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Šibanc N, Clark DR, Helgason T, Dumbrell AJ, Maček I. Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi. mSystems 2024; 9:e0133123. [PMID: 38376262 PMCID: PMC10949450 DOI: 10.1128/msystems.01331-23] [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: 12/13/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem-mofettes or natural CO2 springs caused by geological CO2 exhalations-are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, "stress tolerant" taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.IMPORTANCEArbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.
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Affiliation(s)
- Nataša Šibanc
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of forest physiology and genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Dave R. Clark
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- Institute for Analytics and Data Science, University of Essex, Colchester, United Kingdom
| | - Thorunn Helgason
- Department of Biology, University of York, York, United Kingdom
- Institute for Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Alex J. Dumbrell
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Irena Maček
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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2
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De Castro O, Avino M, Carraturo F, Di Iorio E, Giovannelli D, Innangi M, Menale B, Mormile N, Troisi J, Guida M. Profiling microbial communities in an extremely acidic environment influenced by a cold natural carbon dioxide spring: A study of the Mefite in Ansanto Valley, Southern Italy. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13241. [PMID: 38407001 PMCID: PMC10895555 DOI: 10.1111/1758-2229.13241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
The Ansanto Valley's Mefite, one of the Earth's largest non-volcanic CO2 gas emissions, is distinguished by its cold natural carbon dioxide springs. These emissions originate from the intricate tectonics and geodynamics of the southern Apennines in Italy. Known for over two millennia for its lethal concentration of CO2 and other harmful gases, the Mefite has a reputation for being toxic and dangerous. Despite its historical significance and unique geological features, there is a lack of information on the microbial diversity associated with the Mefite's gas emissions. This study presents an integrated exploration of the microbial diversity in the mud soil, using high-throughput sequencing of 16S rRNA (Prokaryotes) and ITS2 (Fungi), alongside a geochemical site characterisation. Our findings reveal that the Mefite's unique environment imposes a significant bottleneck on microbial diversity, favouring a select few microbial groups such as Actinobacteria and Firmicutes for Prokaryotes, and Basidiomycota for Fungi.
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Affiliation(s)
- Olga De Castro
- Department of BiologyUniversity of Naples Federico IINaplesItaly
- Botanical GardenNaplesItaly
| | - Mariano Avino
- Department of Biochemistry and Functional GenomicsSherbrooke UniversitySherbrookeQuebecCanada
| | | | | | - Donato Giovannelli
- Department of BiologyUniversity of Naples Federico IINaplesItaly
- National Research CouncilInstitute of Marine Biological Resources and Biotechnologies—CNR‐IRBIMAnconaItaly
- Department of Marine and Coastal ScienceRutgers UniversityNew BrunswickNew JerseyUSA
- Marine Chemistry & Geochemistry DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - Michele Innangi
- EnvixLab, Department of Biosciences and TerritoryUniversity of Molise Contrada Fonte LapponePesche (IS)Italy
| | - Bruno Menale
- Department of BiologyUniversity of Naples Federico IINaplesItaly
- Botanical GardenNaplesItaly
| | - Nicolina Mormile
- Department of BiologyUniversity of Naples Federico IINaplesItaly
| | - Jacopo Troisi
- European Biomedical Research Institute of Salerno (EBRIS)SalernoItaly
- Theoreo srlMontecorvino Pugliano (SA)Italy
| | - Marco Guida
- Department of BiologyUniversity of Naples Federico IINaplesItaly
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3
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Jasechko S, Seybold H, Perrone D, Fan Y, Shamsudduha M, Taylor RG, Fallatah O, Kirchner JW. Rapid groundwater decline and some cases of recovery in aquifers globally. Nature 2024; 625:715-721. [PMID: 38267682 PMCID: PMC10808077 DOI: 10.1038/s41586-023-06879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/14/2023] [Indexed: 01/26/2024]
Abstract
Groundwater resources are vital to ecosystems and livelihoods. Excessive groundwater withdrawals can cause groundwater levels to decline1-10, resulting in seawater intrusion11, land subsidence12,13, streamflow depletion14-16 and wells running dry17. However, the global pace and prevalence of local groundwater declines are poorly constrained, because in situ groundwater levels have not been synthesized at the global scale. Here we analyse in situ groundwater-level trends for 170,000 monitoring wells and 1,693 aquifer systems in countries that encompass approximately 75% of global groundwater withdrawals18. We show that rapid groundwater-level declines (>0.5 m year-1) are widespread in the twenty-first century, especially in dry regions with extensive croplands. Critically, we also show that groundwater-level declines have accelerated over the past four decades in 30% of the world's regional aquifers. This widespread acceleration in groundwater-level deepening highlights an urgent need for more effective measures to address groundwater depletion. Our analysis also reveals specific cases in which depletion trends have reversed following policy changes, managed aquifer recharge and surface-water diversions, demonstrating the potential for depleted aquifer systems to recover.
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Affiliation(s)
- Scott Jasechko
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Hansjörg Seybold
- Department of Environmental Systems Sciences, ETH Zürich, Zürich, Switzerland
| | - Debra Perrone
- Environmental Studies Program, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Ying Fan
- Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Mohammad Shamsudduha
- Institute for Risk and Disaster Reduction, University College London, London, UK
| | | | - Othman Fallatah
- Department of Nuclear Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
- Center for Training and Radiation Protection, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
| | - James W Kirchner
- Department of Environmental Systems Sciences, ETH Zürich, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
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4
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Zhou N, Kupper RJ, Catalano JG, Thompson A, Chan CS. Biological Oxidation of Fe(II)-Bearing Smectite by Microaerophilic Iron Oxidizer Sideroxydans lithotrophicus Using Dual Mto and Cyc2 Iron Oxidation Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17443-17453. [PMID: 36417801 PMCID: PMC9731265 DOI: 10.1021/acs.est.2c05142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Fe(II) clays are common across many environments, making them a potentially significant microbial substrate, yet clays are not well established as an electron donor. Therefore, we explored whether Fe(II)-smectite supports the growth of Sideroxydans lithotrophicus ES-1, a microaerophilic Fe(II)-oxidizing bacterium (FeOB), using synthesized trioctahedral Fe(II)-smectite and 2% oxygen. S. lithotrophicus grew substantially and can oxidize Fe(II)-smectite to a higher extent than abiotic oxidation, based on X-ray near-edge spectroscopy (XANES). Sequential extraction showed that edge-Fe(II) is oxidized before interior-Fe(II) in both biotic and abiotic experiments. The resulting Fe(III) remains in smectite, as secondary minerals were not detected in biotic and abiotic oxidation products by XANES and Mössbauer spectroscopy. To determine the genes involved, we compared S. lithotrophicus grown on smectite versus Fe(II)-citrate using reverse-transcription quantitative PCR and found that cyc2 genes were highly expressed on both substrates, while mtoA was upregulated on smectite. Proteomics confirmed that Mto proteins were only expressed on smectite, indicating that ES-1 uses the Mto pathway to access solid Fe(II). We integrate our results into a biochemical and mineralogical model of microbial smectite oxidation. This work increases the known substrates for FeOB growth and expands the mechanisms of Fe(II)-smectite alteration in the environment.
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Affiliation(s)
- Nanqing Zhou
- School
of Marine Science and Policy, University
of Delaware, Newark, Delaware 19716, United
States
| | - Robert J. Kupper
- Department
of Earth and Planetary Sciences, Washington
University in St. Louis, Saint
Louis, Missouri 63130, United States
| | - Jeffrey G. Catalano
- Department
of Earth and Planetary Sciences, Washington
University in St. Louis, Saint
Louis, Missouri 63130, United States
| | - Aaron Thompson
- Department
of Crop and Soil Sciences, University of
Georgia, Athens, Georgia 30602, United States
| | - Clara S. Chan
- School
of Marine Science and Policy, University
of Delaware, Newark, Delaware 19716, United
States
- Department
of Earth Sciences, University of Delaware, Newark, Delaware 19716, United States
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5
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Smrhova T, Jani K, Pajer P, Kapinusova G, Vylita T, Suman J, Strejcek M, Uhlik O. Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis. ENVIRONMENTAL MICROBIOME 2022; 17:48. [PMID: 36089611 PMCID: PMC9465906 DOI: 10.1186/s40793-022-00440-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition. RESULTS Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaClw/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs. CONCLUSIONS Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Tomas Vylita
- Institute of Balneology and Spa Sciences, Karlovy Vary, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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6
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Perez‐Molphe‐Montoya E, Küsel K, Overholt WA. Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota. Environ Microbiol 2022; 24:5437-5449. [DOI: 10.1111/1462-2920.16170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | - Kirsten Küsel
- Institute of Biodiversity Friedrich Schiller University Jena Germany
- The German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐ Leipzig Germany
| | - Will A. Overholt
- Institute of Biodiversity Friedrich Schiller University Jena Germany
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7
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Zavarzina DG, Prokofeva MI, Pikhtereva VA, Klyukina AA, Maslov AA, Merkel AY, Gavrilov SN. Deferrivibrio essentukiensis sp. nov., gen. nov., a Representative of Deferrivibrionaceae fam. nov., Isolated from the Subsurface Aquifer of Caucasian Mineral Drinking Waters. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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8
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Gavrilov SN, Potapov EG, Prokof’eva MI, Klyukina AA, Merkel AY, Maslov AA, Zavarzina DG. Diversity of Novel Uncultured Prokaryotes in Microbial Communities of the Yessentukskoye Underground Mineral Water Deposit. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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9
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Spieck E, Wegen S, Keuter S. Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems. Appl Microbiol Biotechnol 2021; 105:7123-7139. [PMID: 34508283 PMCID: PMC8494671 DOI: 10.1007/s00253-021-11487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/10/2023]
Abstract
Abstract Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11487-5.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Simone Wegen
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
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10
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Liu Q, Adler K, Lipus D, Kämpf H, Bussert R, Plessen B, Schulz HM, Krauze P, Horn F, Wagner D, Mangelsdorf K, Alawi M. Microbial Signatures in Deep CO 2-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic). Front Microbiol 2020; 11:543260. [PMID: 33381087 PMCID: PMC7768021 DOI: 10.3389/fmicb.2020.543260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 11/20/2020] [Indexed: 01/04/2023] Open
Abstract
The Hartoušov mofette system is a natural CO2 degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO2 on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO2 blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO2 reservoir associated with a deep low-permeable CO2-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO2 starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO2-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO2-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO2 accumulation in the mofette system.
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Affiliation(s)
- Qi Liu
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Karsten Adler
- Institute of Geosciences, University of Potsdam, Potsdam, Germany.,Section Organic Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Daniel Lipus
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Horst Kämpf
- Section Organic Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Robert Bussert
- Section Applied Geochemistry, Institute of Applied Geosciences, Technische Universität Berlin, Berlin, Germany
| | - Birgit Plessen
- Section Climate Dynamics and Landscape Evolution, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Hans-Martin Schulz
- Section Organic Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Patryk Krauze
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Fabian Horn
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Dirk Wagner
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Kai Mangelsdorf
- Section Organic Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Mashal Alawi
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
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11
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Laport MS, Pinheiro U, Rachid CTCDC. Freshwater Sponge Tubella variabilis Presents Richer Microbiota Than Marine Sponge Species. Front Microbiol 2019; 10:2799. [PMID: 31849922 PMCID: PMC6902092 DOI: 10.3389/fmicb.2019.02799] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/18/2019] [Indexed: 02/02/2023] Open
Abstract
Sponges can host diverse and abundant communities of microorganisms, which constitute an interesting source of bioactive compounds. Thus, to broaden our knowledge about the diversity of the microbiota that is found in freshwater sponges, the microbial community of Tubella variabilis was analyzed using culture-independent and culture-dependent approaches. Additionally, sponge-associated bacteria were compared with those living in the surrounding waters. Bacteria were also tested for antimicrobial production. Overall, the microbial composition identified comprises at least 44 phyla belonging mainly to Proteobacteria and low percentages of Bacteroidetes, Acidobacteria, and Verrucomicrobia. Alphaproteobacteria was the dominant class in T. variabilis while Betaproteobacteria was dominant in freshwater. Our data also revealed a high richness of bacteria in comparison to another freshwater sponge and 32 marine sponges. A global comparison of the structure of microbiota of different sponges showed that the main structuring factor may be the sponge environment, with T. variabilis and all freshwater sponges clustering together, and far away from the marine sponges. Bacterial strains from sponges and from freshwater were isolated and 163 morphotypes were phylogenetically identified. These belong to 26 genera, of which 12 were exclusively found in sponge samples and three only in freshwater. Inhibitory activities were also detected among 20–25% of the isolates from sponges and freshwater, respectively. This study presents new information on the composition of the microbial community found in freshwater sponges, which is diverse, abundant and distinct from some marine sponges. Moreover, the antimicrobial activity observed from the bacterial strains might play an important role in shaping microbial communities of the environment.
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Affiliation(s)
- Marinella Silva Laport
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ulisses Pinheiro
- Department of Zoology, Federal University of Pernambuco, Recife, Brazil
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12
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Klasek SA, Torres ME, Loher M, Bohrmann G, Pape T, Colwell FS. Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion. Front Microbiol 2019; 10:1436. [PMID: 31281306 PMCID: PMC6596357 DOI: 10.3389/fmicb.2019.01436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li+ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K+ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats.
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Affiliation(s)
- Scott A Klasek
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Marta E Torres
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Markus Loher
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Frederick S Colwell
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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13
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Gulliver D, Lipus D, Ross D, Bibby K. Insights into microbial community structure and function from a shallow, simulated CO 2 -leakage aquifer demonstrate microbial selection and adaptation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:338-351. [PMID: 29984552 DOI: 10.1111/1758-2229.12675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/30/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2 ), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO2 -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1.15 g l-1 . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO2 exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO2 utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO2 leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.
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Affiliation(s)
- Djuna Gulliver
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, USA
| | - Daniel Lipus
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Daniel Ross
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, USA
- AECOM, Pittsburgh, PA, USA
| | - Kyle Bibby
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, South Bend, IN, USA
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14
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Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Martínez-Cruz M, de Moor JM, Pieper DH, Chavarría M. Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO 2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica. Extremophiles 2019; 23:177-187. [PMID: 30600357 DOI: 10.1007/s00792-018-01072-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
Here we report the chemical and microbial characterization of the surface water of a CO2-rich hydrothermal vent known in Costa Rica as Borbollones, located at Tenorio Volcano National Park. The Borbollones showed a temperature surrounding 60 °C, a pH of 2.4 and the gas released has a composition of ~ 97% CO2, ~ 0.07% H2S, ~ 2.3% N2 and ~ 0.12% CH4. Other chemical species such as sulfate and iron were found at high levels with respect to typical fresh water bodies. Analysis by 16S rRNA gene metabarcoding revealed that in Borbollones predominates an archaeon from the order Thermoplasmatales and one bacterium from the genus Sulfurimonas. Other sulfur- (genera Thiomonas, Acidithiobacillus, Sulfuriferula, and Sulfuricurvum) and iron-oxidizing bacteria (genera Sideroxydans, Gallionella, and Ferrovum) were identified. Our results show that CO2-influenced surface water of Borbollones contains microorganisms that are usually found in acid rock drainage environments or sulfur-rich hydrothermal vents. To our knowledge, this is the first microbiological characterization of a CO2-dominated hydrothermal spring from Central America and expands our understanding of those extreme ecosystems.
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Affiliation(s)
- Alejandro Arce-Rodríguez
- Institute of Microbiology, Technical University of Braunschweig, 38106, Brunswick, Germany.,Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany.,Molecular Bacteriology Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - María Martínez-Cruz
- Observatorio Vulcanológico y Sismológico de Costa Rica, Universidad Nacional (OVSICORI-UNA), 2386-3000, Heredia, Costa Rica
| | - J Maarten de Moor
- Observatorio Vulcanológico y Sismológico de Costa Rica, Universidad Nacional (OVSICORI-UNA), 2386-3000, Heredia, Costa Rica
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica. .,Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, 11501-2060, San José, Costa Rica. .,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, 11501-2060, San José, Costa Rica.
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15
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Mehlhorn J, Besold J, Lezama Pacheco JS, Gustafsson JP, Kretzschmar R, Planer-Friedrich B. Copper Mobilization and Immobilization along an Organic Matter and Redox Gradient-Insights from a Mofette Site. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13698-13707. [PMID: 30199245 DOI: 10.1021/acs.est.8b02668] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mofettes (natural geogenic CO2 exhalations) represent excellent sites to study the behavior of Cu in soils and the co-occurrence of different mobilization and immobilization processes since they exhibit both a gradient in redox conditions (oxic to permanently anoxic) and in soil organic matter (SOM; low to high contents). Soil and pore water samples from an 18 m-transect over a mofette showed a complex behavior of Cu, with highest mobility in the transition between oxic and anoxic conditions. Cu(II) sorption experiments on SOM-rich topsoil revealed that Cu mobility under oxic conditions was confined by adsorption to SOM while in the oxygen-free mofette center reduction and precipitation of sulfides was the dominating Cu-sequestering process. In transition areas with low amounts of oxygen (<10%), there was no mineral precipitation, instead high dissolved-to-soil organic carbon ratios strongly increased Cu mobility. Our results show that low stability of SOM formed under oxygen-limited conditions leads to increased Cu mobility unless sulfur-reducing conditions cause Cu sequestration by sulfide precipitation. The interplay of these (im)mobilization processes and especially the unexpectedly high mobility under suboxic conditions have to be considered when assessing Cu mobility along spatial or temporal redox gradients, e.g., at contamination sites or periodically flooded soils.
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Affiliation(s)
- Judith Mehlhorn
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER) , University of Bayreuth , D-95440 Bayreuth , Germany
| | - Johannes Besold
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER) , University of Bayreuth , D-95440 Bayreuth , Germany
| | - Juan S Lezama Pacheco
- Department of Environmental Earth System Science , Stanford University , Stanford , California 94305 , United States
| | - Jon Petter Gustafsson
- Department of Soil and Environment , Swedish University of Agricultural Sciences , 75007 Uppsala , Sweden
| | - Ruben Kretzschmar
- Soil Chemistry Group , Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, CHN , CH-8092 Zurich , Switzerland
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER) , University of Bayreuth , D-95440 Bayreuth , Germany
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16
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Liu Q, Kämpf H, Bussert R, Krauze P, Horn F, Nickschick T, Plessen B, Wagner D, Alawi M. Influence of CO 2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift). Front Microbiol 2018; 9:2787. [PMID: 30524401 PMCID: PMC6258768 DOI: 10.3389/fmicb.2018.02787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/30/2018] [Indexed: 01/13/2023] Open
Abstract
The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartoušov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km2 and a soil gas concentration of up to 100% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.
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Affiliation(s)
- Qi Liu
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Horst Kämpf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Potsdam, Germany
| | - Robert Bussert
- Institute of Applied Geosciences, Technische Universität Berlin, Berlin, Germany
| | - Patryk Krauze
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Tobias Nickschick
- Institute for Geophysics and Geology, University of Leipzig, Leipzig, Germany
| | - Birgit Plessen
- GFZ German Research Centre for Geosciences, Section Climate Dynamics and Landscape Evolution, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany.,Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
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