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Knisz J, Eckert R, Gieg LM, Koerdt A, Lee JS, Silva ER, Skovhus TL, An Stepec BA, Wade SA. Microbiologically influenced corrosion-more than just microorganisms. FEMS Microbiol Rev 2023; 47:fuad041. [PMID: 37437902 PMCID: PMC10479746 DOI: 10.1093/femsre/fuad041] [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: 02/24/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/14/2023] Open
Abstract
Microbiologically influenced corrosion (MIC) is a phenomenon of increasing concern that affects various materials and sectors of society. MIC describes the effects, often negative, that a material can experience due to the presence of microorganisms. Unfortunately, although several research groups and industrial actors worldwide have already addressed MIC, discussions are fragmented, while information sharing and willingness to reach out to other disciplines are limited. A truly interdisciplinary approach, which would be logical for this material/biology/chemistry-related challenge, is rarely taken. In this review, we highlight critical non-biological aspects of MIC that can sometimes be overlooked by microbiologists working on MIC but are highly relevant for an overall understanding of this phenomenon. Here, we identify gaps, methods, and approaches to help solve MIC-related challenges, with an emphasis on the MIC of metals. We also discuss the application of existing tools and approaches for managing MIC and propose ideas to promote an improved understanding of MIC. Furthermore, we highlight areas where the insights and expertise of microbiologists are needed to help progress this field.
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Affiliation(s)
- J Knisz
- Department of Water Supply and Sewerage, Faculty of Water Sciences, University of Public Service, 6500, Baja, Hungary
| | - R Eckert
- Microbial Corrosion Consulting, LLC, Commerce Township, 48382, MI, USA
| | - L M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - A Koerdt
- Federal Institute for Materials Research and Testing (BAM), 12205, Berlin, Germany
| | - J S Lee
- Naval Research Laboratory, Ocean Sciences Division, Stennis Space Center, 39529, MS, USA
| | - E R Silva
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal
- CERENA - Centre for Natural Resources and the Environment, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1, 1049-001, Lisboa, Portugal
| | - T L Skovhus
- Research Center for Built Environment, Energy, Water and Climate, VIA, University College, 8700, Horsens, Denmark
| | - B A An Stepec
- Department of Energy and Technology, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | - S A Wade
- Bioengineering Research Group, Swinburne University of Technology, 3122, Melbourne, Australia
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2
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de Smit S, Langedijk JJH, van Haalen LCA, Lin SH, Bitter JH, Strik DPBTB. Methodology for In Situ Microsensor Profiling of Hydrogen, pH, Oxidation-Reduction Potential, and Electric Potential throughout Three-Dimensional Porous Cathodes of (Bio)Electrochemical Systems. Anal Chem 2023; 95:2680-2689. [PMID: 36715453 PMCID: PMC9909735 DOI: 10.1021/acs.analchem.2c03121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/17/2023] [Indexed: 01/31/2023]
Abstract
We developed a technique based on the use of microsensors to measure pH and H2 gradients during microbial electrosynthesis. The use of 3D electrodes in (bio)electrochemical systems likely results in the occurrence of gradients from the bulk conditions into the electrode. Since these gradients, e.g., with respect to pH and reactant/product concentrations determine the performance of the electrode, it is essential to be able to accurately measure them. Apart from these parameters, also local oxidation-reduction potential and electric field potential were determined in the electrolyte and throughout the 3D porous electrodes. Key was the realization that the presence of an electric field disturbed the measurements obtained by the potentiometric type of microsensor. To overcome the interference on the pH measure, a method was validated where the signal was corrected for the local electric field measured with the electric potential microsensor. The developed method provides a useful tool for studies about electrode design, reactor engineering, measuring gradients in electroactive biofilms, and flow dynamics in and around 3D porous electrodes of (bio)electrochemical systems.
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Affiliation(s)
- Sanne
M. de Smit
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
- Biobased
Chemistry and Technology, Wageningen University
and Research, Wageningen 6708WG, The Netherlands
| | - Jelle J. H. Langedijk
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
| | - Lennert C. A. van Haalen
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
| | - Shih Hsuan Lin
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
| | - Johannes H. Bitter
- Biobased
Chemistry and Technology, Wageningen University
and Research, Wageningen 6708WG, The Netherlands
| | - David P. B. T. B. Strik
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
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3
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Burgstaller H, Wang Y, Caliebe J, Hueren V, Appel J, Boehm M, Leitzke S, Theune M, King PW, Gutekunst K. Synechocystis sp. PCC 6803 Requires the Bidirectional Hydrogenase to Metabolize Glucose and Arginine Under Oxic Conditions. Front Microbiol 2022; 13:896190. [PMID: 35711753 PMCID: PMC9195167 DOI: 10.3389/fmicb.2022.896190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
The cyanobacterium Synechocystis sp.PCC 6803 possesses a bidirectional NiFe-hydrogenase, HoxEFUYH. It functions to produce hydrogen under dark, fermentative conditions and photoproduces hydrogen when dark-adapted cells are illuminated. Unexpectedly, we found that the deletion of the large subunit of the hydrogenase (HoxH) in Synechocystis leads to an inability to grow on arginine and glucose under continuous light in the presence of oxygen. This is surprising, as the hydrogenase is an oxygen-sensitive enzyme. In wild-type (WT) cells, thylakoid membranes largely disappeared, cyanophycin accumulated, and the plastoquinone (PQ) pool was highly reduced, whereas ΔhoxH cells entered a dormant-like state and neither consumed glucose nor arginine at comparable rates to the WT. Hydrogen production was not traceable in the WT under these conditions. We tested and could show that the hydrogenase does not work as an oxidase on arginine and glucose but has an impact on the redox states of photosynthetic complexes in the presence of oxygen. It acts as an electron valve as an immediate response to the supply of arginine and glucose but supports the input of electrons from arginine and glucose oxidation into the photosynthetic electron chain in the long run, possibly via the NDH-1 complex. Despite the data presented in this study, the latter scenario requires further proof. The exact role of the hydrogenase in the presence of arginine and glucose remains unresolved. In addition, a unique feature of the hydrogenase is its ability to shift electrons between NAD(H), NADP(H), ferredoxin, and flavodoxin, which was recently shown in vitro and might be required for fine-tuning. Taken together, our data show that Synechocystis depends on the hydrogenase to metabolize organic carbon and nitrogen in the presence of oxygen, which might be an explanation for its prevalence in aerobic cyanobacteria.
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Affiliation(s)
- Heinrich Burgstaller
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Yingying Wang
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Johanna Caliebe
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Vanessa Hueren
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Jens Appel
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Marko Boehm
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Sinje Leitzke
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany
| | - Marius Theune
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Kirstin Gutekunst
- Plant Cell Physiology and Biotechnology, Botanical Institute, University of Kiel, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
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4
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Berlanga M, Palau M, Guerrero R. Community homeostasis of coastal microbial mats from the Camargue during winter (cold) and summer (hot) seasons. Ecosphere 2022. [DOI: 10.1002/ecs2.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences University of Barcelona Barcelona Spain
| | - Montserrat Palau
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences University of Barcelona Barcelona Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine University of Barcelona Barcelona Spain
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5
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Martinez JN, Nishihara A, Lichtenberg M, Trampe E, Kawai S, Tank M, Kühl M, Hanada S, Thiel V. Vertical Distribution and Diversity of Phototrophic Bacteria within a Hot Spring Microbial Mat (Nakabusa Hot Springs, Japan). Microbes Environ 2019; 34:374-387. [PMID: 31685759 PMCID: PMC6934398 DOI: 10.1264/jsme2.me19047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phototrophic microbial mats are assemblages of vertically layered microbial populations dominated by photosynthetic microorganisms. In order to elucidate the vertical distribution and diversity of phototrophic microorganisms in a hot spring-associated microbial mat in Nakabusa (Japan), we analyzed the 16S rRNA gene amplicon sequences of the microbial mat separated into five depth horizons, and correlated them with microsensor measurements of O2 and spectral scalar irradiance. A stable core community and high diversity of phototrophic organisms dominated by the filamentous anoxygenic phototrophs, Roseiflexus castenholzii and Chloroflexus aggregans were identified together with the spectral signatures of bacteriochlorophylls (BChls) a and c absorption in all mat layers. In the upper mat layers, a high abundance of cyanobacteria (Thermosynechococcus sp.) correlated with strong spectral signatures of chlorophyll a and phycobiliprotein absorption near the surface in a zone of high O2 concentrations during the day. Deeper mat layers were dominated by uncultured chemotrophic Chlorobi such as the novel putatively sulfate-reducing “Ca. Thermonerobacter sp.”, which showed increasing abundance with depth correlating with low O2 in these layers enabling anaerobic metabolism. Oxygen tolerance and requirements for the novel phototroph “Ca. Chloroanaerofilum sp.” and the uncultured chemotrophic Armatimonadetes member type OS-L detected in Nakabusa hot springs, Japan appeared to differ from previously suggested lifestyles for close relatives identified in hot springs in Yellowstone National Park, USA. The present study identified various microenvironmental gradients and niche differentiation enabling the co-existence of diverse chlorophototrophs in metabolically diverse communities in hot springs.
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Affiliation(s)
- Joval N Martinez
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University.,Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle
| | - Arisa Nishihara
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Mads Lichtenberg
- Marine Biological Section, Department of Biology, University of Copenhagen
| | - Erik Trampe
- Marine Biological Section, Department of Biology, University of Copenhagen
| | - Shigeru Kawai
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Marcus Tank
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen
| | - Satoshi Hanada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
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6
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Haro S, Brodersen KE, Bohórquez J, Papaspyrou S, Corzo A, Kühl M. Radiative Energy Budgets in a Microbial Mat Under Different Irradiance and Tidal Conditions. MICROBIAL ECOLOGY 2019; 77:852-865. [PMID: 30852639 DOI: 10.1007/s00248-019-01350-6] [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: 10/29/2018] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Irradiance and temperature variations during tidal cycles modulate microphytobenthic primary production potentially by changing the radiative energy balance of photosynthetic mats between immersion and emersion and thus sediment daily net metabolism. To test the effect of tidal stages on the radiative energy budget, we used microsensor measurements of oxygen, temperature, and scalar irradiance to estimate the radiative energy budget in a coastal photosynthetic microbial mat during immersion (constant water column of 2 cm) and emersion under increasing irradiance. Total absorbed light energy was higher in immersion than emersion, due to a lower reflectance of the microbial mat, while most (> 97%) of the absorbed light energy was dissipated as heat irrespective of tidal conditions. During immersion, the upward heat flux was higher than the downward one, whereas the opposite occurred during emersion. At highest photon irradiance (800 μmol photon m-2 s-1), the sediment temperature increased ~ 2.5 °C after changing the conditions from immersion to emersion. The radiative energy balance showed that less than 1% of the incident light energy (PAR, 400-700 nm) was conserved by photosynthesis under both tidal conditions. At low to moderate incident irradiances, the light use efficiency was similar during the tidal stages. In contrast, we found an ~ 30% reduction in the light use efficiency during emersion as compared to immersion under the highest irradiance likely due to the rapid warming of the sediment during emersion and increased non-photochemical quenching. These changes in the photosynthetic efficiency and radiative energy budget could affect both primary producers and temperature-dependent bacterial activity and consequently daily net metabolism rates having important ecological consequences.
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Affiliation(s)
- S Haro
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, 11510, Puerto Real, Cádiz, Spain.
- University Institute of Marine Research (INMAR), University of Cádiz, Cadiz, Spain.
| | - K E Brodersen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - J Bohórquez
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, 11510, Puerto Real, Cádiz, Spain
- University Institute of Marine Research (INMAR), University of Cádiz, Cadiz, Spain
| | - S Papaspyrou
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, 11510, Puerto Real, Cádiz, Spain
- University Institute of Marine Research (INMAR), University of Cádiz, Cadiz, Spain
| | - A Corzo
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, 11510, Puerto Real, Cádiz, Spain
- University Institute of Marine Research (INMAR), University of Cádiz, Cadiz, Spain
| | - M Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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7
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Teng Y, Xu Y, Wang X, Christie P. Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation. Front Microbiol 2019; 10:106. [PMID: 30837956 PMCID: PMC6383490 DOI: 10.3389/fmicb.2019.00106] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Hydrogen (H2) metabolism has attracted considerable interest because the activities of H2-producing and consuming microbes shape the global H2 cycle and may have vital relationships with the global cycling of other elements. There are many pathways of microbial H2 emission and consumption which may affect the structure and function of microbial communities. A wide range of microbial groups employ H2 as an electron donor to catalyze the reduction of pollutants such as organohalides, azo compounds, and trace metals. Syntrophy coupled mutualistic interaction between H2-producing and H2-consuming microorganisms can transfer H2 and be accompanied by the removal of toxic compounds. Moreover, hydrogenases have been gradually recognized to have a key role in the progress of pollutant degradation. This paper reviews recent advances in elucidating role of H2 metabolism involved in syntrophy and hydrogenases in environmental bioremediation. Further investigations should focus on the application of bioenergy in bioremediation to make microbiological H2 metabolism a promising remediation strategy.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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8
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Li T, Sharp CE, Ataeian M, Strous M, de Beer D. Role of Extracellular Carbonic Anhydrase in Dissolved Inorganic Carbon Uptake in Alkaliphilic Phototrophic Biofilm. Front Microbiol 2018; 9:2490. [PMID: 30405559 PMCID: PMC6204761 DOI: 10.3389/fmicb.2018.02490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/28/2018] [Indexed: 11/22/2022] Open
Abstract
Alkaline Soda Lakes are extremely productive ecosystems, due to their high dissolved inorganic carbon (DIC) concentrations. Here, we studied the dynamics of the carbonate system, in particular, the role of extracellular carbonic anhydrase (eCA) of an alkaliphilic phototrophic biofilm composed of bacteria enriched from soda lake benthic mats. By using measurements with microsensors and membrane inlet mass spectrometry, combined with mathematical modeling, we show how eCA controls DIC uptake. In our experiments, the activity of eCA varied four-fold, and was controlled by the bicarbonate concentration during growth: a higher bicarbonate concentration led to lower eCA activity. Inhibition of eCA decreased both the net and the gross photosynthetic productivities of the investigated biofilms. After eCA inhibition, the efflux of carbon dioxide (CO2) from the biofilms increased two- to four-fold. This could be explained by the conversion of CO2, leaking from cyanobacterial cells, by eCA, to bicarbonate. Bicarbonate is then taken up again by the cyanobacteria. In suspensions, eCA reduced the CO2 leakage to the bulk medium from 90 to 50%. In biofilms cultivated at low bicarbonate concentration (~0.13 mM), the oxygen production was reduced by a similar ratio upon eCA inhibition. The role of eCA in intact biofilms was much less significant compared to biomass suspensions, as CO2 loss to the medium is reduced due to mass transfer resistance.
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Affiliation(s)
- Tong Li
- Microsensor Group, Max-Planck-Insititute for Marine Microbiology, Bremen, Germany
| | | | - Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Dirk de Beer
- Microsensor Group, Max-Planck-Insititute for Marine Microbiology, Bremen, Germany
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9
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Schrameyer V, York PH, Chartrand K, Ralph PJ, Kühl M, Brodersen KE, Rasheed MA. Contrasting impacts of light reduction on sediment biogeochemistry in deep- and shallow-water tropical seagrass assemblages (Green Island, Great Barrier Reef). MARINE ENVIRONMENTAL RESEARCH 2018; 136:38-47. [PMID: 29472034 DOI: 10.1016/j.marenvres.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/11/2018] [Indexed: 06/08/2023]
Abstract
Seagrass meadows increasingly face reduced light availability as a consequence of coastal development, eutrophication, and climate-driven increases in rainfall leading to turbidity plumes. We examined the impact of reduced light on above-ground seagrass biomass and sediment biogeochemistry in tropical shallow- (∼2 m) and deep-water (∼17 m) seagrass meadows (Green Island, Australia). Artificial shading (transmitting ∼10-25% of incident solar irradiance) was applied to the shallow- and deep-water sites for up to two weeks. While above-ground biomass was unchanged, higher diffusive O2 uptake (DOU) rates, lower O2 penetration depths, and higher volume-specific O2 consumption (R) rates were found in seagrass-vegetated sediments as compared to adjacent bare sand (control) areas at the shallow-water sites. In contrast, deep-water sediment characteristics did not differ between bare sand and vegetated sites. At the vegetated shallow-water site, shading resulted in significantly lower hydrogen sulphide (H2S) levels in the sediment. No shading effects were found on sediment biogeochemistry at the deep-water site. Overall, our results show that the sediment biogeochemistry of shallow-water (Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata and C. serrulata) and deep-water (Halophila decipiens) seagrass meadows with different species differ in response to reduced light. The light-driven dynamics of the sediment biogeochemistry at the shallow-water site could suggest the presence of a microbial consortium, which might be stimulated by photosynthetically produced exudates from the seagrass, which becomes limited due to lower seagrass photosynthesis under shaded conditions.
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Affiliation(s)
- Verena Schrameyer
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Paul H York
- Centre for Tropical Water & Aquatic Ecosystem Research, James Cook University, Cairns, QLD, Australia
| | - Kathryn Chartrand
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Centre for Tropical Water & Aquatic Ecosystem Research, James Cook University, Cairns, QLD, Australia
| | - Peter J Ralph
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Michael Kühl
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Kasper Elgetti Brodersen
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
| | - Michael A Rasheed
- Centre for Tropical Water & Aquatic Ecosystem Research, James Cook University, Cairns, QLD, Australia
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10
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Prieto-Barajas CM, Valencia-Cantero E, Santoyo G. Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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11
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Berlanga M, Palau M, Guerrero R. Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats. Front Microbiol 2017; 8:2619. [PMID: 29312277 PMCID: PMC5744480 DOI: 10.3389/fmicb.2017.02619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/15/2017] [Indexed: 01/11/2023] Open
Abstract
Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0–2, 2–4, and 4–6 mm). To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%), followed by Archaea (∼4%) and Eukarya (∼1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0–2 mm) than in the lower layers (2–4 and 4–6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat.
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Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Montserrat Palau
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona - Institut d'Investigació Biomédica de Bellvitge, Barcelona, Spain.,Academia Europaea-Barcelona Knowledge Hub, Barcelona, Spain
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12
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Maegaard K, Nielsen LP, Revsbech NP. Hydrogen Dynamics in Cyanobacteria Dominated Microbial Mats Measured by Novel Combined H 2/H 2S and H 2/O 2 Microsensors. Front Microbiol 2017; 8:2022. [PMID: 29093704 PMCID: PMC5651244 DOI: 10.3389/fmicb.2017.02022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Hydrogen may accumulate to micromolar concentrations in cyanobacterial mat communities from various environments, but the governing factors for this accumulation are poorly described. We used newly developed sensors allowing for simultaneous measurement of H2S and H2 or O2 and H2 within the same point to elucidate the interactions between oxygen, sulfate reducing bacteria, and H2 producing microbes. After onset of darkness and subsequent change from oxic to anoxic conditions within the uppermost ∼1 mm of the mat, H2 accumulated to concentrations of up to 40 μmol L-1 in the formerly oxic layer, but with high variability among sites and sampling dates. The immediate onset of H2 production after darkening points to fermentation as the main H2 producing process in this mat. The measured profiles indicate that a gradual disappearance of the H2 peak was mainly due to the activity of sulfate reducing bacteria that invaded the formerly oxic surface layer from below, or persisted in an inactive state in the oxic mat during illumination. The absence of significant H2 consumption in the formerly oxic mat during the first ∼30 min after onset of anoxic conditions indicated absence of active sulfate reducers in this layer during the oxic period. Addition of the methanogenesis inhibitor BES led to increase in H2, indicating that methanogens contributed to the consumption of H2. Both H2 formation and consumption seemed unaffected by the presence/absence of H2S.
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Affiliation(s)
| | | | - Niels P. Revsbech
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Thiel V, Hügler M, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses. Front Microbiol 2017. [PMID: 28634470 PMCID: PMC5459899 DOI: 10.3389/fmicb.2017.00943] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States
| | - Michael Hügler
- Department Microbiology and Molecular Biology, DVGW-Technologiezentrum WasserKarlsruhe, Germany
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States.,Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, United States
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The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil. Appl Environ Microbiol 2017; 83:AEM.00275-17. [PMID: 28363961 DOI: 10.1128/aem.00275-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/27/2017] [Indexed: 11/20/2022] Open
Abstract
The enrichment of H2-oxidizing bacteria (HOB) by H2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H2 mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H2 while enhancing community level carbon substrate utilization potential and lowering CH4 uptake activity in soil. We found that H2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H2 on soil microbial communities will lead to a better understanding of the H2 fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H2 diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH4 oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H2 rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.
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Lichtenberg M, Brodersen KE, Kühl M. Radiative Energy Budgets of Phototrophic Surface-Associated Microbial Communities and their Photosynthetic Efficiency Under Diffuse and Collimated Light. Front Microbiol 2017; 8:452. [PMID: 28400749 PMCID: PMC5368174 DOI: 10.3389/fmicb.2017.00452] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/03/2017] [Indexed: 11/13/2022] Open
Abstract
We investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O2, temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under low light conditions and amounted to 18.1% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis, and light distribution. The light acclimation index, Ek, i.e., the irradiance at the onset of saturation of photosynthesis, was >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. The aim was to investigate how the physical structure and light propagation affected energy budgets and light utilization efficiencies in loosely organized vs. compact phototrophic sediment under diffuse and collimated light. Our results suggest that the optical properties and the structural organization of phytoelements are important traits affecting the photosynthetic efficiency of biofilms and sediments.
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Affiliation(s)
- Mads Lichtenberg
- Marine Biological Section, Department of Biology, University of Copenhagen Helsingør, Denmark
| | - Kasper E Brodersen
- Marine Biological Section, Department of Biology, University of Copenhagen Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of CopenhagenHelsingør, Denmark; Climate Change Cluster, University of Technology SydneyUltimo, NSW, Australia
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In Situ Hydrogen Dynamics in a Hot Spring Microbial Mat during a Diel Cycle. Appl Environ Microbiol 2016; 82:4209-4217. [PMID: 27208140 DOI: 10.1128/aem.00710-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Microbes can produce molecular hydrogen (H2) via fermentation, dinitrogen fixation, or direct photolysis, yet the H2 dynamics in cyanobacterial communities has only been explored in a few natural systems and mostly in the laboratory. In this study, we investigated the diel in situ H2 dynamics in a hot spring microbial mat, where various ecotypes of unicellular cyanobacteria (Synechococcus sp.) are the only oxygenic phototrophs. In the evening, H2 accumulated rapidly after the onset of darkness, reaching peak values of up to 30 μmol H2 liter(-1) at about 1-mm depth below the mat surface, slowly decreasing to about 11 μmol H2 liter(-1) just before sunrise. Another pulse of H2 production, reaching a peak concentration of 46 μmol H2 liter(-1), was found in the early morning under dim light conditions too low to induce accumulation of O2 in the mat. The light stimulation of H2 accumulation indicated that nitrogenase activity was an important source of H2 during the morning. This is in accordance with earlier findings of a distinct early morning peak in N2 fixation and expression of Synechococcus nitrogenase genes in mat samples from the same location. Fermentation might have contributed to the formation of H2 during the night, where accumulation of other fermentation products lowered the pH in the mat to less than pH 6 compared to a spring source pH of 8.3. IMPORTANCE Hydrogen is a key intermediate in anaerobic metabolism, and with the development of a sulfide-insensitive microsensor for H2, it is now possible to study the microdistribution of H2 in stratified microbial communities such as the photosynthetic microbial mat investigated here. The ability to measure H2 profiles within the mat compared to previous measurements of H2 emission gives much more detailed information about the sources and sinks of H2 in such communities, and it was demonstrated that the high rates of H2 formation in the early morning when the mat was exposed to low light intensities might be explained by nitrogen fixation, where H2 is formed as a by-product.
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