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Hou Z, Zhou X, Zhao Z, Dong W, Wang H, Liu H, Zeng Z, Xie J. Advanced aromatic organic compounds removal from refractory coking wastewater in a step-feed three-stage integrated A/O bio-filter: Spectrum characterization and biodegradation mechanism. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116140. [PMID: 36070652 DOI: 10.1016/j.jenvman.2022.116140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/20/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Extensive presence of aromatic organic compounds (AOCs) is a major course for the non-biodegradability of coking wastewater (COW). In-depth understanding of bio-degradation of AOCs is crucial for optimizing the design and operation of COW biological treatment systems in practical applications. Herein, the behavior and fate of AOCs were explored in a lab-scale step-feed three-stage integrated A/O biofilter (SFTIAOB) treating synthetic COW. Long-term operation demonstrated that COD, phenol, indole, quinoline and pyridine could be simultaneously removed. Phenol and indole were chiefly removed by anoxic zones, while quinoline and pyridine removal occurred in both anoxic and aerobic zones. Ultraviolet-visible spectrum observed that initial carboxylation and subsequent ring cracking and mineralization. Infrared spectroscopy also confirmed that key functional groups were cracked and produced during AOCs bio-degradation. Three-dimensional fluorescence spectrum indicated that significant transformation and elimination of tryptophan and humic acid with high molecular weight. Ring cleavage, distinct degradation and even complete mineralization of complex AOCs were further verified by gas chromatography-mass spectrometry. Moreover, functional degrading bacteria and aromatic ring-cleavage enzymes was successfully identified. Finally, AOCs biodegradation mechanisms by alternating anoxic and aerobic treatment was unraveled. This research provides thorough insights on AOCs biodegradation using a step-feed multi-stage alternating anoxic/oxic COW treatment process.
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Affiliation(s)
- Zilong Hou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Xin Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.
| | - Zilong Zhao
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Wenyi Dong
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China; Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen, 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Hongjie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China; Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen, 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Huaguang Liu
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Zhiwei Zeng
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Jin Xie
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
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102
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Wang W, Chang JS, Show KY, Lee DJ. Anaerobic recalcitrance in wastewater treatment: A review. BIORESOURCE TECHNOLOGY 2022; 363:127920. [PMID: 36087651 DOI: 10.1016/j.biortech.2022.127920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic treatment is applied as an alternative to traditional aerobic treatment for recalcitrant compound degradation. This review highlighted the recalcitrant compounds in wastewaters and their pathways under aerobic and anaerobic conditions. Forty-one recalcitrant compounds commonly found in wastewater along with associated anaerobic removal performance were summarized from current research. Anaerobic degradability of wastewater could not be appropriately evaluated by BOD/COD ratio, which should only be suitable for determining aerobic degradability. Recalcitrant wastewaters with a low BOD/COD ratio may be handled by anaerobic treatments after the adaption and provision of sufficient electron donors. Novel indicator characterizing the anaerobic recalcitrance of wastewater is called for, essential for emergent needs to resource recovery from high-strength recalcitrant wastewater for fulfilling appeals of circular bioeconomy of modern societies.
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Affiliation(s)
- Wei Wang
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan
| | - Kuan-Yeow Show
- Puritek Research Institute, Puritec Co., Ltd., Nanjing, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong; Department of Chemical Engineering & Materials Science, Yuan Ze University, Chung-Li 32003, Taiwan.
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103
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Roth HK, Nelson AR, McKenna AM, Fegel TS, Young RB, Rhoades CC, Wilkins MJ, Borch T. Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1661-1677. [PMID: 36004537 DOI: 10.1039/d2em00184e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.
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Affiliation(s)
- Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University, FL, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis & Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
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104
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Somee MR, Amoozegar MA, Dastgheib SMM, Shavandi M, Maman LG, Bertilsson S, Mehrshad M. Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea. BMC Genomics 2022; 23:690. [PMID: 36203131 PMCID: PMC9535955 DOI: 10.1186/s12864-022-08906-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08906-w.
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Affiliation(s)
- Maryam Rezaei Somee
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | | | - Mahmoud Shavandi
- Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Leila Ghanbari Maman
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden.
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105
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Tang H, Wang MJ, Gan XF, Li YQ. Funneling lignin-derived compounds into polyhydroxyalkanoate by Halomonas sp. Y3. BIORESOURCE TECHNOLOGY 2022; 362:127837. [PMID: 36031122 DOI: 10.1016/j.biortech.2022.127837] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Lignin-derived compounds (LDCs) biological funneling for polyhydroxyalkanoate (PHA) synthesis has been attractive but elusive. Herein, the Halomonas sp. Y3 is isolated and developed for PHA production from LDCs. Of the tested 13 LDCs, 4-hydroxybenzoic acid (4-HBA), protocatechuate (PA), catechol (CAT), and vanillic acid (VA) exhibit a hyper-degradation and production with 87.2 %, 85.8 %, 84.7 %, and 83.4 % TOC removal rate and 535.2 mg/L, 506.5 mg/L, 435.6 mg/L, and 440.8 mg/L PHA concentration, respectively. The Halomonas sp. Y3 genome is sequenced by identifying numerous genes responsible for LDCs funneling, stress response, and PHA biosynthesis. An open unsterilized fermentation with optimal conditions of pH 9.0 and NaCl 60 g/L is investigated, achieving a completely aseptic effect and significantly improved PHA production from LDCs. Overall, the results indicate that the Halomonas sp. Y3 is an ideal candidate for LDC bioconversion and exhibits a great potential to realize black liquor valorization.
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Affiliation(s)
- Hao Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Ming-Jun Wang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Xiao-Feng Gan
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Yuan-Qiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China; College of Life Sciences, Capital Normal University, Beijing 100048, China.
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106
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Junghare M, Frey J, Naji KM, Spiteller D, Vaaje-Kolstad G, Schink B. Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate. BMC Microbiol 2022; 22:227. [PMID: 36171563 PMCID: PMC9516798 DOI: 10.1186/s12866-022-02630-x] [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: 04/28/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA. Results Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6 kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg2+ and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between pH 7.0 to 7.5. The optimal temperature was between 25 °C and 37 °C. Denaturation temperature (Tm) of IPCL was found to be at about 63 °C. The apparent KM values for isophthalate, CoA, and ATP were 409 μM, 642 μM, and 3580 μM, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions. Conclusion We have successfully cloned the ipcl gene, expressed and characterized the corresponding IPCL enzyme, which plays a key role in isophthalate activation that initiates its activation and further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02630-x.
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Affiliation(s)
- Madan Junghare
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany. .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway.
| | - Jasmin Frey
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Khalid M Naji
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Dieter Spiteller
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway
| | - Bernhard Schink
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
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107
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Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
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Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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108
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He J, Zhang K, Wang L, Du Y, Yang Y, Yuan C. Highly efficient degradation of cypermethrin by a co-culture of Rhodococcus sp. JQ-L and Comamonas sp. A-3. Front Microbiol 2022; 13:1003820. [PMID: 36188009 PMCID: PMC9522905 DOI: 10.3389/fmicb.2022.1003820] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Cypermethrin is an important synthetic pyrethroid pesticide that widely used to control pests in agriculture. However, extensive use has caused its residue and the metabolite 3-phenoxybenzoic acid (3-PBA) to seriously pollute the environments and agricultural products. In this study, a highly efficient cypermethrin-degrading bacterial consortium was acclimated from long-term pyrethroid-contaminated soil. Two strains, designated JQ-L and A-3, were screened from the consortium, and identified as Rhodococcus sp. and Comamonas sp., respectively. Strain JQ-L transformed 100 mg/L of cypermethrin to 3-PBA within 60 h of incubation; however, 3-PBA could not be further degraded by the strain. Strain A-3 utilized 3-PBA as sole carbon for growth, and completely degraded 100 mg/L of 3-PBA within 15 h of incubation. Co-culture of JQ-L and A-3 completely degraded 100 mg/L of cypermethrin within 24 h of incubation. Furthermore, a complete catabolic pathway of cypermethrin and the metabolite 3-PBA by the co-culture was proposed. This study provided a promising strategy for efficient elimination of cypermethrin residue-contaminated environments and agricultural products.
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Affiliation(s)
- Jian He
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kaiyun Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lin Wang
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Yingchun Du
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Ying Yang
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Cansheng Yuan
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
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Rawat D, Sharma U, Poria P, Finlan A, Parker B, Sharma RS, Mishra V. Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system. ISME COMMUNICATIONS 2022; 2:83. [PMID: 36407791 PMCID: PMC9476460 DOI: 10.1038/s43705-022-00161-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 06/15/2022] [Accepted: 07/14/2022] [Indexed: 01/11/2023]
Abstract
Phototrophic communities of autotrophic microalgae and heterotrophic bacteria perform complex tasks of nutrient acquisition and tackling environmental stress but remain underexplored as a basis for the bioremediation of emerging pollutants. In industrial monoculture designs, poor iron uptake by microalgae limits their productivity and biotechnological efficacy. Iron supplementation is expensive and ineffective because iron remains insoluble in an aqueous medium and is biologically unavailable. However, microalgae develop complex interkingdom associations with siderophore-producing bacteria that help solubilize iron and increase its bioavailability. Using dye degradation as a model, we combined environmental isolations and synthetic ecology as a workflow to design a simplified microbial community based on iron and carbon exchange. We established a mutualism between the previously non-associated alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii. Siderophore-mediated increase in iron bioavailability alleviated Fe stress for algae and increased the reductive iron uptake mechanism and bioremediation potential. In exchange, C. sorokiniana produced galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose that extracellular iron reduction by ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. These results demonstrate that iron bioavailability, often overlooked in cultivation, governs microalgal growth, enzymatic processes, and bioremediation potential. Our results suggest that phototrophic communities with an active association for iron and carbon exchange have the potential to overcome challenges associated with micronutrient availability, while scaling up bioremediation designs.
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Affiliation(s)
- Deepak Rawat
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
- Department of Biochemical Engineering, Bernard Katz Building, University College London, Gower Street, London, WC1E 6BT UK
- Department of Environmental Studies, Janki Devi Memorial College, University of Delhi, Delhi, 110060 India
| | - Udita Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
| | - Pankaj Poria
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
| | - Arran Finlan
- Department of Biochemical Engineering, Bernard Katz Building, University College London, Gower Street, London, WC1E 6BT UK
| | - Brenda Parker
- Department of Biochemical Engineering, Bernard Katz Building, University College London, Gower Street, London, WC1E 6BT UK
| | - Radhey Shyam Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
- Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi, 110007 India
| | - Vandana Mishra
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007 India
- Centre for Interdisciplinary Studies on Mountain & Hill Environment, University of Delhi, Delhi, 110007 India
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Jiao M, He W, Ouyang Z, Shi Q, Wen Y. Progress in structural and functional study of the bacterial phenylacetic acid catabolic pathway, its role in pathogenicity and antibiotic resistance. Front Microbiol 2022; 13:964019. [PMID: 36160191 PMCID: PMC9493321 DOI: 10.3389/fmicb.2022.964019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Phenylacetic acid (PAA) is a central intermediate metabolite involved in bacterial degradation of aromatic components. The bacterial PAA pathway mainly contains 12 enzymes and a transcriptional regulator, which are involved in biofilm formation and antimicrobial activity. They are present in approximately 16% of the sequenced bacterial genome. In this review, we have summarized the PAA distribution in microbes, recent structural and functional study progress of the enzyme families of the bacterial PAA pathway, and their role in bacterial pathogenicity and antibiotic resistance. The enzymes of the bacterial PAA pathway have shown potential as an antimicrobial drug target for biotechnological applications in metabolic engineering.
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Affiliation(s)
- Min Jiao
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wenbo He
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Zhenlin Ouyang
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Qindong Shi
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Yurong Wen
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an, China
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111
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Ong CT, Ross EM, Boe-Hansen G, Turni C, Hayes BJ, Fordyce G, Tabor AE. Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes. Sci Rep 2022; 12:15075. [PMID: 36065055 PMCID: PMC9445037 DOI: 10.1038/s41598-022-19022-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies’ adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.
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Affiliation(s)
- Chian Teng Ong
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gry Boe-Hansen
- Faculty of Science, School of Veterinary Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Geoffry Fordyce
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ala E Tabor
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Faculty of Science, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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112
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Weidenweber S, Schühle K, Lippert M, Mock J, Seubert A, Demmer U, Ermler U, Heider J. Finis tolueni
: a new type of thiolase with an integrated Zn‐finger subunit catalyzes the final step of anaerobic toluene metabolism. FEBS J 2022; 289:5599-5616. [DOI: 10.1111/febs.16443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 03/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Sina Weidenweber
- Max‐Planck‐Institut für Biophysik Frankfurt am Main Germany
- Technische Hochschule Mittelhessen Gießen Germany
| | - Karola Schühle
- Laboratorium für Mikrobiologie Fachbereich Biologie and SYNMIKRO Center Philipps‐Universität Marburg Germany
| | - Marie‐Luise Lippert
- Laboratorium für Mikrobiologie Fachbereich Biologie and SYNMIKRO Center Philipps‐Universität Marburg Germany
| | - Johanna Mock
- Laboratorium für Mikrobiologie Fachbereich Biologie and SYNMIKRO Center Philipps‐Universität Marburg Germany
| | - Andreas Seubert
- Analytische Chemie Fachbereich Chemie Philipps‐Universität Marburg Germany
| | - Ulrike Demmer
- Max‐Planck‐Institut für Biophysik Frankfurt am Main Germany
| | - Ulrich Ermler
- Max‐Planck‐Institut für Biophysik Frankfurt am Main Germany
| | - Johann Heider
- Laboratorium für Mikrobiologie Fachbereich Biologie and SYNMIKRO Center Philipps‐Universität Marburg Germany
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113
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Ganesan M, Mani R, Sai S, Kasivelu G, Awasthi MK, Rajagopal R, Wan Azelee NI, Selvi PK, Chang SW, Ravindran B. Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes. CHEMOSPHERE 2022; 303:134956. [PMID: 35588873 DOI: 10.1016/j.chemosphere.2022.134956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.
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Affiliation(s)
- Mirunalini Ganesan
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Ravi Mani
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Sakthinarenderan Sai
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Govindaraju Kasivelu
- Centre for Ocean Research, Col. Dr. Jeppiaar Ocean Research Field Facility, ESTC Cell Marine Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 712100, PR China.
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Nur Izyan Wan Azelee
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, 81310, Johor, Malaysia
| | - P K Selvi
- Central Pollution Control Board, Nisarga Bhawan, Shivanagar, Bengaluru, India
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| | - Balasubramani Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea; Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai 602 105, Tamil Nadu, India.
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114
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Nelson AR, Narrowe AB, Rhoades CC, Fegel TS, Daly RA, Roth HK, Chu RK, Amundson KK, Young RB, Steindorff AS, Mondo SJ, Grigoriev IV, Salamov A, Borch T, Wilkins MJ. Wildfire-dependent changes in soil microbiome diversity and function. Nat Microbiol 2022; 7:1419-1430. [PMID: 36008619 PMCID: PMC9418001 DOI: 10.1038/s41564-022-01203-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, and the frequency and size of severe fires have increased owing to climate change. Fires affect ecosystem recovery and modify soil microbiomes and microbially mediated biogeochemical processes. To study wildfire-dependent changes in soil microbiomes, we characterized functional shifts in the soil microbiota (bacteria, fungi and viruses) across burn severity gradients (low, moderate and high severity) 1 yr post fire in coniferous forests in Colorado and Wyoming, USA. We found severity-dependent increases of Actinobacteria encoding genes for heat resistance, fast growth, and pyrogenic carbon utilization that might enhance post-fire survival. We report that increased burn severity led to the loss of ectomycorrhizal fungi and less tolerant microbial taxa. Viruses remained active in post-fire soils and probably influenced carbon cycling and biogeochemistry via turnover of biomass and ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link post-fire soil microbial taxonomy to functions and reveal the complexity of post-fire soil microbiome activity.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, PA, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kaela K Amundson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Andrei S Steindorff
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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115
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Vila-Costa M, Lundin D, Casamayor EO, Meijer SN, Fernández P, Dachs J. Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119592. [PMID: 35688389 DOI: 10.1016/j.envpol.2022.119592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/20/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Semivolatile organic pollutants have potential for long range atmospheric transport and can thus reach pristine remote lakes by atmospheric deposition. Polycyclic aromatic hydrocarbons (PAHs) are among the most abundant and toxic semivolatile pollutants affecting lakes, however, the main factors controlling their fate are still poorly known. Here we show two contrasting lines of evidence for the importance of microbial degradation on the environmental fate of PAHs in a high altitude deep lake. The first evidence is given by an assessment of the metagenomes from surface and deep waters from Lake Redon (Pyrenees Mountains), which shows the occurrence of the initial ring hydroxylating dioxygenases as well as other PAH degrading genes from the complete metabolic route of PAH degradation. The second line of evidence is by the application of an environmental fate model for PAHs to Lake Redon under two contrasting scenarios considering the inclusion or not of degradation. When degradation is included in the model, PAH concentrations in the sediment are predicted within a factor of two of those measured in Lake Redon. Finally, the extent of the degradation sink is quantified and compared to other cycling PAH fluxes in the lake.
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Affiliation(s)
- Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain.
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Sweden
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes, CEAB-CSIC, Blanes, Catalunya, Spain
| | - Sandra N Meijer
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pilar Fernández
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
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116
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Ling C, Peabody GL, Salvachúa D, Kim YM, Kneucker CM, Calvey CH, Monninger MA, Munoz NM, Poirier BC, Ramirez KJ, St John PC, Woodworth SP, Magnuson JK, Burnum-Johnson KE, Guss AM, Johnson CW, Beckham GT. Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering. Nat Commun 2022; 13:4925. [PMID: 35995792 PMCID: PMC9395534 DOI: 10.1038/s41467-022-32296-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Muconic acid is a bioprivileged molecule that can be converted into direct replacement chemicals for incumbent petrochemicals and performance-advantaged bioproducts. In this study, Pseudomonas putida KT2440 is engineered to convert glucose and xylose, the primary carbohydrates in lignocellulosic hydrolysates, to muconic acid using a model-guided strategy to maximize the theoretical yield. Using adaptive laboratory evolution (ALE) and metabolic engineering in a strain engineered to express the D-xylose isomerase pathway, we demonstrate that mutations in the heterologous D-xylose:H+ symporter (XylE), increased expression of a major facilitator superfamily transporter (PP_2569), and overexpression of aroB encoding the native 3-dehydroquinate synthase, enable efficient muconic acid production from glucose and xylose simultaneously. Using the rationally engineered strain, we produce 33.7 g L−1 muconate at 0.18 g L−1 h−1 and a 46% molar yield (92% of the maximum theoretical yield). This engineering strategy is promising for the production of other shikimate pathway-derived compounds from lignocellulosic sugars. Muconic acid is a platform chemical with wide industrial applicability. Here, the authors report efficient muconate production from glucose and xylose by engineered Pseudomonas putida strain using adaptive laboratory evolution, metabolic modeling, and rational strain engineering strategies.
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Affiliation(s)
- Chen Ling
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - George L Peabody
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Young-Mo Kim
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Colin M Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher H Calvey
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michela A Monninger
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Nathalie Munoz Munoz
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Brenton C Poirier
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Peter C St John
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean P Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jon K Magnuson
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam M Guss
- Agile BioFoundry, Emeryville, CA, 94608, USA. .,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Agile BioFoundry, Emeryville, CA, 94608, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Agile BioFoundry, Emeryville, CA, 94608, USA.
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117
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Xu T, Zong QJ, Liu H, Wang L, Liu ZH, Li BZ, Yuan YJ. Identifying ligninolytic bacteria for lignin valorization to bioplastics. BIORESOURCE TECHNOLOGY 2022; 358:127383. [PMID: 35644455 DOI: 10.1016/j.biortech.2022.127383] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Biological valorization of lignin to bioplastics is a promising route to improve biorefinery efficiency and address environmental challenges. A two-stage screening procedure had been designed to successfully identify four ligninolytic bacteria from soil samples. The isolated bacteria displayed substrate preference of guaiacyl- and hydroxyphenyl-based aromatics, but they effectively synthesized polyhydroxyalkanoates (PHAs). B. cepacia B1-2 and P. putida KT3-1 accumulated 27.3% and 20.9% PHA in cells and achieved a titer of 280.9 and 204.1 mg/L, respectively, from p-hydroxybenzoic acid. The isolated bacteria exhibited good ligninolytic performance indicated by the degradation of β-O-4 linkage and small molecules. B. cepacia B1-2 grew well on actual lignin substrate and yielded a PHA titer of 87.2 mg/L. With the design of fed-batch mode, B. cepacia B1-2 produced the highest PHA titer of 1420 mg/L from lignin-derived aromatics. Overall, isolated ligninolytic bacteria show good PHA accumulation capacity, which are the promising host strains for lignin valorization.
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Affiliation(s)
- Tao Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Qiu-Jin Zong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - He Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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118
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Tang G, Zheng X, Hu S, Li B, Chen S, Liu T, Zhang B, Liu C. Microbial metabolism changes molecular compositions of riverine dissolved organic matter as regulated by temperature. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119416. [PMID: 35526649 DOI: 10.1016/j.envpol.2022.119416] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/15/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the control of dissolved organic matter (DOM) molecular compositions by microbial community shifts under temperature regulation (range from 5 to 35 °C), using riverine DOM and in situ microorganisms as examples. The functioning of different microbial metabolisms, including the utilization and generation processes, was comprehensively analyzed. Though the overall quantity of DOM was less temperature-affected, more molecules were identified at moderate temperatures (e.g., 15 and 25 °C) and their accumulated mass peak intensities increased with the temperature. The results were ascribed to 1) the microbial production of macromolecular (m/z > 600) CHO, CHON, and CHONS species was stimulated at higher temperatures; 2) the microorganisms consumed more DOM molecules at both higher and lower temperatures; and 3) the simultaneously decreased utilization and increased generation of recalcitrant CHO and CHON molecules with m/z < 600 at higher temperatures. The strong correlations among the temperature, community structures, and DOM chemodiversity suggested that temperature promoted the community evenness to increase the DOM generation. In addition, the higher temperature decreased the abundance of microorganisms that utilized more recalcitrant molecules and produced fewer new molecules (e.g., Proteobacteria, Acinetobacter, and Erythrobacter) while increased others that functioned the opposite (e.g., Verrucomicrobia, Bacteroidetes, and Flavobacterium) to increase the DOM production. The constructed temperature-community-DOM chemistry relationship deepened the molecular-level understanding of DOM variations and provided implications for the warming future.
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Affiliation(s)
- Gang Tang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, China.
| | - Xing Zheng
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, China
| | - Shiwen Hu
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Binrui Li
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Civil and Environmental Engineering Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Shuling Chen
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Tong Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, China
| | - Bowei Zhang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chongxuan Liu
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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119
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Chen K, Xu X, Yang M, Liu T, Liu B, Zhu J, Wang B, Jiang J. Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats. Environ Microbiol 2022; 24:5123-5138. [PMID: 35876302 DOI: 10.1111/1462-2920.16141] [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: 04/04/2022] [Revised: 07/17/2022] [Accepted: 07/17/2022] [Indexed: 11/28/2022]
Abstract
Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Muji Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tairong Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Bin Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jianchun Zhu
- Laboratory Centre of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
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Jamal M, Awadasseid A, Su X. Exploring potential bacterial populations for enhanced anthraquinone dyes biodegradation: a critical review. Biotechnol Lett 2022; 44:1011-1025. [DOI: 10.1007/s10529-022-03279-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/04/2022] [Indexed: 11/02/2022]
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121
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Wang Q, Liu Y, Su Y, Cheng C, Shang B, Agathokleous E, Feng Z. Effects of elevated ozone on bacterial communities inhabiting the phyllo- and endo-spheres of rice plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154705. [PMID: 35318051 DOI: 10.1016/j.scitotenv.2022.154705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
To explore the effects of elevated ozone (O3) on microbial communities inhabiting phyllo- and endo-spheres of Japonica rice leaves, cultivars Nangeng 5055 (NG5055) and Wuyujing 27 (WYJ27) were grown in either charcoal-filtered air (CF) or elevated O3 (ambient O3 + 40 ppb, E-O3) in field open-top chambers (OTCs) during a growing season. E-O3 increased the values of the Shannon (43-80%) and Simpson (34-51%) indexes of the phyllo-and endo-spheric bacterial communities in NG5055. E-O3 also increased the values of the phyllosphere Simpson index by 58% and the endosphere Shannon index by 54% in WYJ27. Both diversity indexes positively correlated with the contents of nitrogen, phosphorus, magnesium, and soluble sugar, and negatively correlated with the contents of starch and condensed tannins. The leaf-associated bacterial community composition significantly changed in both rice cultivars under E-O3. Moreover, the leaf-associated bacterial communities in NG5055 were more sensitive to E-O3 than those in WYJ27. The chemical properties explained 70% and 98% of variations in the phyllosphere and endosphere bacterial communities, respectively, suggesting a predominant role of chemical status for the endospheric bacterial community. Most variation (57.3%) in the endosphere bacterial community assembly was explained by phosphorus. Gammaproteobacteria and Pantoea were found to be the most abundant class (63-76%) and genus (38-48%) in the phyllosphere and endosphere, respectively. E-O3 significantly increased the relative abundance of Bacteroidetes in the phyllosphere bacterial community and decreased the relative abundance of Gammaproteobacteria in the endophytic community. In conclusion, elevated O3 increased the diversity of bacterial communities of leaf phyllosphere and endosphere, and leaf chemical properties had a more pronounced effect on the endosphere bacterial community.
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Affiliation(s)
- Qi Wang
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yuanyuan Liu
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yi Su
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Cheng Cheng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Bo Shang
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Evgenios Agathokleous
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhaozhong Feng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
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122
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Góngora E, Chen YJ, Ellis M, Okshevsky M, Whyte L. Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119247. [PMID: 35390417 DOI: 10.1016/j.envpol.2022.119247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.
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Affiliation(s)
- Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Madison Ellis
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Mira Okshevsky
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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123
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The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α
3
β
3
-Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site. Appl Environ Microbiol 2022; 88:e0083522. [PMID: 35862661 PMCID: PMC9361823 DOI: 10.1128/aem.00835-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cumene dioxygenase (CumDO) is an initial enzyme in the cumene degradation pathway of Pseudomonas fluorescens IP01 and is a Rieske non-heme iron oxygenase (RO) that comprises two electron transfer components (reductase [CumDO-R] and Rieske-type ferredoxin [CumDO-F]) and one catalytic component (α3β3-type oxygenase [CumDO-O]). Catalysis is triggered by electrons that are transferred from NAD(P)H to CumDO-O by CumDO-R and CumDO-F. To investigate the binding mode between CumDO-F and CumDO-O and to identify the key CumDO-O amino acid residues for binding, we simulated docking between the CumDO-O crystal structure and predicted model of CumDO-F and identified two potential binding sites: one is at the side-wise site and the other is at the top-wise site in mushroom-like CumDO-O. Then, we performed alanine mutagenesis of 16 surface amino acid residues at two potential binding sites. The results of reduction efficiency analyses using the purified components indicated that CumDO-F bound at the side-wise site of CumDO-O, and K117 of the α-subunit and R65 of the β-subunit were critical for the interaction. Moreover, these two positively charged residues are well conserved in α3β3-type oxygenase components of ROs whose electron donors are Rieske-type ferredoxins. Given that these residues were not conserved if the electron donors were different types of ferredoxins or reductases, the side-wise site of the mushroom-like structure is thought to be the common binding site between Rieske-type ferredoxin and α3β3-type oxygenase components in ROs. IMPORTANCE We clarified the critical amino acid residues of the oxygenase component (Oxy) of Rieske non-heme iron oxygenase (RO) for binding with Rieske-type ferredoxin (Fd). Our results showed that Rieske-type Fd-binding site is commonly located at the stem (side-wise site) of the mushroom-like α3β3 quaternary structure in many ROs. The resultant binding site was totally different from those reported at the top-wise site of the doughnut-like α3-type Oxy, although α3-type Oxys correspond to the cap (α3 subunit part) of the mushroom-like α3β3-type Oxys. Critical amino acid residues detected in this study were not conserved if the electron donors of Oxys were different types of Fds or reductases. Altogether, we can suggest that unique binding modes between Oxys and electron donors have evolved, depending on the nature of the electron donors, despite Oxy molecules having shared α3β3 quaternary structures.
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124
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Schut GJ, Haja DK, Feng X, Poole FL, Li H, Adams MWW. An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism. Front Microbiol 2022; 13:946711. [PMID: 35875533 PMCID: PMC9304861 DOI: 10.3389/fmicb.2022.946711] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD+ and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP+, cofactor F420, formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.
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Affiliation(s)
- Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Dominik K. Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Michael W. W. Adams, ; orcid.org/0000-0002-9796-5014
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Ma Q, Xu Y, Xiao H, Mariga AM, Chen Y, Zhang X, Wang L, Li D, Li L, Luo Z. Rethinking of botanical volatile organic compounds applied in food preservation: Challenges in acquisition, application, microbial inhibition and stimulation. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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126
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Cruz Viggi C, Tucci M, Resitano M, Crognale S, Di Franca ML, Rossetti S, Aulenta F. Coupling of bioelectrochemical toluene oxidation and trichloroethene reductive dechlorination for single-stage treatment of groundwater containing multiple contaminants. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 11:100171. [PMID: 36158759 PMCID: PMC9488093 DOI: 10.1016/j.ese.2022.100171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 05/12/2023]
Abstract
Bioremediation of groundwater contaminated by a mixture of aromatic hydrocarbons and chlorinated solvents is typically challenged because these contaminants are degraded via distinctive oxidative and reductive pathways, thus requiring different amendments and redox conditions. Here, we provided the proof-of-concept of a single-stage treatment of synthetic groundwater containing toluene and trichloroethene (TCE) in a tubular bioelectrochemical reactor, known as a "bioelectric well". Toluene was degraded by a microbial bioanode (up to 150 μmol L-1 d-1) with a polarized graphite anode (+0.2 V vs. SHE) serving as the terminal electron acceptor. The electric current deriving from microbially-driven toluene oxidation resulted in (abiotic) hydrogen production (at a stainless-steel cathode), which sustained the reductive dechlorination of TCE to less-chlorinated intermediates (i.e., cis-DCE, VC, and ETH), at a maximum rate of 500 μeq L-1 d-1, in the bulk of the reactor. A phylogenetic and functional gene-based analysis of the "bioelectric well" confirmed the establishment of a microbiome harboring the metabolic potential for anaerobic toluene oxidation and TCE reductive dechlorination. However, Toluene degradation and current generation were found to be rate-limited by external mass transport phenomena, thus indicating the existing potential for further process optimization.
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127
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Davenport EJ, Bose A. Taxonomic Re-Evaluation and Genomic Comparison of Novel Extracellular Electron Uptake-Capable Rhodovulum visakhapatnamense and Rhodovulum sulfidophilum Isolates. Microorganisms 2022; 10:1235. [PMID: 35744753 PMCID: PMC9230146 DOI: 10.3390/microorganisms10061235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022] Open
Abstract
Rhodovulum spp. are anoxygenic phototrophic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). A total of 15 strains of Rhodovulum sulfidophilum were isolated from a marine estuary to observe these metabolisms in marine phototrophs. One representative strain, Rhodovulum sulfidophilum strain AB26, can perform phototrophic iron oxidation (photoferrotrophy) and couples carbon dioxide fixation to pEEU. Here, we reclassify two R. sulfidophilum isolates, strainAB26 and strain AB19, as Rhodovulum visakhapatnamense using taxonomic re-evaluation based on 16S and pufM phylogenetic analyses. The strain AB26 genome consists of 4,380,746 base-pairs, including two plasmids, and encodes 4296 predicted protein-coding genes. Strain AB26 contains 22 histidine kinases, 20 response regulators, and dedicates ~16% of its genome to transport. Transcriptomic data under aerobic, photoheterotrophy, photoautotrophy, and pEEU reveals how gene expression varies between metabolisms in a novel R. visakhapatnamense strain. Genome comparison led by transcriptomic data under pEEU reveals potential pEEU-relevant genes both unique to R. visakhapatnamense strains and shared within the R. sulfidophilum genomes. With these data we identify potential pEEU-important transcripts and how speciation may affect molecular mechanisms of pEEU in Rhodovulum species from the same environment.
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Affiliation(s)
| | - Arpita Bose
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA;
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128
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An Isolated Arthrobacter sp. Enhances Rice ( Oryza sativa L.) Plant Growth. Microorganisms 2022; 10:microorganisms10061187. [PMID: 35744704 PMCID: PMC9228311 DOI: 10.3390/microorganisms10061187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022] Open
Abstract
Rice is a symbol of life and a representation of prosperity in South Korea. However, studies on the diversity of the bacterial communities in the rhizosphere of rice plants are limited. In this study, four bundles of root samples were collected from the same rice field located in Goyang, South Korea. These were systematically analyzed to discover the diversity of culturable bacterial communities through culture-dependent methods. A total of 504 culturable bacteria were isolated and evaluated for their plant growth-promoting abilities in vitro. Among them, Arthrobacter sp. GN70 was selected for inoculation into the rice plants under laboratory and greenhouse conditions. The results showed a significantly positive effect on shoot length, root length, fresh plant weight, and dry plant weight. Moreover, scanning electron microscopic (SEM) images demonstrated the accumulation of bacterial biofilm networks at the junction of the primary roots, confirming the root-colonizing ability of the bacterium. The strain also exhibited a broad spectrum of in vitro antimicrobial activities against bacteria and fungi. Here, we first report the rice plant growth-promoting ability of the Arthrobacter species with the biofilm-producing and antimicrobial activities against plant and human pathogens. Genome analyses revealed features attributable to enhance rice plant growth, including the genes involved in the synthesis of plant hormones, biofilm production, and secondary metabolites. This study revealed that the rhizobacteria isolated from the roots of rice plants have dual potential to be utilized as a plant growth promoter and antimicrobial agent.
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129
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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130
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Wang A, Shao P. Effects of Organic Maceral on Biogenic Coalbed Gas Generation from Bituminous Coal. ACS OMEGA 2022; 7:18139-18145. [PMID: 35664615 PMCID: PMC9161391 DOI: 10.1021/acsomega.2c01821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Clarifying the effect of organic maceral on biogenic coalbed gas generation is important to understand the mechanism of biogenic coalbed gas generation and to develop bioengineering of coalbed gas. Bituminous coals in the Huainan mining area of China were selected as the research object, and the organic macerals were enriched through manual separation and floatation-sedimentation experiments first. Then, the simulated biogas generation experiments were carried out by using raw coal, single vitrinite, and inertinite, respectively. The results showed that all the bituminous coal, vitrinite, and inertinite could be biodegraded to generate biogas. The gas production yield of vitrinite was11.5 mL/g, which was more than that of raw coal (9.8 mL/g) and inertinite (6.26 mL/g). The production processes showed the stage characteristics of rapid increase and continuous decrease, but the gas production peak of inertinite lagged behind that of raw coal and vitrinite. Vitrinite content was positively correlated with total gas production, while inertinite could inhibit biogas production. CH4 composition in simulated biogas from vitrinite was the most, and that from inertinite was the least, while there was a positive correlation between vitrinite content and CH4 composition. The above evidence showed that vitrinite in bituminous coal is more easily biodegradable. There were significant positive correlations between chloroform bitumen "A", H, and H/C to total gas production, and they can be used as important indicators to evaluate the output of coalbed biogas.
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Affiliation(s)
- Aikuan Wang
- Key
Laboratory of Coalbed Methane Resources & Reservoir Formation
Process, Ministry of Education, China University
of Mining & Technology, Xuzhou 221008, China
- School
of Resources and Geosciences, China University
of Mining & Technology, Xuzhou 221116, China
| | - Pei Shao
- Department
of Surveying and Planning, Shangqiu Normal
University, Shangqiu 476000, China
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131
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Optimized Operating Conditions for a Biological Treatment Process of Industrial Residual Process Brine Using a Halophilic Mixed Culture. FERMENTATION 2022. [DOI: 10.3390/fermentation8060246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Residual process brine is a sustainable raw material for chlor-alkali electrolysis processes. This study investigates the influence of critical process parameters on the performance of a continuous treatment process for residual process brine using halophilic microorganisms. The goal of the bioprocess is an efficient degradation of the organic impurities formate, aniline, phenol, and 4,4′-methylenedianline from this residual stream. It was shown that formate could be degraded with high efficiencies (89–98%) during the treatment process. It was observed that formate degradation was influenced by the co-substrate glycerol. The lowest residual formate concentrations were achieved with specific glycerol uptake rates of 8.0–16.0 × 10−3 g L−1 h−1 OD600−1. Moreover, a triple-nutrient limitation for glycerol, ammonium, and phosphate was successfully applied for continuous cultivations. Furthermore, it was shown that all aromatic impurities were degraded with an efficiency of 100%. Ultimately, this study proposed optimized operating conditions, allowing the efficient degradation of organics in the residual process brine under various process conditions. Future optimization steps will require a strategy to prevent the accumulation of potential intermediate degradation products formed at high aniline feed concentrations and increase the liquid dilution rates of the system to achieve a higher throughput of brines.
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132
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Yang R, Zhang B, Xu Y, Zhang G, Liu Y, Zhang D, Zhang W, Chen T, Liu G. Genomic insights revealed the environmental adaptability of Planococcus halotolerans Y50 isolated from petroleum-contaminated soil on the Qinghai-Tibet Plateau. Gene 2022; 823:146368. [PMID: 35240255 DOI: 10.1016/j.gene.2022.146368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/28/2022]
Abstract
The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C11-C23, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 103 J/m2 UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.
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Affiliation(s)
- Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China.
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Dongming Zhang
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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Becker P, Döhmann A, Wöhlbrand L, Thies D, Hinrichs C, Buschen R, Wünsch D, Neumann-Schaal M, Schomburg D, Winklhofer M, Reinhardt R, Rabus R. Complex and flexible catabolism in Aromatoleum aromaticum pCyN1. Environ Microbiol 2022; 24:3195-3211. [PMID: 35590445 DOI: 10.1111/1462-2920.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
Abstract
Large quantities of organic matter are continuously deposited, and (a)biotic gradients intersect in the soil-rhizosphere, where biodegradation contributes to the global cycles of elements. The betaproteobacterial genus Aromatoleum comprises cosmopolitan, facultative denitrifying degradation specialists. A. aromaticum pCyN1 stands out for anaerobically decomposing plant-derived monoterpenes in addition to monoaromatic hydrocarbons, polar aromatics and aliphatics. The catabolic network's structure and flexibility in A. aromaticum pCyN1 was studied across 34 growth conditions by superimposing proteome profiles onto the manually annotated 4.37 Mbp genome. Strain pCyN1 employs three fundamentally different enzymes for C-H-bond cleavage at the methyl groups of p-cymene/4-ethyltoluene, toluene and p-cresol, respectively. Regulation of degradation modules displayed substrate specificities ranging from narrow (toluene and cyclohexane carboxylate) via medium-wide (one module shared by p-cymene, 4-ethyltoluene, α-phellandrene, α-terpinene, γ-terpinene and limonene) to broad (central benzoyl-CoA pathway serving 16 aromatic substrates). Remarkably, three variants of ATP-dependent (class I) benzoyl-CoA reductase and four different β-oxidation routes establish a degradation hub that accommodates the substrate diversity. The respiratory system displayed several conspicuous profiles, e.g., the presence of nitrous oxide reductase under oxic and of low-affinity oxidase under anoxic conditions. Overall, nutritional versatility in conjunction with network regulation endow A. aromaticum pCyN1 with broad adaptability. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Patrick Becker
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Annemieke Döhmann
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Daniela Thies
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ramona Buschen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolism, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany.,Department of Analytics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Dietmar Schomburg
- Research Group Bacterial Metabolism, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany
| | - Michael Winklhofer
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.,Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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134
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Ghimire N, Kim B, Lee CM, Oh TJ. Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660. BMC Genomics 2022; 23:375. [PMID: 35585492 PMCID: PMC9115942 DOI: 10.1186/s12864-022-08589-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Background While the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 is a lichen-associated bacterium isolated from Antarctica. The work presents the genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp. PAMC26660. Additionally, the accessory, core and unique genes were identified among Variovorax species using the pan genome analysis tool. A detailed analysis of the genes related to xenobiotic metabolism revealed the potential roles of Variovorax sp. PAMC26660 and other species in bioremediation. Results TYGS analysis, dDDH, phylogenetic placement and average nucleotide identity (ANI) analysis identified the strain as Variovorax sp. Cell morphology was assessed using scanning electron microscopy (SEM). On analysis of the core, accessory, and unique genes, xenobiotic metabolism accounted only for the accessory and unique genes. On detailed analysis of the aromatic compound catabolic genes, peripheral pathway related to 4-hydroxybenzoate (4-HB) degradation was found among all species while phenylacetate and tyrosine degradation pathways were present in most of the species including PAMC26660. Likewise, central catabolic pathways, like protocatechuate, gentisate, homogentisate, and phenylacetyl-CoA, were also present. The peripheral pathway for 4-HB degradation was functionally tested using PAMC26660, which resulted in the growth using it as a sole source of carbon. Conclusions Computational tools for genome and pan genome analysis are important to understand the behavior of an organism. Xenobiotic metabolism-related genes, that only account for the accessory and unique genes infer evolution through events like lateral gene transfer, mutation and gene rearrangement. 4-HB, an aromatic compound present among lichen species is utilized by lichen-associated Variovorax sp. PAMC26660 as the sole source of carbon. The strain holds genes and pathways for its utilization. Overall, this study outlines the importance of Variovorax in bioremediation and presents the genomic information of the species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08589-3.
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Affiliation(s)
- Nisha Ghimire
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea
| | - Chang-Muk Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 55365, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea. .,Genome-based BioIT Convergence Institute, Asan, 31460, Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, South Korea.
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135
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Jung GY, Nam IH, Kim SJ. Undibacter mobilis gen. nov., sp. nov. isolated from an artificial wetland in Okcheon, Korea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005369] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain GY_HT was isolated from an artificial wetland in Okcheon, Chungcheongbuk-do Province, Republic of Korea. Strain GY_HT was closely related to
Pseudolabrys taiwanensis
CC-BB4T based on 16S rRNA gene sequences (94.7 % similarity) and clustered within the family
Nitrobacteraceae
. Cells of the isolate were Gram-stain-negative, catalase-negative and oxidase-positive, and colonies were white or pale transparent. A flagellum was observed, and the isolate could respire both aerobically and anaerobically. Growth of GY_ HT was observed in the following conditions: 10–45 °C, pH 5–11 and 0–4 % NaCl. The optimal conditions for growth were 25 °C, pH 6.5–7.5 and 0.5–1.5 % NaCl. The major fatty acids were C19 : 0 cyclo ω8c (35.8 %) and summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c; 27.4 %). The major quinone was found to be ubiquinone-10. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The G+C content of the genome of GY_HT was 63.3 mol%. Based on its phylogenomic, physiological and biochemical attributes, strain GY_HT represents a novel species of a novel genus of the family
Nitrobacteraceae
. We propose the name as Undibacter mobilis gen. nov., sp. nov. The type strain is GY_HT (=KCTC 62792T=JCM 32856T).
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Affiliation(s)
- Gi-Yong Jung
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
- Mineral Resources Division, Korea Institute of Geoscience and Mineral resources, Daejeon 34132, Republic of Korea
| | - In-Hyun Nam
- Mineral Resources Division, Korea Institute of Geoscience and Mineral resources, Daejeon 34132, Republic of Korea
| | - So-Jeong Kim
- Mineral Resources Division, Korea Institute of Geoscience and Mineral resources, Daejeon 34132, Republic of Korea
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136
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Carstensen L, Beil S, Börnick H, Stolte S. Structure-related endocrine-disrupting potential of environmental transformation products of benzophenone-type UV filters: A review. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128495. [PMID: 35739676 DOI: 10.1016/j.jhazmat.2022.128495] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 06/15/2023]
Abstract
Benzophenone-type UV filters (BPs) represent a very diverse group of chemicals that are used across a range of industrial sectors around the world. They are found within different environmental compartments (e.g. surface water, groundwater, wastewater, sediments and biota) at concentrations ranging from ng/L to mg/L. Some are known as endocrine disruptors and are currently within the scope of international regulations. A structural alert for high potential of endocrine disrupting activity was assigned to 11 BP derivatives. Due to the widespread use, distribution and disruptive effects of some BPs, knowledge of their elimination pathways is required. This review demonstrates that biodegradation and photolytic decomposition are the major elimination processes for BP-type UV filters in the environment. Under aerobic conditions, transformation pathways have only been reported for BP, BP-3 and BP-4, which are also the most common derivatives. Primary biodegradation mainly results in the formation of hydroxylated BPs, which exhibit a structure-related increase in endocrine activity when compared to their parent substances. By combining 76 literature-based transformation products (TPs) with in silico results relating to their receptor activity, it is demonstrated that 32 TPs may retain activity and that further knowledge of the degradation of BPs in the environment is needed.
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Affiliation(s)
- Lale Carstensen
- Institute of Water Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Stephan Beil
- Institute of Water Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Hilmar Börnick
- Institute of Water Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Stefan Stolte
- Institute of Water Chemistry, Technische Universität Dresden, 01069 Dresden, Germany.
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137
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Jabłońska J, Tawfik DS. Innovation and tinkering in the evolution of oxidases. Protein Sci 2022; 31:e4310. [PMID: 35481655 PMCID: PMC9040561 DOI: 10.1002/pro.4310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/25/2022] [Accepted: 04/01/2022] [Indexed: 12/19/2022]
Abstract
Although molecular oxygen is a relative newcomer to the biosphere, it has had a profound impact on metabolism. About 700 oxygen‐dependent enzymatic reactions are known, the vast majority of which emerged only after the appearance of oxygen in the biosphere, circa 3 billion years ago. Oxygen was a major driving force for evolutionary innovation—~60% of all known oxygen‐dependent enzyme families emerged as such; that is, the founding ancestor was an O2‐dependent enzyme. The other 40% seem to have diverged by tinkering from pre‐existing proteins whose function was not related to oxygen. Here, we focus on the latter. We describe transitions from various enzyme classes, as well as from non‐enzymatic proteins, and we explore these transitions in terms of catalytic chemistry, metabolism, and protein structure. These transitions vary from subtle ones, such as simply repurposing oxidoreductases by replacing an electron acceptor such as NAD by O2, to drastic changes in reaction mechanism, such as turning carboxylases and hydrolases into oxidases. The latter is more common and can occur with strikingly minor changes, for example, only one mutation in the active site. We further suggest that engineering enzymes to harness the extraordinary reactivity of oxygen may yield higher catabolic power and versatility.
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Affiliation(s)
- Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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138
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Biodegradation of Naphthalene and Anthracene by Aspergillus glaucus Strain Isolated from Antarctic Soil. Processes (Basel) 2022. [DOI: 10.3390/pr10050873] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biotechnologies based on microbial species capable of destroying harmful pollutants are a successful way to solve some of the most important problems associated with a clean environment. The subject of investigation is the Antarctic fungal strain Aspergillus glaucus AL1. The culturing of the examined strain was performed with 70 mg of wet mycelium being inoculated in a Czapek Dox liquid medium containing naphthalene, anthracene, or phenanthrene (0.3 g/L) as the sole carbon source. Progressively decreasing naphthalene and anthracene concentrations were monitored in the culture medium until the 15th day of the cultivation of A. glaucus AL1. The degradation was determined through gas chromatography–mass spectrometry. Both decreased by 66% and 44%, respectively, for this period. The GC-MS analyses were applied to identify salicylic acid, catechol, and ketoadipic acid as intermediates in the naphthalene degradation. The intermediates identified in anthracene catabolism are 2-hydroxy-1-naphthoic acid, o-phthalic acid, and protocatechuic acid. The enzyme activities for phenol 2-monooxygenase (1.14.13.7) and catechol 1,2-dioxygenase (1.13.11.1) were established. A gene encoding an enzyme with catechol 1,2-dioxygenase activity was identified and sequenced (GeneBank Ac. No KM360483). The recent study provides original data on the potential of an ascomycete’s fungal strain A. glaucus strain AL 1 to degrade naphthalene and anthracene.
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139
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Liu J, Lorraine SC, Dolinar BS, Hoover JM. Aerobic Oxidation Reactivity of Well-Defined Cobalt(II) and Cobalt(III) Aminophenol Complexes. Inorg Chem 2022; 61:6008-6016. [PMID: 35414172 PMCID: PMC9328405 DOI: 10.1021/acs.inorgchem.1c03686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This paper describes the synthesis and reactivity studies of three cobalt complexes bearing aminophenol-derived ligands without nitrogen substitution: CoII(tBu2APH)2(tBu2AP)2 (1), CoIII2(tBu2APH)2(tBu2AP)2(μ-tBu2BAP)2 (2), and CoIII(tBu2AP)3 (3), where tBu2APH = 2-amino-4,6-di-tert-butylphenol, tBu2AP = 2-amino-4,6-di-tert-butylphenolate, and μ-tBu2BAP = bridging 2-amido-4,6-di-tert-butylphenolate. Stoichiometric reactivity studies of these well-defined complexes demonstrate the catalytic competency of both cobalt(II) and cobalt(III) complexes in the aerobic oxidative cyclization of tBu2APH with tert-butylisonitrile. Reactions with O2 reveal the aerobic oxidation of the cobalt(II) complex 1 to generate the cobalt(III) species 2 and 3. UV-visible time-course studies and electron paramagnetic resonance spectroscopy indicate that this oxidation proceeds through a ligand-based radical intermediate. These studies represent the first example of well-defined cobalt aminophenol complexes that participate in catalytic aerobic oxidation reactions and highlight a key role for a ligand radical in the oxidation sequence.
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140
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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141
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Tartaglia M, Sciarrillo R, Zuzolo D, Postiglione A, Prigioniero A, Scarano P, Ruggieri V, Guarino C. Exploring an enhanced rhizospheric phenomenon for pluricontaminated soil remediation: Insights from tripartite metatranscriptome analyses. JOURNAL OF HAZARDOUS MATERIALS 2022; 428:128246. [PMID: 35030484 DOI: 10.1016/j.jhazmat.2022.128246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 05/20/2023]
Abstract
Phytoremediation involving the use of microorganisms with tolerant plant species represents a new frontier for on-site remediation of pluricontaminated soils. In this study, the effectiveness of a biotechnological strategy, involving the use of Festuca arundinacea and a pool of microorganisms, was assessed by a mesocosm experiment and an in-depth rhizospheric metatranscriptomic analysis. The chemical profile of mesocosm soil at the end of the experiment (240 days) showed that the decrease of trace elements such as Cd, Hg, Pb, Sn, Tl, V and Zn in the soil was enhanced by our biological combination. Additionally, also the organic pollutants (PAHs and PCBs) were strongly reduced up to 40.5%. About two million transcripts were identified and used for taxonomic and functional profiling. Transcripts read counts, tripartite among plant, bacteria and fungi were identified and quantified to provide an overview of the complex soil community composition. We observed that Actinobacteria and fungi abundance might be involved in remediation success. Functional analyses showed that Trehalose Biosynthesis and the antioxidant activity might have played a key-role in metaorganism effective interactions. The biotechnological approach remodeled the transcriptional profile toward organic pollutant degradation and heavy metal stress response.
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Affiliation(s)
- Maria Tartaglia
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Daniela Zuzolo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Alessia Postiglione
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | - Pierpaolo Scarano
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | - Carmine Guarino
- Department of Science and Technologies, University of Sannio, Benevento, Italy.
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142
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Sun H, Chang H, Tang W, Zhang X, Yang H, Zhang F, Zhang Y. Effects of influent immigration and environmental factors on bacterial assembly of activated sludge microbial communities. ENVIRONMENTAL RESEARCH 2022; 205:112426. [PMID: 34843723 DOI: 10.1016/j.envres.2021.112426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 05/13/2023]
Abstract
The functional mechanism of microbial assembly of activated sludge (AS) in urban wastewater treatment plants (UWTPs) remains unclear. A comprehensive quantitative evaluation of the contribution of influent immigration and environmental factors to AS community composition requires investigation. In this study, the microbial characteristics of six full-scale UWTPs with different influent compositions and environmental factors (altitude, temperature, dissolved oxygen (DO), pH, chemical oxygen demand (COD), total nitrogen (TN), ammonia nitrogen (NH4+-N), and total phosphorus (TP)) were analyzed to determine the main forces affecting the bacterial assembly of AS microbial communities. Abundant and core taxa were screened out based on the abundance and frequency of operational taxonomic units (OTUs) occurrence in all samples. Abundant OTUs (18.7% occurrence) accounted for 87.7% of the total 16S rRNA sequences, while rare OTUs (71.7% occurrence) accounted for only 7.8% of the total 16S rRNA sequences. A total of 135 OTUs were identified as core taxa, accounting for 14.6-26.2% of the total reads, of which 83 OTUs belonged to abundant taxa. The richness and uniformity of the influent community were significantly lower than those of the AS system. The community composition in influent varied from that in AS. Moreover, about 89.7% (86.5% of 16S rRNA sequences) OTUs in AS samples showed positive growth rates, indicating that immigration of influent communities had a limited effect on the microbial composition of AS. Redundancy analysis (RDA) combined with co-occurrence network showed that the bacterial assembly of microbial communities was significantly correlated with altitude, pH, and TN (P < 0.05), and these three parameters could explain 23.3%, 21.1%, and 17.7% of the bacterial assembly of AS microbial communities in UWTPs, respectively.
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Affiliation(s)
- Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China.
| | - Huanhuan Chang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Wei Tang
- Yantai City Drainage Service Center, Yantai, 264000, China
| | | | - Hao Yang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Feng Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China
| | - Yanxiang Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China.
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143
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Sun H, Huang K, Zhang X, Ren H, Ye L. Stable isotope probing reveals specific assimilating bacteria of refractory organic compounds in activated sludge. WATER RESEARCH 2022; 212:118105. [PMID: 35074670 DOI: 10.1016/j.watres.2022.118105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Activated sludge in wastewater treatment bioreactors contains diverse bacteria, while little is known about the community structure of bacteria responsible for degradation of refractory organic compounds (ROCs). In this study, 10 ROCs frequently detected in sewage were investigated, and the potential bacteria degrading these ROCs were analyzed by DNA stable isotope probing and high-throughput sequencing. The results showed that the bacterial communities responsible for degradation of different ROCs were largely different. A total of 84 bacterial genera were found to be involved in degrading at least one of the 10 ROCs, however, only six genera (Acinetobacter, Bacteroides, Bosea, Brevundimonas, Lactobacillus and Pseudomonas) were common to all 10 ROCs. This suggests that different ROCs may have specific assimilating bacteria in the activated sludge. Our results also showed that these ROC-degrading bacteria are difficult to isolate by conventional methods and that most of them have relatively low relative abundance in municipal wastewater treatment bioreactors. Development of new technologies to increase the abundance and activity of these bacteria may significantly improve the removal efficiency of ROCs from wastewater.
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Affiliation(s)
- Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China.
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144
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Zhu D, Qaria MA, Zhu B, Sun J, Yang B. Extremophiles and extremozymes in lignin bioprocessing. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 157:112069. [DOI: 10.1016/j.rser.2021.112069] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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145
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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146
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Csizi K, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non-heme iron family of oxygenases and catalyze important cis-dihydroxylation as well as O-/N-dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non-heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O 2 activation. Here, we studied the role of the substrate in the key elementary reaction leading to O 2 activation from a theoretical perspective by systematically considering (i) the 6-coordinate to 5-coordinate conversion of the non-heme FeII upon abstraction of a water ligand, (ii) binding of O 2 , and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin-state-dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non-heme FeII center through thermoneutral H2 O reorientation and exothermic O 2 binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe-oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6-coordinate non-heme FeII sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non-heme FeII in agreement with a strategy that avoids unproductive O 2 activation.
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Affiliation(s)
- Katja‐Sophia Csizi
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Lina Eckert
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Christoph Brunken
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas B. Hofstetter
- EawagSwiss Federal Institute of Aquatic Science and TechnologyÜberlandstrasse 1338600DübendorfSwitzerland
| | - Markus Reiher
- ETH ZürichLaboratory for Physical ChemistryVladimir-Prelog-Weg 28093ZürichSwitzerland
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147
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Wang Q, Geng S, Wang L, Wen Z, Sun X, Huang H. Bacterial mandelic acid degradation pathway and its application in biotechnology. J Appl Microbiol 2022; 133:273-286. [PMID: 35294082 DOI: 10.1111/jam.15529] [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: 05/06/2021] [Revised: 12/22/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analyzed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyze various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Shanshan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Lingru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, People's Republic of China
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148
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Ortega Ramírez CA, Ching T, Yoza B, Li QX. Glycerol-assisted degradation of dibenzothiophene by Paraburkholderia sp. C3 is associated with polyhydroxyalkanoate granulation. CHEMOSPHERE 2022; 291:133054. [PMID: 34838841 DOI: 10.1016/j.chemosphere.2021.133054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/06/2021] [Accepted: 11/22/2021] [Indexed: 05/28/2023]
Abstract
Glycerol is a biodiesel byproduct. In the present study, glycerol was used as a co-substrate during biodegradation of dibenzothiophene (DBT) by Paraburkholderia sp. C3. Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent, ubiquitous and carcinogenic chemicals found in the environment. DBT is a major sulfur-containing PAH. The chemical properties of DBT make it an ideal model pollutant for examining the bioremediation of higher molecular weight PAHs. Bioremediation uses microbial catalysis for removal of environmental pollutants. Environmental microorganisms that encounter aromatic substrates such as heterocyclic PAHs develop unique characteristics that allow the uptake and assimilation of these cytotoxic substrates. Microbial adaptations include changes in membrane lipid composition, secretion of surface-active compounds and accumulation of lipid granules to withstand chemical toxicity. Biostimulation using more readily metabolized substrates can increase the biodegradation rate of PAHs, but the molecular mechanisms are not well understood. We analyzed the DBT biodegradation kinetics in C3, proteome changes and TEM micrographs in different culturing conditions. We utilized 2-bromoalkanoic lipid metabolic inhibitors to establish a correlation between polyhydroxyalkanoate (PHA) granule formation and the enhancement of DBT biodegradation induced by glycerol. This is the first description linking PHA biosynthesis, DBT biodegradation and 2-bromoalkanoic acids in a Paraburkholderia species.
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Affiliation(s)
- Camila A Ortega Ramírez
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Travers Ching
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Brandon Yoza
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
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149
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Ummara U, Noreen S, Afzal M, Zafar ZU, Akhter MS, Iqbal S, Hefft DI, Kazi M, Ahmad P. Induced systemic tolerance mediated by plant-microbe interaction in maize (Zea mays L.) plants under hydrocarbon contamination. CHEMOSPHERE 2022; 290:133327. [PMID: 34929274 DOI: 10.1016/j.chemosphere.2021.133327] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/05/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The present investigation was committed to examining the effect of soil spiked with diesel contamination (0, 1.5, 2.5, 3.5 g diesel kg-1 soil) on maize (Zea mays L) varieties (MMRI yellow and Pearl white) with or without bacterial consortium (Pseudomonas aeruginosa BRRI54, Acinetobacter sp. strain BRSI56, Acinetobacter sp. strain ACRH80). Seed and soil bacterial inoculation were done. The studied morphological attributes were fresh and dry weight of shoot and root of both maize varieties. The results documented that bacterial consortium caused 21%, 0.06% and 29%, 34% higher shoot and root fresh/dry weights in "Pearl white" and 14%, 15% and 32%, 22% shoot and root fresh/dry weights respectively in MMRI yellow under control conditions. The biochemical attributes of shoot and root were affected negatively by the 3.5 g diesel kg-1 soil contamination. Bacterial consortium enhanced enzymatic activity (APX, CAT, POD, SOD, GR) and non-enzymatic (AsA, GSH, Pro, α-Toco) antioxidant and reduction in oxidative stress (H2O2, MDA) under hydrocarbon stress as compared to non-inoculated ones in both root and shoot organs. Among both varieties, the highest hydrocarbon removal (75, 64, and 69%) was demonstrated by MMRI yellow with bacterial consortium as compare to Pearl white showed 73, 57, 65% hydrocarbon degradation at 1.5 2.5, 3.5 g diesel kg-1 soil contamination. Consequently, the microbe mediated biotransformation of hydrocarbons suggested that the use of PGPB would be the most beneficial selection in diesel fuel contaminated soil to overcome the abiotic stress in plants and successfully remediation of hydrocarbon in contaminated soil.
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Affiliation(s)
- Ume Ummara
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sibgha Noreen
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan.
| | - Muhammad Afzal
- National Institute of Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Zafar Ullah Zafar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Salim Akhter
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sehrish Iqbal
- Department of Environment Science, Bahauddin Zakariya University, Multan, Pakistan
| | - Daniel Ingo Hefft
- Department of Food Sciences, University Centre Reaseheath, Reaseheath College, Nantwich, CW5 6DF, UK.
| | - Mohsin Kazi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh, 11451, Saudi Arabia
| | - Parvaiz Ahmad
- Department of Botany, GDC Pulwama, 192301, Jammu and Kashmir, India.
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150
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Prediction of Second-Order Rate Constants of Sulfate Radical with Aromatic Contaminants Using Quantitative Structure-Activity Relationship Model. WATER 2022. [DOI: 10.3390/w14050766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Predicting the second-order rate constants between aromatic contaminants and a sulfate radical (kSO4•−) is vital for the screening of pollutants resistant to sulfate radical-based advanced oxidation processes. In this study, a quantitative structure-activity relationship (QSAR) model was developed to predict the values for aromatic contaminants. The relationship between logkSO4•− and three molecular descriptors (electron density, steric energy, and ratio between oxygen atoms and carbon atoms) was built through multiple linear regression. The goodness-of-fit, robustness, and predictive ability of the model were characterized statistically with indicators showing that the model was reliable and applicable. Electron density was found to be the most influential descriptor that contributed the most to logkSO4•−. All data points fell within the applicability domain, and no outliers existed in the training set. The comparison with other models indicates that the QSAR model performs well in elucidating the mechanism of the reaction between aromatic compounds and sulfate radicals.
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