51
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Savio D, Stadler P, Reischer GH, Demeter K, Linke RB, Blaschke AP, Mach RL, Kirschner AKT, Stadler H, Farnleitner AH. Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community. Front Microbiol 2019; 10:28. [PMID: 30828319 PMCID: PMC6385617 DOI: 10.3389/fmicb.2019.00028] [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] [Received: 07/31/2018] [Accepted: 01/09/2019] [Indexed: 11/13/2022] Open
Abstract
Alpine karst aquifers are important groundwater resources for the provision of drinking water all around the world. Yet, due to difficult accessibility and long-standing methodological limitations, the microbiology of these systems has long been understudied. The aim of the present study was to investigate the structure and dynamics of bacterial communities in spring water of an alpine limestone karst aquifer (LKAS2) under different hydrological conditions (base vs. event flow). The study was based on high-throughput 16S rRNA gene amplicon sequencing, study design and sample selection were guided by hydrology and pollution microbiology data. Spanning more than 27 months, our analyses revealed a taxonomically highly stable bacterial community, comprising high proportions of yet uncultivated bacteria in the suspended bacterial community fraction. Only the three candidate phyla Parcubacteria (OD1), Gracilibacteria (GN02), Doudnabacteria (SM2F11) together with Proteobacteria and Bacteroidetes contributed between 70.0 and 88.4% of total reads throughout the investigation period. A core-community of 300 OTUs consistently contributed between 37.6 and 56.3% of total reads, further supporting the hypothesis of a high temporal stability in the bacterial community in the spring water. Nonetheless, a detectable response in the bacterial community structure of the spring water was discernible during a high-discharge event. Sequence reads affiliated to the class Flavobacteriia clearly increased from a mean proportion of 2.3% during baseflow to a maximum of 12.7% during the early phase of the studied high-discharge event, suggesting direct impacts from changing hydrological conditions on the bacterial community structure in the spring water. This was further supported by an increase in species richness (Chao1) at higher discharge. The combination of these observations allowed the identification and characterization of three different discharge classes (Q1-Q3). In conclusion, we found a taxonomically stable bacterial community prevailing in spring waters from an alpine karst aquifer over the entire study period of more than 2 years. Clear response to changing discharge conditions could be detected for particular bacterial groups, whereas the most responsive group - bacteria affiliated to the class of Flavobacteriia - might harbor potential as a valuable natural indicator of "system disturbances" in karst aquifers.
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Affiliation(s)
- Domenico Savio
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
| | - Philipp Stadler
- Centre for Water Resource Systems, TU Wien, Vienna, Austria
- Research Unit for Water Quality Management, Institute for Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Georg H. Reischer
- Molecular Diagnostics Group, Institute of Chemical, Environmental and Bioscience Engineering, Department of Agrobiotechnology, IFA-Tulln, TU Wien, Tulln an der Donau, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katalin Demeter
- Centre for Water Resource Systems, TU Wien, Vienna, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Rita B. Linke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alfred P. Blaschke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alexander K. T. Kirschner
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Hermann Stadler
- Department for Water Resources Management and Environmental Analytics, Institute for Water, Energy and Sustainability, Joanneum Research, Graz, Austria
| | - Andreas H. Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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52
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Eveillard D, Bouskill NJ, Vintache D, Gras J, Ward BB, Bourdon J. Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle. Front Microbiol 2019; 9:3298. [PMID: 30745899 PMCID: PMC6360161 DOI: 10.3389/fmicb.2018.03298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/18/2018] [Indexed: 11/15/2022] Open
Abstract
Understanding the interactions between microbial communities and their environment sufficiently to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is problematic, because (i) communities are complex, (ii) most descriptions are qualitative, and (iii) quantitative understanding of the way communities interact with their surroundings remains incomplete. One approach to overcoming such complications is the integration of partial qualitative and quantitative descriptions into more complex networks. Here we outline the development of a probabilistic framework, based on Event Transition Graph (ETG) theory, to predict microbial community structure across observed chemical data. Using reverse engineering, we derive probabilities from the ETG that accurately represent observations from experiments and predict putative constraints on communities within dynamic environments. These predictions can feedback into the future development of field experiments by emphasizing the most important functional reactions, and associated microbial strains, required to characterize microbial ecosystems.
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Affiliation(s)
- Damien Eveillard
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France.,Research Federation (FR2022) Tara Oceans GO-SEE, Paris, France
| | - Nicholas J Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Damien Vintache
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France.,Research Federation (FR2022) Tara Oceans GO-SEE, Paris, France
| | - Julien Gras
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France
| | - Bess B Ward
- Geoscience Department, Princeton University, Princeton, NJ, United States
| | - Jérémie Bourdon
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France
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53
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Saleem M, Lavagnolo MC, Campanaro S, Squartini A. Dynamic membrane bioreactor (DMBR) for the treatment of landfill leachate; bioreactor's performance and metagenomic insights into microbial community evolution. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:326-335. [PMID: 30195162 DOI: 10.1016/j.envpol.2018.08.090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
The use of dynamic membranes as a low-cost alternative for conventional membrane for the treatment of landfill leachate (LFL) was investigated in this study. For this purpose a lab-scale, submerged pre-anoxic and post-aerobic bioreactor configuration was used with nylon mesh as dynamic membrane support. The study was conducted at ambient temperature and LFL was fed to the bioreactor in gradually increasing concentration mixed with tap water (from 20% to 100%). The results of this study demonstrated that lower mesh pore size of 52 μm achieved better results in terms of solid-liquid separation performance (turbidity <10 NTU) of the formed dynamic membrane layer as compared to 200 and 85 μm meshes while treating LFL. Consistently high NH4+-N conversion efficiency of more than 98% was achieved under all nitrogen loading conditions, showing effectiveness of the formed dynamic membrane in retaining slow growing nitrifying species. Total nitrogen removal reached more than 90% however, the denitrification activity showed a fluctuating profile and found to be inhibited by elevated concentrations of free nitrous acid and NO2--N at low pH values inside the anoxic bioreactor. A detailed metagenomic analysis allowed a taxonomic investigation over time and revealed the potential biochemical pathways involved in NH4+-N conversion. This study led to the identification of a dynamic system in which nitrite concentration is determined by the contribution of NH4+ oxidizers (Nitrosomonas), and by a competition between nitrite oxidizers (Nitrospira and Nitrobacter) and reducers (Thauera).
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Affiliation(s)
- Mubbshir Saleem
- Department of Civil, Environmental and Architectural Engineering, University of Padova, via Marzolo 9, 35131, Padova, Italy.
| | - Maria Cristina Lavagnolo
- Department of Civil, Environmental and Architectural Engineering, University of Padova, via Marzolo 9, 35131, Padova, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Legnaro, Padova, Italy
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54
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Wilmoth JL, Moran MA, Thompson A. Transient O 2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome. MICROBIOME 2018; 6:189. [PMID: 30352628 PMCID: PMC6199725 DOI: 10.1186/s40168-018-0574-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O2). METHODS We repeatedly exposed anoxic (4% H2:96% N2) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 102, 1.05 × 103, and 1.05 × 104 mmol O2 kg-1 soil h-1 during pulsed oxygenation treatments. Metatranscriptomic analysis and 57Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively. RESULTS Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO2 to CH4 and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation. CONCLUSIONS This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O2 influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments.
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Affiliation(s)
- Jared Lee Wilmoth
- Department of Crop and Soil Sciences, University of Georgia, Athens, 30602, GA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Aaron Thompson
- Department of Crop and Soil Sciences, University of Georgia, Athens, 30602, GA, USA.
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55
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Bryce C, Blackwell N, Schmidt C, Otte J, Huang YM, Kleindienst S, Tomaszewski E, Schad M, Warter V, Peng C, Byrne JM, Kappler A. Microbial anaerobic Fe(II) oxidation - Ecology, mechanisms and environmental implications. Environ Microbiol 2018; 20:3462-3483. [DOI: 10.1111/1462-2920.14328] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/15/2018] [Accepted: 06/16/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Casey Bryce
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Nia Blackwell
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | | | - Julia Otte
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Yu-Ming Huang
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | | | | | - Manuel Schad
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Viola Warter
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Chao Peng
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - James M. Byrne
- Geomicrobiology; University of Tübingen; Tübingen Germany
| | - Andreas Kappler
- Geomicrobiology; University of Tübingen; Tübingen Germany
- Center for Geomicrobiology, Department of Bioscience; Aarhus University; Aarhus Denmark
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56
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Xu Z, Dai X, Chai X. Effect of different carbon sources on denitrification performance, microbial community structure and denitrification genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:195-204. [PMID: 29627542 DOI: 10.1016/j.scitotenv.2018.03.348] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Solid and liquid organic substances as carbon sources for denitrification process were deeply explored. In this study, the effect of three carbon sources, referred to as poly (3-hydroxybutyrate-co-3-hydroxyvalerate)/poly (lactic acid) (PHBV/PLA) polymer, glucose and CH3COONa, on denitrification performance, microbial community and functional genes were investigated. It was found that maximum denitrification rates of 0.37, 0.46 and 0.39gN/(L·d) were achieved in PHBV/PLA, glucose and CH3COONa supported denitrification systems, respectively. Meanwhile, Illumina MiSeq sequencing revealed that three carbon sources led to different microbial community structures. It can be seen that Brevinema/Thauera/Dechloromonas, Tolumonas/Thauera/Dechloromonas, Thauera dominated in the PHBV/PLA, glucose and CH3COONa supported denitrification systems, respectively. Transcriptome-based analysis further indicated that the glucose supported denitrification system showed the highest FPKM values (the fragments per kilobase per million mapped reads) of the genes participating in the dissimilatory nitrate reduction process, corresponding to the greatest effluent NH4+-N concentration. A better knowledge of effect of different carbon sources on denitrification process will be significant for nitrate removal in practice.
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Affiliation(s)
- Zhongshuo Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaoli Chai
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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57
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Sirisena KA, Daughney CJ, Moreau M, Sim DA, Lee CK, Cary SC, Ryan KG, Chambers GK. Bacterial bioclusters relate to hydrochemistry in New Zealand groundwater. FEMS Microbiol Ecol 2018; 94:5078342. [DOI: 10.1093/femsec/fiy170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/31/2022] Open
Affiliation(s)
- Kosala A Sirisena
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
- Center for Water Quality and Algae Research, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | | | - Magali Moreau
- GNS Science, PO Box 30368, Lower Hutt 5040, New Zealand
| | - Dalice A Sim
- School of Mathematics, Statistics and Operations Research, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Charles K Lee
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Stephen C Cary
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Ken G Ryan
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Geoffrey K Chambers
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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58
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Schlosser C, Streu P, Frank M, Lavik G, Croot PL, Dengler M, Achterberg EP. H 2S events in the Peruvian oxygen minimum zone facilitate enhanced dissolved Fe concentrations. Sci Rep 2018; 8:12642. [PMID: 30140004 PMCID: PMC6107642 DOI: 10.1038/s41598-018-30580-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/23/2018] [Indexed: 11/09/2022] Open
Abstract
Dissolved iron (DFe) concentrations in oxygen minimum zones (OMZs) of Eastern Boundary Upwelling Systems are enhanced as a result of high supply rates from anoxic sediments. However, pronounced variations in DFe concentrations in anoxic coastal waters of the Peruvian OMZ indicate that there are factors in addition to dissolved oxygen concentrations (O2) that control Fe cycling. Our study demonstrates that sediment-derived reduced Fe (Fe(II)) forms the main DFe fraction in the anoxic/euxinic water column off Peru, which is responsible for DFe accumulations of up to 200 nmol L-1. Lowest DFe values were observed in anoxic shelf waters in the presence of nitrate and nitrite. This reflects oxidation of sediment-sourced Fe(II) associated with nitrate/nitrite reduction and subsequent removal as particulate Fe(III) oxyhydroxides. Unexpectedly, the highest DFe levels were observed in waters with elevated concentrations of hydrogen sulfide (up to 4 µmol L-1) and correspondingly depleted nitrate/nitrite concentrations (<0.18 µmol L-1). Under these conditions, Fe removal was reduced through stabilization of Fe(II) as aqueous iron sulfide (FeSaqu) which comprises complexes (e.g., FeSH+) and clusters (e.g., Fe2S2|4H2O). Sulfidic events on the Peruvian shelf consequently enhance Fe availability, and may increase in frequency in future due to projected expansion and intensification of OMZs.
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Affiliation(s)
- Christian Schlosser
- Marine Biogeochemie, Helmholtz-Zentrum für Ozeanforschung, GEOMAR, Kiel, Germany.
| | - Peter Streu
- Marine Biogeochemie, Helmholtz-Zentrum für Ozeanforschung, GEOMAR, Kiel, Germany
| | - Martin Frank
- Marine Biogeochemie, Helmholtz-Zentrum für Ozeanforschung, GEOMAR, Kiel, Germany
| | - Gaute Lavik
- Max-Plank-Institut für Mikrobiologie, 28359, Bremen, Germany
| | - Peter L Croot
- Marine Biogeochemie, Helmholtz-Zentrum für Ozeanforschung, GEOMAR, Kiel, Germany.,iCRAG (Irish Centre for Research in Applied Geoscience), Earth and Ocean Sciences, NUI Galway, Galway, Ireland
| | - Marcus Dengler
- Marine Biogeochemie, Helmholtz-Zentrum für Ozeanforschung, GEOMAR, Kiel, Germany
| | - Eric P Achterberg
- Marine Biogeochemie, Helmholtz-Zentrum für Ozeanforschung, GEOMAR, Kiel, Germany
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59
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Taş N, Brandt BW, Braster M, van Breukelen BM, Röling WFM. Subsurface landfill leachate contamination affects microbial metabolic potential and gene expression in the Banisveld aquifer. FEMS Microbiol Ecol 2018; 94:5074391. [DOI: 10.1093/femsec/fiy156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/13/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Neslihan Taş
- Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085 HV Amsterdam, the Netherlands
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 70A-331794720 Berkeley CA, United States of America
- Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 70A-331794720 Berkeley CA, Berkeley, United States of America
| | - Bernd W Brandt
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Gustav Mahlerlaan 3004 1081 LA, Amsterdam, the Netherlands
| | - Martin Braster
- Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085 HV Amsterdam, the Netherlands
| | - Boris M van Breukelen
- Department of Water Management, Delft University of Technology, Gebouw 23 Stevinweg 1 2628 CN, Delft, the Netherlands
| | - Wilfred F M Röling
- Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085 HV Amsterdam, the Netherlands
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60
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Kumar S, Herrmann M, Blohm A, Hilke I, Frosch T, Trumbore SE, Küsel K. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol Ecol 2018; 94:5056153. [DOI: 10.1093/femsec/fiy141] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/18/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Swatantar Kumar
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Annika Blohm
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, D-07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Torsten Frosch
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, D-07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Albert-Einstein-Strasse 6, D-07745, Jena, Germany
| | - Susan E Trumbore
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
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61
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Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS. Appl Environ Microbiol 2018; 84:AEM.02173-17. [PMID: 29500257 DOI: 10.1128/aem.02173-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/20/2018] [Indexed: 11/20/2022] Open
Abstract
Most isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer, Gallionellaceae sp., and less abundant heterotrophic strains (e.g., Bradyrhizobium sp., Nocardioides sp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the family Gallionellaceae dominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated with Bradyrhizobium sp. Gallionellaceae sp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II). Bradyrhizobium spp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O2IMPORTANCE Nitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizer Gallionellaceae sp. and several heterotrophic strains (e.g., Bradyrhizobium sp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed and Bradyrhizobium became the dominant community member, Fe(II) was still oxidized by Gallionellaceae sp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate.
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62
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Insights into Carbon Metabolism Provided by Fluorescence In Situ Hybridization-Secondary Ion Mass Spectrometry Imaging of an Autotrophic, Nitrate-Reducing, Fe(II)-Oxidizing Enrichment Culture. Appl Environ Microbiol 2018; 84:AEM.02166-17. [PMID: 29500258 DOI: 10.1128/aem.02166-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/20/2018] [Indexed: 01/03/2023] Open
Abstract
The enrichment culture KS is one of the few existing autotrophic, nitrate-reducing, Fe(II)-oxidizing cultures that can be continuously transferred without an organic carbon source. We used a combination of catalyzed amplification reporter deposition fluorescence in situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) to analyze community dynamics, single-cell activities, and interactions among the two most abundant microbial community members (i.e., Gallionellaceae sp. and Bradyrhizobium spp.) under autotrophic and heterotrophic growth conditions. CARD-FISH cell counts showed the dominance of the Fe(II) oxidizer Gallionellaceae sp. under autotrophic conditions as well as of Bradyrhizobium spp. under heterotrophic conditions. We used NanoSIMS to monitor the fate of 13C-labeled bicarbonate and acetate as well as 15N-labeled ammonium at the single-cell level for both taxa. Under autotrophic conditions, only the Gallionellaceae sp. was actively incorporating 13C-labeled bicarbonate and 15N-labeled ammonium. Interestingly, both Bradyrhizobium spp. and Gallionellaceae sp. became enriched in [13C]acetate and [15N]ammonium under heterotrophic conditions. Our experiments demonstrated that Gallionellaceae sp. was capable of assimilating [13C]acetate while Bradyrhizobium spp. were not able to fix CO2, although a metagenomics survey of culture KS recently revealed that Gallionellaceae sp. lacks genes for acetate uptake and that the Bradyrhizobium sp. carries the genetic potential to fix CO2 The study furthermore extends our understanding of the microbial reactions that interlink the nitrogen and Fe cycles in the environment.IMPORTANCE Microbial mechanisms by which Fe(II) is oxidized with nitrate as the terminal electron acceptor are generally referred to as "nitrate-dependent Fe(II) oxidation" (NDFO). NDFO has been demonstrated in laboratory cultures (such as the one studied in this work) and in a variety of marine and freshwater sediments. Recently, the importance of NDFO for the transport of sediment-derived Fe in aquatic ecosystems has been emphasized in a series of studies discussing the impact of NDFO for sedimentary nutrient cycling and redox dynamics in marine and freshwater environments. In this article, we report results from an isotope labeling study performed with the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS, which was first described by Straub et al. (1) about 20 years ago. Our current study builds on the recently published metagenome of culture KS (2).
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Aquilina L, Roques C, Boisson A, Vergnaud-Ayraud V, Labasque T, Pauwels H, Pételet-Giraud E, Pettenati M, Dufresne A, Bethencourt L, Bour O. Autotrophic denitrification supported by biotite dissolution in crystalline aquifers (1): New insights from short-term batch experiments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:842-853. [PMID: 29734630 DOI: 10.1016/j.scitotenv.2017.11.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 06/08/2023]
Abstract
We investigate denitrification mechanisms through batch experiments using crushed rock and groundwater from a granitic aquifer subject to long term pumping (Ploemeur, France). Except for sterilized experiments, extensive denitrification reaction induces NO3 decreases ranging from 0.3 to 0.6mmol/L. Carbon concentrations, either organic or inorganic, remain relatively stable and do not document potential heterotrophic denitrification. Batch experiments show a clear effect of mineral dissolution which is documented through cation (K, Na, Ca) and Fluoride production. These productions are tightly related to denitrification progress during the experiment. Conversely, limited amounts of SO4, systematically lower than autotrophic denitrification coupled to sulfur oxidation stoichiometry, are produced during the experiments which indicates that sulfur oxidation is not likely even when pyrite is added to the experiments. Analysis of cation ratios, both in isolated minerals of the granite and within water of the batch, allow the mineral dissolution during the experiments to be quantified. Using cation ratios, we show that batch experiments are characterized mainly by biotite dissolution. As biotite contains 21 to 30% of Fe and 0.3 to 1.7% of F, it constitutes a potential source for these two elements. Denitrification could be attributed to the oxidation of Fe(II) contained in biotite. We computed the amount of K and F produced through biotite dissolution when entirely attributing denitrification to biotite dissolution. Computed amounts show that this process may account for the observed K and F produced. We interpret these results as the development of microbial activity which induces mineral dissolution in order to uptake Fe(II) which is used for denitrification. Although pyrite is probably available, SO4 and cation measurements favor a large biotite dissolution reaction which could account for all the observed Fe production. Chemical composition of groundwater produced from the Ploemeur site indicates similar denitrification processes although original composition shows mainly plagioclase dissolution.
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Affiliation(s)
- Luc Aquilina
- Université Rennes 1 - CNRS, OSUR - Géosciences Rennes, Av. du Général Leclerc, 35 042 Rennes, France.
| | - Clément Roques
- ETH Zürich, Department of Earth Sciences, Sonneggstrasse 5, 8092 Zürich, Switzerland.
| | - Alexandre Boisson
- BRGM DAT Bretagne, Rennes Atalante Beaulieu 2 rue de Jouanet, 35700 Rennes, France
| | - Virginie Vergnaud-Ayraud
- Université Rennes 1 - CNRS, OSUR - Géosciences Rennes, Av. du Général Leclerc, 35 042 Rennes, France
| | - Thierry Labasque
- Université Rennes 1 - CNRS, OSUR - Géosciences Rennes, Av. du Général Leclerc, 35 042 Rennes, France
| | - Hélène Pauwels
- BRGM D3E, 3 av. Guillemin, BP 36009, 45060 Orléans Cedex 2, France
| | | | - Marie Pettenati
- BRGM D3E, 3 av. Guillemin, BP 36009, 45060 Orléans Cedex 2, France
| | - Alexis Dufresne
- Université Rennes 1 - CNRS, OSUR - Ecobio, Av. du Général Leclerc, 35 042 Rennes, France
| | - Lorine Bethencourt
- Université Rennes 1 - CNRS, OSUR - Ecobio, Av. du Général Leclerc, 35 042 Rennes, France
| | - Olivier Bour
- Université Rennes 1 - CNRS, OSUR - Géosciences Rennes, Av. du Général Leclerc, 35 042 Rennes, France
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Yang X, Chen Z, Wu Q, Xu M. Enhanced phenanthrene degradation in river sediments using a combination of biochar and nitrate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:600-605. [PMID: 29156278 DOI: 10.1016/j.scitotenv.2017.11.130] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 06/07/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) pollution in urban river sediments is a serious problem to ecological systems and human health. We examined novel remediation approaches, using a biochar amendment combined with bioaugmentation or/and nitrate stimulation, to degrade phenanthrene in sediment. Biochar amendment combined with nitrate stimulation enhanced phenanthrene degradation by 2.3 times that of the control and 1.9 times that of biochar alone. Nitrate stimulation altered the microbial succession and encouraged the growth of potential nitrate-reducing PAH-degraders Thiobacillus and Stenotrophomonas. Biochar was an excellent sorbent for phenanthrene and the shelter that it provided PAH-degraders increased contact between phenanthrene and PAH-degraders. Biochar also enhanced the aging effects of phenanthrene and reduced the ecological risk by 7.7% to 11%. These results suggest that biochar amendment combined with nitrate stimulation can achieve high-efficiency phenanthrene degradation in sediments.
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Affiliation(s)
- Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China; Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China
| | - Zefang Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Qunhe Wu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China; Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China
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Jemison NE, Shiel AE, Johnson TM, Lundstrom CC, Long PE, Williams KH. Field Application of 238U/ 235U Measurements To Detect Reoxidation and Mobilization of U(IV). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3422-3430. [PMID: 29464949 DOI: 10.1021/acs.est.7b05162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biostimulation to induce reduction of soluble U(VI) to relatively immobile U(IV) is an effective strategy for decreasing aqueous U(VI) concentrations in contaminated groundwater systems. If oxidation of U(IV) occurs following the biostimulation phase, U(VI) concentrations increase, challenging the long-term effectiveness of this technique. However, detecting U(IV) oxidation through dissolved U concentrations alone can prove difficult in locations with few groundwater wells to track the addition of U to a mass of groundwater. We propose the 238U/235U ratio of aqueous U as an independent, reliable tracer of U(IV) remobilization via oxidation or mobilization of colloids. Reduction of U(VI) produces 238U-enriched U(IV), whereas remobilization of solid U(IV) should not induce isotopic fractionation. The incorporation of remobilized U(IV) with a high 238U/235U ratio into the aqueous U(VI) pool produces an increase in 238U/235U of aqueous U(VI). During several injections of nitrate to induce U(IV) oxidation, 238U/235U consistently increased, suggesting 238U/235U is broadly applicable for detecting mobilization of U(IV).
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Affiliation(s)
- Noah E Jemison
- Department of Geology , University of Illinois at Urbana-Champaign , 3081 Natural History Building, 1301 W. Green St. , Urbana , Illinois 61801 , United States
| | - Alyssa E Shiel
- College of Earth, Ocean, and Atmospheric Sciences , Oregon State University , 104 CEOAS Administration Building, 101 SW 26th St. , Corvallis , Oregon 97331 , United States
| | - Thomas M Johnson
- Department of Geology , University of Illinois at Urbana-Champaign , 3081 Natural History Building, 1301 W. Green St. , Urbana , Illinois 61801 , United States
| | - Craig C Lundstrom
- Department of Geology , University of Illinois at Urbana-Champaign , 3081 Natural History Building, 1301 W. Green St. , Urbana , Illinois 61801 , United States
| | - Philip E Long
- Earth Sciences Division , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Kenneth H Williams
- Earth Sciences Division , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
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High reactivity of deep biota under anthropogenic CO 2 injection into basalt. Nat Commun 2017; 8:1063. [PMID: 29051484 PMCID: PMC5648843 DOI: 10.1038/s41467-017-01288-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 09/01/2017] [Indexed: 11/21/2022] Open
Abstract
Basalts are recognized as one of the major habitats on Earth, harboring diverse and active microbial populations. Inconsistently, this living component is rarely considered in engineering operations carried out in these environments. This includes carbon capture and storage (CCS) technologies that seek to offset anthropogenic CO2 emissions into the atmosphere by burying this greenhouse gas in the subsurface. Here, we show that deep ecosystems respond quickly to field operations associated with CO2 injections based on a microbiological survey of a basaltic CCS site. Acidic CO2-charged groundwater results in a marked decrease (by ~ 2.5–4) in microbial richness despite observable blooms of lithoautotrophic iron-oxidizing Betaproteobacteria and degraders of aromatic compounds, which hence impact the aquifer redox state and the carbon fate. Host-basalt dissolution releases nutrients and energy sources, which sustain the growth of autotrophic and heterotrophic species whose activities may have consequences on mineral storage. The impacts of carbon capture and storage (CCS) on subsurface microorganisms are poorly understood. Here, the authors show that deep ecosystems respond quickly to CO2 injections and that the environmental consequences of their metabolic activities need to be properly assessed for sustainable CCS in basalt.
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Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō'ihi Seamount, Hawai'i. ISME JOURNAL 2017; 11:1900-1914. [PMID: 28362721 PMCID: PMC5520029 DOI: 10.1038/ismej.2017.40] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/21/2017] [Accepted: 01/27/2017] [Indexed: 01/16/2023]
Abstract
The Zetaproteobacteria are ubiquitous in marine environments, yet this class of Proteobacteria is only represented by a few closely-related cultured isolates. In high-iron environments, such as diffuse hydrothermal vents, the Zetaproteobacteria are important members of the community driving its structure. Biogeography of Zetaproteobacteria has shown two ubiquitous operational taxonomic units (OTUs), yet much is unknown about their genomic diversity. Genome-resolved metagenomics allows for the specific binning of microbial genomes based on genomic signatures present in composite metagenome assemblies. This resulted in the recovery of 93 genome bins, of which 34 were classified as Zetaproteobacteria. Form II ribulose 1,5-bisphosphate carboxylase genes were recovered from nearly all the Zetaproteobacteria genome bins. In addition, the Zetaproteobacteria genome bins contain genes for uptake and utilization of bioavailable nitrogen, detoxification of arsenic, and a terminal electron acceptor adapted for low oxygen concentration. Our results also support the hypothesis of a Cyc2-like protein as the site for iron oxidation, now detected across a majority of the Zetaproteobacteria genome bins. Whole genome comparisons showed a high genomic diversity across the Zetaproteobacteria OTUs and genome bins that were previously unidentified by SSU rRNA gene analysis. A single lineage of cosmopolitan Zetaproteobacteria (zOTU 2) was found to be monophyletic, based on cluster analysis of average nucleotide identity and average amino acid identity comparisons. From these data, we can begin to pinpoint genomic adaptations of the more ecologically ubiquitous Zetaproteobacteria, and further understand their environmental constraints and metabolic potential.
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Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One 2017; 12:e0174930. [PMID: 28384184 PMCID: PMC5383146 DOI: 10.1371/journal.pone.0174930] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/18/2017] [Indexed: 12/12/2022] Open
Abstract
Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds.
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Affiliation(s)
- William B. Ludington
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
- * E-mail:
| | - Thaddeus D. Seher
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
| | - Olin Applegate
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Xunde Li
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Joseph I. Kliegman
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Charles Langelier
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Edward R. Atwill
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Thomas Harter
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Joseph L. DeRisi
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Yabusaki SB, Wilkins MJ, Fang Y, Williams KH, Arora B, Bargar J, Beller HR, Bouskill NJ, Brodie EL, Christensen JN, Conrad ME, Danczak RE, King E, Soltanian MR, Spycher NF, Steefel CI, Tokunaga TK, Versteeg R, Waichler SR, Wainwright HM. Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3307-3317. [PMID: 28218533 DOI: 10.1021/acs.est.6b04873] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling, based on published and newly generated data, is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain. In this system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs (e.g., oxidizing Fe(II), S compounds, and ammonium) is linked to the presence of DO, which has higher concentrations near the water table.
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Affiliation(s)
- Steven B Yabusaki
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | | | - Yilin Fang
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Bhavna Arora
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - John Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Harry R Beller
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Nicholas J Bouskill
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - John N Christensen
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Mark E Conrad
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | - Eric King
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | - Nicolas F Spycher
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Carl I Steefel
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Tetsu K Tokunaga
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Roelof Versteeg
- Subsurface Insights , Hanover, New Hampshire 03755, United States
| | - Scott R Waichler
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Haruko M Wainwright
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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Jewell TNM, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, Beller HR. Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer. Front Microbiol 2017; 8:40. [PMID: 28179898 PMCID: PMC5264521 DOI: 10.3389/fmicb.2017.00040] [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: 10/09/2016] [Accepted: 01/06/2017] [Indexed: 02/05/2023] Open
Abstract
Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with an initial N2 headspace and were sampled every 5 days for metagenome and metatranscriptome profiles in combination with biogeochemical measurements. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO2 during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after 2 weeks. A pulse of methanogenesis co-occurred with acetogenesis, but only accounted for a small fraction of carbon flux. The depletion of DOM over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, H2 oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates (numerous lesser expressed cell-wall-associated hydrolases targeted peptidoglycan). Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.
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Affiliation(s)
- Talia N M Jewell
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Markus Bill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Kenneth H Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Harry R Beller
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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Starke R, Müller M, Gaspar M, Marz M, Küsel K, Totsche KU, von Bergen M, Jehmlich N. Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer. J Proteomics 2017; 152:153-160. [DOI: 10.1016/j.jprot.2016.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/28/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
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Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219. [PMID: 27774985 PMCID: PMC5079060 DOI: 10.1038/ncomms13219] [Citation(s) in RCA: 594] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Christopher T. Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Laura A. Hug
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Alexander J. Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Michael J. Wilkins
- School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment. Appl Environ Microbiol 2016; 82:6120-6131. [PMID: 27496777 PMCID: PMC5068159 DOI: 10.1128/aem.01570-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/02/2016] [Indexed: 11/23/2022] Open
Abstract
Nitrate-reducing Fe(II)-oxidizing microorganisms were described for the first time ca. 20 years ago. Most pure cultures of nitrate-reducing Fe(II) oxidizers can oxidize Fe(II) only under mixotrophic conditions, i.e., when an organic cosubstrate is provided. A small number of nitrate-reducing Fe(II)-oxidizing cultures have been proposed to grow autotrophically, but unambiguous evidence for autotrophy has not always been provided. Thus, it is still unclear whether or to what extent Fe(II) oxidation coupled to nitrate reduction is an enzymatically catalyzed and energy-yielding autotrophic process or whether Fe(II) is abiotically oxidized by nitrite from heterotrophic nitrate reduction. The aim of the present study was to find evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. Microcosm incubations showed that with increasing incubation times, the stoichiometric ratio of reduced nitrate/oxidized Fe(II) [NO3−reduced/Fe(II)oxidized] decreased, indicating a decreasing contribution of heterotrophic denitrification and/or an increasing contribution of autotrophic nitrate-reducing Fe(II) oxidation over time. After incubations of sediment slurries for >10 weeks, nitrate-reducing activity ceased, although nitrate was still present. This suggests that heterotrophic nitrate reduction had ceased due to the depletion of readily available organic carbon. However, after the addition of Fe(II) to these batch incubation mixtures, the nitrate-reducing activity resumed, and Fe(II) was oxidized, indicating the activity of autotrophic nitrate-reducing Fe(II) oxidizers. The concurrent reduction of 14C-labeled bicarbonate concentrations unambiguously proved that autotrophic C fixation occurred during Fe(II) oxidation and nitrate reduction. Our results clearly demonstrated that autotrophic nitrate-reducing Fe(II)-oxidizing bacteria were present in the investigated coastal marine sediments.
IMPORTANCE Twenty years after the discovery of nitrate-reducing Fe(II) oxidizers, it is still controversially discussed whether autotrophic nitrate-reducing Fe(II)-oxidizing microorganisms exist and to what extent Fe(II) oxidation in this reduction/oxidation process is enzymatically catalyzed or which role abiotic side reactions of Fe(II) with reactive N species play. Most pure cultures of nitrate-reducing Fe(II) oxidizers are mixotrophic; i.e., they need an organic cosubstrate to maintain their activity over several cultural transfers. For the few existing autotrophic isolates and enrichment cultures, either the mechanism of nitrate-reducing Fe(II) oxidation is not known or evidence for their autotrophic lifestyle is controversial. In the present study, we provide evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. The evidence is based on stoichiometries of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and the incorporation of carbon from CO2 under conditions that favor the activity of nitrate-reducing Fe(II) oxidizers.
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Chan CS, Emerson D, Luther GW. The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations. GEOBIOLOGY 2016; 14:509-528. [PMID: 27392195 DOI: 10.1111/gbi.12192] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.
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Affiliation(s)
- C S Chan
- Department of Geological Sciences, University of Delaware, and the Delaware Biotechnology Institute, Newark, DE, USA
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - G W Luther
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
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Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes. Trends Microbiol 2016; 24:600-610. [DOI: 10.1016/j.tim.2016.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 11/24/2022]
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