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Kadnikov VV, Mardanov AV, Beletsky AV, Banks D, Pimenov NV, Frank YA, Karnachuk OV, Ravin NV. A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition. FEMS Microbiol Ecol 2018; 94:5067867. [DOI: 10.1093/femsec/fiy152] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia
| | - David Banks
- School of Engineering, Systems Power & Energy, Glasgow University, Glasgow G12 8QQ, and Holymoor Consultancy Ltd., 360 Ashgate Road, Chesterfield, Derbyshire S40 4BW, UK
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp 33-2, Moscow, 119071, Russia
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenina prosp. 35, Tomsk, 634050, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenina prosp. 35, Tomsk, 634050, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow, 119071, Russia
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52
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Lopez-Fernandez M, Broman E, Turner S, Wu X, Bertilsson S, Dopson M. Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. FEMS Microbiol Ecol 2018; 94:5040220. [PMID: 29931252 PMCID: PMC6030916 DOI: 10.1093/femsec/fiy121] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/15/2018] [Indexed: 11/14/2022] Open
Abstract
The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligotrophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modern marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligotrophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoautotrophic deep biosphere.
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Affiliation(s)
- Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Xiaofen Wu
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
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53
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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54
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Ancient Microbial Activity in Deep Hydraulically Conductive Fracture Zones within the Forsmark Target Area for Geological Nuclear Waste Disposal, Sweden. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8060211] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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55
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Escudero C, Oggerin M, Amils R. The deep continental subsurface: the dark biosphere. Int Microbiol 2018; 21:3-14. [DOI: 10.1007/s10123-018-0009-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 11/28/2022]
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56
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Deng Y, Li B, Zhang T. Bacteria That Make a Meal of Sulfonamide Antibiotics: Blind Spots and Emerging Opportunities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3854-3868. [PMID: 29498514 DOI: 10.1021/acs.est.7b06026] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The release of sulfonamide antibiotics into the environment is alarming because the existence of these antibiotics in the environment may promote resistance in clinically relevant microorganisms, which is a potential threat to the effectiveness of antibiotic therapies. Controllable biodegradation processes are of particular significance for the inexpensive yet effective restoration of sulfonamide-contaminated environments. Cultivation-based techniques have already made great strides in successfully isolating bacteria with promising sulfonamide degradation abilities, but the implementation of these isolates in bioremediation has been limited by unknown microbial diversity, vast population responsiveness, and the impact of perturbations from open and complex environments. Advances in DNA sequencing technologies and metagenomic analyses are being used to complement the information derived from cultivation-based procedures. In this Review, we provide an overview of the growing understanding of isolated sulfonamide degraders and identify shortcomings of the prevalent literature in this field. In addition, we propose a technical paradigm that integrates experimental testing with metagenomic analysis to pave the way for improved understanding and exploitation of these ecologically important isolates. Overall, this Review aims to outline how metagenomic studies of isolated sulfonamide degraders are being applied for the advancement of bioremediation strategies for sulfonamide contamination.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , PR China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen , Tsinghua University , Shenzhen 518055 , PR China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , PR China
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57
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Deng Y, Wang Y, Mao Y, Zhang T. Partnership of Arthrobacter and Pimelobacter in Aerobic Degradation of Sulfadiazine Revealed by Metagenomics Analysis and Isolation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:2963-2972. [PMID: 29378398 DOI: 10.1021/acs.est.7b05913] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study, metagenomic analyses were combined with cultivation-based techniques as a nested approach to identify functionally significant bacteria for sulfadiazine biodegradation within enrichment communities. The metagenomic investigations indicated that our previously isolated sulfadiazine degrader, Arthrobacter sp. D2, and another Pimelobacter bacterium concomitantly occurred as most abundant members in the community of an enrichment culture that performed complete sulfadiazine mineralization for over two years. Responses of the enriched populations to sole carbon source alternation further suggested the ability of this Pimelobacter member to grow on 2-aminopyrimidine, the most prominent intermediate metabolite of sulfadiazine. Taking advantage of this propensity, additional cultivation procedures have enabled the successful isolation of Pimelobacter sp. LG209, whose genomic sequences exactly matched that of the dominant Pimelobacter bacterium in the sulfadiazine enrichment culture. Integration of metagenomic investigations with the physiological characteristics of the isolates conclusively demonstrated that the sulfadiazine mineralization in a long-running enrichment culture was prominently mediated by primary sulfadiazine-degrading specialist strain Arthrobacter sp. D2 in association with the 2-aminopyrimidine-degrading partner strain Pimelobacter sp. LG209. Here, we provided the first mechanistic insight into microbial interactions in steady sulfadiazine mineralization processes, which will help develop appropriate bioremediation strategies for sulfadiazine-contaminated hotspot sites.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , 518060 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
- International Center for Antibiotic Resistance in the Environment , Southern University of Science and Technology , Shenzhen , 518055 China
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58
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Wenk CB, Wing BA, Halevy I. Electron carriers in microbial sulfate reduction inferred from experimental and environmental sulfur isotope fractionations. THE ISME JOURNAL 2018; 12:495-507. [PMID: 29087380 PMCID: PMC5776465 DOI: 10.1038/ismej.2017.185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/26/2017] [Accepted: 09/24/2017] [Indexed: 01/29/2023]
Abstract
Dissimilatory sulfate reduction (DSR) has been a key process influencing the global carbon cycle, atmospheric composition and climate for much of Earth's history, yet the energy metabolism of sulfate-reducing microbes remains poorly understood. Many organisms, particularly sulfate reducers, live in low-energy environments and metabolize at very low rates, requiring specific physiological adaptations. We identify one such potential adaptation-the electron carriers selected for survival under energy-limited conditions. Employing a quantitative biochemical-isotopic model, we find that the large S isotope fractionations (>55‰) observed in a wide range of natural environments and culture experiments at low respiration rates are only possible when the standard-state Gibbs free energy (ΔG'°) of all steps during DSR is more positive than -10 kJ mol-1. This implies that at low respiration rates, only electron carriers with modestly negative reduction potentials are involved, such as menaquinone, rubredoxin, rubrerythrin or some flavodoxins. Furthermore, the constraints from S isotope fractionation imply that ferredoxins with a strongly negative reduction potential cannot be the direct electron donor to S intermediates at low respiration rates. Although most sulfate reducers have the genetic potential to express a variety of electron carriers, our results suggest that a key physiological adaptation of sulfate reducers to low-energy environments is to use electron carriers with modestly negative reduction potentials.
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Affiliation(s)
- Christine B Wenk
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
| | - Itay Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.
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59
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60
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Ivarsson M, Bengtson S, Drake H, Francis W. Fungi in Deep Subsurface Environments. ADVANCES IN APPLIED MICROBIOLOGY 2018; 102:83-116. [PMID: 29680127 DOI: 10.1016/bs.aambs.2017.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.
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Affiliation(s)
- Magnus Ivarsson
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark; Swedish Museum of Natural History, Stockholm, Sweden.
| | | | | | - Warren Francis
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
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61
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Brailsford FL, Glanville HC, Marshall MR, Golyshin PN, Johnes PJ, Yates CA, Owen AT, Jones DL. Microbial use of low molecular weight DOM in filtered and unfiltered freshwater: Role of ultra-small microorganisms and implications for water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:377-384. [PMID: 28448929 DOI: 10.1016/j.scitotenv.2017.04.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 06/07/2023]
Abstract
Dissolved organic matter (DOM) plays a central role in regulating productivity and nutrient cycling in freshwaters. It is therefore vital that we can representatively sample and preserve DOM in freshwaters for subsequent analysis. Here we investigated the effect of filtration, temperature (5 and 25°C) and acidification (HCl) on the persistence of low molecular weight (MW) dissolved organic carbon (DOC), nitrogen (DON) and orthophosphate in oligotrophic and eutrophic freshwater environments. Our results showed the rapid loss of isotopically-labelled glucose and amino acids from both filtered (0.22 and 0.45μm) and unfiltered waters. We ascribe this substrate depletion in filtered samples to the activity of ultra-small (<0.45μm) microorganisms (bacteria and archaea) present in the water. As expected, the rate of C, N and P loss was much greater at higher temperatures and was repressed by the addition of HCl. Based on our results and an evaluation of the protocols used in recently published studies, we conclude that current techniques used to sample water for low MW DOM characterisation are frequently inadequate and lack proper validation. In contrast to the high degree of analytical precision and rigorous statistical analysis of most studies, we argue that insufficient consideration is still given to the presence of ultra-small microorganisms and potential changes that can occur in the low MW fraction of DOM prior to analysis.
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Affiliation(s)
- F L Brailsford
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - H C Glanville
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - M R Marshall
- Centre for Ecology and Hydrology (CEH), Environment Centre Wales, Bangor, Gwynedd LL57 2UW, UK
| | - P N Golyshin
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - P J Johnes
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK
| | - C A Yates
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK
| | - A T Owen
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK
| | - D L Jones
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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62
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Tully BJ, Wheat CG, Glazer BT, Huber JA. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME JOURNAL 2017; 12:1-16. [PMID: 29099490 PMCID: PMC5739024 DOI: 10.1038/ismej.2017.187] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 11/29/2022]
Abstract
The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.
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Affiliation(s)
- Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - C Geoff Wheat
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Brain T Glazer
- Department of Oceanography, University of Hawaii, Honolulu, HI, USA
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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63
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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions. mSystems 2017; 2:mSystems00038-17. [PMID: 29104938 PMCID: PMC5663940 DOI: 10.1128/msystems.00038-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022] Open
Abstract
Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems. Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.
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64
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Ino K, Hernsdorf AW, Konno U, Kouduka M, Yanagawa K, Kato S, Sunamura M, Hirota A, Togo YS, Ito K, Fukuda A, Iwatsuki T, Mizuno T, Komatsu DD, Tsunogai U, Ishimura T, Amano Y, Thomas BC, Banfield JF, Suzuki Y. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. ISME JOURNAL 2017; 12:31-47. [PMID: 28885627 DOI: 10.1038/ismej.2017.140] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 07/06/2017] [Accepted: 07/25/2017] [Indexed: 01/14/2023]
Abstract
Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.
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Affiliation(s)
- Kohei Ino
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Alex W Hernsdorf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Uta Konno
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsunori Yanagawa
- Graduate School of Environmental Engineering, The University of Kitakyushu, Kitakyushu, Fukuoka, Japan
| | - Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC (Japan Agency for Marine-Earth Science and Technology), Yokosuka City, Kanagawa, Japan
| | - Michinari Sunamura
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akinari Hirota
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Yoko S Togo
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Kazumasa Ito
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Akari Fukuda
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.,Japan Atomic Energy Agency, Naka-gun, Ibaraki, Japan
| | | | | | - Daisuke D Komatsu
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Toyoho Ishimura
- National Institute of Technology, Ibaraki College, Hitachinaka-shi, Ibaraki, Japan
| | - Yuki Amano
- Japan Atomic Energy Agency, Naka-gun, Ibaraki, Japan
| | - Brian C Thomas
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yohey Suzuki
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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65
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Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN. 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ. Nat Commun 2017; 8:60. [PMID: 28680072 PMCID: PMC5498576 DOI: 10.1038/s41467-017-00104-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/31/2017] [Indexed: 11/09/2022] Open
Abstract
Intriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction. In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.
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Affiliation(s)
- Olga V Golyshina
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK.
| | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine-National Institutes of Health, Bethesda, MD, 20894, USA
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia
| | | | - Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Erika Arcadi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Taras Y Nechitaylo
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, Jena, 07745, Germany
| | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049, Madrid, Spain
| | - Ilya V Kublanov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236040, Russia.,Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine-National Institutes of Health, Bethesda, MD, 20894, USA
| | - Michail M Yakimov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236040, Russia.,Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
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66
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Drake H, Ivarsson M, Bengtson S, Heim C, Siljeström S, Whitehouse MJ, Broman C, Belivanova V, Åström ME. Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures. Nat Commun 2017; 8:55. [PMID: 28676652 PMCID: PMC5496868 DOI: 10.1038/s41467-017-00094-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/31/2017] [Indexed: 11/08/2022] Open
Abstract
The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (-740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.Deep subsurface microorganisms play an important role in nutrient cycling, yet little is known about deep continental fungal communities. Here, the authors show organically preserved and partly mineralized fungi at 740 m depth, and find evidence of an anaerobic fungi and sulfate reducing bacteria consortium.
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Affiliation(s)
- Henrik Drake
- Department of Biology and Environmental Science, Linnæus University, Kalmar, 39182, Sweden.
| | - Magnus Ivarsson
- Department of Palaeobiology and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50 007, Stockholm, 10405, Sweden
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50 007, Stockholm, 10405, Sweden
| | - Christine Heim
- Geoscience Centre Göttingen of the Georg-August University (Department of Geobiology), Goldschmidtstr. 3, Göttingen, 37077, Germany
| | - Sandra Siljeström
- Department of Surfaces, Chemistry and Materials, SP Technical Research Institute of Sweden, P.O. Box 857, Borås, 50115, Sweden
| | - Martin J Whitehouse
- Department of Geosciences and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50007, Stockholm, 10405, Sweden
| | - Curt Broman
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Veneta Belivanova
- Department of Palaeobiology and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50 007, Stockholm, 10405, Sweden
| | - Mats E Åström
- Department of Biology and Environmental Science, Linnæus University, Kalmar, 39182, Sweden
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67
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Zhang X, Liu X, Liang Y, Xiao Y, Ma L, Guo X, Miao B, Liu H, Peng D, Huang W, Yin H. Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps. Front Microbiol 2017; 8:790. [PMID: 28529505 PMCID: PMC5418355 DOI: 10.3389/fmicb.2017.00790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
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68
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Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF. Potential for microbial H 2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME JOURNAL 2017; 11:1915-1929. [PMID: 28350393 PMCID: PMC5520028 DOI: 10.1038/ismej.2017.39] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/02/2017] [Accepted: 02/05/2017] [Indexed: 01/24/2023]
Abstract
Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.
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Affiliation(s)
- Alex W Hernsdorf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.,Horonobe Underground Research Center, Japan Atomic Energy Agency, Horonobe, Hokkaido, Japan
| | - Kazuya Miyakawa
- Horonobe Underground Research Center, Japan Atomic Energy Agency, Horonobe, Hokkaido, Japan
| | - Kotaro Ise
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Yohey Suzuki
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | | | - David Burstein
- Department of Earth and Planetary Sciences, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
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69
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Wu X, Pedersen K, Edlund J, Eriksson L, Åström M, Andersson AF, Bertilsson S, Dopson M. Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters. MICROBIOME 2017; 5:37. [PMID: 28335808 PMCID: PMC5364579 DOI: 10.1186/s40168-017-0253-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 03/12/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. CONCLUSIONS Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.
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Affiliation(s)
- Xiaofen Wu
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | | | | | | | - Mats Åström
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
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70
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Rajala P, Bomberg M. Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment. Front Microbiol 2017; 8:431. [PMID: 28367144 PMCID: PMC5355647 DOI: 10.3389/fmicb.2017.00431] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/28/2017] [Indexed: 02/01/2023] Open
Abstract
Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions.
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Affiliation(s)
- Pauliina Rajala
- Materials Performance, VTT Technical Research Centre of Finland Espoo, Finland
| | - Malin Bomberg
- Materials Performance, VTT Technical Research Centre of FinlandEspoo, Finland; Material Processing and Geotechnology, VTT Technical Research Centre of FinlandEspoo, Finland
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71
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Rempfert KR, Miller HM, Bompard N, Nothaft D, Matter JM, Kelemen P, Fierer N, Templeton AS. Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman. Front Microbiol 2017; 8:56. [PMID: 28223966 PMCID: PMC5293757 DOI: 10.3389/fmicb.2017.00056] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H2, CH4, Ca2+, Mg2+, NO3-, SO42-, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.
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Affiliation(s)
- Kaitlin R Rempfert
- Department of Geological Sciences, University of Colorado Boulder, CO, USA
| | - Hannah M Miller
- Department of Geological Sciences, University of Colorado Boulder, CO, USA
| | - Nicolas Bompard
- National Oceanography Centre, University of Southampton Southampton, UK
| | - Daniel Nothaft
- Department of Geological Sciences, University of Colorado Boulder, CO, USA
| | - Juerg M Matter
- National Oceanography Centre, University of Southampton Southampton, UK
| | - Peter Kelemen
- Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA
| | - Noah Fierer
- Cooperate Institute for Research in Environmental Sciences, University of ColoradoBoulder, CO, USA; Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Alexis S Templeton
- Department of Geological Sciences, University of Colorado Boulder, CO, USA
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72
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Frank YA, Kadnikov VV, Gavrilov SN, Banks D, Gerasimchuk AL, Podosokorskaya OA, Merkel AY, Chernyh NA, Mardanov AV, Ravin NV, Karnachuk OV, Bonch-Osmolovskaya EA. Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study. Front Microbiol 2016; 7:2101. [PMID: 28082967 PMCID: PMC5187383 DOI: 10.3389/fmicb.2016.02101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.
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Affiliation(s)
- Yulia A. Frank
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Vitaly V. Kadnikov
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Sergey N. Gavrilov
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - David Banks
- Glasgow and Holymoor Consultancy Ltd., Glasgow UniversityChesterfield, UK
| | - Anna L. Gerasimchuk
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Olga A. Podosokorskaya
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Alexander Y. Merkel
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Nikolai A. Chernyh
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Andrey V. Mardanov
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Nikolai V. Ravin
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Olga V. Karnachuk
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Elizaveta A. Bonch-Osmolovskaya
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
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73
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Bagnoud A, Chourey K, Hettich RL, de Bruijn I, Andersson AF, Leupin OX, Schwyn B, Bernier-Latmani R. Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock. Nat Commun 2016; 7:12770. [PMID: 27739431 PMCID: PMC5067608 DOI: 10.1038/ncomms12770] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/29/2016] [Indexed: 11/25/2022] Open
Abstract
The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. Hydrogen build-up in geological nuclear waste repositories poses risks, but it may be alleviated by H2 consumption by deep subsurface microbial communities. Here, the authors inject H2 in a borehole and use metagenomics and metaproteomics to identify a carbon cycle driven by autotrophic H2 oxidizers.
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Affiliation(s)
- Alexandre Bagnoud
- Ecole Polytechnique Fédérale de Lausanne, Environmental Microbiology Laboratory, Station 6, Lausanne CH-1015, Switzerland
| | - Karuna Chourey
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee 37831, USA
| | - Robert L Hettich
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee 37831, USA
| | - Ino de Bruijn
- Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm 171 65, Sweden.,KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm 171 65, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm 171 65, Sweden
| | | | | | - Rizlan Bernier-Latmani
- Ecole Polytechnique Fédérale de Lausanne, Environmental Microbiology Laboratory, Station 6, Lausanne CH-1015, Switzerland
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Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME JOURNAL 2016; 10:2447-58. [PMID: 27022994 PMCID: PMC5030689 DOI: 10.1038/ismej.2016.36] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 01/29/2016] [Accepted: 02/07/2016] [Indexed: 11/14/2022]
Abstract
Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.
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