta FF, Fariña JI, Delgado OD, Sánchez LA. Cold-adapted strains as plant growth-promoting bacteria on soybean seeds and biocontrol agents against Macrophomina phaseolina. J Appl Microbiol 2022; 133:2835-2850. [PMID: 35921041 DOI: 10.1111/jam.15759] [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: 05/31/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 12/01/2022]
Abstract
AIM To characterise cold-adapted bacteria by testing their PGP features and antagonistic activity against Macrophomina phaseolina, both in vitro and coating soybean seeds (Glycine max (L.) Merr.). METHODS AND RESULTS Burkholderia gladioli MB39, Serratia proteamaculans 136 and Serratia proteamaculans 137 were evaluated. In vitro tests showed that S. proteamaculans 136 and 137 produce siderophore and indole-acetic acid (IAA), solubilise phosphate and fix nitrogen. Additionally, B. gladioli MB39 and S. proteamaculans 137 showed hydrolase activity and potent antifungal effects. The biocontrol efficacy over soybean seeds was evaluated using in vitro and green-house methods by immersing seeds into each bacterial suspension. As a result, S. proteamaculans 136 has improved the performance in all the seed-germination evaluated parameters. In addition, S. proteamaculans 137 and B. gladioli MB39 strongly inhibited M. phaseolina, reducing the infection index values to 10% and 0%, respectively. CONCLUSION Serratia proteamaculans 136, 137 and Burkholderia gladioli MB39 showed plant growth promotion features and inhibition of Macrophomina phaseolina infection by producing different antifungal compounds. SIGNIFICANCE AND IMPACT OF THE STUDY Our results reinforce the application of cold-adapted Serratia proteamaculans and Burkholderia gladioli bacterial strains as candidates for developing microbial formulation to promote plant growth and guarantee antifungal protection in soybean crops.
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Affiliation(s)
- Dinorah Anabella Sarli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET. Av. Belgrano y Pje. Caseros, (T4001MVB). San Miguel de Tucumán, Tucumán, Argentina
| | - Gisele Teixeira Gomes
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET. Av. Belgrano y Pje. Caseros, (T4001MVB). San Miguel de Tucumán, Tucumán, Argentina
| | - Sebastián Reznikov
- Estación Experimental Agroindustrial Obispo Colombres (EEAOC), Av. William, W. Cross 3150 (T4101XAC) Las Talitas, Tucumán, Argentina
| | - Federico Francisco Acosta
- Instituto de Ciencias Veterinarias del Litoral [ICIVET-LITORAL]. Centro Científico Tecnológico CONICET - Santa Fé, [CCT SANTA FE]
| | - Julia Inés Fariña
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET. Av. Belgrano y Pje. Caseros, (T4001MVB). San Miguel de Tucumán, Tucumán, Argentina
| | - Osvaldo Daniel Delgado
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET. Av. Belgrano y Pje. Caseros, (T4001MVB). San Miguel de Tucumán, Tucumán, Argentina.,Universidad Nacional de Catamarca (UNCa). Facultad de Ciencias Exactas y Naturales. Centro de Biología Molecular y Biotecnología (CEBIOTEC). Av. Belgrano 300, (K4751XAK) San Fernando del Valle de Catamarca, Catamarca, Argentina
| | - Leandro A Sánchez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET. Av. Belgrano y Pje. Caseros, (T4001MVB). San Miguel de Tucumán, Tucumán, Argentina
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Santos Correa S, Schultz J, Lauersen KJ, Soares Rosado A. Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways. J Adv Res 2022; 47:75-92. [PMID: 35918056 PMCID: PMC10173188 DOI: 10.1016/j.jare.2022.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms. AIM OF REVIEW In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field. KEY SCIENTIFIC CONCEPTS OF REVIEW Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.
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Affiliation(s)
- Sulamita Santos Correa
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Junia Schultz
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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10
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Mesbah NM. Industrial Biotechnology Based on Enzymes From Extreme Environments. Front Bioeng Biotechnol 2022; 10:870083. [PMID: 35480975 PMCID: PMC9036996 DOI: 10.3389/fbioe.2022.870083] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.
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Affiliation(s)
- Noha M Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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11
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Canhos DAL, Almeida EAB, Assad AL, Cunha Bustamante MMD, Canhos VP, Chapman AD, Giovanni RD, Imperatriz-Fonseca VL, Lohmann LG, Maia LC, Miller JT, Nelson G, Peterson AT, Pirani JR, Souza SD, Stehmann JR, Thiers B. speciesLink: rich data and novel tools for digital assessments of biodiversity. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract speciesLink is a large-scale biodiversity information portal that exists thanks to a broad collaborative network of people and institutions. CRIA’s involvement with the scientific community of Brazil and other countries is responsible for the significant results achieved, currently reaching more than 15 million primary biodiversity data records, 95% of which are associated with preserved specimens and about 25% with high-quality digital images. The network provides data on over 200,000 species, of which over 110,000 occur in Brazil. This article describes thematic networks within speciesLink, as well as some of the most useful tools developed. The importance and contributions of speciesLink are outlined, as are concerns about securing stable budgetary support for such biodiversity data e-infrastructures. Here we review the value of speciesLink as a major source of biodiversity information for research, education, informed decision-making, policy development, and bioeconomy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Gil Nelson
- Integrated Digitized Biocollections, USA
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Fodelianakis S, Washburne AD, Bourquin M, Pramateftaki P, Kohler TJ, Styllas M, Tolosano M, De Staercke V, Schön M, Busi SB, Brandani J, Wilmes P, Peter H, Battin TJ. Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome. ISME JOURNAL 2021; 16:666-675. [PMID: 34522009 PMCID: PMC8857233 DOI: 10.1038/s41396-021-01106-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 02/01/2023]
Abstract
Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.
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Affiliation(s)
- Stilianos Fodelianakis
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| | | | - Massimo Bourquin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tyler J Kohler
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Michail Styllas
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Matteo Tolosano
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vincent De Staercke
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Martina Schön
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Susheel Bhanu Busi
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jade Brandani
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paul Wilmes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hannes Peter
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tom J Battin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
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13
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Šovljanski O, Pezo L, Stanojev J, Bajac B, Kovač S, Tóth E, Ristić I, Tomić A, Ranitović A, Cvetković D, Markov S. Comprehensive Profiling of Microbiologically Induced CaCO 3 Precipitation by Ureolytic Bacillus Isolates from Alkaline Soils. Microorganisms 2021; 9:1691. [PMID: 34442771 PMCID: PMC8400936 DOI: 10.3390/microorganisms9081691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/26/2022] Open
Abstract
Microbiologically induced CaCO3 precipitation (MICP) is a well-known bio-based solution with application in environmental, geotechnical, and civil engineering. The significance of the MICP has increased explorations of process efficiency and specificity via natural bacterial isolates. In this study, comprehensive profiling of five soil ureolytic Bacillus strains was performed through a newly formed procedure that involved six steps from selection and identification, through kinetic study, to the characterization of the obtained precipitates, for the first time. To shorten the whole selection procedure of 43 bioagents with the MICP potential, Standard Score Analysis was performed and five selected bacteria were identified as Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis by the MALDI-TOF mass spectrometry. Despite following the targeted activity, kinetic studies were included important aspects of ureolysis and the MICP such as cell concentration, pH profiling, and reduction in calcium ion concentration. At the final step, characterization of the obtained precipitates was performed using FTIR, XRD, Raman, DTA/TGA, and SEM analysis. Although all tested strains showed significant potential in terms of precipitation of calcite or calcite and vaterite phase, the main differences in the MICP behavior can be observed at the bacterial strain level. B. licheniformis showed favorable behavior compared to the reference Sporosarcina pasteurii DSM 33.
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Affiliation(s)
- Olja Šovljanski
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia; (I.R.); (A.T.); (A.R.); (D.C.); (S.M.)
| | - Lato Pezo
- Institute of General and Physical Chemistry, Studenski Trg 12/V, 11000 Belgrade, Serbia;
| | - Jovana Stanojev
- BioSense Institute, University of Novi Sad, Dr Zorana Đinđića 1, 21000 Novi Sad, Serbia; (J.S.); (B.B.)
| | - Branimir Bajac
- BioSense Institute, University of Novi Sad, Dr Zorana Đinđića 1, 21000 Novi Sad, Serbia; (J.S.); (B.B.)
| | - Sabina Kovač
- Department of Crystallography and Mineralogy, Faculty of Mining and Geology, University of Belgrade, Đušina 7, 11000 Belgrade, Serbia;
| | - Elvira Tóth
- Department of Physics, Faculty of Science, University of Novi Sad, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia;
| | - Ivan Ristić
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia; (I.R.); (A.T.); (A.R.); (D.C.); (S.M.)
| | - Ana Tomić
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia; (I.R.); (A.T.); (A.R.); (D.C.); (S.M.)
| | - Aleksandra Ranitović
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia; (I.R.); (A.T.); (A.R.); (D.C.); (S.M.)
| | - Dragoljub Cvetković
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia; (I.R.); (A.T.); (A.R.); (D.C.); (S.M.)
| | - Siniša Markov
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar Cara Lazara 1, 21000 Novi Sad, Serbia; (I.R.); (A.T.); (A.R.); (D.C.); (S.M.)
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14
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Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods. Front Microbiol 2021; 12:630013. [PMID: 33643258 PMCID: PMC7902512 DOI: 10.3389/fmicb.2021.630013] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
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Affiliation(s)
- Maksim Sysoev
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan W. Grötzinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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15
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Isolation and Characterization of Cold-Tolerant Hyper-ACC-Degrading Bacteria from the Rhizosphere, Endosphere, and Phyllosphere of Antarctic Vascular Plants. Microorganisms 2020; 8:microorganisms8111788. [PMID: 33202619 PMCID: PMC7697395 DOI: 10.3390/microorganisms8111788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022] Open
Abstract
1-Aminociclopropane-1-carboxylate (ACC)-degrading bacteria having been widely studied for their use in alleviating abiotic stresses in plants. In the present study, we isolated and characterized ACC-degrading bacteria from the rhizosphere, phyllosphere, and endosphere of the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis. One hundred and eighty of the 578 isolates (31%) were able to grow on minimal medium containing ACC, with 101 isolates (23, 37, and 41 endosphere-, phyllosphere- and rhizosphere-associated isolates, respectively) identified as being genetically unique by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Subsequently, freeze/thaw treatments and ice-recrystallization-inhibition (IRI) activity assays were performed, the results of which revealed that 77 (13%) of cold-tolerant isolates exhibited putative ACC deaminase activity. Significant (p ≤ 0.05) differences in IRI activity were also observed between the studied plant niches. Surprisingly, all the cold-tolerant isolates showed ACC deaminase activity, independent of the plant niches, with 12 isolates showing the highest ACC deaminase activities of 13.21-39.56 mmol α KB mg protein-1 h-1. These isolates were categorized as 'cold-tolerant hyper-ACC-degrading bacteria', and identified as members of Pseudomonas, Serratia, and Staphylococcus genera. The results revealed the occurrence of cold-tolerant hyper-ACC-degrading bacteria in diverse plant niches of Antarctic vascular plants, that could be investigated as novel microbial inoculants to alleviate abiotic stresses in plants.
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16
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Hu W, Feng S, Tong Y, Zhang H, Yang H. Adaptive defensive mechanism of bioleaching microorganisms under extremely environmental acid stress: Advances and perspectives. Biotechnol Adv 2020; 42:107580. [DOI: 10.1016/j.biotechadv.2020.107580] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/26/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
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17
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Zhang Q, Campos M, Larama G, Acuña JJ, Valenzuela B, Solis F, Zamorano P, Araya R, Sadowsky MJ, Jorquera MA. Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile. Arch Microbiol 2020; 203:389-397. [PMID: 32816051 DOI: 10.1007/s00203-020-02020-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 10/23/2022]
Abstract
The El Tatio Geyser Field (ETGF), located in Northern Chile, is the main geyser field in the southern hemisphere. Despite this, details of its microbial ecology are still unknown. Here, we briefly report on the composition and predicted functions of the bacterial community in spouting pool sediments from the ETGF as revealed by high-throughput sequencing of 16S rRNA genes. Results of this analysis showed that while there were differences in richness and diversity between samples, bacterial communities were primarily dominated by the phyla Proteobacteria, followed Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by sulfur (respiration of sulfur compounds and sulfate) and nitrogen (nitrate reduction, respiration of nitrogen and nitrate) cycling. Taken together, our results suggest a high diversity in taxonomy and predictive functions of bacterial communities in sediments from spouting pools. This study provides fundamentally important information on the structure and function predictive functions of microbiota communities in spouting pools. Moreover, since the ETGF is intensively visited and impacted by tens of thousands of tourists every year, our results can be used to help guide the design of sustainable conservation strategies.
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Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St Paul, MN, 55108-6106, USA
| | - Marco Campos
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Giovanni Larama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Bernardita Valenzuela
- Laboratorio de Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Francisco Solis
- Laboratorio de Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Pedro Zamorano
- Laboratorio de Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile.,Departamento Biomédico, Universidad de Antofagasta, Antofagasta, Chile
| | - Rubén Araya
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Av. Angamos 601, Antofagasta, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St Paul, MN, 55108-6106, USA.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. .,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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18
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Gaete A, Mandakovic D, González M. Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics. Microorganisms 2020; 8:microorganisms8081213. [PMID: 32785053 PMCID: PMC7466141 DOI: 10.3390/microorganisms8081213] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/15/2022] Open
Abstract
The isolation of soil bacteria from extreme environments represents a major challenge, but also an opportunity to characterize the metabolic potential of soil bacteria that could promote the growth of plants inhabiting these harsh conditions. The aim of this study was to isolate and identify bacteria from two Chilean desert environments and characterize the beneficial traits for plants through a biochemical approach. By means of different culture strategies, we obtained 39 bacterial soil isolates from the Coppermine Peninsula (Antarctica) and 32 from Lejía Lake shore soil (Atacama Desert). The results obtained from the taxonomic classification and phylogenetic analysis based on 16S rDNA sequences indicated that the isolates belonged to four phyla (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes), and that the most represented genus at both sites was Pseudomonas. Regarding biochemical characterization, all strains displayed in vitro PGP capabilities, but these were in different proportions that grouped them according to their site of origin. This study contributes with microbial isolates from natural extreme environments with biotechnological potentials in improving plant growth under cold stress.
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Affiliation(s)
- Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile;
- Center for Genome Regulation, El Libano 5524, Santiago 7810000, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile. Santa Rosa 11315, 8820808 Santiago, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Camino La Pirámide 5750, 8320000 Santiago, Chile;
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LGIB). Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile. El Líbano 5524, 7810000 Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile;
- Center for Genome Regulation, El Libano 5524, Santiago 7810000, Chile
- Correspondence:
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19
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Dávila AM. Rethinking Omics Education in Brazil and South America: From Genomics to Multiomics and Critical Policy Studies. OMICS: A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:391-393. [PMID: 32412823 PMCID: PMC7368383 DOI: 10.1089/omi.2020.0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Alberto M.R. Dávila
- Computational and Systems Biology Laboratory, Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
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20
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Zhu D, Adebisi WA, Ahmad F, Sethupathy S, Danso B, Sun J. Recent Development of Extremophilic Bacteria and Their Application in Biorefinery. Front Bioeng Biotechnol 2020; 8:483. [PMID: 32596215 PMCID: PMC7303364 DOI: 10.3389/fbioe.2020.00483] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.
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Affiliation(s)
- Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Wasiu Adewale Adebisi
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Fiaz Ahmad
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Blessing Danso
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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21
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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