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Frolova AA, Merkel AY, Kevbrin VV, Kopitsyn DS, Slobodkin AI. Sulfurospirillum tamanensis sp. nov., a Facultatively Anaerobic Alkaliphilic Bacterium from a Terrestrial Mud Volcano. Microbiology (Reading) 2023. [DOI: 10.1134/s0026261722602226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Dominance of Sulfurospirillum in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola). Appl Environ Microbiol 2022; 88:e0029022. [PMID: 35867581 PMCID: PMC9365241 DOI: 10.1128/aem.00290-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Sirsoe methanicola, commonly known as the methane ice worm, is the only macrofaunal species known to inhabit the Gulf of Mexico methane hydrates. Little is known about this elusive marine polychaete that can colonize rich carbon and energy reserves. Metagenomic analysis of gut contents and worm fragments predicted diverse metabolic capabilities with the ability to utilize a range of nitrogen, sulfur, and organic carbon compounds through microbial taxa affiliated with Campylobacterales, Desulfobacterales, Enterobacterales, SAR324, Alphaproteobacteria, and Mycoplasmatales. Entomoplasmatales and Chitinivibrionales were additionally identified from extracted full-length 16S rRNA sequences, and read analysis identified 196 bacterial families. Overall, the microbial community appeared dominated by uncultured Sulfurospirillum, a taxon previously considered free-living rather than host-associated. Metagenome-assembled genomes (MAGs) classified as uncultured Sulfurospirillum predicted thiosulfate disproportionation and the reduction of tetrathionate, sulfate, sulfide/polysulfide, and nitrate. Microbial amino acid and vitamin B12 biosynthesis genes were identified in multiple MAGs, suggesting nutritional value to the host. Reads assigned to aerobic or anaerobic methanotrophic taxa were rare. IMPORTANCE Methane hydrates represent vast reserves of natural gas with roles in global carbon cycling and climate change. This study provided the first analysis of metagenomes associated with Sirsoe methanicola, the only polychaete species known to colonize methane hydrates. Previously unrecognized participation of Sulfurospirillum in a gut microbiome is provided, and the role of sulfur compound redox reactions within this community is highlighted. The comparative biology of S. methanicola is of general interest given research into the adverse effects of sulfide production in human gut microbiomes. In addition, taxonomic assignments are provided for nearly 200 bacterial families, expanding our knowledge of microbiomes in the deep sea.
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Hieu DQ, Hang BTB, Lokesh J, Garigliany MM, Huong DTT, Yen DT, Liem PT, Tam BM, Hai DM, Son VN, Phuong NT, Farnir F, Kestemont P. Salinity significantly affects intestinal microbiota and gene expression in striped catfish juveniles. Appl Microbiol Biotechnol 2022; 106:3245-3264. [PMID: 35366085 DOI: 10.1007/s00253-022-11895-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/08/2022] [Accepted: 03/19/2022] [Indexed: 12/17/2022]
Abstract
In the present study, juvenile striped catfish (Pangasianodon hypophthalmus), a freshwater fish species, have been chronically exposed to a salinity gradient from freshwater to 20 psu (practical salinity unit) and were sampled at the beginning (D20) and the end (D34) of exposure. The results revealed that the intestinal microbial profile of striped catfish reared in freshwater conditions were dominated by the phyla Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Alpha diversity measures (observed OTUs (operational taxonomic units), Shannon and Faith's PD (phylogenetic diversity)) showed a decreasing pattern as the salinities increased, except for the phylogenetic diversity at D34, which was showing an opposite trend. Furthermore, the beta diversity between groups was significantly different. Vibrio and Akkermansia genera were affected differentially with increasing salinity, the former being increased while the latter was decreased. The genus Sulfurospirillium was found predominantly in fish submitted to salinity treatments. Regarding the host response, the fish intestine likely contributed to osmoregulation by modifying the expression of osmoregulatory genes such as nka1a, nka1b, slc12a1, slc12a2, cftr, and aqp1, especially in fish exposed to 15 and 20 psu. The expression of heat shock proteins (hsp) hsp60, hsp70, and hsp90 was significantly increased in fish reared in 15 and 20 psu. On the other hand, the expression of pattern recognition receptors (PRRs) were inhibited in fish exposed to 20 psu at D20. In conclusion, the fish intestinal microbiota was significantly disrupted in salinities higher than 10 psu and these effects were proportional to the exposure time. In addition, the modifications of intestinal gene expression related to ion exchange and stressful responses may help the fish to adapt hyperosmotic environment. KEY POINTS: • It is the first study to provide detailed information on the gut microbiota of fish using the amplicon sequencing method. • Salinity environment significantly modified the intestinal microbiota of striped catfish. • Intestinal responses may help the fish adapt to hyperosmotic environment.
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Affiliation(s)
- Dang Quang Hieu
- Research Unit in Environmental and Evolutionary Biology, Institute of Life Earth & Environment (ILEE), University of Namur, Namur, Belgium.
| | - Bui Thi Bich Hang
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Jep Lokesh
- Université de Pau Et Des Pays de L'Adour, Saint-Pee-sur-Nivelle, E2S UPPA, INRAE, NuMéA, France
| | - Mutien-Marie Garigliany
- Department of Pathology, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Do Thi Thanh Huong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Duong Thuy Yen
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Pham Thanh Liem
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Bui Minh Tam
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Dao Minh Hai
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam.,Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Vo Nam Son
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Frédéric Farnir
- Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, Institute of Life Earth & Environment (ILEE), University of Namur, Namur, Belgium.
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Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains. mSphere 2022; 7:e0093121. [PMID: 35196120 PMCID: PMC8865925 DOI: 10.1128/msphere.00931-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Sulfurospirillum species strains are frequently detected in various pristine and contaminated environments and participate in carbon, sulfur, nitrogen, and halogen elements cycling. Recently we obtained the complete genome sequences of two newly isolated Sulfurospirillum strains, ACSDCE and ACSTCE, capable of dechlorinating tetrachloroethene to cis-1,2-dichloroethene and trichloroethene under low-pH conditions, but a detailed analysis of these two genomes in reference to other Sulfurospirillum genomes for an improved understanding of Sulfurospirillum evolution and ecophysiology has not been accomplished. Here, we performed phylogenetic and pangenome analyses with 12 completed Sulfurospirillum genomes, including those of strain ACSTCE and strain ACSDCE, to unravel the evolutionary and metabolic potentials in the genus Sulfurospirillum. Based on 16S rRNA gene and whole-genome phylogenies, strains ACSTCE, ACSDCE, and JPD-1 could be clustered into a single species, proposed as “Candidatus Sulfurospirillum acididehalogenans.” TimeTree analysis suggested that the organohalide-respiring (OHR) Sulfurospirillum might acquire the ability to use chlorinated electron acceptors later than other energy conservation processes. Nevertheless, the ambiguity of the phylogenetic relations among Sulfurospirillum strains complicated the interpretation of acquisition and loss of metabolic traits. Interestingly, all OHR Sulfurospirillum genomes except the ones of Sulfurospirillum multivorans strains harbor a well-aligned and conserved region comprising the genetic components required for the organohalide respiration chain. Pangenome results further revealed that a total of 34,620 gene products, annotated from the 12 Sulfurospirillum genomes, can be classified into 4,118 homolog families and 2,075 singleton families. Various Sulfurospirillum species strains have conserved metabolisms as well as individual enzymes and biosynthesis capabilities. For instance, only the OHR Sulfurospirillum species strains possess the quinone-dependent pyruvate dehydrogenase (PoxB) gene, and only “Ca. Sulfurospirillum acididehalogenans” strains harbor urea transporter and urease genes. The plasmids found in strain ACSTCE and strain ACSDCE feature genes coding for type II toxin-antitoxin systems and transposases and are promising tools for the development of robust gene editing tools for Sulfurospirillum. IMPORTANCE Organohalide-respiring bacteria (OHRB) play critical roles in the detoxification of chlorinated pollutants and bioremediation of subsurface environments (e.g., groundwater and sediment) impacted by anthropogenic chlorinated solvents. The majority of known OHRB cannot perform reductive dechlorination below neutral pH, hampering the applications of OHRB for remediating acidified groundwater due to fermentation and reductive dechlorination. Previously we isolated two Sulfurospirillum strains, ACSTCE and ACSDCE, capable of dechlorinating tetrachloroethene under acidic conditions (e.g., pH 5.5), and obtained the complete genomes of both strains. Notably, two plasmid sequences were identified in the genomes of strain ACSTCE and strain ACSDCE that may be conducive to unraveling the genetic modification mechanisms in the genus Sulfurospirillum. Our findings improve the current understanding of Sulfurospirillum species strains regarding their biogeographic evolution, genome dynamics, and functional diversity. This study has applied values for the bioremediation of toxic and persistent organohalide pollutants in low-pH environments.
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Palma TL, Costa MC. Anaerobic biodegradation of fluoxetine using a high-performance bacterial community. Anaerobe 2021; 68:102356. [PMID: 33766774 DOI: 10.1016/j.anaerobe.2021.102356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 02/11/2021] [Accepted: 03/06/2021] [Indexed: 01/13/2023]
Abstract
Fluoxetine (FLX), an antidepressant extensively used worldwide is considered an emerging pollutant. The present work intends to investigate for the first time the capacity of a bacterial community containing sulphate-reducing bacteria (SRB) enriched from an anaerobic sludge to biodegrade and use FLX as sole carbon source, since current literature suggests that this drug is poorly biodegraded being mainly removed by adsorption to sediments, where it persists. FLX was biodegraded under sulphate reducing conditions until reaching its lowest and reliably detectable concentration, when 20 mg/L of the drug was used as sole carbon source, while 66 ± 9% of 50 mg/L FLX was removed, after 31 days. The initial bacterial population was mainly constituted by Desulfomicrobium and Desulfovibrio whereas during the experiments using FLX as unique carbon source a clear shift occurred with the increase of vadinBC27 wastewater-sludge group, Macellibacteroidetes, Dethiosulfovibrio, Bacteroides, Tolumonas, Sulfuricurvum, f_Enterobacteriaceae_OTU_18 that are assumed for the first time as FLX degrading bacteria. Although the main mechanism of FLX removal described in literature is by adsorption, in the results herein presented anaerobic biodegradation appears to play the main role in the removal of the FLX, thus demonstrating the potentialities that the anaerobic processes can play in wastewater treatment aiming the removal of new emerging compounds.
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Affiliation(s)
- Tânia Luz Palma
- Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, Building 7, 8005-139, Faro, Portugal; Faculdade de Ciências e Tecnologias, University of Algarve, Campus de Gambelas, Building 8, 8005-139, Faro, Portugal.
| | - Maria Clara Costa
- Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, Building 7, 8005-139, Faro, Portugal; Faculdade de Ciências e Tecnologias, University of Algarve, Campus de Gambelas, Building 8, 8005-139, Faro, Portugal.
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Ma X, Zhang G, Li F, Jiao M, Yao S, Chen Z, Liu Z, Zhang Y, Lv M, Liu L. Boosting the Microbial Electrosynthesis of Acetate from CO2 by Hydrogen Evolution Catalysts of Pt Nanoparticles/rGO. Catal Letters 2021. [DOI: 10.1007/s10562-021-03537-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Dessì P, Sánchez C, Mills S, Cocco FG, Isipato M, Ijaz UZ, Collins G, Lens PNL. Carboxylic acids production and electrosynthetic microbial community evolution under different CO 2 feeding regimens. Bioelectrochemistry 2020; 137:107686. [PMID: 33142136 DOI: 10.1016/j.bioelechem.2020.107686] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 11/17/2022]
Abstract
Microbial electrosynthesis (MES) is a potential technology for CO2 recycling, but insufficient information is available on the microbial interactions underpinning electrochemically-assisted reactions. In this study, a MES reactor was operated for 225 days alternately with bicarbonate or CO2 as carbon source, under batch or continuous feeding regimens, to evaluate the response of the microbial communities, and their productivity, to dynamic operating conditions. A stable acetic acid production rate of 9.68 g m-2 d-1, and coulombic efficiency up to 40%, was achieved with continuous CO2 sparging, higher than the rates obtained with bicarbonate (0.94 g m-2 d-1) and CO2 under fed-batch conditions (2.54 g m-2 d-1). However, the highest butyric acid production rate (0.39 g m-2 d-1) was achieved with intermittent CO2 sparging. The microbial community analyses focused on differential amplicon sequence variants (ASVs), allowing detection of ASVs significantly different across consecutive samples. This analysis, combined with co-occurence network analysis, and cyclic voltammetry, indicated that hydrogen-mediated acetogenesis was carried out by Clostridium, Eubacterium and Acetobacterium, whereas Oscillibacter and Caproiciproducens were involved in butyric acid production. The cathodic community was spatially inhomogeneous, with potential electrotrophs, such as Sulfurospirillum and Desulfovibrio, most prevalent near the current collector. The abundance of Sulfurospirillum positively correlated with that of Acetobacterium, supporting the syntrophic metabolism of both organisms.
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Affiliation(s)
- Paolo Dessì
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.
| | - Carlos Sánchez
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Simon Mills
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Francesco Giuseppe Cocco
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Department of Civil and Environmental Engineering and Architecture, University of Cagliari, Piazza d'Armi, 09123 Cagliari, Italy
| | - Marco Isipato
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Department of Civil and Environmental Engineering and Architecture, University of Cagliari, Piazza d'Armi, 09123 Cagliari, Italy
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Gavin Collins
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Piet N L Lens
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
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Mardanov AV, Kadnikov VV, Beletsky AV, Ravin NV. Sulfur and Methane-Oxidizing Microbial Community in a Terrestrial Mud Volcano Revealed by Metagenomics. Microorganisms 2020; 8:microorganisms8091333. [PMID: 32878336 PMCID: PMC7565565 DOI: 10.3390/microorganisms8091333] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using a metagenomics approach, we analyzed the microbial community of bubbling fluids retrieved from an active mud volcano in eastern Crimea. The microbial community was dominated by chemolithoautotrophic Campylobacterota and Gammaproteobacteria, which are capable of sulfur oxidation coupled to aerobic and anaerobic respiration. Methane oxidation could be enabled by aerobic Methylococcales bacteria and anaerobic methanotrophic archaea (ANME), while methanogens were nearly absent. The ANME community was dominated by a novel species of Ca. Methanoperedenaceae that lacked nitrate reductase and probably couple methane oxidation to the reduction of metal oxides. Analysis of two Ca. Bathyarchaeota genomes revealed the lack of mcr genes and predicted that they could grow on fatty acids, sugars, and proteinaceous substrates performing fermentation. Thermophilic sulfate reducers indigenous to the deep subsurface, Thermodesulfovibrionales (Nitrospirae) and Ca. Desulforudis (Firmicutes), were found in minor amounts. Overall, the results obtained suggest that reduced compounds delivered from the deep subsurface support the development of autotrophic microorganisms using various electron acceptors for respiration.
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van Grinsven S, Sinninghe Damsté JS, Villanueva L. Assessing the Effect of Humic Substances and Fe(III) as Potential Electron Acceptors for Anaerobic Methane Oxidation in a Marine Anoxic System. Microorganisms 2020; 8:E1288. [PMID: 32846903 PMCID: PMC7564286 DOI: 10.3390/microorganisms8091288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/06/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Marine anaerobic methane oxidation (AOM) is generally assumed to be coupled to sulfate reduction, via a consortium of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). ANME-1 are, however, often found as single cells, or only loosely aggregated with SRB, suggesting they perform a form of AOM independent of sulfate reduction. Oxidized metals and humic substances have been suggested as potential electron acceptors for ANME, but up to now, AOM linked to reduction of these compounds has only been shown for the ANME-2 and ANME-3 clades. Here, the effect of the electron acceptors anthraquinone-disulfonate (AQDS), a humic acids analog, and Fe3+ on anaerobic methane oxidation were assessed by incubation experiments with anoxic Black Sea water containing ANME-1b. Incubation experiments with 13C-methane and AQDS showed a stimulating effect of AQDS on methane oxidation. Fe3+ enhanced the ANME-1b abundance but did not substantially increase methane oxidation. Sodium molybdate, which was added as an inhibitor of sulfate reduction, surprisingly enhanced methane oxidation, possibly related to the dominant abundance of Sulfurospirillum in those incubations. The presented data suggest the potential involvement of ANME-1b in AQDS-enhanced anaerobic methane oxidation, possibly via electron shuttling to AQDS or via interaction with other members of the microbial community.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
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LaBelle EV, Marshall CW, May HD. Microbiome for the Electrosynthesis of Chemicals from Carbon Dioxide. Acc Chem Res 2020; 53:62-71. [PMID: 31809012 DOI: 10.1021/acs.accounts.9b00522] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The price for renewable electricity is rapidly decreasing, and the availability of such energy is expected to increase in the coming years. This is a welcomed outcome considering that mitigation of climate disruption due to the use of fossil carbon is reaching a critical stage. However, the economy will remain dependent on carbon-based chemicals and the problem of electricity storage persists. Therefore, the development of electrosynthetic processes that convert electricity and CO2 into chemicals and energy dense fuels, perhaps even food, would be desirable. Electrochemistry has been applied to the manufacture of many valuable products and at a large industrial scale, but it is difficult to produce multicarbon chemicals from CO2 by chemistry alone. Being that the biological world possesses expertise at the construction of C-C bonds, it is being examined in conjunction with electrochemistry to discover new ways of synthesizing chemicals from electricity and CO2. One approach is microbial electrosynthesis. This Account describes the development of a microbial electrosynthesis system by the authors. A biocathode consisting of a carbon-based electrode and a microbial community produced short chain fatty acids, primarily acetate. The device works by electrolysis of water, but microbes facilitate electron transfer from the cathode while reducing CO2 by the Wood-Ljungdahl pathway possessed by an Acetobacterium sp. While this acetogenic microorganism dominates the microbiome growing on the cathode surface, 13 total species of microbes overall were ecologically selected on the cathode and genomes for each have been assembled. The combined species may contribute to the stability of the microbiome, a common feature of naturally selected microbial communities. The microbial electrosynthesis system was demonstrated to operate continuously at a cathode for more than 2 years and could also be used with intermittent power, thus demonstrating the stability of the microbiome living at the cathode. In addition to the description of reactor design and startup procedures, the possible mechanisms of electron transfer are described in this Account. While mysteries remain to be solved, much evidence indicates that the microbiome may facilitate electron transfer by supplying catalyst(s) external to the bacterial cells and onto the cathode surface. This may be in the form of a hydrogen-producing catalyst that enhances hydrogen generation by an inert carbon-based electrode. Through the enrichment of the electrosynthetic microbiome along with several modifications in reactor design and operation, the productivity and efficiency were improved. In addition to the intrinsic value of the current products, coupling the process with a secondary stage might be used to produce more valuable products from the acetic acid stream such as lipids, biocrude oil, or higher value food supplements. Alternatively, additional work on the mechanism of electron transfer, reactor design/operation, and modification of the microbes through synthetic biology, particularly to enhance carbon efficiency into higher value chemicals, are the needed next steps to advance microbial electrosynthesis so that it may be used to transform renewable electrons and CO2 directly into products and help solve the problem of climate disruption.
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Affiliation(s)
- Edward V. LaBelle
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christopher W. Marshall
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Harold D. May
- Department of Microbiology & Immunology, Hollings Marine Laboratory, Medical University of South Carolina, Charleston, South Carolina 29412, United States
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Akhtar N, Ghauri MA, Akhtar K, Parveen S, Farooq M, Ali A, Schierack P. Comparative Analysis of Draft Genome Sequence of Rhodococcus sp. Eu-32 with Other Rhodococcus Species for Its Taxonomic Status and Sulfur Metabolism Potential. Curr Microbiol 2019; 76:1207-1214. [PMID: 31300840 DOI: 10.1007/s00284-019-01737-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
Rhodococcus sp. Eu-32 has shown an extended novel dibenzothiophene desulfurization sulfur-specific 4S pathway and could remove significant amounts of organic sulfur from coal. Here, we present the draft genome sequence of Eu-32 with a genome size of approximately 5.61 Mb, containing 5065 protein coding sequences with a G+C content of 65.1%. The Rhodococcus sp. Eu-32 showed ~ 99% identity at the 16S rRNA gene sequence level while < 34% digital DNA-DNA hybridization and < 81% average nucleotide identity values with the genome sequence of most closely related known Rhodococcus species, suggesting that it is taxonomically different from the already reported Rhodococcus species. Among the annotated genes, 90 are involved in the metabolism of sulfur. Comparative genome analysis suggests many commonalities in sulfur metabolism gene sets that may have evolved due to many factors including ecological pressures. Our study and the genome sequence data will be available for further research and will provide insights into potential biotechnological and industrial applications of this bacterium.
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Affiliation(s)
- Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P. O. Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Muhammad A Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P. O. Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P. O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P. O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P. O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Aamir Ali
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P. O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
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Kruse S, Goris T, Westermann M, Adrian L, Diekert G. Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria. Nat Commun 2018; 9:4872. [PMID: 30451902 PMCID: PMC6242987 DOI: 10.1038/s41467-018-07342-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 10/24/2018] [Indexed: 02/04/2023] Open
Abstract
Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production upon pyruvate fermentation for free-living Epsilonproteobacteria, Sulfurospirillum spp. The amount of hydrogen produced is different in two subgroups of Sulfurospirillum spp., represented by S. cavolei and S. multivorans. The former produces more hydrogen and excretes acetate as sole organic acid, while the latter additionally produces lactate and succinate. Hydrogen production can be assigned by differential proteomics to a hydrogenase (similar to hydrogenase 4 from E. coli) that is more abundant during fermentation. A syntrophic interaction is established between Sulfurospirillum multivorans and Methanococcus voltae when cocultured with lactate as sole substrate, as the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen for growth. This might hint to a yet unrecognized role of Epsilonproteobacteria as hydrogen producers in anoxic microbial communities. Epsilonproteobacteria, such as Sulfurospirillum, can use molecular hydrogen as an electron donor for respiration. Here, the authors show that Sulfurospirillum can, in addition, release hydrogen during fermentation, allowing metabolic interactions with other hydrogen-consuming microorganisms.
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Affiliation(s)
- Stefan Kruse
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743, Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743, Jena, Germany.
| | - Martin Westermann
- Center for Electron Microscopy of the University Hospital Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.,Fachgebiet Geobiotechnologie, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743, Jena, Germany
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Metagenome-Assembled Genome Sequences of Acetobacterium sp. Strain MES1 and Desulfovibrio sp. Strain MES5 from a Cathode-Associated Acetogenic Microbial Community. GENOME ANNOUNCEMENTS 2017; 5:5/36/e00938-17. [PMID: 28883141 PMCID: PMC5589535 DOI: 10.1128/genomea.00938-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 were obtained from the metagenome of a cathode-associated community enriched within a microbial electrosynthesis system (MES). The draft genome sequences provide insight into the functional potential of these microorganisms within an MES and a foundation for future comparative analyses.
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14
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Metabolic Reconstruction and Modeling Microbial Electrosynthesis. Sci Rep 2017; 7:8391. [PMID: 28827682 PMCID: PMC5566340 DOI: 10.1038/s41598-017-08877-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022] Open
Abstract
Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial cells to capture electrons from a cathode and fix carbon. Yet despite the promise of this technology, the metabolic capacity of the microbes that inhabit the electrode surface and catalyze electron transfer in these systems remains largely unknown. We assembled thirteen draft genomes from a microbial electrosynthesis system producing primarily acetate from carbon dioxide, and their transcriptional activity was mapped to genomes from cells on the electrode surface and in the supernatant. This allowed us to create a metabolic model of the predominant community members belonging to Acetobacterium, Sulfurospirillum, and Desulfovibrio. According to the model, the Acetobacterium was the primary carbon fixer, and a keystone member of the community. Transcripts of soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were found in high abundance near the electrode surface. Cytochrome c oxidases of facultative members of the community were highly expressed in the supernatant despite completely sealed reactors and constant flushing with anaerobic gases. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.
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15
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Goris T, Schenz B, Zimmermann J, Lemos M, Hackermüller J, Schubert T, Diekert G. The complete genome of the tetrachloroethene-respiring Epsilonproteobacterium Sulfurospirillum halorespirans. J Biotechnol 2017. [DOI: 10.1016/j.jbiotec.2017.06.1197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Altermann E, Lu J, McCulloch A. GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes. Front Microbiol 2017; 8:346. [PMID: 28386247 PMCID: PMC5362640 DOI: 10.3389/fmicb.2017.00346] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 02/20/2017] [Indexed: 11/13/2022] Open
Abstract
Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.
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Affiliation(s)
- Eric Altermann
- AgResearch Limited, Grasslands Research CentrePalmerston North, New Zealand; Riddet Institute, Massey UniversityPalmerston North, New Zealand
| | - Jingli Lu
- AgResearch Limited, Grasslands Research Centre Palmerston North, New Zealand
| | - Alan McCulloch
- AgResearch Limited, Invermay Agricultural Centre Mosgiel, New Zealand
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17
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Ribeiro H, Mucha AP, Azevedo I, Salgado P, Teixeira C, Almeida CMR, Joye SB, Magalhães C. Differential effects of crude oil on denitrification and anammox, and the impact on N2O production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 216:391-399. [PMID: 27395442 DOI: 10.1016/j.envpol.2016.05.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Denitrification and anammox are key processes for reducing the external nitrogen loads delivered to coastal ecosystems, and these processes can be affected by pollutants. In this study, we investigated the effect of crude oil on denitrification and anammox. Controlled laboratory experiments were performed using sediment slurries from the Lima Estuary (NW Portugal). Anammox and denitrification rates were measured using (15)N-labeled NO3(-), and the production of (29)N2 and (30)N2 quantified by membrane inlet mass spectrometry. Results revealed that while denitrification rates were stimulated between 10 and 25 000 times after crude oil amendment, anammox activity was partially (between 2 and 5 times) or completely inhibited by the addition of crude oil when comparing to rates in unamended controls. Similar results were observed across four estuarine sediment types, despite their different physical-chemical characteristics. Moreover, N2O production was reduced by 2-36 times following crude oil addition. Further work is required to fully understand the mechanism(s) of the observed reduction in N2O production. This study represents one of the first contributions to the understanding of the impact of crude oil pollution on denitrification and anammox, with profound implications for the management of aquatic ecosystems regarding eutrophication (N-removal).
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Affiliation(s)
- Hugo Ribeiro
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
| | - Ana P Mucha
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Isabel Azevedo
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Paula Salgado
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Porto, Portugal
| | - Catarina Teixeira
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Porto, Portugal
| | - C Marisa R Almeida
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Catarina Magalhães
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
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