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Valzelli A, Boschetti A, Mattiotti F, Kargol A, Green C, Borgonovi F, Celardo GL. Large Scale Simulations of Photosynthetic Antenna Systems: Interplay of Cooperativity and Disorder. J Phys Chem B 2024; 128:9643-9655. [PMID: 39351757 DOI: 10.1021/acs.jpcb.4c02406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
Abstract
Large-scale simulations of light-matter interaction in natural photosynthetic antenna complexes containing more than one hundred thousands of chlorophyll molecules, comparable with natural size, have been performed. Photosynthetic antenna complexes present in Green sulfur bacteria and Purple bacteria have been analyzed using a radiative non-Hermitian Hamiltonian, well-known in the field of quantum optics, instead of the widely used dipole-dipole Frenkel Hamiltonian. This approach allows us to study ensembles of emitters beyond the small volume limit (system size much smaller than the absorbed wavelength), where the Frenkel Hamiltonian fails. When analyzed on a large scale, such structures display superradiant states much brighter than their single components. An analysis of the robustness to static disorder and dynamical (thermal) noise shows that exciton coherence in the whole photosynthetic complex is larger than the coherence found in its parts. This provides evidence that the photosynthetic complex as a whole plays a predominant role in sustaining coherences in the system even at room temperature. Our results allow a better understanding of natural photosynthetic antennae and could drive experiments to verify how the response to electromagnetic radiation depends on the size of the photosynthetic antenna.
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Affiliation(s)
- Alessia Valzelli
- Dipartimento di Ingegneria dell'Informazione, Università degli Studi di Firenze, 50139 Firenze, Italy
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze e CSDC, 50019 Sesto Fiorentino,Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, 50019 Sesto Fiorentino,Italy
| | - Alice Boschetti
- European Laboratory for Non-Linear Spectroscopy (LENS), Università degli Studi di Firenze, 50019 Sesto Fiorentino,Italy
- Istituto Nazionale di Ricerca Metrologica (INRiM), 10135 Torino, Italy
| | - Francesco Mattiotti
- CESQ and ISIS (UMR 7006), aQCess, University of Strasbourg and CNRS, 67000 Strasbourg, France
| | - Armin Kargol
- Department of Physics, Loyola University New Orleans, New Orleans, Louisiana 70118, United States
| | - Coleman Green
- Department of Physics, Loyola University New Orleans, New Orleans, Louisiana 70118, United States
| | - Fausto Borgonovi
- Dipartimento di Matematica e Fisica and Interdisciplinary Laboratories for Advanced Materials Physics, Università Cattolica, 25133 Brescia,Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Milano, 20133 Milano,Italy
| | - G Luca Celardo
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze e CSDC, 50019 Sesto Fiorentino,Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, 50019 Sesto Fiorentino,Italy
- European Laboratory for Non-Linear Spectroscopy (LENS), Università degli Studi di Firenze, 50019 Sesto Fiorentino,Italy
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2
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Ochoa-Hernández ME, Reynoso-Varela A, Martínez-Córdova LR, Rodelas B, Durán U, Alcántara-Hernández RJ, Serrano-Palacios D, Calderón K. Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118435. [PMID: 37379625 DOI: 10.1016/j.jenvman.2023.118435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.
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Affiliation(s)
- María E Ochoa-Hernández
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Andrea Reynoso-Varela
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico
| | - Luis R Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Belén Rodelas
- Department of Microbiology and Institute of Water Research, University of Granada, Spain
| | - Ulises Durán
- Universidad Autónoma Metropolitana, Biotechnology Dept., P.A. 55-535, 09340, Iztapalapa, Mexico City, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, Mexico
| | - Denisse Serrano-Palacios
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico.
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
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3
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Frehan SK, Dsouza L, Li X, Eríc V, Jansen TLC, Mul G, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Huijser A. Photon Energy-Dependent Ultrafast Exciton Transfer in Chlorosomes of Chlorobium tepidum and the Role of Supramolecular Dynamics. J Phys Chem B 2023; 127:7581-7589. [PMID: 37611240 PMCID: PMC10493955 DOI: 10.1021/acs.jpcb.3c05282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/09/2023] [Indexed: 08/25/2023]
Abstract
The antenna complex of green sulfur bacteria, the chlorosome, is one of the most efficient supramolecular systems for efficient long-range exciton transfer in nature. Femtosecond transient absorption experiments provide new insight into how vibrationally induced quantum overlap between exciton states supports highly efficient long-range exciton transfer in the chlorosome of Chlorobium tepidum. Our work shows that excitation energy is delocalized over the chlorosome in <1 ps at room temperature. The following exciton transfer to the baseplate occurs in ∼3 to 5 ps, in line with earlier work also performed at room temperature, but significantly faster than at the cryogenic temperatures used in previous studies. This difference can be attributed to the increased vibrational motion at room temperature. We observe a so far unknown impact of the excitation photon energy on the efficiency of this process. This dependency can be assigned to distinct optical domains due to structural disorder, combined with an exciton trapping channel competing with exciton transfer toward the baseplate. An oscillatory transient signal damped in <1 ps has the highest intensity in the case of the most efficient exciton transfer to the baseplate. These results agree well with an earlier computational finding of exciton transfer driven by low-frequency rotational motion of molecules in the chlorosome. Such an exciton transfer process belongs to the quantum coherent regime, for which the Förster theory for intermolecular exciton transfer does not apply. Our work hence strongly indicates that structural flexibility is important for efficient long-range exciton transfer in chlorosomes.
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Affiliation(s)
- Sean K. Frehan
- MESA+
Institute for Nanotechnology, University
of Twente, 7500 AE Enschede, The Netherlands
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Xinmeng Li
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315 Oslo, Norway
| | - Vesna Eríc
- Zernike
Institute of Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute of Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Guido Mul
- MESA+
Institute for Nanotechnology, University
of Twente, 7500 AE Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, 7500 AE Enschede, The Netherlands
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Cerruti M, Kim JH, Pabst M, Van Loosdrecht MCM, Weissbrodt DG. Light intensity defines growth and photopigment content of a mixed culture of purple phototrophic bacteria. Front Microbiol 2022; 13:1014695. [DOI: 10.3389/fmicb.2022.1014695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Purple bacteria (PPB), anoxygenic photoorganoheterotrophic organisms with a hyper-versatile metabolism and high biomass yields over substrate, are promising candidates for the recovery of nutrient resources from wastewater. Infrared light is a pivotal parameter to control and design PPB-based resource recovery. However, the effects of light intensities on the physiology and selection of PPB in mixed cultures have not been studied to date. Here, we examined the effect of infrared irradiance on PPB physiology, enrichment, and growth over a large range of irradiance (0 to 350 W m−2) in an anaerobic mixed-culture sequencing batch photobioreactor. We developed an empirical mathematical model that suggests higher PPB growth rates as response to higher irradiance. Moreover, PPB adapted to light intensity by modulating the abundances of their phototrophic complexes. The obtained results provide an in-depth phylogenetic and metabolic insight the impact of irradiance on PPB. Our findings deliver the fundamental information for guiding the design of light-driven, anaerobic mixed-culture PPB processes for wastewater treatment and bioproduct valorization.
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5
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Tang K, Jia L, Yuan B, Yang S, Li H, Meng J, Zeng Y, Feng F. Aerobic Anoxygenic Phototrophic Bacteria Promote the Development of Biological Soil Crusts. Front Microbiol 2018; 9:2715. [PMID: 30483234 PMCID: PMC6243035 DOI: 10.3389/fmicb.2018.02715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/23/2018] [Indexed: 12/14/2022] Open
Abstract
Chlorophyll-containing oxygenic photoautotrophs have been well known to play a fundamental role in the development of biological soil crusts (BSCs) by harvesting solar radiations and providing fixed carbon to the BSCs ecosystems. Although the same functions can be theoretically fulfilled by the widespread bacteriochlorophyll-harboring aerobic anoxygenic phototrophic bacteria (AAnPB), whether AAnPB play a role in the formation of BSCs and how important they are to this process remain largely unknown. To address these questions, we set up a microcosm system with surface sands of the Hopq desert in northern China and observed the significant effects of near-infrared illumination on the development of BSCs. Compared to near-infrared or red light alone, the combined use of near-infrared and red lights for illumination greatly increased the thickness of BSCs, their organic matter contents and the microalgae abundance by 24.0, 103.7, and 1447.6%, respectively. These changes were attributed to the increasing abundance of AAnPB that can absorb near-infrared radiations. Our data suggest that AAnPB is a long-overlooked driver in promoting the development of BSCs in drylands.
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Affiliation(s)
- Kai Tang
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Lijuan Jia
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Bo Yuan
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China.,College of Life Science, Inner Mongolia Normal University, Huhhot, China
| | - Shanshan Yang
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Heng Li
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Jianyu Meng
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China
| | - Yonghui Zeng
- Aarhus Institute of Advanced Studies, Aarhus, Denmark.,Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Fuying Feng
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Huhhot, China
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6
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A weak infrared light strengthens anoxygenic photosynthetic bacteria activated sludge for the anaerobic biodegradation of polylactic acid in microbial fuel cell systems. Polym Degrad Stab 2018. [DOI: 10.1016/j.polymdegradstab.2018.09.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Qi X, Ren Y, Liang P, Wang X. New insights in photosynthetic microbial fuel cell using anoxygenic phototrophic bacteria. BIORESOURCE TECHNOLOGY 2018; 258:310-317. [PMID: 29571891 DOI: 10.1016/j.biortech.2018.03.058] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/05/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Anoxygenic phototrophic bacteria (APB) pay a key role in biogeochemical cycles, and it can convert light energy to chemical energy by photosynthesis process. Photosynthetic microbial fuel cell (photo-MFC) is regarded as a promising energy-harvesting technology, which is also applied to environment treatment in recent years. The previous studies show that photo-MFC with APB have higher power putout than other bioelectrochemical systems. However, photo-MFC with APB is not reviewed due to some limited factors in the development process. In this review, photo-MFC with APB is treated according to its electron transfer pathways, the current understanding, APB strains, application, influence of substrates, and economic assessment. Meanwhile, knowledge of photosynthesis components and electron transfer pathways of APB is crucial for developing new energy and easing the serious energy crisis. Moreover, some new insights (the optimization of light source and self-sustaining bioelectricity generation) are proposed for the future explorations.
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Affiliation(s)
- Xiang Qi
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment, Tsinghua University, Beijing 100084, PR China; University of Chinese Academy of Sciences, Beijing 101407, PR China
| | - Yiwei Ren
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; University of Chinese Academy of Sciences, Beijing 101407, PR China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xingzu Wang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; University of Chinese Academy of Sciences, Beijing 101407, PR China.
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8
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Coles D, Flatten LC, Sydney T, Hounslow E, Saikin SK, Aspuru-Guzik A, Vedral V, Tang JKH, Taylor RA, Smith JM, Lidzey DG. A Nanophotonic Structure Containing Living Photosynthetic Bacteria. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701777. [PMID: 28809455 DOI: 10.1002/smll.201701777] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/08/2017] [Indexed: 06/07/2023]
Abstract
Photosynthetic organisms rely on a series of self-assembled nanostructures with tuned electronic energy levels in order to transport energy from where it is collected by photon absorption, to reaction centers where the energy is used to drive chemical reactions. In the photosynthetic bacteria Chlorobaculum tepidum, a member of the green sulfur bacteria family, light is absorbed by large antenna complexes called chlorosomes to create an exciton. The exciton is transferred to a protein baseplate attached to the chlorosome, before migrating through the Fenna-Matthews-Olson complex to the reaction center. Here, it is shown that by placing living Chlorobaculum tepidum bacteria within a photonic microcavity, the strong exciton-photon coupling regime between a confined cavity mode and exciton states of the chlorosome can be accessed, whereby a coherent exchange of energy between the bacteria and cavity mode results in the formation of polariton states. The polaritons have energy distinct from that of the exciton which can be tuned by modifying the energy of the optical modes of the microcavity. It is believed that this is the first demonstration of the modification of energy levels within living biological systems using a photonic structure.
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Affiliation(s)
- David Coles
- Department of Physics and Astronomy, University of Sheffield, Sheffield, S3 7RH, UK
| | - Lucas C Flatten
- Department of Materials, University of Oxford, Sheffield, OX1 3PH, UK
| | - Thomas Sydney
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Emily Hounslow
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Semion K Saikin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Institute of Physics, Kazan Federal University, Kazan, 420008, Russian Federation
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Vlatko Vedral
- Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph Kuo-Hsiang Tang
- Department of Chemistry and Biochemistry, Clark University, Worcester, MA, 01610-1477, USA
| | - Robert A Taylor
- Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Jason M Smith
- Department of Materials, University of Oxford, Sheffield, OX1 3PH, UK
| | - David G Lidzey
- Department of Physics and Astronomy, University of Sheffield, Sheffield, S3 7RH, UK
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9
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Qi X, Ren Y, Tian E, Wang X. The exploration of monochromatic near-infrared LED improved anoxygenic photosynthetic bacteria Rhodopseudomonas sp. for wastewater treatment. BIORESOURCE TECHNOLOGY 2017; 241:620-626. [PMID: 28605726 DOI: 10.1016/j.biortech.2017.05.202] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/27/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
The future wastewater treatment requires high-efficiency and energy-saving technology. Anoxygenic photosynthetic bacteria (APB) is deemed as an eco-friendly microorganism, which could be employed in wastewater treatment. Here, monochromatic near-infrared (MNIR) light emitting diode (LED) was used, and three key factors (light quality, light intensity and photoperiod) of it were analyzed by a response surface methodology (RSM) in APB wastewater treatment. The results showed that light quality was the biggest impact factor in APB wastewater treatment, and nearly 58.07% of NH4+-N and 70.62% of chemical oxygen demand (COD) could be removed based on 46.4% of that theoretically possible. The light quality's study revealed that APB had the highest NH4+-N and COD removal, biomass production, and bacteriochlorophyll a production with 850nm IR LED. Moreover, the application of optimal MNIR LED could not only save energy, but also avoid algae bloom of photo-bioreactors (PBR).
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Affiliation(s)
- Xiang Qi
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; College of Resource and Environment, University of Chinese Academy of Sciences, Beijing 101407, China
| | - Yiwei Ren
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing Industrial Technology Innovation Institute of Environmental Protection Membrane Materials and Equipment Technology, Chongqing 408400, China
| | - Enling Tian
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Xingzu Wang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
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10
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Schütte UME, Cadieux SB, Hemmerich C, Pratt LM, White JR. Unanticipated Geochemical and Microbial Community Structure under Seasonal Ice Cover in a Dilute, Dimictic Arctic Lake. Front Microbiol 2016; 7:1035. [PMID: 27458438 PMCID: PMC4932660 DOI: 10.3389/fmicb.2016.01035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/20/2016] [Indexed: 11/13/2022] Open
Abstract
Despite most lakes in the Arctic being perennially or seasonally frozen for at least 40% of the year, little is known about microbial communities and nutrient cycling under ice cover. We assessed the vertical microbial community distribution and geochemical composition in early spring under ice in a seasonally ice-covered lake in southwest Greenland using amplicon-based sequencing that targeted 16S rRNA genes and using a combination of field and laboratory aqueous geochemical methods. Microbial communities changed consistently with changes in geochemistry. Composition of the abundant members responded strongly to redox conditions, shifting downward from a predominantly heterotrophic aerobic community in the suboxic waters to a heterotrophic anaerobic community in the anoxic waters. Operational taxonomic units (OTUs) of Sporichthyaceae, Comamonadaceae, and the SAR11 Clade had higher relative abundances above the oxycline and OTUs within the genus Methylobacter, the phylum Lentisphaerae, and purple sulfur bacteria (PSB) below the oxycline. Notably, a 13-fold increase in sulfide at the oxycline was reflected in an increase and change in community composition of potential sulfur oxidizers. Purple non-sulfur bacteria were present above the oxycline and green sulfur bacteria and PSB coexisted below the oxycline, however, PSB were most abundant. For the first time we show the importance of PSB as potential sulfur oxidizers in an Arctic dimictic lake.
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Affiliation(s)
- Ursel M E Schütte
- Integrated Program in the Environment, Indiana University, BloomingtonIN, USA; Institute of Arctic Biology, University of Alaska Fairbanks, FairbanksAK, USA
| | - Sarah B Cadieux
- Department of Geological Sciences, Indiana University, BloomingtonIN, USA; University of Illinois at Chicago, ChicagoIL, USA
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington IN, USA
| | - Lisa M Pratt
- Department of Geological Sciences, Indiana University, Bloomington IN, USA
| | - Jeffrey R White
- Integrated Program in the Environment, Indiana University, BloomingtonIN, USA; School of Public and Environmental Affairs, Indiana University, BloomingtonIN, USA
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11
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Tao MJ, Ai Q, Deng FG, Cheng YC. Proposal for probing energy transfer pathway by single-molecule pump-dump experiment. Sci Rep 2016; 6:27535. [PMID: 27277702 PMCID: PMC4899753 DOI: 10.1038/srep27535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 12/25/2022] Open
Abstract
The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.
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Affiliation(s)
- Ming-Jie Tao
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Qing Ai
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Fu-Guo Deng
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Yuan-Chung Cheng
- Department of Chemistry, Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan
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12
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Sawaya NPD, Huh J, Fujita T, Saikin SK, Aspuru-Guzik A. Fast delocalization leads to robust long-range excitonic transfer in a large quantum chlorosome model. NANO LETTERS 2015; 15:1722-1729. [PMID: 25694170 DOI: 10.1021/nl504399d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chlorosomes are efficient light-harvesting antennas containing up to hundreds of thousands of bacteriochlorophyll molecules. With massively parallel computer hardware, we use a nonperturbative stochastic Schrödinger equation, while including an atomistically derived spectral density, to study excitonic energy transfer in a realistically sized chlorosome model. We find that fast short-range delocalization leads to robust long-range transfer due to the antennae's concentric-roll structure. Additionally, we discover anomalous behavior arising from different initial conditions, and outline general considerations for simulating excitonic systems on the nanometer to micrometer scale.
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Affiliation(s)
- Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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Peroxidase activity and involvement in the oxidative stress response of roseobacter denitrificans truncated hemoglobin. PLoS One 2015; 10:e0117768. [PMID: 25658318 PMCID: PMC4319818 DOI: 10.1371/journal.pone.0117768] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/01/2015] [Indexed: 11/19/2022] Open
Abstract
Roseobacter denitrificans is a member of the widespread marine Roseobacter genus. We report the first characterization of a truncated hemoglobin from R. denitrificans (Rd. trHb) that was purified in the heme-bound form from heterologous expression of the protein in Escherichia coli. Rd. trHb exhibits predominantly alpha-helical secondary structure and absorbs light at 412, 538 and 572 nm. The phylogenetic classification suggests that Rd. trHb falls into group II trHbs, whereas sequence alignments indicate that it shares certain important heme pocket residues with group I trHbs in addition to those of group II trHbs. The resonance Raman spectra indicate that the isolated Rd. trHb contains a ferric heme that is mostly 6-coordinate low-spin and that the heme of the ferrous form displays a mixture of 5- and 6-coordinate states. Two Fe-His stretching modes were detected, notably one at 248 cm-1, which has been reported in peroxidases and some flavohemoglobins that contain an Fe-His-Asp (or Glu) catalytic triad, but was never reported before in a trHb. We show that Rd. trHb exhibits a significant peroxidase activity with a (kcat/Km) value three orders of magnitude higher than that of bovine Hb and only one order lower than that of horseradish peroxidase. This enzymatic activity is pH-dependent with a pKa value ~6.8. Homology modeling suggests that residues known to be important for interactions with heme-bound ligands in group II trHbs from Mycobacterium tuberculosis and Bacillus subtilis are pointing toward to heme in Rd. trHb. Genomic organization and gene expression profiles imply possible functions for detoxification of reactive oxygen and nitrogen species in vivo. Altogether, Rd. trHb exhibits some distinctive features and appears equipped to help the bacterium to cope with reactive oxygen/nitrogen species and/or to operate redox biochemistry.
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León-Montiel RDJ, Kassal I, Torres JP. Importance of Excitation and Trapping Conditions in Photosynthetic Environment-Assisted Energy Transport. J Phys Chem B 2014; 118:10588-94. [DOI: 10.1021/jp505179h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Roberto de J. León-Montiel
- ICFO−Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
| | - Ivan Kassal
- Centre
for Engineered Quantum Systems, Centre for Quantum Computation and
Communication Technology, and School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072, Australia
| | - Juan P. Torres
- ICFO−Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
- Department
of Signal Theory and Communications, Campus Nord D3, Universitat Politecnica de Catalunya, 08034 Barcelona, Spain
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