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Nien TS, Chan TH, Li YY, Liu TS, Shiau YJ, Ho MY. Two cyanobacterial species exhibit stress responses when grown together in visible light or far-red light. mSphere 2024:e0025124. [PMID: 39120135 DOI: 10.1128/msphere.00251-24] [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: 03/25/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Although most cyanobacteria grow in visible light (VL; λ = 400-700 nm), some cyanobacteria can also use far-red light (FRL; λ = 700-800 nm) for oxygenic photosynthesis by performing far-red light photoacclimation. These two types of cyanobacteria can be found in the same environment. However, how they respond to each other remains unknown. Here, we reveal that coculture stresses FRL-using Chlorogloeopsis fritschii PCC 9212 and VL-using Synechocystis sp. PCC 6803. No significant growth difference was found in Synechocystis sp. PCC 6803 between the coculture and the monoculture. Conversely, the growth of Chlorogloeopsis fritschii PCC 9212 was suppressed in VL under coculture. According to transcriptomic analysis, Chlorogloeopsis fritschii PCC 9212 in coculture shows low transcript levels of metabolic activities and high transcript levels of ion transporters, with the differences being more noticeable in VL than in FRL. The transcript levels of stress responses in coculture were likewise higher than in monoculture in Synechocystis sp. PCC 6803 under FRL. The low transcript level of metabolic activities in coculture or the inhibition of cyanobacterial growth indicates a possible negative interaction between these two cyanobacterial strains.IMPORTANCEThe interaction between two cyanobacterial species is the primary focus of this study. One species harvests visible light, while the other can harvest far-red and visible light. Prior research on cyanobacteria interaction concentrated on its interactions with algal, coral, and fungal species. Interactions between cyanobacterial species were, nevertheless, rarely discussed. Thus, we characterized the interaction between two cyanobacterial species, one capable of photosynthesis using far-red light and the other not. Through experimental and bioinformatic approaches, we demonstrate that when one cyanobacterium thrives under optimal light conditions, it stresses the remaining cyanobacterial species. We contribute to an ecological understanding of these two kinds of cyanobacteria distribution patterns. Cyanobacteria that utilize far-red light probably disperse in environments with limited visible light to avoid competition with other cyanobacteria. From a biotechnological standpoint, this study suggests that the simultaneous cultivation of two cyanobacterial species in large-scale cultivation facilities may reduce the overall biomass yield.
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Affiliation(s)
- Ting-Shuo Nien
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Ying-Yang Li
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Ting-So Liu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yo-Jin Shiau
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Ming-Yang Ho
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
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2
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Broniatowski M, Wydro P. Interactions of Brominated Flame Retardants with Membrane Models of Dehalogenating Bacteria: Langmuir Monolayer and Grazing Incidence X-ray Diffraction Studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10600-10614. [PMID: 38721840 PMCID: PMC11112749 DOI: 10.1021/acs.langmuir.4c00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024]
Abstract
Brominated flame retardants (BFRs) are small organic molecules containing several bromine substituents added to plastics to limit their flammability. BFRs can constitute up to 30% of the weight of some plastics, which is why they are produced in large quantities. Along with plastic waste and microplastic particles, BFRs end up in the soil and can easily leach causing contamination. As polyhalogenated molecules, multiple BFRs were classified as persistent organic pollutants (POPs), meaning that their biodegradation in the soils is especially challenging. However, some anaerobic bacteria as Dehaloccocoides can dehalogenate BFRs, which is important in the bioremediation of contaminated soils. BFRs are hydrophobic, can accumulate in plasma membranes, and disturb their function. On the other hand, limited membrane accumulation is necessary for BFR dehalogenation. To study the BFR-membrane interaction, we created membrane models of soil dehalogenating bacteria and tested their interactions with seven legacy and novel BFRs most common in soils. Phospholipid Langmuir monolayers with appropriate composition were used as membrane models. These membranes were doped in the selected BFRs, and the incorporation of BFR molecules into the phospholipid matrix and also the effects of BFR presence on membrane physical properties and morphology were studied. It turned out that the seven BFRs differed significantly in their membrane affinity. For some, the incorporation was very limited, and others incorporated effectively and could affect membrane properties, while one of the tested molecules induced the formation of bilayer domains in the membranes. Thus, Langmuir monolayers can be effectively used for pretesting BFR membrane activity.
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Affiliation(s)
- Marcin Broniatowski
- Department
of Environmental Chemistry, Faculty of Chemistry, the Jagiellonian University in Kraków, ul. Gronostajowa 2, Kraków 30-387, Poland
| | - Paweł Wydro
- Department
of Physical Chemistry and Electrochemistry, Faculty of Chemistry, the Jagiellonian University in Kraków, ul. Gronostajowa 2, Kraków 30-387, Poland
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3
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Plummer SM, Plummer MA, Merkel PA, Waidner LA. Using directed evolution to improve hydrogen production in chimeric hydrogenases from algal species. Enzyme Microb Technol 2024; 173:110349. [PMID: 37984199 DOI: 10.1016/j.enzmictec.2023.110349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
Algae generate hydrogen from sunlight and water utilizing high-energy electrons generated during photosynthesis. The amount of hydrogen produced in heterologous expression of the wild-type hydrogenase is currently insufficient for industrial applications. One approach to improve hydrogen yields is through directed evolution of the DNA of the native hydrogenase. Here, we created 113 chimeric algal hydrogenase gene variants derived from combining segments of three parent hydrogenases, two from Chlamydomonas reinhardtii (CrHydA1 and CrHydA2) and one from Scenedesmus obliquus (HydA1). To generate chimeras, there were seven segments into which each of the parent hydrogenase genes was divided and recombined in a variety of combinations. The chimeric and parental hydrogenase sequences were cloned for heterologous expression in Escherichia coli, and 40 of the resultant enzymes expressed were assayed for H2 production. Chimeric clones that resulted in equal or greater production obtained with the cloned CrHydA1 parent hydrogenase were those comprised of CrHydA1 sequence in segments #1, 2, 3, and/or 4. These best-performing chimeras all contained one common region, segment #2, the part of the sequence known to contain important amino acids involved in proton transfer or hydrogen cluster coordination. The amino acid sequence distances among all chimeric clones to that of the CrHydA1 parent were determined, and the relationship between sequence distances and experimentally-derived H2 production was evaluated. An additional model determined the correlation between electrostatic potential energy surface area ratios and H2 production. The model yielded several algal mutants with predicted hydrogen productions in a range of two to three times that of the wild-type hydrogenase. The mutant data and the model can now be used to predict which specific mutant sequences may result in even higher hydrogen yields. Overall, results provide more precise details in planning future directed evolution to functionally improve algal hydrogenases.
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Affiliation(s)
| | | | - Patricia A Merkel
- H2OPE Biofuels LLC, Greenwood Village, CO, USA; Children's Hospital, 3123 East 16th Avenue, B518, Aurora, CO, USA
| | - Lisa A Waidner
- H2OPE Biofuels LLC, Greenwood Village, CO, USA; University of West Florida, Pensacola, FL USA.
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4
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Lee WH, Yoon CK, Park H, Park GH, Jeong JH, Cha GD, Lee BH, Lee J, Lee CW, Bootharaju MS, Sunwoo SH, Ryu J, Lee C, Cho YJ, Nam TW, Ahn KH, Hyeon T, Seok YJ, Kim DH. Highly Efficient Nitrogen-Fixing Microbial Hydrogel Device for Sustainable Solar Hydrogen Production. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2306092. [PMID: 37739451 DOI: 10.1002/adma.202306092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/20/2023] [Indexed: 09/24/2023]
Abstract
Conversion of sunlight and organic carbon substrates to sustainable energy sources through microbial metabolism has great potential for the renewable energy industry. Despite recent progress in microbial photosynthesis, the development of microbial platforms that warrant efficient and scalable fuel production remains in its infancy. Efficient transfer and retrieval of gaseous reactants and products to and from microbes are particular hurdles. Here, inspired by water lily leaves floating on water, a microbial device designed to operate at the air-water interface and facilitate concomitant supply of gaseous reactants, smooth capture of gaseous products, and efficient sunlight delivery is presented. The floatable device carrying Rhodopseudomonas parapalustris, of which nitrogen fixation activity is first determined through this study, exhibits a hydrogen production rate of 104 mmol h-1 m-2 , which is 53 times higher than that of a conventional device placed at a depth of 2 cm in the medium. Furthermore, a scaled-up device with an area of 144 cm2 generates hydrogen at a high rate of 1.52 L h-1 m-2 . Efficient nitrogen fixation and hydrogen generation, low fabrication cost, and mechanical durability corroborate the potential of the floatable microbial device toward practical and sustainable solar energy conversion.
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Affiliation(s)
- Wang Hee Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Kyu Yoon
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunseo Park
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ga-Hee Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Hwan Jeong
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Gi Doo Cha
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung-Hoon Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Juri Lee
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chan Woo Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Megalamane S Bootharaju
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Hyuk Sunwoo
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaeyune Ryu
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Changha Lee
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Tae-Wook Nam
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
- MightyBugs, Inc., Busan, 46918, Republic of Korea
| | - Kyung Hyun Ahn
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Hyeong Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
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5
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Chanderban M, Hill CA, Dhamad AE, Lessner DJ. Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl Environ Microbiol 2023; 89:e0103323. [PMID: 37695043 PMCID: PMC10537573 DOI: 10.1128/aem.01033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
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Affiliation(s)
- Melissa Chanderban
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Christopher A. Hill
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Ahmed E. Dhamad
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
- Department of Biological Sciences, Wasit University, Wasit, Iraq
| | - Daniel J. Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
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6
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Griesemer M, Navid A. Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites. Microorganisms 2023; 11:2149. [PMID: 37763993 PMCID: PMC10536367 DOI: 10.3390/microorganisms11092149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
Secondary metabolites are not essential for the growth of microorganisms, but they play a critical role in how microbes interact with their surroundings. In addition to this important ecological role, secondary metabolites also have a variety of agricultural, medicinal, and industrial uses, and thus the examination of secondary metabolism of plants and microbes is a growing scientific field. While the chemical production of certain secondary metabolites is possible, industrial-scale microbial production is a green and economically attractive alternative. This is even more true, given the advances in bioengineering that allow us to alter the workings of microbes in order to increase their production of compounds of interest. This type of engineering requires detailed knowledge of the "chassis" organism's metabolism. Since the resources and the catalytic capacity of enzymes in microbes is finite, it is important to examine the tradeoffs between various bioprocesses in an engineered system and alter its working in a manner that minimally perturbs the robustness of the system while allowing for the maximum production of a product of interest. The in silico multi-objective analysis of metabolism using genome-scale models is an ideal method for such examinations.
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Affiliation(s)
| | - Ali Navid
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Division, Physical & Life Sciences Directorate, Livermore, CA 94550, USA
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7
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Lozano DA, Niño-Navarro C, Chairez I, Salgado-Manjarrez E, García-Peña EI. Intensification of Hydrogen Production by a Co-culture of Syntrophomonas wolfei and Rhodopseudomonas palustris Employing High Concentrations of Butyrate as a Substrate. Appl Biochem Biotechnol 2023; 195:1800-1822. [PMID: 36399303 DOI: 10.1007/s12010-022-04220-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/19/2022]
Abstract
The purpose of this study is to present an effective form of developing a sequential dark (DF) and photo (PF) fermentation using volatile fatty acids (VFAs) and nitrogen compounds as bonding components between both metabolic networks of microbial growing in each fermentation. A simultaneous (co-)culture of Syntrophomonas wolfei (with its ability to consume butyrate and produce acetate) and Rhodopseudomonas palustris (that can use the produced acetate as a carbon source) performed a syntrophic metabolism. The former bacteria consumed the acetate/butyrate mixture reducing the butyrate concentration below 2.0 g/L, permitting Rhodopseudomonas palustris to produce hydrogen. Considering that the inoculum composition (Syntrophomonas wolfei/Rhodopseudomonas palustris) and the nitrogen source (yeast extract) define the microbial biomass specific productivity and the butyrate consumption, a response surface methodology defined the best inoculum design and yeast extract (YE) yielding to the highest biomass concentration of 1.1 g/L after 380.00 h. A second culture process (without a nitrogen source) showed the biomass produced in the previous culture process yields to produce a total cumulated hydrogen concentration of 3.4 mmol. This value was not obtained previously with the pure strain Rhodopseudomonas palustris if the culture medium contained butyrate concentration above 2.0 g/L, representing a contribution to the sequential fermentation scheme based on DF and PF.
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Affiliation(s)
- D A Lozano
- Bioprocesses Department, UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico
| | - C Niño-Navarro
- Bioprocesses Department, UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico
| | - I Chairez
- Bioprocesses Department, UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico.
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey, Mexico.
| | - E Salgado-Manjarrez
- Bioengineering Department, UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico
| | - E I García-Peña
- Bioengineering Department, UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico
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8
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Xuan J, He L, Wen W, Feng Y. Hydrogenase and Nitrogenase: Key Catalysts in Biohydrogen Production. Molecules 2023; 28:molecules28031392. [PMID: 36771068 PMCID: PMC9919214 DOI: 10.3390/molecules28031392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Hydrogen with high energy content is considered to be a promising alternative clean energy source. Biohydrogen production through microbes provides a renewable and immense hydrogen supply by utilizing raw materials such as inexhaustible natural sunlight, water, and even organic waste, which is supposed to solve the two problems of "energy supply and environment protection" at the same time. Hydrogenases and nitrogenases are two classes of key enzymes involved in biohydrogen production and can be applied under different biological conditions. Both the research on enzymatic catalytic mechanisms and the innovations of enzymatic techniques are important and necessary for the application of biohydrogen production. In this review, we introduce the enzymatic structures related to biohydrogen production, summarize recent enzymatic and genetic engineering works to enhance hydrogen production, and describe the chemical efforts of novel synthetic artificial enzymes inspired by the two biocatalysts. Continual studies on the two types of enzymes in the future will further improve the efficiency of biohydrogen production and contribute to the economic feasibility of biohydrogen as an energy source.
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Affiliation(s)
- Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Correspondence: (J.X.); (Y.F.)
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wen Wen
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.X.); (Y.F.)
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9
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Simultaneous Production of Biohydrogen (bioH2) and Poly-Hydroxy-Alkanoates (PHAs) by a Photoheterotrophic Consortium Bioaugmented with Syntrophomonas wolfei. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mixed cultures represent better alternatives to ferment organic waste and dark fermentation products in anerobic conditions because the microbial associations contribute to electron transfer mechanisms and combine metabolic possibilities. The understanding of the microbial interactions in natural and synthetic consortia and the strategies to improve the performance of the processes by bioaugmentation provide insight into the physiology and ecology of the mixed cultures used for biotechnological purposes. Here, synthetic microbial communities were built from three hydrogen (bioH2) and poly-hydroxy-alkanoates (PHA) producers, Clostridium pasteurianum, Rhodopseudomonas palustris and Syntrophomonas wolfei, and a photoheterotrophic mixed consortium C4, and their performance was evaluated during photofermentation. Higher hydrogen volumetric production rates (H2VPR) were determined with the consortia (28–40 mL/Lh) as compared with individual strains (20–27 mL/Lh). The designed consortia reached the highest bioH2 and PHA productions of 44.3 mmol and 50.46% and produced both metabolites simultaneously using dark fermentation effluents composed of a mixture of lactic, butyric, acetic, and propionic acids. When the mixed culture C4 was bioaugmented with S. wolfei, the bioH2 and PHA production reached 32 mmol and 50%, respectively. Overall, the consumption of organic acids was above 50%, which accounted up to 55% of total chemical oxygen demand (COD) removed. Increased bioH2 was observed in the condition when S. wolfei was added as the bioaugmentation agent, reaching up to 562 mL of H2 produced per gram of COD. The enhanced production of bioH2 and PHA can be explained by the metabolic interaction between the three selected strains, which likely include thermodynamic equilibrium, the assimilation of organic acids via beta-oxidation, and the production of bioH2 using a proton driving force derived from reduced menaquinone or via electron bifurcation.
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10
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Syed Z, Sogani M, Sharma G, Sonu K, Rajvanshi J, Gupta NS. Framework to improve biohydrogen generation with estrogen co-metabolism under complete suppression of nitrogen source. BIORESOURCE TECHNOLOGY 2022; 360:127595. [PMID: 35803446 DOI: 10.1016/j.biortech.2022.127595] [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: 06/06/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 06/15/2023]
Abstract
The current work provides insights for improving the hydrogen output while degrading emerging contaminants using Rhodopseudomonas palustris. The changes in the growth rate of a microorganism due to different substrate inputs affects the hydrogen production due to metabolic route changes. The different ratios of glutamate and glycerol as nitrogen and carbon sources along with the presence of ethinylestradiol (EE2) in the photofermenter affected the flux of electrons being directed towards biosynthesis and biohydrogen generation. The combination of glutamate and glycerol in different ratios (Glu:Gly; 0, 0.20 and 0.54) along with estrogen showed no significant difference in the bacteriochlorophyll concentrations. The highest biomass concentration (0.013 h-1) was in ratio of 0.54 while maximum specific hydrogen production (1.9 ± 0.05 ml g-1 biomass h-1) was observed under complete suppression of nitrogen (0; without Glu; non-growing condition) with resultant improved estrogen degradation of about 78% in 168 h by R. palustris strain MDOC01.
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Affiliation(s)
- Zainab Syed
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, Rajasthan, India
| | - Monika Sogani
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, Rajasthan, India.
| | - Gopesh Sharma
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, Rajasthan, India
| | - Kumar Sonu
- Department of Mechanical Engineering, Kashi Institute of Technology, Varanasi 221307, Uttar Pradesh, India
| | - Jayana Rajvanshi
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, Rajasthan, India
| | - Nishan Sen Gupta
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, Rajasthan, India
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11
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Pansook S, Incharoensakdi A, Phunpruch S. Simazine Enhances Dark Fermentative H2 Production by Unicellular Halotolerant Cyanobacterium Aphanothece halophytica. Front Bioeng Biotechnol 2022; 10:904101. [PMID: 35910023 PMCID: PMC9335942 DOI: 10.3389/fbioe.2022.904101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
The halotolerant cyanobacterium Aphanothece halophytica is a potential H2 producer that induces H2 evolution under nitrogen deprivation. H2 is mainly produced via the catabolism of stored glycogen under dark anaerobic condition. H2 evolution is catalyzed by O2-sensitive bidirectional hydrogenase. The aim of this study was to improve H2 production by A. halophytica using various kinds of inhibitors. Among all types of inhibitors, simazine efficiently promoted the highest H2 production under dark conditions. High simazine concentration and long-term incubation resulted in a decrease in cell and chlorophyll concentrations. The optimal simazine concentration for H2 production by A. halophytica was 25 µM. Simazine inhibited photosynthetic O2 evolution but promoted dark respiration, resulting in a decrease in O2 level. Hence, the bidirectional hydrogenase activity and H2 production was increased. A. halophytica showed the highest H2 production rate at 58.88 ± 0.22 µmol H2 g−1 dry weight h−1 and H2 accumulation at 356.21 ± 6.04 μmol H2 g−1 dry weight after treatment with 25 µM simazine under dark anaerobic condition for 2 and 24 h, respectively. This study demonstrates the potential of simazine for the enhancement of dark fermentative H2 production by A. halophytica.
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Affiliation(s)
- Sunisa Pansook
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Aran Incharoensakdi
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Saranya Phunpruch
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
- Bioenergy Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
- *Correspondence: Saranya Phunpruch,
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12
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Iqbal K, Saxena A, Pande P, Tiwari A, Chandra Joshi N, Varma A, Mishra A. Microalgae-bacterial granular consortium: Striding towards sustainable production of biohydrogen coupled with wastewater treatment. BIORESOURCE TECHNOLOGY 2022; 354:127203. [PMID: 35462016 DOI: 10.1016/j.biortech.2022.127203] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Anthropogenic activities have drastically affected the environment, leading to increased waste accumulation in atmospheric bodies, including water. Wastewater treatment is an energy-consuming process and typically requires thousands of kilowatt hours of energy. This enormous energy demand can be fulfilled by utilizing the microbial electrolysis route to breakdown organic pollutants in wastewater which produces clean water and biohydrogen as a by-product of the reaction. Microalgae are the promising microorganism for the biohydrogen production, and it has been investigated that the interaction between microalgae and bacteria can be used to boost the yield of biohydrogen. Consortium of algae and bacteria resulting around 50-60% more biohydrogen production compared to the biohydrogen production of algae and bacteria separately. This review summarises the recent development in different microalgae-bacteria granular consortium systems successfully employed for biohydrogen generation. We also discuss the limitations in biohydrogen production and factors affecting its production from wastewater.
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Affiliation(s)
- Khushboo Iqbal
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Abhishek Saxena
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India
| | - Priyanshi Pande
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Arti Mishra
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India.
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13
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Li M, Ning P, Sun Y, Luo J, Yang J. Characteristics and Application of Rhodopseudomonas palustris as a Microbial Cell Factory. Front Bioeng Biotechnol 2022; 10:897003. [PMID: 35646843 PMCID: PMC9133744 DOI: 10.3389/fbioe.2022.897003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/27/2022] [Indexed: 01/20/2023] Open
Abstract
Rhodopseudomonas palustris, a purple nonsulfur bacterium, is a bacterium with the properties of extraordinary metabolic versatility, carbon source diversity and metabolite diversity. Due to its biodetoxification and biodegradation properties, R. palustris has been traditionally applied in wastewater treatment and bioremediation. R. palustris is rich in various metabolites, contributing to its application in agriculture, aquaculture and livestock breeding as additives. In recent years, R. palustris has been engineered as a microbial cell factory to produce valuable chemicals, especially photofermentation of hydrogen. The outstanding property of R. palustris as a microbial cell factory is its ability to use a diversity of carbon sources. R. palustris is capable of CO2 fixation, contributing to photoautotrophic conversion of CO2 into valuable chemicals. R. palustris can assimilate short-chain organic acids and crude glycerol from industrial and agricultural wastewater. Lignocellulosic biomass hydrolysates can also be degraded by R. palustris. Utilization of these feedstocks can reduce the industry cost and is beneficial for environment. Applications of R. palustris for biopolymers and their building blocks production, and biofuels production are discussed. Afterward, some novel applications in microbial fuel cells, microbial electrosynthesis and photocatalytic synthesis are summarized. The challenges of the application of R. palustris are analyzed, and possible solutions are suggested.
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Affiliation(s)
- Meijie Li
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, Qingdao, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Peng Ning
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, Qingdao, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yi Sun
- Haiyang Comprehensive Administrative Law Enforcement Bureau (Agriculture), Haiyang, China
| | - Jie Luo
- Qingdao Garden Forestry Technology School, Qingdao, China
- *Correspondence: Jie Luo, ; Jianming Yang,
| | - Jianming Yang
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, Qingdao, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Jie Luo, ; Jianming Yang,
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14
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Luxem KE, Kraepiel AML, Zhang L, Waldbauer JR, Zhang X. Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation. Environ Microbiol 2022; 24:2170-2176. [PMID: 35478483 DOI: 10.1111/1462-2920.16001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, Chen H, Duan Y, Pandey A, Kumar S, Taherzadeh MJ, Li J, Zhang Z. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: A review. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 156:111987. [DOI: 10.1016/j.rser.2021.111987] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
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16
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Mapstone LJ, Leite MN, Purton S, Crawford IA, Dartnell L. Cyanobacteria and microalgae in supporting human habitation on Mars. Biotechnol Adv 2022; 59:107946. [DOI: 10.1016/j.biotechadv.2022.107946] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 12/16/2022]
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Autenrieth C, Shaw S, Ghosh R. New Approach for the Construction and Calibration of Gas-Tight Setups for Biohydrogen Production at the Small Laboratory Scale. Metabolites 2021; 11:metabo11100667. [PMID: 34677382 PMCID: PMC8541310 DOI: 10.3390/metabo11100667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/21/2021] [Accepted: 09/25/2021] [Indexed: 11/25/2022] Open
Abstract
Biohydrogen production in small laboratory scale culture vessels is often difficult to perform and quantitate. One problem is that commonly used silicon tubing and improvised plastic connections used for constructing apparatus are cheap and easy to connect but are generally not robust for gases such as hydrogen. In addition, this type of apparatus presents significant safety concerns. Here, we demonstrate the construction of hydrogen-tight apparatus using a commercially available modular system, where plastic tubing and connections are made of explosion-proof dissipative plastic material. Using this system, we introduce a gas chromatograph calibration procedure, which can be easily performed without necessarily resorting to expensive commercial gas standards for the calibration of hydrogen gas concentrations. In this procedure, the amount of hydrogen produced by the reaction of sodium borohydride with water in a closed air-filled bottle is deduced from the observed decrease of the oxygen partial pressure, using the ideal gas law. Finally, the determined calibration coefficients and the gas-tight apparatus are used for the analysis of simultaneous oxygen consumption and hydrogen production of the purple photosynthetic bacterium, Rhodospirillum rubrum, during semi-aerobic growth in the dark.
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Affiliation(s)
- Caroline Autenrieth
- Institute of Biomaterials and Biomolecular Systems, Department of Bioenergetics, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; (S.S.); (R.G.)
- Correspondence: ; Tel.: +49-711-685-65048
| | - Shreya Shaw
- Institute of Biomaterials and Biomolecular Systems, Department of Bioenergetics, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; (S.S.); (R.G.)
- School of Molecular Sciences, Tempe Campus, Mailcode 1604, Arizona State University, Tempe, AZ 85281, USA
| | - Robin Ghosh
- Institute of Biomaterials and Biomolecular Systems, Department of Bioenergetics, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; (S.S.); (R.G.)
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18
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du Toit JP, Lea-Smith DJ, Git A, Hervey JRD, Howe CJ, Pott RWM. Expression of Alternative Nitrogenases in Rhodopseudomonas palustris Is Enhanced Using an Optimized Genetic Toolset for Rapid, Markerless Modifications. ACS Synth Biol 2021; 10:2167-2178. [PMID: 34431288 DOI: 10.1021/acssynbio.0c00496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The phototrophic bacterium Rhodopseudomonas palustris is emerging as a promising biotechnological chassis organism, due to its resilience to a range of harsh conditions, a wide metabolic repertoire, and the ability to quickly regenerate ATP using light. However, realization of this promise is impeded by a lack of efficient, rapid methods for genetic modification. Here, we present optimized tools for generating chromosomal insertions and deletions employing electroporation as a means of transformation. Generation of markerless strains can be completed in 12 days, approximately half the time for previous conjugation-based methods. This system was used for overexpression of alternative nitrogenase isozymes with the aim of improving biohydrogen productivity. Insertion of the pucBa promoter upstream of vnf and anf nitrogenase operons drove robust overexpression up to 4000-fold higher than wild-type. Transcript quantification was facilitated by an optimized high-quality RNA extraction protocol employing lysis using detergent and heat. Overexpression resulted in increased nitrogenase protein levels, extending to superior hydrogen productivity in bioreactor studies under nongrowing conditions, where promoter-modified strains better utilized the favorable energy state created by reduced competition from cell division. Robust heterologous expression driven by the pucBa promoter is thus attractive for energy-intensive biosyntheses suited to the capabilities of R. palustris. Development of this genetic modification toolset will accelerate the advancement of R. palustris as a biotechnological chassis organism, and insights into the effects of nitrogenase overexpression will guide future efforts in engineering strains for improved hydrogen production.
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Affiliation(s)
- Jan-Pierre du Toit
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, 7600, South Africa
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - John R. D. Hervey
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Christopher J. Howe
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Robert W. M. Pott
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, 7600, South Africa
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19
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Schmid F, Novion Ducassou J, Couté Y, Gescher J. Developing Rhodobacter sphaeroides for cathodic biopolymer production. BIORESOURCE TECHNOLOGY 2021; 336:125340. [PMID: 34090098 DOI: 10.1016/j.biortech.2021.125340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
In this work, Rhodobacter sphaeroides was identified as a potential cathodic production strain for photoautotrophic production processes. First, a stable cultivation in a bioelectrochemical system (BES) was established under conditions in which hydrogen produced by a poised cathode served as an electron donor. It was shown that both the introduction of a plasmid vector and exposure to the corresponding antibiotic selection pressure caused a strong improvement in both cathodic biofilm formation and electrochemical properties. A quantitative proteomic analysis identified key players in the molecular adaptation to biofilm growth on the cathodic surface. Furthermore, biofilm formation kinetics were quantified by optical coherence tomography measurements, which showed a strong tendency for biofilm formation together with a robust biofilm architecture. A media switch to N2-limited conditions resulted in increased cathodic poly(3-hydroxybutyrate) (PHB) accumulation, suggesting R. sphaeroides as a potential strain for photoautotrophic PHB production in future industrial applications.
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Affiliation(s)
- Ferdinand Schmid
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe Germany
| | - Julia Novion Ducassou
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048 38000, Grenoble France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048 38000, Grenoble France
| | - Johannes Gescher
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe Germany.
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20
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Shepard EM, Impano S, Duffus BR, Pagnier A, Duschene KS, Betz JN, Byer AS, Galambas A, McDaniel EC, Watts H, McGlynn SE, Peters JW, Broderick WE, Broderick JB. HydG, the "dangler" iron, and catalytic production of free CO and CN -: implications for [FeFe]-hydrogenase maturation. Dalton Trans 2021; 50:10405-10422. [PMID: 34240096 PMCID: PMC9154046 DOI: 10.1039/d1dt01359a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The organometallic H-cluster of the [FeFe]-hydrogenase consists of a [4Fe-4S] cubane bridged via a cysteinyl thiolate to a 2Fe subcluster ([2Fe]H) containing CO, CN-, and dithiomethylamine (DTMA) ligands. The H-cluster is synthesized by three dedicated maturation proteins: the radical SAM enzymes HydE and HydG synthesize the non-protein ligands, while the GTPase HydF serves as a scaffold for assembly of [2Fe]H prior to its delivery to the [FeFe]-hydrogenase containing the [4Fe-4S] cubane. HydG uses l-tyrosine as a substrate, cleaving it to produce p-cresol as well as the CO and CN- ligands to the H-cluster, although there is some question as to whether these are formed as free diatomics or as part of a [Fe(CO)2(CN)] synthon. Here we show that Clostridium acetobutylicum (C.a.) HydG catalyzes formation of multiple equivalents of free CO at rates comparable to those for CN- formation. Free CN- is also formed in excess molar equivalents over protein. A g = 8.9 EPR signal is observed for C.a. HydG reconstituted to load the 5th "dangler" iron of the auxiliary [4Fe-4S][FeCys] cluster and is assigned to this "dangler-loaded" cluster state. Free CO and CN- formation and the degree of activation of [FeFe]-hydrogenase all occur regardless of dangler loading, but are increased 10-35% in the dangler-loaded HydG; this indicates the dangler iron is not essential to this process but may affect relevant catalysis. During HydG turnover in the presence of myoglobin, the g = 8.9 signal remains unchanged, indicating that a [Fe(CO)2(CN)(Cys)] synthon is not formed at the dangler iron. Mutation of the only protein ligand to the dangler iron, H272, to alanine nearly completely abolishes both free CO formation and hydrogenase activation, however results show this is not due solely to the loss of the dangler iron. In experiments with wild type and H272A HydG, and with different degrees of dangler loading, we observe a consistent correlation between free CO/CN- formation and hydrogenase activation. Taken in full, our results point to free CO/CN-, but not an [Fe(CO)2(CN)(Cys)] synthon, as essential species in hydrogenase maturation.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Benjamin R Duffus
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kaitlin S Duschene
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Jeremiah N Betz
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda S Byer
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda Galambas
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Hope Watts
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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21
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Sarma S, Sharma S, Rudakiya D, Upadhyay J, Rathod V, Patel A, Narra M. Valorization of microalgae biomass into bioproducts promoting circular bioeconomy: a holistic approach of bioremediation and biorefinery. 3 Biotech 2021; 11:378. [PMID: 34367870 DOI: 10.1007/s13205-021-02911-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/28/2021] [Indexed: 11/30/2022] Open
Abstract
The need for alternative source of fuel has demanded the cultivation of 3rd generation feedstock which includes microalgae, seaweed and cyanobacteria. These phototrophic organisms are unique in a sense that they utilise natural sources like sunlight, water and CO2 for their growth and metabolism thereby producing diverse products that can be processed to produce biofuel, biochemical, nutraceuticals, feed, biofertilizer and other value added products. But due to low biomass productivity and high harvesting cost, microalgae-based production have not received much attention. Therefore, this review provides the state of the art of the microalgae based biorefinery approach to define an economical and sustainable process. The three major segments that need to be considered for economic microalgae biorefinery is low cost nutrient source, efficient harvesting methods and production of by-products with high market value. This review has outlined the use of various wastewater as nutrient source for simultaneous biomass production and bioremediation. Further, it has highlighted the common harvesting methods used for microalgae and also described various products from both raw biomass and delipidified microalgae residues in order to establish a sustainable, economical microalgae biorefinery with a touch of circular bioeconomy. This review has also discussed various challenges to be considered followed by a techno-economic analysis of the microalgae based biorefinery model.
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Affiliation(s)
- Shyamali Sarma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
| | - Shaishav Sharma
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
| | - Darshan Rudakiya
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
| | - Jinal Upadhyay
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
| | - Vinod Rathod
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
| | - Aesha Patel
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
| | - Madhuri Narra
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Post Box No. 2, Anand, Gujarat 388120 India
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22
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Saye LMG, Navaratna TA, Chong JPJ, O’Malley MA, Theodorou MK, Reilly M. The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production. Microorganisms 2021; 9:694. [PMID: 33801700 PMCID: PMC8065543 DOI: 10.3390/microorganisms9040694] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass. However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel. Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum Neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores. Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to H2 and ethanol. Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to H2 or CH4 by other microorganisms. The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth. Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering. In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.
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Affiliation(s)
- Luke M. G. Saye
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Tejas A. Navaratna
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - James P. J. Chong
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - Michael K. Theodorou
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Matthew Reilly
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
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23
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Policastro G, Luongo V, Fabbricino M. Biohydrogen and poly-β-hydroxybutyrate production by winery wastewater photofermentation: Effect of substrate concentration and nitrogen source. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:111006. [PMID: 32778291 DOI: 10.1016/j.jenvman.2020.111006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/07/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
The applicability and convenience of biohydrogen and poly-β-hydroxybutyrate production through single-stage photofermentation of winery wastewater is demonstrated in the present study. Experiments are conducted using a purple non-sulfur bacteria mixed consortium, subject to variable nutrient conditions, to analyze the effect of initial chemical oxygen demand and the available nitrogen source on the metabolic response. Results show that winery wastewater is a promising substrate for photofermentation processes, despite the presence of inhibiting compounds such as phenolics. Nonetheless, the initial chemical oxygen demand must be carefully controlled to maximize hydrogen production. Up to 468 mL L-1 of hydrogen and 203 mg L-1 of poly-β-hydroxybutyrate can be produced starting from an initial chemical oxygen demand of 1500 mg L-1. The used nitrogen source may direct substrate transformation through different metabolic pathways. Interestingly, the maximum production of both hydrogen and poly-β-hydroxybutyrate occurred when glutamate was used as the nitrogen source.
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Affiliation(s)
- Grazia Policastro
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy.
| | - Vincenzo Luongo
- Department of Mathematics and Applications Renato Caccioppoli, University of Naples Federico II, via Cintia, Monte S. Angelo, I-80126 Naples, Italy.
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy.
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24
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Abstract
The enzyme molybdenum nitrogenase converts atmospheric nitrogen gas to ammonia and is of critical importance for the cycling of nitrogen in the biosphere and for the sustainability of life. Alternative vanadium and iron-only nitrogenases that are homologous to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transition metal, either vanadium or iron, at their active sites. So far alternative nitrogenases have only been found in microbes that also have molybdenum nitrogenase. They are less widespread than molybdenum nitrogenase in bacteria and archaea, and they are less efficient. The presumption has been that alternative nitrogenases are fail-safe enzymes that are used in situations where molybdenum is limiting. Recent work indicates that vanadium nitrogenase may play a role in the global biological nitrogen cycle and iron-only nitrogenase may contribute products that shape microbial community interactions in nature.
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Affiliation(s)
- Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA;
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25
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Production of polyhydroxybutyrate by pure and mixed cultures of purple non-sulfur bacteria: A review. J Biotechnol 2020; 317:39-47. [DOI: 10.1016/j.jbiotec.2020.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 11/24/2022]
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26
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Capson-Tojo G, Batstone DJ, Grassino M, Vlaeminck SE, Puyol D, Verstraete W, Kleerebezem R, Oehmen A, Ghimire A, Pikaar I, Lema JM, Hülsen T. Purple phototrophic bacteria for resource recovery: Challenges and opportunities. Biotechnol Adv 2020; 43:107567. [PMID: 32470594 DOI: 10.1016/j.biotechadv.2020.107567] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
Sustainable development is driving a rapid focus shift in the wastewater and organic waste treatment sectors, from a "removal and disposal" approach towards the recovery and reuse of water, energy and materials (e.g. carbon or nutrients). Purple phototrophic bacteria (PPB) are receiving increasing attention due to their capability of growing photoheterotrophically under anaerobic conditions. Using light as energy source, PPB can simultaneously assimilate carbon and nutrients at high efficiencies (with biomass yields close to unity (1 g CODbiomass·g CODremoved-1)), facilitating the maximum recovery of these resources as different value-added products. The effective use of infrared light enables selective PPB enrichment in non-sterile conditions, without competition with other phototrophs such as microalgae if ultraviolet-visible wavelengths are filtered. This review reunites results systematically gathered from over 177 scientific articles, aiming at producing generalized conclusions. The most critical aspects of PPB-based production and valorisation processes are addressed, including: (i) the identification of the main challenges and potentials of different growth strategies, (ii) a critical analysis of the production of value-added compounds, (iii) a comparison of the different value-added products, (iv) insights into the general challenges and opportunities and (v) recommendations for future research and development towards practical implementation. To date, most of the work has not been executed under real-life conditions, relevant for full-scale application. With the savings in wastewater discharge due to removal of organics, nitrogen and phosphorus as an important economic driver, priorities must go to using PPB-enriched cultures and real waste matrices. The costs associated with artificial illumination, followed by centrifugal harvesting/dewatering and drying, are estimated to be 1.9, 0.3-2.2 and 0.1-0.3 $·kgdry biomass-1. At present, these costs are likely to exceed revenues. Future research efforts must be carried out outdoors, using sunlight as energy source. The growth of bulk biomass on relatively clean wastewater streams (e.g. from food processing) and its utilization as a protein-rich feed (e.g. to replace fishmeal, 1.5-2.0 $·kg-1) appears as a promising valorisation route.
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Affiliation(s)
- Gabriel Capson-Tojo
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072, Australia; CRETUS Institute, Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Damien J Batstone
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - María Grassino
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
| | - Daniel Puyol
- Department of Chemical and Environmental Technology, ESCET, Rey Juan Carlos University, Móstoles, Spain.
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium; Avecom NV, Industrieweg 122P, 9032 Wondelgem, Belgium.
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands.
| | - Adrian Oehmen
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Anish Ghimire
- Department of Environmental Science and Engineering, Kathmandu University, Dhulikhel, Nepal.
| | - Ilje Pikaar
- School of Civil Engineering, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Juan M Lema
- CRETUS Institute, Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Tim Hülsen
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072, Australia.
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27
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Luxem KE, Kraepiel AML, Zhang L, Waldbauer JR, Zhang X. Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation. Environ Microbiol 2020; 22:1397-1408. [PMID: 32090445 PMCID: PMC7187303 DOI: 10.1111/1462-2920.14955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/07/2020] [Indexed: 01/21/2023]
Abstract
Biological nitrogen fixation is catalyzed by the molybdenum (Mo), vanadium (V) and iron (Fe)‐only nitrogenase metalloenzymes. Studies with purified enzymes have found that the ‘alternative’ V‐ and Fe‐nitrogenases generally reduce N2 more slowly and produce more byproduct H2 than the Mo‐nitrogenase, leading to an assumption that their usage results in slower growth. Here we show that, in the metabolically versatile photoheterotroph Rhodopseudomonas palustris, the type of carbon substrate influences the relative rates of diazotrophic growth based on different nitrogenase isoforms. The V‐nitrogenase supports growth as fast as the Mo‐nitrogenase on acetate but not on the more oxidized substrate succinate. Our data suggest that this is due to insufficient electron flux to the V‐nitrogenase isoform on succinate compared with acetate. Despite slightly faster growth based on the V‐nitrogenase on acetate, the wild‐type strain uses exclusively the Mo‐nitrogenase on both carbon substrates. Notably, the differences in H2:N2 stoichiometry by alternative nitrogenases (~1.5 for V‐nitrogenase, ~4–7 for Fe‐nitrogenase) and Mo‐nitrogenase (~1) measured here are lower than prior in vitro estimates. These results indicate that the metabolic costs of V‐based nitrogen fixation could be less significant for growth than previously assumed, helping explain why alternative nitrogenase genes persist in diverse diazotroph lineages and are broadly distributed in the environment.
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Affiliation(s)
- Katja E Luxem
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Anne M L Kraepiel
- Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.,Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
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28
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Craven J, Sultan MA, Sarma R, Wilson S, Meeks N, Kim DY, Hastings JT, Bhattacharyya D. Rhodopseudomonas palustris-based conversion of organic acids to hydrogen using plasmonic nanoparticles and near-infrared light. RSC Adv 2019; 9:41218-41227. [PMID: 35540054 PMCID: PMC9076380 DOI: 10.1039/c9ra08747h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/28/2019] [Indexed: 11/21/2022] Open
Abstract
The simultaneous elimination of organic waste and the production of clean fuels will have an immense impact on both the society and the industrial manufacturing sector. The enhanced understanding of the interface between nanoparticles and photo-responsive bacteria will further advance the knowledge of their interactions with biological systems. Although literature shows the production of gases by photobacteria, herein, we demonstrated the integration of photonics, biology, and nanostructured plasmonic materials for hydrogen production with a lower greenhouse CO2 gas content at quantified light energy intensity and wavelength. Phototrophic purple non-sulfur bacteria were able to generate hydrogen as a byproduct of nitrogen fixation using the energy absorbed from visible and near-IR (NIR) light. This type of biological hydrogen production has suffered from low efficiency of converting light energy into hydrogen in part due to light sources that do not exploit the organisms' capacity for NIR absorption. We used NIR light sources and optically resonant gold-silica core-shell nanoparticles to increase the light utilization of the bacteria to convert waste organic acids such as acetic and maleic acids to hydrogen. The batch growth studies for the small cultures (40 mL) of Rhodopseudomonas palustris demonstrated >2.5-fold increase in hydrogen production when grown under an NIR source (167 ± 18 μmol H2) compared to that for a broad-band light source (60 ± 6 μmol H2) at equal light intensity (130 W m-2). The addition of the mPEG-coated optically resonant gold-silica core-shell nanoparticles in the solution further improved the hydrogen production from 167 ± 18 to 398 ± 108 μmol H2 at 130 W m-2. The average hydrogen production rate with the nanoparticles was 127 ± 35 μmol L-1 h-1 at 130 W m-2.
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Affiliation(s)
- John Craven
- Department of Chemical and Materials Engineering, University of Kentucky 177 FPAT Bldg Lexington KY 40506 USA +1 859 312 7790
| | - Mansoor A Sultan
- Department of Electrical and Computer Engineering, University of Kentucky Lexington KY 40506 USA
| | - Rupam Sarma
- Department of Chemical and Materials Engineering, University of Kentucky 177 FPAT Bldg Lexington KY 40506 USA +1 859 312 7790
| | - Sarah Wilson
- Department of Chemical and Materials Engineering, University of Kentucky 177 FPAT Bldg Lexington KY 40506 USA +1 859 312 7790
| | - Noah Meeks
- Southern Company Services, Inc. Birmingham AL 35203 USA
| | - Doo Young Kim
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - J Todd Hastings
- Department of Electrical and Computer Engineering, University of Kentucky Lexington KY 40506 USA
| | - Dibakar Bhattacharyya
- Department of Chemical and Materials Engineering, University of Kentucky 177 FPAT Bldg Lexington KY 40506 USA +1 859 312 7790
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29
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Higuchi-Takeuchi M, Morisaki K, Numata K. Method for the facile transformation of marine purple photosynthetic bacteria using chemically competent cells. Microbiologyopen 2019; 9:e00953. [PMID: 31638342 PMCID: PMC6957439 DOI: 10.1002/mbo3.953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 02/03/2023] Open
Abstract
Marine purple photosynthetic bacteria are ideal organisms for the production of useful materials at reduced costs and contributing to a sustainable society because they can utilize sunlight, seawater, and components of air, including carbon dioxide and nitrogen gases, for their growth. However, conjugation is the only applicable method for the transformation of marine purple photosynthetic bacteria so far. Here, we examined a calcium chloride‐mediated method for the transformation of marine purple photosynthetic bacteria. Plasmid DNAs containing the kanamycin resistance gene were successfully transferred into chemically competent cells of two strains of marine purple photosynthetic bacteria (Rhodovulum sulfidophilum and Roseospira marina). Heat shock treatment increased the transformation efficiency in R. sulfidophilum, whereas the addition of cell‐penetrating peptide did not improve it. We also found that prolonged incubation in agar plates containing kanamycin led to spontaneous mutation of the 16S rRNA, resulting in kanamycin resistance in R. marina. Thus, we developed an efficient and facile transformation method using chemically competent cells of marine purple photosynthetic bacteria with calcium chloride.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Kumiko Morisaki
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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30
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Higuchi-Takeuchi M, Numata K. Marine Purple Photosynthetic Bacteria as Sustainable Microbial Production Hosts. Front Bioeng Biotechnol 2019; 7:258. [PMID: 31681740 PMCID: PMC6798066 DOI: 10.3389/fbioe.2019.00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/25/2019] [Indexed: 12/01/2022] Open
Abstract
Photosynthetic microorganisms can serve as the ideal hosts for the sustainable production of high-value compounds. Purple photosynthetic bacteria are typical anoxygenic photosynthetic microorganisms and are expected to be one of the suitable microorganisms for industrial production. Purple photosynthetic bacteria are reported to produce polyhydroxyalkanoate (PHA), extracellular nucleic acids and hydrogen gas. We characterized PHA production as a model compound in purple photosynthetic bacteria, especially focused on marine strains. PHA is a family of biopolyesters synthesized by a variety of microorganisms as carbon and energy storage materials. PHA have recently attracted attention as an alternative to conventional petroleum-based plastics. Production of extracellular nucleic acids have been studied in Rhodovulum sulfidophilum, a marine purple non-sulfur bacterium. Several types of artificial RNAs have been successfully produced in R. sulfidophilum. Purple photosynthetic bacteria produce hydrogen via nitrogenase, and genetic engineering strategies have been investigated to enhance the hydrogen production. This mini review describes the microbial production of these high-value compounds using purple photosynthetic bacteria as the host microorganism.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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31
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Sangani AA, McCully AL, LaSarre B, McKinlay JB. Fermentative Escherichia coli makes a substantial contribution to H2 production in coculture with phototrophic Rhodopseudomonas palustris. FEMS Microbiol Lett 2019; 366:5536938. [PMID: 31329226 DOI: 10.1093/femsle/fnz162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/17/2019] [Indexed: 11/14/2022] Open
Abstract
Individual species within microbial communities can combine their attributes to produce services that benefit society, such as the transformation of renewable resources into valuable chemicals. Under defined genetic and environmental conditions, fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris exchange essential carbon and nitrogen, respectively, to establish a mutualistic relationship. In this relationship, each species produces H2 biofuel as a byproduct of its metabolism. However, the extent to which each species contributes to H2 production and the factors that influence their relative contributions were previously unknown. By comparing H2 yields in cocultures pairing R. palustris with either wild-type E. coli or a formate hydrogenlyase mutant that is incapable of H2 production, we determined the relative contribution of each species to total H2 production. Our results indicate that E. coli contributes between 32 and 86% of the H2 produced in coculture depending on the level of ammonium excreted by the R. palustris partner. The level of ammonium excretion influenced the time over which E. coliwas exposed to formate, the types of E. colifermentation products available to R. palustris, and the pH of the medium, all of which affected the contribution of each species to H2 production.
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Affiliation(s)
- Amee A Sangani
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,Biology Undergraduate Program, Indiana University, Bloomington, IN 47405, USA
| | | | - Breah LaSarre
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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32
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Higuchi-Takeuchi M, Numata K. Acetate-Inducing Metabolic States Enhance Polyhydroxyalkanoate Production in Marine Purple Non-sulfur Bacteria Under Aerobic Conditions. Front Bioeng Biotechnol 2019; 7:118. [PMID: 31192201 PMCID: PMC6546801 DOI: 10.3389/fbioe.2019.00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are a family of biopolyesters that a variety of microorganisms accumulate as carbon and energy storage molecules under starvation conditions in the presence of excess carbon. Anoxygenic photosynthetic bacteria exhibit a variety of growth styles and high PHA production activity. Here, we characterized PHA production by four marine purple non-sulfur bacteria strains (Rhodovulum sulfidophilum, Rhodovulum euryhalinum, Rhodovulum imhoffii, and Rhodovulum visakhapatnamense) under different growth conditions. Unlike the well-studied PHA-producing bacteria, nutrient limitation is not appropriate for PHA production in marine purple non-sulfur bacteria. We found that marine purple non-sulfur bacteria did not accumulate PHA under aerobic conditions in the presence of malate and pyruvate. Interestingly, PHA accumulation was observed upon the addition of acetate under aerobic conditions but was not observed upon the addition of reductants, suggesting that an acetate-dependent pathway is involved in PHA accumulation. Gene expression analysis revealed that the expression of isocitrate dehydrogenase in the tricarboxylic acid (TCA) cycle decreased under aerobic conditions and increased with the addition of acetate, indicating that TCA cycle activity is involved in PHA production under aerobic conditions. We also found that expression of PdhRrs, which belongs to the GntR family of transcription regulators, in Rhodovulum sulfidophilum was upregulated upon the addition of acetate. Taken together, the results show that the changes in the metabolic state upon the addition of acetate, possibly regulated by PdhR, are important for PHA production under aerobic conditions in marine purple non-sulfur bacteria.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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33
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Navid A, Jiao Y, Wong SE, Pett-Ridge J. System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris. BMC Bioinformatics 2019; 20:233. [PMID: 31072303 PMCID: PMC6509789 DOI: 10.1186/s12859-019-2844-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/24/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Living organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological trade-offs can provide invaluable information regarding the biophysical and biochemical bases behind observed cellular phenotypes. A quantitative knowledge of a cell system's critical objectives is also needed for engineering of cellular metabolism, where there is interest in mitigating the fitness costs that may result from human manipulation. RESULTS To study metabolism in photoheterotrophs, we developed and validated a genome-scale model of metabolism in Rhodopseudomonas palustris, a metabolically versatile gram-negative purple non-sulfur bacterium capable of growing phototrophically on various carbon sources, including inorganic carbon and aromatic compounds. To quantitatively assess trade-offs among a set of important biological objectives during different metabolic growth modes, we used our new model to conduct an 8-dimensional multi-objective flux analysis of metabolism in R. palustris. Our results revealed that phototrophic metabolism in R. palustris is light-limited under anaerobic conditions, regardless of the available carbon source. Under photoheterotrophic conditions, R. palustris prioritizes the optimization of carbon efficiency, followed by ATP production and biomass production rate, in a Pareto-optimal manner. To achieve maximum carbon fixation, cells appear to divert limited energy resources away from growth and toward CO2 fixation, even in the presence of excess reduced carbon. We also found that to achieve the theoretical maximum rate of biomass production, anaerobic metabolism requires import of additional compounds (such as protons) to serve as electron acceptors. Finally, we found that production of hydrogen gas, of potential interest as a candidate biofuel, lowers the cellular growth rates under all circumstances. CONCLUSIONS Photoheterotrophic metabolism of R. palustris is primarily regulated by the amount of light it can absorb and not the availability of carbon. However, despite carbon's secondary role as a regulating factor, R. palustris' metabolism strives for maximum carbon efficiency, even when this increased efficiency leads to slightly lower growth rates.
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Affiliation(s)
- Ali Navid
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550 USA
| | - Yongqin Jiao
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550 USA
| | - Sergio Ernesto Wong
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550 USA
| | - Jennifer Pett-Ridge
- Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550 USA
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Erkal NA, Eser MG, Özgür E, Gündüz U, Eroglu I, Yücel M. Transcriptome analysis of Rhodobacter capsulatus grown on different nitrogen sources. Arch Microbiol 2019; 201:661-671. [PMID: 30796473 DOI: 10.1007/s00203-019-01635-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/10/2018] [Accepted: 02/18/2019] [Indexed: 01/21/2023]
Abstract
This study investigated the effect of different nitrogen sources, namely, ammonium chloride and glutamate, on photoheterotrophic metabolism of Rhodobacter capsulatus grown on acetate as the carbon source. Genes that were significantly differentially expressed according to Affymetrix microarray data were categorized into Clusters of Orthologous Groups functional categories and those in acetate assimilation, hydrogen production, and photosynthetic electron transport pathways were analyzed in detail. Genes related to hydrogen production metabolism were significantly downregulated in cultures grown on ammonium chloride when compared to those grown on glutamate. In contrast, photosynthetic electron transport and acetate assimilation pathway genes were upregulated. In detail, aceA encoding isocitrate lyase, a unique enzyme of the glyoxylate cycle and ccrA encoding the rate limiting crotonyl-CoA carboxylase/reductase enzyme of ethylmalonyl-coA pathway were significantly upregulated. Our findings indicate for the first time that R. capsulatus can operate both glyoxylate and ethylmalonyl-coA cycles for acetate assimilation.
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Affiliation(s)
- Nilüfer Afsar Erkal
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
- Mikro Biyositemler Inc, 06530, Ankara, Turkey
| | | | - Ebru Özgür
- Mikro Biyositemler Inc, 06530, Ankara, Turkey
- Department of Chemical Engineering, Middle East Technical University, 06800, Ankara, Turkey
| | - Ufuk Gündüz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Inci Eroglu
- Department of Chemical Engineering, Middle East Technical University, 06800, Ankara, Turkey
| | - Meral Yücel
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.
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35
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Anandraj A, White S, Mutanda T. Photosystem I fluorescence as a physiological indicator of hydrogen production in Chlamydomonas reinhardtii. BIORESOURCE TECHNOLOGY 2019; 273:313-319. [PMID: 30448683 DOI: 10.1016/j.biortech.2018.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 06/09/2023]
Abstract
This study investigated the interrelations between hydrogen synthesis and Photosystem I electron transport rate in Chlamydomonas reinhardtii. The fluorescence of both photosystems (PS I and PS II) was monitored using a Dual Pulse Amplitude Modulated (PAM) Fluorometer. Hydrogen synthesis was induced by eliminating sulphur from the growth media (TAP-S). Multiple physiological parameters [rETR, Y (I), Y (II), NPQ, α, Fv/Fm and YI:YII] were recorded using the Dual PAM and correlated to hydrogen produced. There was a 66% increase in Photosystem I rETRmax during hydrogen production. A significant direct correlation existed between PS 1 rETRmax and hydrogen evolution values over the ten-day period (r = 0.895, p < 0.01) indicating that PS I can be considered as a driver of H2 production. Significant correlations between rETRmax of PS I and H2 evolution suggest a novel physiological indicator to monitor H2 production during the three critical phases identified in this study.
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Affiliation(s)
- Akash Anandraj
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Jacobs, 4026 Durban, South Africa.
| | - Sarah White
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Jacobs, 4026 Durban, South Africa
| | - Taurai Mutanda
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Jacobs, 4026 Durban, South Africa
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36
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part IV. Canonical, non-canonical and hybrid iron-sulfur proteins. J Struct Biol 2019; 205:103-120. [PMID: 30677521 DOI: 10.1016/j.jsb.2019.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/26/2022]
Abstract
A plethora of proteins are able to express iron-sulfur clusters, but have a clear picture of the different types of proteins and the different iron-sulfur clusters they harbor it is not easy. In the last five years we have reviewed structure/electrochemistry of metalloproteins expressing: (i) single types of iron-sulfur clusters (namely: {Fe(Cys)4}, {[Fe2S2](Cys)4}, {[Fe2S2](Cys)3(X)} (X = Asp, Arg, His), {[Fe2S2](Cys)2(His)2}, {[Fe3S4](Cys)3}, {[Fe4S4](Cys)4} and {[Fe4S4](Cys)3(nonthiolate ligand)} cores); (ii) metalloproteins harboring iron-sulfur centres of different nuclearities (namely: [4Fe-4S] and [2Fe-2S], [4Fe-4S] and [3Fe-4S], and [4Fe-4S], [3Fe-4S] and [2Fe-2S] clusters. Our target is now to review structure and electrochemistry of proteins harboring canonical, non-canonical and hybrid iron-sulfur proteins.
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Affiliation(s)
- Piero Zanello
- Dipartimento di Biotecnologie, Chimica e Farmacia dell'Università di Siena, Via A. De Gasperi 2, 53100 Siena, Italy
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37
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The physiology and biotechnology of dark fermentative biohydrogen production. Biotechnol Adv 2018; 36:2165-2186. [DOI: 10.1016/j.biotechadv.2018.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 02/02/2023]
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Rosa LT, Dix SR, Rafferty JB, Kelly DJ. Structural basis for high-affinity adipate binding to AdpC (RPA4515), an orphan periplasmic-binding protein from the tripartite tricarboxylate transporter (TTT) family in Rhodopseudomonas palustris. FEBS J 2017; 284:4262-4277. [PMID: 29082669 DOI: 10.1111/febs.14304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/27/2017] [Accepted: 10/19/2017] [Indexed: 01/24/2023]
Abstract
The tripartite tricarboxylate transporter (TTT) family is a poorly characterised group of prokaryotic secondary solute transport systems, which employ a periplasmic substrate-binding protein (SBP) for initial ligand recognition. The substrates of only a small number of TTT systems are known and very few SBP structures have been solved, so the mechanisms of SBP-ligand interactions in this family are not well understood. The SBP RPA4515 (AdpC) from Rhodopseudomonas palustris was found by differential scanning fluorescence and isothermal titration calorimetry to bind aliphatic dicarboxylates of a chain length of six to nine carbons, with KD values in the μm range. The highest affinity was found for the C6-dicarboxylate adipate (1,6-hexanedioate). Crystal structures of AdpC, either adipate or 2-oxoadipate bound, revealed a lack of positively charged amino acids in the binding pocket and showed that water molecules are involved in bridging hydrogen bonds to the substrate, a conserved feature in the TTT SBP family that is distinct from other types of SBP. In AdpC, both of the ligand carboxylate groups and a linear chain conformation are needed for coordination in the binding pocket. RT-PCR showed that adpC expression is upregulated by low environmental adipate concentrations, suggesting adipate is a physiologically relevant substrate but as adpC is not genetically linked to any TTT membrane transport genes, the role of AdpC may be in signalling rather than transport. Our data expand the known ligands for TTT systems and identify a novel high-affinity binding protein for adipate, an important industrial chemical intermediate and food additive. DATABASES Protein structure co-ordinates are available in the PDB under the accession numbers 5OEI and 5OKU.
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Affiliation(s)
- Leonardo T Rosa
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Samuel R Dix
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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Gabrielyan L, Hakobyan L, Trchounian A. Characterization of light-dependent hydrogen production by new green microalga Parachlorella kessleri in various conditions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 175:207-210. [DOI: 10.1016/j.jphotobiol.2017.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/13/2017] [Accepted: 09/05/2017] [Indexed: 11/27/2022]
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40
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Plummer SM, Plummer MA, Merkel PA, Hagen M, Biddle JF, Waidner LA. Using directed evolution to improve hydrogen production in chimeric hydrogenases from Clostridia species. Enzyme Microb Technol 2016; 93-94:132-141. [DOI: 10.1016/j.enzmictec.2016.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 01/28/2023]
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41
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Zou X, Pan T, Chen L, Tian Y, Zhang W. Luminescence materials for pH and oxygen sensing in microbial cells - structures, optical properties, and biological applications. Crit Rev Biotechnol 2016; 37:723-738. [PMID: 27627832 DOI: 10.1080/07388551.2016.1223011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Luminescence including fluorescence and phosphorescence sensors have been demonstrated to be important for studying cell metabolism, and diagnosing diseases and cancer. Various design principles have been employed for the development of sensors in different formats, such as organic molecules, polymers, polymeric hydrogels, and nanoparticles. The integration of the sensing with fluorescence imaging provides valuable tools for biomedical research and applications at not only bulk-cell level but also at single-cell level. In this article, we critically reviewed recent progresses on pH, oxygen, and dual pH and oxygen sensors specifically for their application in microbial cells. In addition, we focused not only on sensor materials with different chemical structures, but also on design and applications of sensors for better understanding cellular metabolism of microbial cells. Finally, we also provided an outlook for future materials design and key challenges in reaching broad applications in microbial cells.
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Affiliation(s)
- Xianshao Zou
- a Department of Materials Science and Engineering , South University of Science and Technology of China , Shenzhen , Guangdong , P.R. China
| | - Tingting Pan
- a Department of Materials Science and Engineering , South University of Science and Technology of China , Shenzhen , Guangdong , P.R. China
| | - Lei Chen
- b Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , P.R. China.,c Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , P.R. China.,d SynBio Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , P.R. China
| | - Yanqing Tian
- a Department of Materials Science and Engineering , South University of Science and Technology of China , Shenzhen , Guangdong , P.R. China
| | - Weiwen Zhang
- b Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , P.R. China.,c Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , P.R. China.,d SynBio Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , P.R. China
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42
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Wecker MS, Beaton SE, Chado RA, Ghirardi ML. Development of a
Rhodobacter capsulatus
self‐reporting model system for optimizing light‐dependent, [FeFe]‐hydrogenase‐driven H
2
production. Biotechnol Bioeng 2016; 114:291-297. [DOI: 10.1002/bit.26076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/29/2016] [Accepted: 08/08/2016] [Indexed: 11/07/2022]
Affiliation(s)
| | - Stephen E. Beaton
- United States Air Force AcademyDepartment of ChemistryColorado SpringsColorado
| | - Robert A. Chado
- United States Air Force AcademyDepartment of ChemistryColorado SpringsColorado
| | - Maria L. Ghirardi
- National Renewable Energy LaboratoryMS 3313, 15013 Denver West ParkwayGoldenColorado80401
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43
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Gabrielyan L, Sargsyan H, Trchounian A. Biohydrogen production by purple non-sulfur bacteria Rhodobacter sphaeroides: Effect of low-intensity electromagnetic irradiation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:592-596. [PMID: 27479839 DOI: 10.1016/j.jphotobiol.2016.07.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 07/23/2016] [Accepted: 07/26/2016] [Indexed: 02/03/2023]
Abstract
The present work was focused on the effects of low-intensity (the flux capacity was of 0.06mWcm(-2)) electromagnetic irradiation (EMI) of extremely high frequencies or millimeter waves on the growth and hydrogen (H2) photoproduction by purple non-sulfur bacteria Rhodobacter sphaeroides MDC6521 (from Armenian mineral springs). After exposure of R. sphaeroides, grown under anaerobic conditions upon illumination, to EMI (51.8GHz and 53.0GHz) for 15min an increase of specific growth rate by ~1.2-fold, in comparison with control (non-irradiated cells), was obtained. However, the effect of EMI depends on the duration of irradiation: the exposure elongation up to 60min caused the delay of the growth lag phase and the decrease specific growth rate by ~1.3-fold, indicating the bactericidal effect of EMI. H2 yield of the culture, irradiated by EMI for 15min, determined during 72h growth, was ~1.2-fold higher than H2 yield of control cells, whereas H2 production by cultures, irradiated by EMI for 60min was not observed during 72h growth. This difference in the effects of extremely high frequency EMI indicates a direct effect of radiation on the membrane transfer and the enzymes of these bacteria. Moreover, EMI increased DCCD-inhibited H(+) fluxes across the bacterial membrane and DCCD-sensitive ATPase activity of membrane vesicles, indicating that the proton FoF1-ATPase is presumably a basic target for extremely high frequency EMI related to H2 production by cultures.
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Affiliation(s)
- Lilit Gabrielyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
| | - Harutyun Sargsyan
- Research Institute of Biology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
| | - Armen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia.
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44
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Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. J Bacteriol 2016; 198:1268-80. [PMID: 26833419 PMCID: PMC4859585 DOI: 10.1128/jb.01025-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethyl sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroidescomplex I enzymes (complex IA and complex IE) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex IA) or NADH oxidation (complex IE). The canonical alphaproteobacterial complex I isozyme (complex IA) was also shown to be important for routing electrons to nitrogenase-mediated H2 production, while the horizontally acquired enzyme (complex IE) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. IMPORTANCE Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides, a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.
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Adessi A, Spini G, Presta L, Mengoni A, Viti C, Giovannetti L, Fani R, De Philippis R. Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL. Stand Genomic Sci 2016; 11:24. [PMID: 26966509 PMCID: PMC4785650 DOI: 10.1186/s40793-016-0145-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/03/2015] [Indexed: 11/17/2022] Open
Abstract
Rhodopseudomonas palustris strain 42OL was isolated in 1973 from a sugar refinery waste treatment pond. The strain has been prevalently used for hydrogen production processes using a wide variety of waste-derived substrates, and cultured both indoors and outdoors, either freely suspended or immobilized. R. palustris 42OL was suitable for many other applications and capable of growing in very different culturing conditions, revealing a wide metabolic versatility. The analysis of the genome sequence allowed to identify the metabolic pathways for hydrogen and poly-β-hydroxy-butyrate production, and confirmed the ability of using a wide range of organic acids as substrates.
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Affiliation(s)
- Alessandra Adessi
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144 Firenze, Italy ; Institute of Chemistry of Organometallic Compounds, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Giulia Spini
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144 Firenze, Italy
| | - Luana Presta
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Carlo Viti
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144 Firenze, Italy
| | - Luciana Giovannetti
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144 Firenze, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144 Firenze, Italy ; Institute of Chemistry of Organometallic Compounds, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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46
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Xie GJ, Liu BF, Wang RQ, Ding J, Ren HY, Zhou X, Ren NQ. Bioaggregate of photo-fermentative bacteria for enhancing continuous hydrogen production in a sequencing batch photobioreactor. Sci Rep 2015; 5:16174. [PMID: 26538350 PMCID: PMC4633638 DOI: 10.1038/srep16174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Hydrogen recovery through solar-driven biomass conversion by photo-fermentative bacteria (PFB) has been regarded as a promising way for sustainable energy production. However, a considerable fraction of organic substrate was consumed for the growth of PFB as biocatalysts, furthermore, these PFB were continuously washed out from the photobioreactor in continuous operation because of their poor flocculation. In this work, PFB bioaggregate induced by L-cysteine was applied in a sequencing batch photobioreactor to enhance continuous hydrogen production and reduce biomass washout. The effects of the hydraulic retention time (HRT), influent concentration and light intensity on hydrogen production of the photobioreactor were investigated. The maximum hydrogen yield (3.35 mol H2/mol acetate) and production rate (1044 ml/l/d) were obtained at the HRT of 96 h, influent concentration of 3.84 g COD/l, and light intensity of 200 W/m2. With excellent settling ability, biomass accumulated in the photobioreactor and reached 2.15 g/l under the optimum conditions. Structural analysis of bioaggregate showed that bacterial cells were covered and tightly linked together by extracellular polymeric substances, and formed a stable structure. Therefore, PFB bioaggregate induced by L-cysteine is an efficient strategy to improve biomass retention capacity of the photobioreactor and enhance hydrogen recovery efficiency from organic wastes.
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Affiliation(s)
- Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.,Advanced Water Management Centre, The University of Queensland, QLD 4072, Australia
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Rui-Qing Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hong-Yu Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xu Zhou
- Advanced Water Management Centre, The University of Queensland, QLD 4072, Australia
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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47
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Ding Q, Chen G, Wang Y, Wei D. Identification of Specific Variations in a Non-Motile Strain of Cyanobacterium Synechocystis sp. PCC 6803 Originated from ATCC 27184 by Whole Genome Resequencing. Int J Mol Sci 2015; 16:24081-93. [PMID: 26473841 PMCID: PMC4632739 DOI: 10.3390/ijms161024081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/23/2015] [Accepted: 09/29/2015] [Indexed: 11/25/2022] Open
Abstract
Cyanobacterium Synechocystis sp. PCC 6803 is a widely used model organism in basic research and biofuel biotechnology application. Here, we report the genomic sequence of chromosome and seven plasmids of a glucose-tolerant, non-motile strain originated from ATCC 27184, GT-G, in use at Guangzhou. Through high-throughput genome re-sequencing and verification by Sanger sequencing, eight novel variants were identified in its chromosome and plasmids. The eight novel variants, especially the five non-silent mutations might have interesting effects on the phenotype of GT-G strains, for example the truncated Sll1895 and Slr0322 protein. These resequencing data provide background information for further research and application based on the GT-G strain and also provide evidence to study the evolution and divergence of Synechocystis 6803 globally.
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Affiliation(s)
- Qinglong Ding
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China.
| | - Gu Chen
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China.
| | - Yuling Wang
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China.
| | - Dong Wei
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China.
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48
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Morra S, Cordara A, Gilardi G, Valetti F. Atypical effect of temperature tuning on the insertion of the catalytic iron-sulfur center in a recombinant [FeFe]-hydrogenase. Protein Sci 2015; 24:2090-4. [PMID: 26362685 DOI: 10.1002/pro.2805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 01/04/2023]
Abstract
The expression of recombinant [FeFe]-hydrogenases is an important step for the production of large amount of these enzymes for their exploitation in biotechnology and for the characterization of the protein-metal cofactor interactions. The correct assembly of the organometallic catalytic site, named H-cluster, requires a dedicated set of maturases that must be coexpressed in the microbial hosts or used for in vitro assembly of the active enzymes. In this work, the effect of the post-induction temperature on the recombinant expression of CaHydA [FeFe]-hydrogenase in E. coli is investigated. The results show a peculiar behavior: the enzyme expression is maximum at lower temperatures (20°C), while the specific activity of the purified CaHydA is higher at higher temperature (30°C), as a consequence of improved protein folding and active site incorporation.
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Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Alessandro Cordara
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
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49
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Heiniger EK, Harwood CS. Posttranslational modification of a vanadium nitrogenase. Microbiologyopen 2015; 4:597-603. [PMID: 26097040 PMCID: PMC4554455 DOI: 10.1002/mbo3.265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/06/2015] [Accepted: 04/13/2015] [Indexed: 11/11/2022] Open
Abstract
In microbes that fix nitrogen, nitrogenase catalyzes the conversion of N2 to ammonia in an ATP-demanding reaction. To help conserve energy some bacteria inhibit nitrogenase activity upon exposure to ammonium. The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 can synthesize three functional nitrogenase isoenzymes: a molybdenum nitrogenase, a vanadium nitrogenase, and an iron nitrogenase. Previous studies showed that in some alphaproteobacteria, including R. palustris, molybdenum nitrogenase activity is inhibited by ADP-ribosylation when cells are exposed to ammonium. Some iron nitrogenases are also posttranslationally modified. However, the posttranslational modification of vanadium nitrogenase has not been reported. Here, we investigated the regulation of the alternative nitrogenases of R. palustris and determined that both its vanadium nitrogenase and its iron nitrogenase activities were inhibited and posttranslationally modified when cells are exposed to ammonium. Vanadium nitrogenase is not found in all strains of R. palustris, suggesting that it may have been acquired by horizontal gene transfer. Also, phylogenetic analyses of the three nitrogenases suggest that VnfH, the target of ADP-ribosylation, may be the product of a gene duplication of nifH, the molybdenum nitrogenase homolog.
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Affiliation(s)
- Erin K Heiniger
- Department of Microbiology, University of Washington, Seattle, Washington, 98195
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, 98195
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50
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Kernan C, Chow PP, Christianson RJ, Huang J. Experimental and Computational Investigation of Biofilm Formation by Rhodopseudomonas palustris Growth under Two Metabolic Modes. PLoS One 2015; 10:e0129354. [PMID: 26087200 PMCID: PMC4472842 DOI: 10.1371/journal.pone.0129354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/08/2015] [Indexed: 11/18/2022] Open
Abstract
We examined biofilms formed by the metabolically versatile bacterium Rhodopseudomonas palustris grown via different metabolic modes. R. palustris was grown in flow cell chambers with identical medium conditions either in the presence or absence of light and oxygen. In the absence of oxygen and the presence of light, R. palustris grew and formed biofilms photoheterotrophically, and in the presence of oxygen and the absence of light, R. palustris grew and formed biofilms heterotrophically. We used confocal laser scanning microscopy and image analysis software to quantitatively analyze and compare R. palustris biofilm formation over time in these two metabolic modes. We describe quantifiable differences in structure between the biofilms formed by the bacterium grown heterotrophically and those grown photoheterotrophically. We developed a computational model to explore ways in which biotic and abiotic parameters could drive the observed biofilm architectures, as well as a random-forest machine-learning algorithm based on structural differences that was able to identify growth conditions from the confocal imaging of the biofilms with 87% accuracy. Insight into the structure of phototrophic biofilms and conditions that influence biofilm formation is relevant for understanding the generation of biofilm structures with different properties, and for optimizing applications with phototrophic bacteria growing in the biofilm state.
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Affiliation(s)
- Chase Kernan
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
| | - Philicia P. Chow
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
| | - Rebecca J. Christianson
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
- * E-mail:
| | - Jean Huang
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
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