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Noori MT, Rossi R, Logan BE, Min B. Hydrogen production in microbial electrolysis cells with biocathodes. Trends Biotechnol 2024; 42:815-828. [PMID: 38360421 DOI: 10.1016/j.tibtech.2023.12.010] [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: 09/11/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 02/17/2024]
Abstract
Electroautotrophic microbes at biocathodes in microbial electrolysis cells (MECs) can catalyze the hydrogen evolution reaction with low energy demand, facilitating long-term stable performance through specific and renewable biocatalysts. However, MECs have not yet reached commercialization due to a lack of understanding of the optimal microbial strains and reactor configurations for achieving high performance. Here, we critically analyze the criteria for the inocula selection, with a focus on the effect of hydrogenase activity and microbe-electrode interactions. We also evaluate the impact of the reactor design and key parameters, such as membrane type, composition, and electrode surface area on internal resistance, mass transport, and pH imbalances within MECs. This analysis paves the way for advancements that could propel biocathode-assisted MECs toward scalable hydrogen gas production.
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Affiliation(s)
- Md Tabish Noori
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, South Korea
| | - Ruggero Rossi
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, Penn State University, Pennsylvania, PA 16801, USA
| | - Booki Min
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, South Korea.
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2
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Ham R, Nielsen CJ, Pullen S, Reek JNH. Supramolecular Coordination Cages for Artificial Photosynthesis and Synthetic Photocatalysis. Chem Rev 2023; 123:5225-5261. [PMID: 36662702 PMCID: PMC10176487 DOI: 10.1021/acs.chemrev.2c00759] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Because sunlight is the most abundant energy source on earth, it has huge potential for practical applications ranging from sustainable energy supply to light driven chemistry. From a chemical perspective, excited states generated by light make thermodynamically uphill reactions possible, which forms the basis for energy storage into fuels. In addition, with light, open-shell species can be generated which open up new reaction pathways in organic synthesis. Crucial are photosensitizers, which absorb light and transfer energy to substrates by various mechanisms, processes that highly depend on the distance between the molecules involved. Supramolecular coordination cages are well studied and synthetically accessible reaction vessels with single cavities for guest binding, ensuring close proximity of different components. Due to high modularity of their size, shape, and the nature of metal centers and ligands, cages are ideal platforms to exploit preorganization in photocatalysis. Herein we focus on the application of supramolecular cages for photocatalysis in artificial photosynthesis and in organic photo(redox) catalysis. Finally, a brief overview of immobilization strategies for supramolecular cages provides tools for implementing cages into devices. This review provides inspiration for future design of photocatalytic supramolecular host-guest systems and their application in producing solar fuels and complex organic molecules.
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Affiliation(s)
- Rens Ham
- Homogeneous and Supramolecular Catalysis, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - C Jasslie Nielsen
- Homogeneous and Supramolecular Catalysis, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Sonja Pullen
- Homogeneous and Supramolecular Catalysis, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Joost N H Reek
- Homogeneous and Supramolecular Catalysis, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
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3
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Stephens S, Mahadevan R, Allen DG. Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review. Front Bioeng Biotechnol 2021; 8:610723. [PMID: 33490053 PMCID: PMC7820810 DOI: 10.3389/fbioe.2020.610723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
Microbial production of chemicals using renewable feedstocks such as glucose has emerged as a green alternative to conventional chemical production processes that rely primarily on petroleum-based feedstocks. The carbon footprint of such processes can further be reduced by using engineered cells that harness solar energy to consume feedstocks traditionally considered to be wastes as their carbon sources. Photosynthetic bacteria utilize sophisticated photosystems to capture the energy from photons to generate reduction potential with such rapidity and abundance that cells often cannot use it fast enough and much of it is lost as heat and light. Engineering photosynthetic organisms could enable us to take advantage of this energy surplus by redirecting it toward the synthesis of commercially important products such as biofuels, bioplastics, commodity chemicals, and terpenoids. In this work, we review photosynthetic pathways in aerobic and anaerobic bacteria to better understand how these organisms have naturally evolved to harness solar energy. We also discuss more recent attempts at engineering both the photosystems and downstream reactions that transfer reducing power to improve target chemical production. Further, we discuss different methods for the optimization of photosynthetic bioprocess including the immobilization of cells and the optimization of light delivery. We anticipate this review will serve as an important resource for future efforts to engineer and harness photosynthetic bacteria for chemical production.
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Affiliation(s)
- Sheida Stephens
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - D Grant Allen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
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Santos-Cortez RLP, Bhutta MF, Earl JP, Hafrén L, Jennings M, Mell JC, Pichichero ME, Ryan AF, Tateossian H, Ehrlich GD. Panel 3: Genomics, precision medicine and targeted therapies. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109835. [PMID: 32007292 PMCID: PMC7155947 DOI: 10.1016/j.ijporl.2019.109835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. DATA SOURCES PubMed articles published since the last meeting in June 2015 up to June 2019. REVIEW METHODS A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. CONCLUSION Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. IMPLICATIONS FOR PRACTICE In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19 Ave., Aurora, CO 80045, USA
| | - Mahmood F. Bhutta
- Department of ENT, Royal Sussex County Hospital, Eastern Road, Brighton BN2 5BE, UK
| | - Joshua P. Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Tukholmankatu 8A, 00290 Helsinki, Finland
| | - Michael Jennings
- Institute for Glycomics, Gold Coast campus, Griffith University, QLD 4222, Australia
| | - Joshua C. Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, 1425 Portland Ave., Rochester, NY 14621, USA
| | - Allen F. Ryan
- Department of Surgery/Otolaryngology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hilda Tateossian
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, Oxford, Didcot OX11 0RD, UK
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
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Liu Z, Wang J, Zhang T, Zhou S, Yan K. The effects of microbial fuel cells coupled with solar cells under intermittent illumination on sediment remediation. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:2141-2149. [PMID: 31701991 DOI: 10.1039/c9em00380k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The purpose of this paper was to examine the effect of microbial fuel cells coupled with solar cells (MFC-SCs). In this study, MFC-SCs were constructed to understand the role of intermittent illumination in electricity generation and sediment remediation based on the sediment microbial fuel cell scenario. Furthermore, the microbial community structure on the anode in the sediment was probed using high-throughput sequencing. We identified that SCs with natural intermittent illumination (12 h per day) can promote the electricity production and nutrient utilization of the sediment of MFCs to the greatest extent, which can help manage solar energy utilization for environmental conversion and control the eutrophication of water bodies.The removal rates of NH3-N, NO3-N, organic matter and TP by the MFC-SC were 46.23% ± 1.06%, 41.50% ± 3.80%, 23.20% ± 1.40% and 24.40 ± 5.50%; in contrast, those of the traditional MFC were 25.10% ± 2.40%, 18.70% ± 4.10%, 14.10% ± 0.90% and 13.00% ± 2.50%, respectively. Meanwhile, the treatment groups in MFC-SCs influenced the species components and microflora structure. The 6329 operational taxonomic units (OTUs) in the control group without solar cells outnumbered those of the treatments of 24 h MFC-SC (5676), 12 h MFC-SC (5664) and 3 h MFC-SC (5592). This can advance the enrichment of dominant bacteria; meanwhile, the microbial process and the mechanisms behind it require further study. These results indicate that MFC-SCs provide a comprehensive method of solar energy utilization and environment remediation.
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Affiliation(s)
- Zidan Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, P. R. China.
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6
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Earl JP, Adappa ND, Krol J, Bhat AS, Balashov S, Ehrlich RL, Palmer JN, Workman AD, Blasetti M, Sen B, Hammond J, Cohen NA, Ehrlich GD, Mell JC. Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. MICROBIOME 2018; 6:190. [PMID: 30352611 PMCID: PMC6199724 DOI: 10.1186/s40168-018-0569-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/02/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences' (PacBio's) long-read technology in particular suffers from high error rates per base. Herein, we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome data. RESULTS Analysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity with regard to taxonomic classification. Examination of a 250-plus species mock community demonstrated correct species-level classification of > 90% of taxa, and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed. Propiniobacterium acnes (recently renamed Cutibacterium acnes) was the predominant species throughout, but was found at distinct relative abundances by site. CONCLUSIONS Our microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt ) overcomes deficits of standard marker gene-based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.
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Affiliation(s)
- Joshua P. Earl
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Nithin D. Adappa
- Veteran’s Administration Medical Center, Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5 Ravdin, Philadelphia, PA 19104-4283 USA
| | - Jaroslaw Krol
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Archana S. Bhat
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Sergey Balashov
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Rachel L. Ehrlich
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - James N. Palmer
- Veteran’s Administration Medical Center, Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5 Ravdin, Philadelphia, PA 19104-4283 USA
| | - Alan D. Workman
- Veteran’s Administration Medical Center, Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5 Ravdin, Philadelphia, PA 19104-4283 USA
| | - Mariel Blasetti
- Veteran’s Administration Medical Center, Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5 Ravdin, Philadelphia, PA 19104-4283 USA
| | - Bhaswati Sen
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Jocelyn Hammond
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Noam A. Cohen
- Veteran’s Administration Medical Center, Department of Otorhinolaryngology: Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5 Ravdin, Philadelphia, PA 19104-4283 USA
| | - Garth D. Ehrlich
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
| | - Joshua Chang Mell
- Department of Microbiology & Immunology, Centers for Genomic Sciences and Advanced Microbial Processing, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102 USA
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Strieth D, Ulber R, Muffler K. Application of phototrophic biofilms: from fundamentals to processes. Bioprocess Biosyst Eng 2017; 41:295-312. [PMID: 29198024 DOI: 10.1007/s00449-017-1870-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 11/24/2017] [Indexed: 01/31/2023]
Abstract
Biotechnological production of valuables by microorganisms is commonly achieved by cultivating the cells as suspended solids in an appropriate liquid medium. However, the main portion of these organisms features a surface-attached growth in their native habitats. The utilization of such biofilms shows significant challenges, e.g. concerning control of pH, nutrient supply, and heat/mass transfer. But the use of biofilms might also enable novel and innovative production processes addressing robustness and strength of the applied biocatalyst, for example if variable conditions might occur in the process or a feedstock (substrate) is changed in its composition. Besides the robustness of a biofilm, the high density of the immobilized biocatalyst facilitates a simple separation of the catalyst and the extracellular product, whereas intracellular target compounds occur in a concentrated form; thus, expenses for downstream processing can be drastically reduced. While phototrophic organisms feature a fabulous spectrum of metabolites ranging from biofuels to biologically active compounds, the low cell density of phototrophic suspension cultures is still limiting their application for production processes. The review is focusing on pro- and eukaryotic microalgae featuring the production of valuable compounds and highlights requirements for their cultivation as phototrophic biofilms, i.e. setup as well as operation of biofilm reactors, and modeling of phototrophic growth.
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Affiliation(s)
- D Strieth
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
| | - R Ulber
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
| | - K Muffler
- Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Berlinstr. 109, 55411, Bingen, Germany.
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Mobberley JM, Lindemann SR, Bernstein HC, Moran JJ, Renslow RS, Babauta J, Hu D, Beyenal H, Nelson WC. Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat. FEMS Microbiol Ecol 2017; 93:3071443. [PMID: 28334407 PMCID: PMC5812542 DOI: 10.1093/femsec/fix028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/13/2017] [Indexed: 02/06/2023] Open
Abstract
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms; however, little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity and metabolic gradient measurements. Draft reconstructed genomes of 34 abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence on metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.
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Affiliation(s)
- Jennifer M Mobberley
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA.,Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Hans C Bernstein
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - James J Moran
- Chemical and Biological Signature Sciences, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ryan S Renslow
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Jerome Babauta
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - William C Nelson
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Matturro B, Cruz Viggi C, Aulenta F, Rossetti S. Cable Bacteria and the Bioelectrochemical Snorkel: The Natural and Engineered Facets Playing a Role in Hydrocarbons Degradation in Marine Sediments. Front Microbiol 2017; 8:952. [PMID: 28611751 PMCID: PMC5447156 DOI: 10.3389/fmicb.2017.00952] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/12/2017] [Indexed: 11/13/2022] Open
Abstract
The composition and metabolic traits of the microbial communities acting in an innovative bioelectrochemical system were here investigated. The system, known as Oil Spill Snorkel, was recently developed to stimulate the oxidative biodegradation of petroleum hydrocarbons in anoxic marine sediments. Next Generation Sequencing was used to describe the microbiome of the bulk sediment and of the biofilm growing attached to the surface of the electrode. The analysis revealed that sulfur cycling primarily drives the microbial metabolic activities occurring in the bioelectrochemical system. In the anoxic zone of the contaminated marine sediment, petroleum hydrocarbon degradation occurred under sulfate-reducing conditions and was lead by different families of Desulfobacterales (46% of total OTUs). Remarkably, the occurrence of filamentous Desulfubulbaceae, known to be capable to vehicle electrons deriving from sulfide oxidation to oxygen serving as a spatially distant electron acceptor, was demonstrated. Differently from the sediment, which was mostly colonized by Deltaproteobacteria, the biofilm at the anode hosted, at high extent, members of Alphaproteobacteria (59%) mostly affiliated to Rhodospirillaceae family (33%) and including several known sulfur- and sulfide-oxidizing genera. Overall, we showed the occurrence in the system of a variety of electroactive microorganisms able to sustain the contaminant biodegradation alone or by means of an external conductive support through the establishment of a bioelectrochemical connection between two spatially separated redox zones and the preservation of an efficient sulfur cycling.
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Ha PT, Lindemann SR, Shi L, Dohnalkova AC, Fredrickson JK, Madigan MT, Beyenal H. Syntrophic anaerobic photosynthesis via direct interspecies electron transfer. Nat Commun 2017; 8:13924. [PMID: 28067226 PMCID: PMC5227917 DOI: 10.1038/ncomms13924] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022] Open
Abstract
Microbial phototrophs, key primary producers on Earth, use H2O, H2, H2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis'. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii does not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. This process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities. Direct interspecies electron transfer has been shown in methane-producing communities, but it is unknown how widespread this mechanism is. Here, Ha et al. show that anoxygenic photosynthesis can be driven by direct electron transfer from a heterotrophic partner bacterium.
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Affiliation(s)
- Phuc T Ha
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, USA
| | - Stephen R Lindemann
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geoscience, Wuhan, Hubei 430074, China
| | - Alice C Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - James K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, USA
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11
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Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene 2016; 594:248-258. [DOI: 10.1016/j.gene.2016.09.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 11/20/2022]
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12
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Renslow RS, Lindemann SR, Song HS. A Generalized Spatial Measure for Resilience of Microbial Systems. Front Microbiol 2016; 7:443. [PMID: 27092116 PMCID: PMC4823267 DOI: 10.3389/fmicb.2016.00443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/18/2016] [Indexed: 11/29/2022] Open
Abstract
The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition; that is, a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse. Typically, resilience is quantified using recovery time, which may be difficult or impossible to directly measure in microbial systems. A recent study in the literature showed that under certain conditions, a set of spatial-based metrics termed recovery length, can be correlated to recovery time, and thus may be a reasonable alternative measure of resilience. However, this spatial metric of resilience is limited to use for step-change perturbations. Building upon the concept of recovery length, we propose a more general form of the spatial metric of resilience that can be applied to any shape of perturbation profiles (for example, either sharp or smooth gradients). We termed this new spatial measure “perturbation-adjusted spatial metric of resilience” (PASMORE). We demonstrate the applicability of the proposed metric using a mathematical model of a microbial mat.
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Affiliation(s)
- Ryan S Renslow
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA, USA
| | - Stephen R Lindemann
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA, USA
| | - Hyun-Seob Song
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA, USA
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Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T. High-resolution phylogenetic microbial community profiling. ISME JOURNAL 2016; 10:2020-32. [PMID: 26859772 PMCID: PMC5029162 DOI: 10.1038/ismej.2015.249] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 02/07/2023]
Abstract
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.
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Affiliation(s)
- Esther Singer
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Brian Bushnell
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Devin Coleman-Derr
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,USDA-ARS, Albany, CA, USA
| | | | - Robert M Bowers
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Asaf Levy
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Esther A Gies
- University of British Columbia, Vancouver, BC, Canada
| | - Jan-Fang Cheng
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Alex Copeland
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Hans-Peter Klenk
- Newcastle University, School of Biology, Newcastle upon Tyne, UK
| | | | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Susannah G Tringe
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
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14
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Photosynthetic, respiratory and extracellular electron transport pathways in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:247-55. [PMID: 26498190 DOI: 10.1016/j.bbabio.2015.10.007] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/05/2023]
Abstract
Cyanobacteria have evolved elaborate electron transport pathways to carry out photosynthesis and respiration, and to dissipate excess energy in order to limit cellular damage. Our understanding of the complexity of these systems and their role in allowing cyanobacteria to cope with varying environmental conditions is rapidly improving, but many questions remain. We summarize current knowledge of cyanobacterial electron transport pathways, including the possible roles of alternative pathways in photoprotection. We describe extracellular electron transport, which is as yet poorly understood. Biological photovoltaic devices, which measure electron output from cells, and which have been proposed as possible means of renewable energy generation, may be valuable tools in understanding cyanobacterial electron transfer pathways, and enhanced understanding of electron transfer may allow improvements in the efficiency of power output. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
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15
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Franzén O, Hu J, Bao X, Itzkowitz SH, Peter I, Bashir A. Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering. MICROBIOME 2015; 3:43. [PMID: 26434730 PMCID: PMC4593230 DOI: 10.1186/s40168-015-0105-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 08/31/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation along the 16S rRNA gene is only partially captured by short reads. The recent emergence of long-read platforms, such as single-molecule real-time (SMRT) sequencing from Pacific Biosciences, offers the potential for improved taxonomic and phylogenetic profiling. Here, we evaluate the performance of long- and short-read 16S rRNA gene sequencing using simulated and experimental data, followed by OTU inference using computational pipelines based on heuristic and complete-linkage hierarchical clustering. RESULTS In simulated data, long-read sequencing was shown to improve OTU quality and decrease variance. We then profiled 40 human gut microbiome samples using a combination of Illumina MiSeq and Blautia-specific SMRT sequencing, further supporting the notion that long reads can identify additional OTUs. We implemented a complete-linkage hierarchical clustering strategy using a flexible computational pipeline, tailored specifically for PacBio circular consensus sequencing (CCS) data that outperforms heuristic methods in most settings: https://github.com/oscar-franzen/oclust/ . CONCLUSION Our data demonstrate that long reads can improve OTU inference; however, the choice of clustering algorithm and associated clustering thresholds has significant impact on performance.
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Affiliation(s)
- Oscar Franzén
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Xiuliang Bao
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Steven H Itzkowitz
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Ha PT, Renslow RS, Atci E, Reardon PN, Lindemann SR, Fredrickson JK, Call DR, Beyenal H. Regulation of electron transfer processes affects phototrophic mat structure and activity. Front Microbiol 2015; 6:909. [PMID: 26388853 PMCID: PMC4558538 DOI: 10.3389/fmicb.2015.00909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/19/2015] [Indexed: 11/24/2022] Open
Abstract
Phototrophic microbial mats are among the most diverse ecosystems in nature. These systems undergo daily cycles in redox potential caused by variations in light energy input and metabolic interactions among the microbial species. In this work, solid electrodes with controlled potentials were placed under mats to study the electron transfer processes between the electrode and the microbial mat. The phototrophic microbial mat was harvested from Hot Lake, a hypersaline, epsomitic lake located near Oroville (Washington, USA). We operated two reactors: graphite electrodes were polarized at potentials of -700 mVAg/AgCl [cathodic (CAT) mat system] and +300 mVAg/AgCl [anodic (AN) mat system] and the electron transfer rates between the electrode and mat were monitored. We observed a diel cycle of electron transfer rates for both AN and CAT mat systems. Interestingly, the CAT mats generated the highest reducing current at the same time points that the AN mats showed the highest oxidizing current. To characterize the physicochemical factors influencing electron transfer processes, we measured depth profiles of dissolved oxygen (DO) and sulfide in the mats using microelectrodes. We further demonstrated that the mat-to-electrode and electrode-to-mat electron transfer rates were light- and temperature-dependent. Using nuclear magnetic resonance (NMR) imaging, we determined that the electrode potential regulated the diffusivity and porosity of the microbial mats. Both porosity and diffusivity were higher in the CAT mats than in the AN mats. We also used NMR spectroscopy for high-resolution quantitative metabolite analysis and found that the CAT mats had significantly higher concentrations of osmoprotectants such as betaine and trehalose. Subsequently, we performed amplicon sequencing across the V4 region of the 16S rRNA gene of incubated mats to understand the impact of electrode potential on microbial community structure. These data suggested that variation in the electrochemical conditions under which mats were generated significantly impacted the relative abundances of mat members and mat metabolism.
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Affiliation(s)
- Phuc T Ha
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA USA
| | - Ryan S Renslow
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA USA
| | - Erhan Atci
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA USA
| | - Patrick N Reardon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA USA
| | - Stephen R Lindemann
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - James K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA USA
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17
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Li SL, Nealson KH. Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes. Front Microbiol 2015; 6:111. [PMID: 25741331 PMCID: PMC4330880 DOI: 10.3389/fmicb.2015.00111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/29/2015] [Indexed: 11/13/2022] Open
Abstract
Sulfide is a common product of marine anaerobic respiration, and a potent reactant biologically and geochemically. Here we demonstrate the impact on microbial communities with the removal of sulfide via electrochemical methods. The use of differential pulse voltammetry revealed that the oxidation of soluble sulfide was seen at +30 mV (vs. SHE) at all pH ranges tested (from pH = 4 to 8), while non-ionized sulfide, which dominated at pH = 4 was poorly oxidized via this process. Two mixed cultures (CAT and LA) were enriched from two different marine sediments (from Catalina Island, CAT; from the Port of Los Angeles, LA) in serum bottles using a seawater medium supplemented with lactate, sulfate, and yeast extract, to obtain abundant biomass. Both CAT and LA cultures were inoculated in electrochemical cells (using yeast-extract-free seawater medium as an electrolyte) equipped with carbon-felt electrodes. In both cases, when potentials of +630 or +130 mV (vs. SHE) were applied, currents were consistently higher at +630 then at +130 mV, indicating more sulfide being oxidized at the higher potential. In addition, higher organic-acid and sulfate conversion rates were found at +630 mV with CAT, while no significant differences were found with LA at different potentials. The results of microbial-community analyses revealed a decrease in diversity for both CAT and LA after electrochemical incubation. In addition, some bacteria (e.g., Clostridium and Arcobacter) not well-known to be capable of extracellular electron transfer, were found to be dominant in the electrochemical cells. Thus, even though the different mixed cultures have different tolerances for sulfide, electrochemical-sulfide removal can lead to major population changes.
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Affiliation(s)
- Shiue-Lin Li
- Department of Earth Science, University of Southern California Los Angeles, CA, USA
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California Los Angeles, CA, USA
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