1
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Coskun ÖK, Gomez-Saez GV, Beren M, Özcan D, Günay SD, Elkin V, Hoşgörmez H, Einsiedl F, Eisenreich W, Orsi WD. Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community. FEMS Microbiol Ecol 2024; 100:fiae062. [PMID: 38632042 DOI: 10.1093/femsec/fiae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Doğacan Özcan
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Suna D Günay
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Viktor Elkin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Hakan Hoşgörmez
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Florian Einsiedl
- Chair of Hydrogeology, School of Engineering and Design, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstraße, 85748 Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
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2
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Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
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Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
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3
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Lopez-Fernandez M, Westmeijer G, Turner S, Broman E, Ståhle M, Bertilsson S, Dopson M. Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield. NPJ Biofilms Microbiomes 2023; 9:41. [PMID: 37349512 DOI: 10.1038/s41522-023-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the Äspö Hard Rock Laboratory, Sweden. Metatranscriptomes showed Thiobacillus, Sideroxydans, and Desulforegula to be abundant and together accounted for 31% of the transcripts in the biofilm communities. Differential expression analysis highlighted Thiobacillus to have a principal role in biofilm formation in these oligotrophic groundwaters by being involved in relevant processes such as the formation of extracellular matrix, quorum sensing, and cell motility. The findings revealed an active biofilm community with sulfur cycling as a prominent mode of energy conservation in the deep biosphere.
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Affiliation(s)
- Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden.
- Department of Microbiology, Faculty of Sciences, University of Granada, Avenida Fuentenueva s/n, 18071, Granada, Spain.
| | - George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20 A, 106 91, Stockholm, Sweden
| | - Magnus Ståhle
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Box 7050, SE75007, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
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4
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Osterholz H, Turner S, Alakangas LJ, Tullborg EL, Dittmar T, Kalinowski BE, Dopson M. Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield. Nat Commun 2022; 13:4837. [PMID: 35977924 PMCID: PMC9385861 DOI: 10.1038/s41467-022-32457-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
The deep terrestrial biosphere encompasses the life below the photosynthesis-fueled surface that perseveres in typically nutrient and energy depleted anoxic groundwaters. The composition and cycling of this vast dissolved organic matter (DOM) reservoir relevant to the global carbon cycle remains to be deciphered. Here we show that recent Baltic Sea-influenced to ancient pre-Holocene saline Fennoscandian Shield deep bedrock fracture waters carried DOM with a strong terrigenous signature and varying contributions from abiotic and biotic processes. Removal of easily degraded carbon at the surface-to-groundwater transition and corresponding microbial community assembly processes likely resulted in the highly similar DOM signatures across the notably different water types that selected for a core microbiome. In combination with the aliphatic character, depleted δ13C signatures in DOM indicated recent microbial production in the oldest, saline groundwater. Our study revealed the persistence of terrestrially-sourced carbon in severely energy limited deep continental groundwaters supporting deep microbial life.
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Affiliation(s)
- Helena Osterholz
- Marine Chemistry, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
| | - Stephanie Turner
- Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Linda J Alakangas
- Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.,Swedish Nuclear Fuel and Waste Management Company, Äspö Hard Rock Laboratory, Oskarshamn, Sweden
| | | | - Thorsten Dittmar
- Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky University, Oldenburg, Germany
| | - Birgitta E Kalinowski
- Swedish Nuclear Fuel and Waste Management Company, Äspö Hard Rock Laboratory, Oskarshamn, Sweden
| | - Mark Dopson
- Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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5
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Westmeijer G, Mehrshad M, Turner S, Alakangas L, Sachpazidou V, Bunse C, Pinhassi J, Ketzer M, Åström M, Bertilsson S, Dopson M. Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities. Commun Biol 2022; 5:37. [PMID: 35017653 PMCID: PMC8752596 DOI: 10.1038/s42003-021-02980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/15/2021] [Indexed: 12/20/2022] Open
Abstract
The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions. Westmeijer et al. employ high-throughput sequencing to investigate the connection between deep biosphere groundwaters and surface microbial communities. They suggest that the microbial communities of deep biosphere groundwaters in the Fennoscandian Shield are mostly comprised of autochthonous species, rather than migratory surface representatives.
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Affiliation(s)
- George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Linda Alakangas
- Swedish Nuclear Fuel and Waste Management Co (SKB), 57 229, Oskarshamn, Sweden
| | - Varvara Sachpazidou
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.,Helmholtz-Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Marcelo Ketzer
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Mats Åström
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
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6
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Zhang L, Zhang C, Lian K, Ke D, Xie T, Liu C. River restoration changes distributions of antibiotics, antibiotic resistance genes, and microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147873. [PMID: 34134371 DOI: 10.1016/j.scitotenv.2021.147873] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Although river restoration has been increasingly implemented to restore water quality in ecosystems, its effect on the removal of emerging pollutant antibiotics, and their resultant influence on microbial community structure and functions in river water is still unclear. This study investigated the changes of antibiotics, antibiotic resistant genes (ARGs), microbial communities, and their spatial distributions in a megacity river before and after river restoration. Results indicated that although the restoration activities including riverbed dredging, riverbank hardening, sewage and storm water separation and re-pipelining improved water quality such as by decreasing total phosphorus (TP) content from 4.60 ± 6.38 mg/L in 2018 to 0.98 ± 0.44 mg/L in 2020, the antibiotic concentrations in river water increased. Total antibiotic concentrations in the water samples were higher in 2020 (506.89-6952.50 ng/L) than those in 2018 (137.93-1751.51 ng/L), likely caused by increased usage of antibiotics in 2020 for COVID-19 treatment. The spatial distributions of antibiotics were less varied likely as a result of less retardation and fast mixing during antibiotic transport. The result also found that the abundance of Actinobacteria and Proteobacteria, and their correlations with ARGs increased. The spatial distributions of ARGs and microbial communities became less varied in the river water, consistent with the antibiotic variations before and after river restoration. Physicochemical changes such as decreased TP and dissolved organic carbon content may also be a factor. The results indicated that the current river restoration efforts were not effective in removing antibiotics, and implied that further studies are needed to investigate their subsequent transformation and transport, and to assess their risks to the health of ecosystems.
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Affiliation(s)
- Lili Zhang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Cheng Zhang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Keting Lian
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dongfang Ke
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ting Xie
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chongxuan Liu
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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7
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Povedano-Priego C, Jroundi F, Lopez-Fernandez M, Shrestha R, Spanek R, Martín-Sánchez I, Villar MV, Ševců A, Dopson M, Merroun ML. Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124600. [PMID: 33339698 DOI: 10.1016/j.jhazmat.2020.124600] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Compacted bentonites are one of the best sealing and backfilling clays considered for use in Deep Geological Repositories of radioactive wastes. However, an in-depth understanding of their behavior after placement in the repository is required, including if the activity of indigenous microorganisms affects safety conditions. Here we provide an optimized phenol:chloroform based protocol that facilitates higher DNA-yields when other methods failed. To demonstrate the efficiency of this method, DNA was extracted from acetate-treated bentonites compacted at 1.5 and 1.7 g/cm3 densities after 24 months anoxic incubation. Among the 16S rRNA gene sequences identified, those most similar to taxa mediating biogeochemical sulfur cycling included sulfur oxidizing (e.g., Thiobacillus, and Sulfurimonas) and sulfate reducing (e.g., Desulfuromonas and Desulfosporosinus) bacteria. In addition, iron-cycling populations included iron oxidizing (e.g., Thiobacillus and Rhodobacter) plus reducing taxa (e.g., Geobacillus). Genera described for their capacity to utilize acetate as a carbon source were also detected such as Delftia and Stenotrophomonas. Lastly, microscopic analyses revealed pores and cracks that could host nanobacteria or spores. This study highlights the potential role of microbial driven biogeochemical processes in compacted bentonites and the effect of high compaction on microbial diversity in Deep Geological Repositories.
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Affiliation(s)
| | - Fadwa Jroundi
- Departmento de Microbiología, Facultad de Ciencias, University of Granada, Granada, Spain.
| | - Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Rojina Shrestha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic.
| | - Roman Spanek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic.
| | - Inés Martín-Sánchez
- Departmento de Microbiología, Facultad de Ciencias, University of Granada, Granada, Spain.
| | - María Victoria Villar
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Mohamed L Merroun
- Departmento de Microbiología, Facultad de Ciencias, University of Granada, Granada, Spain.
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8
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles. Commun Biol 2021; 4:307. [PMID: 33686191 PMCID: PMC7940616 DOI: 10.1038/s42003-021-01810-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles. Karin Holmfeldt et al. sequence metagenomes and metatranscriptomes of viruses in deep groundwaters down to 448 m below the surface. The results reveal ecological dynamics of viruses including slow motion ‘boom and burst’ cycles and a ‘kill the winner’ model potentially driven by viral predation.
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9
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Ren CC, Sylvia KE, Munley KM, Deyoe JE, Henderson SG, Vu MP, Demas GE. Photoperiod modulates the gut microbiome and aggressive behavior in Siberian hamsters. ACTA ACUST UNITED AC 2020; 223:jeb.212548. [PMID: 31862850 DOI: 10.1242/jeb.212548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022]
Abstract
Seasonally breeding animals undergo shifts in physiology and behavior in response to changes in photoperiod (day length). Interestingly, some species, such as Siberian hamsters (Phodopus sungorus), are more aggressive during the short-day photoperiods of the non-breeding season, despite gonadal regression. While our previous data suggest that Siberian hamsters employ a 'seasonal switch' from gonadal to adrenal regulation of aggression during short-day photoperiods, there is emerging evidence that the gut microbiome, an environment of symbiotic bacteria within the gastrointestinal tract, may also change seasonally and modulate social behaviors. The goal of this study was to compare seasonal shifts in the gut microbiome, circulating levels of adrenal dehydroepiandrosterone (DHEA) and aggression in male and female Siberian hamsters. Hamsters were housed in either long-day (LD) or short-day (SD) photoperiods for 9 weeks. Fecal samples were collected and behaviors were recorded following 3, 6 and 9 weeks of housing, and circulating DHEA was measured at week 9. SD females that were responsive to changes in photoperiod (SD-R), but not SD-R males, displayed increased aggression following 9 weeks of treatment. SD-R males and females also exhibited distinct changes in the relative abundance of gut bacterial phyla and families, yet showed no change in circulating DHEA. The relative abundance of some bacterial families (e.g. Anaeroplasmataceae in females) was associated with aggression in SD-R but not LD or SD non-responder (SD-NR) hamsters after 9 weeks of treatment. Collectively, this study provides insight into the complex role of the microbiome in regulating social behavior in seasonally breeding species.
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Affiliation(s)
- Clarissa C Ren
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Kristyn E Sylvia
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kathleen M Munley
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Jessica E Deyoe
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Sarah G Henderson
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Michael P Vu
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Gregory E Demas
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
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10
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Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichorst SA, Woebken D, Richter A, Wanek W. Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. SOIL BIOLOGY & BIOCHEMISTRY 2019; 136:107521. [PMID: 31700196 PMCID: PMC6837881 DOI: 10.1016/j.soilbio.2019.107521] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.
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Affiliation(s)
- Qing Zheng
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Yuntao Hu
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shasha Zhang
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Lisa Noll
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Theresa Böckle
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Marlies Dietrich
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Craig W. Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Stephanie A. Eichorst
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Dagmar Woebken
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Andreas Richter
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Wolfgang Wanek
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
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11
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Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters. mBio 2019; 10:mBio.01470-19. [PMID: 31409677 PMCID: PMC6692508 DOI: 10.1128/mbio.01470-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth’s carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water. Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two “modern marine” waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic “thoroughly mixed” water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or “geogases.”
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12
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Christel S, Yu C, Wu X, Josefsson S, Lillhonga T, Högfors-Rönnholm E, Sohlenius G, Åström ME, Dopson M. Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments. Res Microbiol 2019; 170:288-295. [PMID: 31279086 DOI: 10.1016/j.resmic.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
Due to land uplift after the last ice age, previously stable Baltic Sea sulfidic sediments are becoming dry land. When these sediments are drained, the sulfide minerals are exposed to air and can release large amounts of metals and acid into the environment. This can cause severe ecological damage such as fish kills in rivers feeding the northern Baltic Sea. In this study, five sites were investigated for the occurrence of acid sulfate soils and their geochemistry and microbiology was identified. The pH and soil chemistry identified three of the areas as having classical acid sulfate soil characteristics and culture independent identification of 16S rRNA genes identified populations related to acidophilic bacteria capable of catalyzing sulfidic mineral dissolution, including species likely adapted to low temperature. These results were compared to an acid sulfate soil area that had been flooded for ten years and showed that the previously oxidized sulfidic materials had an increased pH compared to the unremediated oxidized layers. In addition, the microbiology of the flooded soil had changed such that alkalinity producing ferric and sulfate reducing reactions had likely occurred. This suggested that flooding of acid sulfate soils mitigates their environmental impact.
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Affiliation(s)
- Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39182 Kalmar, Sweden.
| | - Changxun Yu
- Department of Biology and Environmental Science, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Xiaofen Wu
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39182 Kalmar, Sweden
| | - Sarah Josefsson
- Geological Survey of Sweden, Box 670, 751 28 Uppsala, Sweden
| | - Tom Lillhonga
- Research and Development, Novia University of Applied Sciences, FI-65200, Vaasa, Finland
| | - Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, FI-65200, Vaasa, Finland
| | | | - Mats E Åström
- Department of Biology and Environmental Science, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39182 Kalmar, Sweden
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