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Ghezzi D, Mangiaterra G, Scardino A, Fehervari M, Magnani M, Citterio B, Frangipani E. Characterization of bacterial communities associated with seabed sediments in offshore and nearshore sites to improve Microbiologically Influenced Corrosion mitigation on marine infrastructures. PLoS One 2024; 19:e0309971. [PMID: 39231176 PMCID: PMC11373832 DOI: 10.1371/journal.pone.0309971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/19/2024] [Indexed: 09/06/2024] Open
Abstract
Microbiologically Influenced Corrosion (MIC) is one of the main threats for marine infrastructures, leading to severe safety and environmental risks associated with structural failures and/or leakages of dangerous fluids, together with potential huge economic losses and reputational damage for the involved parts. For a safe design and a proper installation of infrastructure systems in contact with the seabed, a deep knowledge of the site-specific microbial community of the sediments should be beneficial. Therefore, in addition to the simple detection or the sole quantification of Sulphate-Reducing Bacteria (SRB), the whole characterization of the microbial members involved in MIC phenomena is desirable. In this study, 16S rRNA-based comparison between bacterial communities thriving in offshore and nearshore marine sediments was performed, with a focus on the main bacterial groups putatively responsible for MIC. The nearshore sediments were significantly enriched in bacterial members associated with human and organic compounds contamination belonging to the Bacteroidota, Desulfobacterota, and Firmicutes phyla, while the offshore sediments hosted Alphaproteobacteria, Nitrospinota, and Nitrospirota members, representative of a low anthropogenic impact. Quantitative PCR targeting the dsrA gene and detailed community analyses revealed that the nearshore sediments were significantly enriched in SRB mainly affiliated to the Desulfobulbus and Desulfosarcina genera potentially involved in biocorrosion, compared to the offshore ones. These results suggest that the bacterial community associated with the high concentration of organic compounds derived by an elevated anthropogenic impact is likely to favour MIC. Such observations highlight the importance of microbiological investigations as prevention strategy against MIC processes, aiming both at characterizing sites for the establishment of new infrastructures and at monitoring those already installed.
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Affiliation(s)
- Daniele Ghezzi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
| | - Gianmarco Mangiaterra
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
| | - Arianna Scardino
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
| | - Mauro Fehervari
- R&D Engineering, Asset Based Services-Saipem SpA, Fano (PU), Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
| | - Barbara Citterio
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
| | - Emanuela Frangipani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
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Handler ER, Andersen SDJ, Gradinger R, McGovern M, Vader A, Poste AE. Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat. FEMS Microbiol Ecol 2024; 100:fiad162. [PMID: 38111220 PMCID: PMC10799726 DOI: 10.1093/femsec/fiad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.
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Affiliation(s)
- Eleanor R Handler
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Sebastian D J Andersen
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Amanda E Poste
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
- Norwegian Institute for Nature Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
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Jayathilake C, Piyumika G, Nazeer Z, Wijayawardene N, Rajakaruna S, Kumla J, Fernando E. Recent progress in the characterization and application of exo-electrogenic microorganisms. Antonie Van Leeuwenhoek 2024; 117:10. [PMID: 38170279 DOI: 10.1007/s10482-023-01916-y] [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: 07/31/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024]
Abstract
Exo-electrogenic microorganisms are characterized by their special metabolic capability of transferring metabolic electrons out of their cell, into insoluble external electron acceptors such as iron or manganese oxides and electrodes, or vice versa take up electron from electrodes. Their conventional application is primarily limited to microbial fuel cells for electrical power generation and microbial electrolysis cells for the production of value-added products such as biohydrogen, biomethane and hydrogen peroxide. The utility of exo-electrogenic organisms has expanded into many other applications in recent times. Such examples include microbial desalination cells, microbial electro-synthesis cells producing value-added chemicals such as bio-butanol and their applications in other carbon sequestration technologies. Additionally, electrochemically-active organisms are now beginning to be employed in biosensor applications for environmental monitoring. Additionally, the utility of biocathodes in bio-electrochemical systems is also a novel application in catalyzing the cathodic oxygen reduction reaction to enhance their electrochemical performance. Advances have also been made in the expansion and use of other organisms such as the usage of photosynthetic microorganisms for the fabrication of self-sustained bio-electrochemical systems. This review attempts to provide a comprehensive picture of the state-of the art of exo-electrogenic organisms and their novel utility in bioelectrochemical systems.
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Affiliation(s)
| | - Gayani Piyumika
- Department of Biology, Rajarata University, Mihintale, 50300, Sri Lanka
| | - Zumaira Nazeer
- Department of Biology, Rajarata University, Mihintale, 50300, Sri Lanka
| | - Nalin Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, 655011, Yunnan, People's Republic of China
| | | | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Eustace Fernando
- Department of Biology, Rajarata University, Mihintale, 50300, Sri Lanka.
- School of Engineering and Science, Department of Civil, Environmental and Ocean Engineering, Stevens Institute of Technology, Charles V. Schaefer, Hoboken, NJ, 07030, USA.
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Szekeres E, Baricz A, Cristea A, Levei EA, Stupar Z, Brad T, Kenesz M, Moldovan OT, Banciu HL. Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165133. [PMID: 37364839 DOI: 10.1016/j.scitotenv.2023.165133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/19/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Karst aquifers are important water resources for drinking water supplies worldwide. Although they are susceptible to anthropogenic contamination due to their high permeability, there is a lack of detailed knowledge on the stable core microbiome and how contamination may affect these communities. In this study, eight karst springs (distributed across three different regions in Romania) were sampled seasonally for one year. The core microbiota was analysed by 16S rRNA gene amplicon sequencing. To identify bacteria carrying antibiotic resistance genes and mobile genetic elements, an innovative method was applied, consisting of high-throughput antibiotic resistance gene quantification performed on potential pathogen colonies cultivated on Compact Dry™ plates. A taxonomically stable bacterial community consisting of Pseudomonadota, Bacteroidota, and Actinomycetota was revealed. Core analysis reaffirmed these results and revealed primarily freshwater-dwelling, psychrophilic/psychrotolerant species affiliated to Rhodoferax, Flavobacterium, and Pseudomonas genera. Both sequencing and cultivation methods indicated that more than half of the springs were contaminated with faecal bacteria and pathogens. These samples contained high levels of sulfonamide, macrolide, lincosamide and streptogramins B, and trimethoprim resistance genes spread primarily by transposase and insertion sequences. Differential abundance analysis found Synergistota, Mycoplasmatota, and Chlamydiota as suitable candidates for pollution monitoring in karst springs. This is the first study highlighting the applicability of a combined approach based on high-throughput SmartChip™ antibiotic resistance gene quantification and Compact Dry™ pathogen cultivation for estimating microbial contaminants in karst springs and other challenging low biomass environments.
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Affiliation(s)
- Edina Szekeres
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania; National Institute of Research and Development for Biological Sciences, Institute of Biological Research, Cluj-Napoca, Romania
| | - Andreea Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Adorján Cristea
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania; Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Erika Andrea Levei
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Zamfira Stupar
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Traian Brad
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Marius Kenesz
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Oana Teodora Moldovan
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania.
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Baloza M, Henkel S, Kasten S, Holtappels M, Molari M. The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments. Microorganisms 2023; 11:1572. [PMID: 37375074 DOI: 10.3390/microorganisms11061572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.
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Affiliation(s)
- Marwa Baloza
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty 2 Biology/Chemistry, University of Bremen, Leobener Str., 28359 Bremen, Germany
| | - Susann Henkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Sabine Kasten
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Str., 28359 Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Massimiliano Molari
- HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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Zhang B, Shi S, Tang R, Qiao C, Yang M, You Z, Shao S, Wu D, Yu H, Zhang J, Cao Y, Li F, Song H. Recent advances in enrichment, isolation, and bio-electrochemical activity evaluation of exoelectrogenic microorganisms. Biotechnol Adv 2023; 66:108175. [PMID: 37187358 DOI: 10.1016/j.biotechadv.2023.108175] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Exoelectrogenic microorganisms (EEMs) catalyzed the conversion of chemical energy to electrical energy via extracellular electron transfer (EET) mechanisms, which underlay diverse bio-electrochemical systems (BES) applications in clean energy development, environment and health monitoring, wearable/implantable devices powering, and sustainable chemicals production, thereby attracting increasing attentions from academic and industrial communities in the recent decades. However, knowledge of EEMs is still in its infancy as only ~100 EEMs of bacteria, archaea, and eukaryotes have been identified, motivating the screening and capture of new EEMs. This review presents a systematic summarization on EEM screening technologies in terms of enrichment, isolation, and bio-electrochemical activity evaluation. We first generalize the distribution characteristics of known EEMs, which provide a basis for EEM screening. Then, we summarize EET mechanisms and the principles underlying various technological approaches to the enrichment, isolation, and bio-electrochemical activity of EEMs, in which a comprehensive analysis of the applicability, accuracy, and efficiency of each technology is reviewed. Finally, we provide a future perspective on EEM screening and bio-electrochemical activity evaluation by focusing on (i) novel EET mechanisms for developing the next-generation EEM screening technologies, and (ii) integration of meta-omics approaches and bioinformatics analyses to explore nonculturable EEMs. This review promotes the development of advanced technologies to capture new EEMs.
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Affiliation(s)
- Baocai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Sicheng Shi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Tang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chunxiao Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Meiyi Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shulin Shao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Zhong YW, Zhou P, Cheng H, Zhou YD, Pan J, Xu L, Li M, Tao CH, Wu YH, Xu XW. Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge. Microbiol Spectr 2022; 10:e0061422. [PMID: 36286994 PMCID: PMC9769843 DOI: 10.1128/spectrum.00614-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023] Open
Abstract
The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.
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Affiliation(s)
- Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Ya-Dong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Chun-Hui Tao
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Submarine Geosciences, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
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Nixon SL, Bonsall E, Cockell CS. Limitations of microbial iron reduction under extreme conditions. FEMS Microbiol Rev 2022; 46:6645348. [PMID: 35849069 PMCID: PMC9629499 DOI: 10.1093/femsre/fuac033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microbial iron reduction is a widespread and ancient metabolism on Earth, and may plausibly support microbial life on Mars and beyond. Yet, the extreme limits of this metabolism are yet to be defined. To investigate this, we surveyed the recorded limits to microbial iron reduction in a wide range of characterized iron-reducing microorganisms (n = 141), with a focus on pH and temperature. We then calculated Gibbs free energy of common microbially mediated iron reduction reactions across the pH-temperature habitability space to identify thermodynamic limits. Comparing predicted and observed limits, we show that microbial iron reduction is generally reported at extremes of pH or temperature alone, but not when these extremes are combined (with the exception of a small number of acidophilic hyperthermophiles). These patterns leave thermodynamically favourable combinations of pH and temperature apparently unoccupied. The empty spaces could be explained by experimental bias, but they could also be explained by energetic and biochemical limits to iron reduction at combined extremes. Our data allow for a review of our current understanding of the limits to microbial iron reduction at extremes and provide a basis to test more general hypotheses about the extent to which biochemistry establishes the limits to life.
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Affiliation(s)
- Sophie L Nixon
- Corresponding author: Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
| | - Emily Bonsall
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
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Reductive Soil Disinfestation Enhances Microbial Network Complexity and Function in Intensively Cropped Greenhouse Soil. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8060476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Reductive soil disinfestation (RSD) is an effective practice to eliminate plant pathogens and improve the soil microbial community. However, little is known about how RSD treatment affects microbial interactions and functions. Previous study has shown that RSD-regulated microbiomes may degenerate after re-planting with former crops, while the effect of planting with different crops is still unclear. Here, the effects of both RSD treatment and succession planting with different crops on microbial community composition, interactions, and functions were investigated. Results showed that RSD treatment improves the soil microbial community, decreases the relative abundance of plant pathogens, and effectively enhances microbial interactions and functions. The microbial network associated with RSD treatment was more complex and connected. The functions of hydrocarbon (C, H), nitrogen (N), and sulfur (S) cycling were significantly increased in RSD-treated soil, while the functions of bacterial and fungal plant pathogens were decreased. Furthermore, the bacterial and fungal communities present in the RSD-treated soil, and soil succession planted with different crops, were found to be significantly different compared to untreated soil. In summary, we report that RSD treatment can improve soil quality by regulating the interactions of microbial communities and multifunctionality.
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10
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Chaudhary S, Yadav S, Singh R, Sadhotra C, Patil SA. Extremophilic electroactive microorganisms: Promising biocatalysts for bioprocessing applications. BIORESOURCE TECHNOLOGY 2022; 347:126663. [PMID: 35017088 DOI: 10.1016/j.biortech.2021.126663] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Electroactive microorganisms (EAMs) use extracellular electron transfer (EET) processes to access insoluble electron donors or acceptors in cellular respiration. These are used in developing microbial electrochemical technologies (METs) for biosensing and bioelectronics applications and the valorization of liquid and gaseous wastes. EAMs from extreme environments can be useful to overcome the existing limitations of METs operated with non-extreme microorganisms. Studying extreme EAMs is also necessary to improve understanding of respiratory processes involving EET. This article first discusses the advantages of using extreme EAMs in METs and summarizes the diversity of EAMs from different extreme environments. It is followed by a detailed discussion on their use as biocatalysts in various bioprocessing applications via bioelectrochemical systems. Finally, the challenges associated with operating METs under extreme conditions and promising research opportunities on fundamental and applied aspects of extreme EAMs are presented.
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Affiliation(s)
- Srishti Chaudhary
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Sukrampal Yadav
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Ramandeep Singh
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Chetan Sadhotra
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Sunil A Patil
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India.
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11
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Pelovirga terrestris gen. nov., sp. nov., anaerobic, alkaliphilic, fumarate-, arsenate-, Fe(III)- and sulfur-reducing bacterium isolated from a terrestrial mud volcano. Syst Appl Microbiol 2022; 45:126304. [DOI: 10.1016/j.syapm.2022.126304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/14/2022] [Accepted: 01/21/2022] [Indexed: 12/26/2022]
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12
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Wunder LC, Aromokeye DA, Yin X, Richter-Heitmann T, Willis-Poratti G, Schnakenberg A, Otersen C, Dohrmann I, Römer M, Bohrmann G, Kasten S, Friedrich MW. Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments. THE ISME JOURNAL 2021; 15:3587-3604. [PMID: 34155335 PMCID: PMC8630232 DOI: 10.1038/s41396-021-01014-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.
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Affiliation(s)
- Lea C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Graciana Willis-Poratti
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Instituto Antártico Argentino, Buenos Aires, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Annika Schnakenberg
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carolin Otersen
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ingrid Dohrmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Miriam Römer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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13
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Aromokeye DA, Willis-Poratti G, Wunder LC, Yin X, Wendt J, Richter-Heitmann T, Henkel S, Vázquez S, Elvert M, Mac Cormack W, Friedrich MW. Macroalgae degradation promotes microbial iron reduction via electron shuttling in coastal Antarctic sediments. ENVIRONMENT INTERNATIONAL 2021; 156:106602. [PMID: 34051435 DOI: 10.1016/j.envint.2021.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Colonization of newly ice-free areas by marine benthic organisms intensifies burial of macroalgae detritus in Potter Cove coastal surface sediments (Western Antarctic Peninsula). Thus, fresh and labile macroalgal detritus serves as primary organic matter (OM) source for microbial degradation. Here, we investigated the effects on post-depositional microbial iron reduction in Potter Cove using sediment incubations amended with pulverized macroalgal detritus as OM source, acetate as primary product of OM degradation and lepidocrocite as reactive iron oxide to mimic in situ conditions. Humic substances analogue anthraquinone-2,6-disulfonic acid (AQDS) was also added to some treatments to simulate potential for electron shuttling. Microbial iron reduction was promoted by macroalgae and further enhanced by up to 30-folds with AQDS. Notably, while acetate amendment alone did not stimulate iron reduction, adding macroalgae alone did. Acetate, formate, lactate, butyrate and propionate were detected as fermentation products from macroalgae degradation. By combining 16S rRNA gene sequencing and RNA stable isotope probing, we reconstructed the potential microbial food chain from macroalgae degraders to iron reducers. Psychromonas, Marinifilum, Moritella, and Colwellia were detected as potential fermenters of macroalgae and fermentation products such as lactate. Members of class deltaproteobacteria including Sva1033, Desulfuromonas, and Desulfuromusa together with Arcobacter (former phylum Epsilonbacteraeota, now Campylobacterota) acted as dissimilatory iron reducers. Our findings demonstrate that increasing burial of macroalgal detritus in an Antarctic fjord affected by glacier retreat intensifies early diagenetic processes such as iron reduction. Under scenarios of global warming, the active microbial populations identified above will expand their environmental function, facilitate OM remineralisation, and contribute to an increased release of iron and CO2 from sediments. Such indirect consequences of glacial retreat are often overlooked but might, on a regional scale, be relevant for the assessment of future nutrient and carbon fluxes.
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Affiliation(s)
- David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Graciana Willis-Poratti
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany; Instituto Antártico Argentino, San Martín, Buenos Aires, Argentina; Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - Lea C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany; Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Jenny Wendt
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Susann Henkel
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
| | - Susana Vázquez
- CONICET - Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina.
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | - Walter Mac Cormack
- Instituto Antártico Argentino, San Martín, Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina.
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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14
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Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H. Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol 2021; 12:737531. [PMID: 34659166 PMCID: PMC8516083 DOI: 10.3389/fmicb.2021.737531] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Geobacterales is a recently proposed order comprising members who originally belonged to the well-known family Geobacteraceae, which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51T and Red69T, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species Geobacter luticola from other known genera and placed the genus Oryzomonas (fam. Geobacteraceae) into the family ‘Pseudopelobacteraceae’; thus, a novel genus Geomobilimonas is proposed, and the family ‘Pseudopelobacteraceae’ was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species Geobacter argillaceus, Geobacter pelophilus, and Geobacter chapellei should be three novel genera, for which the names Geomobilibacter, Geoanaerobacter, and Pelotalea are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus Geomonas, family Geobacteraceae, and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other Geomonas species, these two strains, Red51T and Red69T, represent two novel species in the genus Geomonas, for which the names Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. are proposed, respectively.
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Affiliation(s)
- Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Xueding Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, Japan
| | | | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Hokkaido, Japan
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15
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Ersoy Omeroglu E, Sudagidan M, Yurt MNZ, Tasbasi BB, Acar EE, Ozalp VC. Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples. Sci Rep 2021; 11:18364. [PMID: 34526632 PMCID: PMC8443733 DOI: 10.1038/s41598-021-97980-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/25/2021] [Indexed: 01/21/2023] Open
Abstract
Soda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.
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Affiliation(s)
- Esra Ersoy Omeroglu
- Biology Department, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, 35040, Bornova, Izmir, Turkey.
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Mediha Nur Zafer Yurt
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Behiye Busra Tasbasi
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Elif Esma Acar
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Veli Cengiz Ozalp
- Department of Medical Biology, Medical School, Atilim University, 06830, Ankara, Turkey
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16
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Pérez-Rodríguez I, Choi JK, Abuyen K, Tyler M, Ronkowski C, Romero E, Trujillo A, Tremblay J, Viney I, Savalia P, Amend JP. Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter. Int J Syst Evol Microbiol 2021; 71. [PMID: 33877046 DOI: 10.1099/ijsem.0.004739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-20 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-25 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4 3-, SO4 2-, SeO4 2-, S2O3 2-, S0 and NO3 - were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii, within the class δ-Proteobacteria (now within the class Desulfuromonadia). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC 20015, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica K Choi
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karla Abuyen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Madeline Tyler
- Present address: College of Pharmacy, Oregon State University, Corvallis, OR 97330, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Cynthia Ronkowski
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Eric Romero
- Present address: Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Anthony Trujillo
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Jason Tremblay
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Isabella Viney
- Present address: Department of Microbiology, University of Arizona, Tucson, AZ 85721, USA.,Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pratixaben Savalia
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
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17
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Kapili BJ, Dekas AE. PPIT: an R package for inferring microbial taxonomy from nifH sequences. Bioinformatics 2021; 37:2289-2298. [PMID: 33580675 DOI: 10.1093/bioinformatics/btab100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. RESULTS We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. AVAILABILITY PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
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18
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Hassan RY, Febbraio F, Andreescu S. Microbial Electrochemical Systems: Principles, Construction and Biosensing Applications. SENSORS (BASEL, SWITZERLAND) 2021; 21:1279. [PMID: 33670122 PMCID: PMC7916843 DOI: 10.3390/s21041279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023]
Abstract
Microbial electrochemical systems are a fast emerging technology that use microorganisms to harvest the chemical energy from bioorganic materials to produce electrical power. Due to their flexibility and the wide variety of materials that can be used as a source, these devices show promise for applications in many fields including energy, environment and sensing. Microbial electrochemical systems rely on the integration of microbial cells, bioelectrochemistry, material science and electrochemical technologies to achieve effective conversion of the chemical energy stored in organic materials into electrical power. Therefore, the interaction between microorganisms and electrodes and their operation at physiological important potentials are critical for their development. This article provides an overview of the principles and applications of microbial electrochemical systems, their development status and potential for implementation in the biosensing field. It also provides a discussion of the recent developments in the selection of electrode materials to improve electron transfer using nanomaterials along with challenges for achieving practical implementation, and examples of applications in the biosensing field.
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Affiliation(s)
- Rabeay Y.A. Hassan
- Nanoscience Program, University of Science and Technology (UST), Zewail City of Science and Technology, 6th October City, Giza 12578, Egypt;
- National Research Centre (NRC), Applied Organic Chemistry Department, El Bohouth st., Dokki, Giza 12622, Egypt
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy;
| | - Silvana Andreescu
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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19
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Biodegradation of acetaminophen and its main by-product 4-aminophenol by Trichoderma harzianum versus mixed biofilm of Trichoderma harzianum/Pseudomonas fluorescens in a fungal microbial fuel cell. J APPL ELECTROCHEM 2021. [DOI: 10.1007/s10800-020-01518-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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20
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline-alkaline environment. NPJ Biofilms Microbiomes 2020; 6:38. [PMID: 33051461 PMCID: PMC7555509 DOI: 10.1038/s41522-020-00147-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/11/2020] [Indexed: 11/08/2022] Open
Abstract
Understanding of the extreme microorganisms that possess extracellular electron transfer (EET) capabilities is pivotal to advance electromicrobiology discipline and to develop niche-specific microbial electrochemistry-driven biotechnologies. Here, we report on the microbial electroactive biofilms (EABs) possessing the outward EET capabilities from a haloalkaline environment of the Lonar lake. We used the electrochemical cultivation approach to enrich haloalkaliphilic EABs under 9.5 pH and 20 g/L salinity conditions. The electrodes controlled at 0.2 V vs. Ag/AgCl yielded the best-performing biofilms in terms of maximum bioelectrocatalytic current densities of 548 ± 23 and 437 ± 17 µA/cm2 with acetate and lactate substrates, respectively. Electrochemical characterization of biofilms revealed the presence of two putative redox-active moieties with the mean formal potentials of 0.183 and 0.333 V vs. Ag/AgCl, which represent the highest values reported to date for the EABs. 16S-rRNA amplicon sequencing of EABs revealed the dominance of unknown Geoalkalibacter sp. at ~80% abundance. Further investigations on the haloalkaliphilic EABs possessing EET components with high formal potentials might offer interesting research prospects in electromicrobiology.
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Yee MO, Deutzmann J, Spormann A, Rotaru AE. Cultivating electroactive microbes-from field to bench. NANOTECHNOLOGY 2020; 31:174003. [PMID: 31931483 DOI: 10.1088/1361-6528/ab6ab5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electromicrobiology is an emerging field investigating and exploiting the interaction of microorganisms with insoluble electron donors or acceptors. Some of the most recently categorized electroactive microorganisms became of interest to sustainable bioengineering practices. However, laboratories worldwide typically maintain electroactive microorganisms on soluble substrates, which often leads to a decrease or loss of the ability to effectively exchange electrons with solid electrode surfaces. In order to develop future sustainable technologies, we cannot rely solely on existing lab-isolates. Therefore, we must develop isolation strategies for environmental strains with electroactive properties superior to strains in culture collections. In this article, we provide an overview of the studies that isolated or enriched electroactive microorganisms from the environment using an anode as the sole electron acceptor (electricity-generating microorganisms) or a cathode as the sole electron donor (electricity-consuming microorganisms). Next, we recommend a selective strategy for the isolation of electroactive microorganisms. Furthermore, we provide a practical guide for setting up electrochemical reactors and highlight crucial electrochemical techniques to determine electroactivity and the mode of electron transfer in novel organisms.
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Affiliation(s)
- Mon Oo Yee
- Nordcee, Department of Biology, University of Southern Denmark, Odense, DK-5230, Denmark
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23
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Scratching and transplanting of electro-active biofilm in fruit peeling leachate by ultrasound: re-inoculation in new microbial fuel cell for enhancement of bio-energy production and organic matter detection. Biotechnol Lett 2020; 42:965-978. [PMID: 32144559 DOI: 10.1007/s10529-020-02858-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/29/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE An electro-active biofilm of Fruit Peeling (FP) leachate was formed onto the Carbon Felt (CF) bio-anode in a Microbial Fuel Cell (MFC), after functioning for a long time. The electro active-biofilm thus formed was then scratched by ultrasound and re-inoculated in a new leachate to be transplanted onto the bio-anode. This procedure allowed the microbial electron charge transfer and therefore the enhancement of the bio-energy production of the fuel cell. RESULTS By using the repetitive mechanical biofilm removal, re-suspension and electrochemically facilitated biofilm formation, the voltage was substantially increased. In effect, the voltage of the 1st G of biofilm, rose gradually and reached its maximum value of 65 mV after 10 days. Whilst the 2nd generation allowed to obtain the maximum voltage 276 mV and without any lag time. The DCO abatement using the 1st G biofilm was 68% greater than the 3rd G 26%. Besides, the electrochemical impedance spectroscopy characterization and cyclic voltammetry of bio-anode with 2nd G biofilm confirmed the ability of electro-active biofilm formation on a new support. The biofilm transplanted showed thus greater kinetic performance, with reduced lag time demonstrating the interest of the selection that took place during the formation of successive biofilms. CONCLUSIONS Despite the transplantation of the electro-active biofilm onto the bio-anode, the MFC still produced relatively lower power output. Nevertheless, it has been tested successfully for monitoring and detecting the oxidation of sodium acetate substrate in the very wide concentration range 0.0025-35 g/l.
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Performance of Exoelectrogenic Bacteria Used in Microbial Desalination Cell Technology. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17031121. [PMID: 32050646 PMCID: PMC7037215 DOI: 10.3390/ijerph17031121] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 11/16/2022]
Abstract
The tri-functional purpose of Microbial Desalination Cell (MDC) has shown a great promise in our current scarcity of water, an increase in water pollution and the high cost of electricity production. As a biological system, the baseline force that drives its performance is the presence of exoelectrogens in the anode chamber. Their presence in the anodic chamber of MDC systems enables the treatment of water, desalination of seawater, and the production of electrical energy. This study reviews the characteristics of exoelectrogens, as a driving force in MDC and examines factors which influence their growth and the performance efficiency of MDC systems. It also addresses the efficiency of mixed cultures with certain predominant species as compared to pure cultures used in MDC systems. Furthermore, the study suggests the need to genetically modify certain predominant strains in mixed cultures to enhance their performance in COD removal, desalination and power output and the integration of MDC with other technologies for cost-effective processes.
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25
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Klasek S, Torres ME, Bartlett DH, Tyler M, Hong W, Colwell F. Microbial communities from Arctic marine sediments respond slowly to methane addition during
ex situ
enrichments. Environ Microbiol 2020; 22:1829-1846. [DOI: 10.1111/1462-2920.14895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/11/2019] [Accepted: 11/30/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Scott Klasek
- Department of Microbiology Oregon State University Corvallis Oregon USA
| | - Marta E. Torres
- College of Earth, Ocean, and Atmospheric Sciences Oregon State University Corvallis Oregon USA
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography University of California San Diego California 92093‐0202 USA
| | - Madeline Tyler
- Department of Microbiology Oregon State University Corvallis Oregon USA
| | - Wei‐Li Hong
- Centre for Arctic Gas Hydrate, Environment and Climate (CAGE), Department of Geosciences UiT The Arctic University of Norway N‐9037 Tromsø Norway
| | - Frederick Colwell
- Department of Microbiology Oregon State University Corvallis Oregon USA
- College of Earth, Ocean, and Atmospheric Sciences Oregon State University Corvallis Oregon USA
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26
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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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27
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Complex Microbial Communities Drive Iron and Sulfur Cycling in Arctic Fjord Sediments. Appl Environ Microbiol 2019; 85:AEM.00949-19. [PMID: 31076435 DOI: 10.1128/aem.00949-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 11/20/2022] Open
Abstract
Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. We hypothesize that in Svalbard fjords, microbes catalyze intense iron and sulfur cycling in low-organic-matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. In this study, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above a 12-cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ13C and C/N ratios) was more abundant at this outer site, and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low availability of organic matter. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.IMPORTANCE Glacial runoff is a key source of iron for primary production in the Arctic. In the fjords of the Svalbard archipelago, glacial retreat is predicted to stimulate phytoplankton blooms that were previously restricted to outer margins. Decreased sediment delivery and enhanced primary production have been hypothesized to alter sediment biogeochemistry, wherein any free reduced iron that could potentially be delivered to the shelf will instead become buried with sulfide generated through microbial sulfate reduction. We support this hypothesis with sequencing data that showed increases in the relative abundance of sulfate reducing taxa and sulfate reduction rates with increasing distance from the glaciers in Van Keulenfjorden, Svalbard. Community structure was driven by organic geochemistry, suggesting that enhanced input of organic material will stimulate sulfate reduction in interior fjord sediments as glaciers continue to recede.
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28
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Zakharyuk AG, Ryzhmanova YV, Avtukh AN, Shcherbakova VA. Iron-Reducing Microbial Communities of the Lake Baikal Low-Temperature Bottom Sediments. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719020139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Abstract
The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.
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30
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Lu S, Xie B, Liu B, Lu B, Xing D. Neglected Effects of Inoculum Preservation on the Start-Up of Psychrophilic Bioelectrochemical Systems and Shaping Bacterial Communities at Low Temperature. Front Microbiol 2019; 10:935. [PMID: 31118927 PMCID: PMC6507619 DOI: 10.3389/fmicb.2019.00935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 01/29/2023] Open
Abstract
Bioelectrochemical systems (BESs) are capable of simultaneous wastewater treatment and resource recovery at low temperatures. However, the direct enrichment of psychrophilic and electroactive biofilms in BESs at 4°C is difficult due to the lack of understanding in the physioecology of psychrophilic exoelectrogens. Here, we report the start-up and operation of microbial fuel cells (MFCs) at 4°C with pre-acclimated inocula at different temperatures (4°C, 10°C, 25°C, and -20°C) for 7 days and 14 days. MFCs with 7-day-pretreated inocula reached higher peak voltages than did those with 14-day-pretreated inocula. The highest power densities were obtained by MFCs with 25°C - 7-day-, 25°C - 14-day-, and 4°C - 7-day-pretreated inocula (650-700 mW/m2). In contrast, the control MFCs with untreated inocula were stable at 450 mW/m2. The power densities of MFCs with 7-day-pretreated inocula were higher than those obtained by MFCs with 14-day-pretreated inocula. The MFCs with 10°C - 7-day-pretreated inocula and the control MFCs showed higher chemical oxygen demand (COD) removal (90-91%) than other MFCs. Illumina HiSeq sequencing based on 16S rRNA gene amplicons indicated that bacterial communities of the anode biofilms were shaped by pretreated inocula at different temperatures. Compared with the control MFCs with untreated inocula, MFCs with temperature-pretreated inocula demonstrated higher microbial diversity, but did not do so with -20°C-pretreated inocula. Principal components analysis (PCA) revealed an obvious separation between the inocula pretreated at 4°C and those pretreated at 10°C, implying that bacterial community structures could be shaped by pretreated inocula at low temperatures. The pretreatment period also had a diverse impact on the abundance of exoelectrogens and non-exoelectrogens in MFCs with inocula pretreated at different temperatures. The majority of the predominant population was affiliated with Geobacter with a relative abundance of 17-70% at different pre-acclimated temperatures, suggesting that the exoelectrogenic Geobacter could be effectively enriched at 4°C even with inocula pretreated at different temperatures. This study provides a strategy that was previously neglected for fast enrichment of psychrophilic exoelectrogens in BESs at low temperatures.
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Affiliation(s)
- Sidan Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Binghan Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Baiyun Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
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31
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Campen R, Kowalski J, Lyons WB, Tulaczyk S, Dachwald B, Pettit E, Welch KA, Mikucki JA. Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert. Environ Microbiol 2019; 21:2290-2306. [PMID: 30927377 DOI: 10.1111/1462-2920.14607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/30/2022]
Abstract
Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.
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Affiliation(s)
- Richard Campen
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | | | - Slawek Tulaczyk
- University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Bernd Dachwald
- Faculty of Aerospace Engineering, FH Aachen University of Applied Sciences, Aachen, Germany
| | - Erin Pettit
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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32
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Logan BE, Rossi R, Ragab A, Saikaly PE. Electroactive microorganisms in bioelectrochemical systems. Nat Rev Microbiol 2019; 17:307-319. [DOI: 10.1038/s41579-019-0173-x] [Citation(s) in RCA: 546] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Shao Q, Li J, Yang S, Sun H. Effects of different substrates on microbial electrolysis cell (MEC) anodic membrane: biodiversity and hydrogen production performance. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:1123-1133. [PMID: 31070592 DOI: 10.2166/wst.2019.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To investigate the effects of different substrates on the biodiversity and hydrogen production performance of microbial electrolysis cell (MEC) anodic membranes, the vital electroactive microorganisms (e.g. in MEC hydrogen production) were worth identifying. In the present study, single-factor experiments were performed. Sodium acetate, sodium propionate, sodium butyrate, glucose and starch served as different substrates for MEC anodic culture experiments under the same condition. The effects of different substrates on the bioactivity, biomass and hydrogen production performance of MEC anodic films were analyzed. Also, the effects of different microbial communities on hydrogen production were studied using 16S rRNA sequencing. According to the experimental results, all the five substrates here can serve as hydrogen-producing raw materials for MEC. All indicators revealed that sodium acetate, sodium propionate and sodium butyrate are excellent biofilm culture materials. The serious acidification of glucose and starch was identified at the same substrate concentration, and the environment of the culture medium was difficult to control, which affected the growth and metabolism of electroactive microorganisms. In comparison, sodium acetate was the best, achieving a maximum output of 23.4 mA and a maximum hydrogen content of 25.85%. The other four were ranked as sodium butyrate > sodium propionate > glucose > starch. According to the results of high-throughput sequencing, when sodium acetate, sodium propionate, sodium butyrate, glucose and starch served as substrates, the number of operational taxonomic units reached 464, 728, 636, 784, and 1,083, respectively. Furthermore, when MEC was cultured with sodium acetate, sodium propionate and sodium butyrate as substrates, the electroactive microorganism Desulfuromonas in the Proteobacteria would contribute the most to producing hydrogen. The relative abundance of the five substrates was ranked as sodium acetate > sodium butyrate > sodium propionate > glucose > starch, suggesting that the MEC anodic film cultured with sodium acetate as the substrate exhibited the best hydrogen production performance, and the starch showed the worst. It is noteworthy that Desulfuromonas was the most abundant species according to sequencing results. When glucose and starch served as substrates, they exhibited high biodiversity. The anodic membranes cultured with sodium acetate, sodium propionate and sodium butyrate were not as good as those cultured with glucose and starch, yet the electroactive microorganisms were up-regulated.
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Affiliation(s)
- Qiongli Shao
- Yunnan Normal University, Kunming 650500, Yunnan, China E-mail:
| | - Jianchang Li
- Yunnan Normal University, Kunming 650500, Yunnan, China E-mail:
| | - Sixia Yang
- Yunnan Normal University, Kunming 650500, Yunnan, China E-mail:
| | - Helin Sun
- Yunnan Normal University, Kunming 650500, Yunnan, China E-mail:
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Cao Y, Mu H, Liu W, Zhang R, Guo J, Xian M, Liu H. Electricigens in the anode of microbial fuel cells: pure cultures versus mixed communities. Microb Cell Fact 2019; 18:39. [PMID: 30782155 PMCID: PMC6380051 DOI: 10.1186/s12934-019-1087-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/12/2019] [Indexed: 11/10/2022] Open
Abstract
Microbial fuel cell (MFC) is an environmentally friendly technology for electricity harvesting from a variety of substrates. Microorganisms used as catalysts in the anodic chamber, which are termed as electricigens, play a major role in the operation of MFCs. This review provides an introduction to the currently identified electricigens on their taxonomical groups and electricity producing abilities. The mechanism of electron transfer from electricigens to electrode is highlighted. The performances of pure culture and mixed communities are compared particularly. It has been proved that the electricity generation capacity and the ability to adapt to the complex environment of MFC systems constructed by pure microbial cultures are less than the systems constructed by miscellaneous consortia. However, pure cultures are useful to clarify the electron transfer mechanism at the microbiological level and further reduce the complexity of mixed communities. Future research trends of electricigens in MFCs should be focused on screening, domestication, modification and optimization of multi-strains to improve their electrochemical activities. Although the MFC techniques have been greatly advanced during the past few years, the present state of this technology still requires to be combined with other processes for cost reduction.
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Affiliation(s)
- Yujin Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| | - Hui Mu
- Shandong Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jing Guo
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| | - Huizhou Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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Jiang Z, Zhang Y, Liu Z, Ma Y, Kang J, Liu Y. Isolation and characterization of an exoelectrogenic strain CL-1 from soil and electron transfer mechanism by linking electrochemistry and spectroscopy. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.09.153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Li M, Zhou M, Tian X, Tan C, McDaniel CT, Hassett DJ, Gu T. Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity. Biotechnol Adv 2018; 36:1316-1327. [DOI: 10.1016/j.biotechadv.2018.04.010] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/28/2018] [Accepted: 04/28/2018] [Indexed: 10/17/2022]
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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: 33] [Impact Index Per Article: 4.7] [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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Sharma SCD, Feng C, Li J, Hu A, Wang H, Qin D, Yu CP. Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei. Microbes Environ 2016; 31:213-25. [PMID: 27396922 PMCID: PMC5017797 DOI: 10.1264/jsme2.me15185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A facultative anaerobic bacterium, designated as strain SCS5, was isolated from the anodic biofilm of a mediator-less microbial fuel cell using acetate as the electron donor and α-FeOOH as the electron acceptor. The isolate was Gram-negative, motile, and shaped as short rods (0.9-1.3 μm in length and 0.4-0.5 μm in width). A phylogenetic analysis of the 16S rRNA, gyrB, and rpoD genes suggested that strain SCS5 belonged to the Aeromonas genus in the Aeromonadaceae family and exhibited the highest 16S rRNA gene sequence similarity (99.45%) with Aeromonas jandaei ATCC 49568. However, phenotypic, cellular fatty acid profile, and DNA G+C content analyses revealed that there were some distinctions between strain SCS5 and the type strain A. jandaei ATCC 49568. The optimum growth temperature, pH, and NaCl (%) for strain SCS5 were 35°C, 7.0, and 0.5% respectively. The DNA G+C content of strain SCS5 was 59.18%. The isolate SCS5 was capable of reducing insoluble iron oxide (α-FeOOH) and transferring electrons to extracellular material (the carbon electrode). The electrochemical activity of strain SCS5 was corroborated by cyclic voltammetry and a Raman spectroscopic analysis. The cyclic voltammogram of strain SCS5 revealed two pairs of oxidation-reduction peaks under anaerobic and aerobic conditions. In contrast, no redox pair was observed for A. jandaei ATCC 49568. Thus, isolated strain SCS5 is a novel exoelectrogenic bacterium phylogenetically related to A. jandaei, but shows distinct electrochemical activity from its close relative A. jandaei ATCC 49568.
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Affiliation(s)
- Subed Chandra Dev Sharma
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
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Badalamenti JP, Summers ZM, Chan CH, Gralnick JA, Bond DR. Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine. Front Microbiol 2016; 7:913. [PMID: 27445996 PMCID: PMC4914508 DOI: 10.3389/fmicb.2016.00913] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/27/2016] [Indexed: 11/25/2022] Open
Abstract
Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, ‘Desulfuromonas soudanensis’ strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that ‘D. soudanensis’ releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. ‘D. soudanensis’ contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of ‘D. soudanensis’ underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.
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Affiliation(s)
| | - Zarath M Summers
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul MN, USA
| | - Chi Ho Chan
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul MN, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint PaulMN, USA; Department of Microbiology, University of Minnesota - Twin Cities, MinneapolisMN, USA
| | - Daniel R Bond
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint PaulMN, USA; Department of Microbiology, University of Minnesota - Twin Cities, MinneapolisMN, USA
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Pierra M, Carmona-Martínez AA, Trably E, Godon JJ, Bernet N. Specific and efficient electrochemical selection of Geoalkalibacter subterraneus and Desulfuromonas acetoxidans in high current-producing biofilms. Bioelectrochemistry 2015; 106:221-5. [DOI: 10.1016/j.bioelechem.2015.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/30/2015] [Accepted: 02/13/2015] [Indexed: 01/27/2023]
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Dopson M, Ni G, Sleutels THJA. Possibilities for extremophilic microorganisms in microbial electrochemical systems. FEMS Microbiol Rev 2015; 40:164-81. [PMID: 26474966 PMCID: PMC4802824 DOI: 10.1093/femsre/fuv044] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 11/12/2022] Open
Abstract
Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Gaofeng Ni
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Tom H J A Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8911 MA Leeuwarden, The Netherlands
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Morrissey EM, Franklin RB. Evolutionary history influences the salinity preference of bacterial taxa in wetland soils. Front Microbiol 2015; 6:1013. [PMID: 26483764 PMCID: PMC4591843 DOI: 10.3389/fmicb.2015.01013] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Salinity is a major driver of bacterial community composition across the globe. Despite growing recognition that different bacterial species are present or active at different salinities, the mechanisms by which salinity structures community composition remain unclear. We tested the hypothesis that these patterns reflect ecological coherence in the salinity preferences of phylogenetic groups using a reciprocal transplant experiment of fresh- and saltwater wetland soils. The salinity of both the origin and host environments affected community composition (16S rRNA gene sequences) and activity (CO2 and CH4 production, and extracellular enzyme activity). These changes in community composition and activity rates were strongly correlated, which suggests the effect of environment on function could be mediated, at least in part, by microbial community composition. Based on their distribution across treatments, each phylotype was categorized as having a salinity preference (freshwater, saltwater, or none) and phylogenetic analyses revealed a significant influence of evolutionary history on these groupings. This finding was corroborated by examining the salinity preferences of high-level taxonomic groups. For instance, we found that the majority of α- and γ-proteobacteria in these wetland soils preferred saltwater, while many β-proteobacteria prefer freshwater. Overall, our results indicate the effect of salinity on bacterial community composition results from phylogenetically-clustered salinity preferences.
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Affiliation(s)
- Ember M Morrissey
- Laboratory of Microbial Ecology, Department of Biology, Virginia Commonwealth University Richmond, VA, USA
| | - Rima B Franklin
- Laboratory of Microbial Ecology, Department of Biology, Virginia Commonwealth University Richmond, VA, USA
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Carmona-Martínez AA, Trably E, Milferstedt K, Lacroix R, Etcheverry L, Bernet N. Long-term continuous production of H2 in a microbial electrolysis cell (MEC) treating saline wastewater. WATER RESEARCH 2015; 81:149-156. [PMID: 26057262 DOI: 10.1016/j.watres.2015.05.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/08/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
A biofilm-based 4 L two chamber microbial electrolysis cell (MEC) was continuously fed with acetate under saline conditions (35 g/L NaCl) for more than 100 days. The MEC produced a biogas highly enriched in H2 (≥90%). Both current (10.6 ± 0.2 A/m(2)Anode or 199.1 ± 4.0 A/m(3)MEC) and H2 production (201.1 ± 7.5 LH2/m(2)Cathode·d or 0.9 ± 0.0 m(3)H2/m(3)MEC·d) rates were highly significant when considering the saline operating conditions. A microbial analysis revealed an important enrichment in the anodic biofilm with five main bacterial groups: 44% Proteobacteria, 32% Bacteroidetes, 18% Firmicutes and 5% Spirochaetes and 1% Actinobacteria. Of special interest is the emergence within the Proteobacteria phylum of the recently described halophilic anode-respiring bacteria Geoalkalibacter (unk. species), with a relative abundance up to 14%. These results provide for the first time a noteworthy alternative for the treatment of saline effluents and continuous production of H2.
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Affiliation(s)
| | - Eric Trably
- INRA, UR0050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, Narbonne F-11100, France
| | - Kim Milferstedt
- INRA, UR0050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, Narbonne F-11100, France
| | - Rémy Lacroix
- 6T-MIC Ingénieries, 4 rue Brindejonc des Moulinais, 31500 Toulouse, France
| | - Luc Etcheverry
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, 4 allée Emile Monso, 31432 Toulouse, France
| | - Nicolas Bernet
- INRA, UR0050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, Narbonne F-11100, France.
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An J, Nam J, Kim B, Lee HS, Kim BH, Chang IS. Performance variation according to anode-embedded orientation in a sediment microbial fuel cell employing a chessboard-like hundred-piece anode. BIORESOURCE TECHNOLOGY 2015; 190:175-181. [PMID: 25941759 DOI: 10.1016/j.biortech.2015.04.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
The effect of two different anode-embedding orientations, lengthwise- and widthwise-embedded anodes was explored, on the performance of sediment microbial fuel cells (SMFCs) using a chessboard anode. The maximum current densities and power densities in SMFCs having lengthwise-embedded anodes (SLA1-SLA10) varied from 38.2mA/m(2) to 121mA/m(2) and from 5.5mW/m(2) to 20mW/m(2). In comparison, the maximum current densities and maximum power densities in SMFCs having anodes widthwise-embedded between 0cm to 8cm (SWA2-SWA5) increased from 82mA/m(2) to 140mA/m(2) and from 14.7mW/m(2) to 31.1mW/m(2) as the anode depth became deeper. Although there was a difference in the performance among SWA5-SWA10, it was considered negligible. Hence, it is concluded that it is important to embed anodes widthwise at the specific anode depths, in order to improve of SMFC performance. Chessboard anode used in this work could be a good option for the determination of optimal anode depths.
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Affiliation(s)
- Junyeong An
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Republic of Korea; Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jonghyun Nam
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Bongkyu Kim
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Hyung-Sool Lee
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Byung Hong Kim
- Fuel Cell Institute, National University of Malaysia, 43600 UKM Bangi, Malaysia; Bioelectrochemistry Laboratory, Water Environment and Remediation Research Centre, Korea Institute of Science and Technology, Republic of Korea
| | - In Seop Chang
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Republic of Korea.
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Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling. Appl Environ Microbiol 2015. [PMID: 26209674 DOI: 10.1128/aem.01382-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem.
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Characterization of a novel strain phylogenetically related to Kocuria rhizophila and its chemical modification to improve performance of microbial fuel cells. Biosens Bioelectron 2015; 69:113-20. [DOI: 10.1016/j.bios.2015.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/02/2015] [Accepted: 02/15/2015] [Indexed: 12/15/2022]
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Nixon SL, Cockell CS. Nonproteinogenic D-amino acids at millimolar concentrations are a toxin for anaerobic microorganisms relevant to early Earth and other anoxic planets. ASTROBIOLOGY 2015; 15:238-246. [PMID: 25695622 DOI: 10.1089/ast.2014.1252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The delivery of extraterrestrial organics to early Earth provided a potentially important source of carbon and energy for microbial life. Optically active organic compounds of extraterrestrial origin exist in racemic form, yet life on Earth has almost exclusively selected for L- over D-enantiomers of amino acids. Although D-enantiomers of proteinogenic amino acids are known to inhibit aerobic microorganisms, the role of concentrated nonproteinogenic meteoritic D-amino acids on anaerobic metabolisms relevant to early Earth and other anoxic planets such as Mars is unknown. Here, we test the inhibitory effect of D-enantiomers of two nonproteinogenic amino acids common to carbonaceous chondrites, norvaline and α-aminobutyric acid, on microbial iron reduction. Three pure strains (Geobacter bemidjiensis, Geobacter metallireducens, Geopsychrobacter electrodiphilus) and an iron-reducing enrichment culture were grown in the presence of 10 mM D-enantiomers of both amino acids. Further tests were conducted to assess the inhibitory effect of these D-amino acids at 1 and 0.1 mM. The presence of 10 mM D-norvaline and D-α-aminobutyric acid inhibited microbial iron reduction by all pure strains and the enrichment. G. bemidjiensis was not inhibited by either amino acid at 0.1 mM, but D-α-aminobutyric acid still inhibited at 1 mM. Calculations using published meteorite accumulation rates to the martian surface indicate D-α-aminobutyric acid may have reached inhibitory concentrations in little over 1000 years during peak infall. These data show that, on a young anoxic planet, the use of one enantiomer over another may render the nonbiological enantiomer an environmental toxin. Processes that generate racemic amino acids in the environment, such as meteoritic infall or impact synthesis, would have been toxic processes and could have been a selection pressure for the evolution of early racemases.
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Affiliation(s)
- Sophie L Nixon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh , Edinburgh, UK
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50
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Nie PF, Li XF, Ren YP, Wang XH. Electricity generation from sulfide tailings using a double-chamber microbial fuel cell. RSC Adv 2015. [DOI: 10.1039/c5ra16459a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pyrrhotite tailings have the potential to drive electricity generation accompanied by microbial leaching of valuable metals using the double-chamber MFC reactor.
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Affiliation(s)
- P. F. Nie
- School of Environmental and Civil Engineering
- Jiangnan University
- Wuxi
- China
- Jiangsu Key Laboratory of Anaerobic Biotechnology
| | - X. F. Li
- School of Environmental and Civil Engineering
- Jiangnan University
- Wuxi
- China
- Jiangsu Key Laboratory of Anaerobic Biotechnology
| | - Y. P. Ren
- School of Environmental and Civil Engineering
- Jiangnan University
- Wuxi
- China
- Jiangsu Key Laboratory of Anaerobic Biotechnology
| | - X. H. Wang
- School of Environmental and Civil Engineering
- Jiangnan University
- Wuxi
- China
- Jiangsu Key Laboratory of Anaerobic Biotechnology
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