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Nagakura T, Morono Y, Ito M, Mangelsdorf K, Pötz S, Schnabel E, Kallmeyer J. Microbial anabolic and catabolic utilization of hydrocarbons in deep subseafloor sediments of Guaymas Basin. FEMS Microbiol Ecol 2024; 100:fiae093. [PMID: 38955392 PMCID: PMC11250447 DOI: 10.1093/femsec/fiae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/02/2024] [Accepted: 07/01/2024] [Indexed: 07/04/2024] Open
Abstract
Guaymas Basin, located in the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nano-scale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Expedition 385 (U1545C and U1546D). These sites are in close proximity of each other (ca. 1 km) and have very similar sedimentology. Site U1546D experienced the intrusion of a sill that has since then thermally equilibrated with the surrounding sediment. Both sites currently have an identical geothermal gradient, despite their different thermal history. The localized heating by the sill led to thermal cracking of sedimentary organic matter and formation of potentially bioavailable organic substrates. There were low levels of hydrocarbon and nitrogen uptake in some samples from both sites, mostly in surficial samples. Hydrocarbon and methane additions stimulated SRR in near-seafloor samples from Site U1545C, while samples from Site U1546D reacted positively only on methane. Our data indicate the potential of microorganisms to metabolize hydrocarbons even in the deep subsurface of Guaymas Basin.
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Affiliation(s)
- Toshiki Nagakura
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Yuki Morono
- JAMSTEC Japan Agency for Marine-Earth Science and Technology, Kochi Institute for Core Sample Research, 200 Monobe Otsu, 783-8502 Nankoku, Kochi, Japan
| | - Motoo Ito
- JAMSTEC Japan Agency for Marine-Earth Science and Technology, Kochi Institute for Core Sample Research, 200 Monobe Otsu, 783-8502 Nankoku, Kochi, Japan
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany
| | - Stefanie Pötz
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany
| | - Ellen Schnabel
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
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Bergsten P, Vannier P, Frion J, Mougeolle A, Marteinsson VÞ. Culturable Bacterial Diversity from the Basaltic Subsurface of the Young Volcanic Island of Surtsey, Iceland. Microorganisms 2022; 10:1177. [PMID: 35744695 PMCID: PMC9229223 DOI: 10.3390/microorganisms10061177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
The oceanic crust is the world's largest and least explored biosphere on Earth. The basaltic subsurface of Surtsey island in Iceland represents an analog of the warm and newly formed-oceanic crust and offers a great opportunity for discovering novel microorganisms. In this study, we collected borehole fluids, drill cores, and fumarole samples to evaluate the culturable bacterial diversity from the subsurface of the island. Enrichment cultures were performed using different conditions, media and temperatures. A total of 195 bacterial isolates were successfully cultivated, purified, and identified based on MALDI-TOF MS analysis and by 16S rRNA gene sequencing. Six different clades belonging to Firmicutes (40%), Gammaproteobacteria (28.7%), Actinobacteriota (22%), Bacteroidota (4.1%), Alphaproteobacteria (3%), and Deinococcota (2%) were identified. Bacillus (13.3%) was the major genus, followed by Geobacillus (12.33%), Enterobacter (9.23%), Pseudomonas (6.15%), and Halomonas (5.64%). More than 13% of the cultured strains potentially represent novel species based on partial 16S rRNA gene sequences. Phylogenetic analyses revealed that the isolated strains were closely related to species previously detected in soil, seawater, and hydrothermal active sites. The 16S rRNA gene sequences of the strains were aligned against Amplicon Sequence Variants (ASVs) from the previously published 16S rRNA gene amplicon sequence datasets obtained from the same samples. Compared with the culture-independent community composition, only 5 out of 49 phyla were cultivated. However, those five phyla accounted for more than 80% of the ASVs. Only 121 out of a total of 5642 distinct ASVs were culturable (≥98.65% sequence similarity), representing less than 2.15% of the ASVs detected in the amplicon dataset. Here, we support that the subsurface of Surtsey volcano hosts diverse and active microbial communities and that both culture-dependent and -independent methods are essential to improving our insight into such an extreme and complex volcanic environment.
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Affiliation(s)
- Pauline Bergsten
- Matís, Exploration and Utilization of Genetic Resources, 113 Reykjavík, Iceland; (P.B.); (P.V.); (J.F.); (A.M.)
- Faculty of Life and Environmental Sciences, University of Iceland, 102 Reykjavík, Iceland
| | - Pauline Vannier
- Matís, Exploration and Utilization of Genetic Resources, 113 Reykjavík, Iceland; (P.B.); (P.V.); (J.F.); (A.M.)
| | - Julie Frion
- Matís, Exploration and Utilization of Genetic Resources, 113 Reykjavík, Iceland; (P.B.); (P.V.); (J.F.); (A.M.)
| | - Alan Mougeolle
- Matís, Exploration and Utilization of Genetic Resources, 113 Reykjavík, Iceland; (P.B.); (P.V.); (J.F.); (A.M.)
| | - Viggó Þór Marteinsson
- Matís, Exploration and Utilization of Genetic Resources, 113 Reykjavík, Iceland; (P.B.); (P.V.); (J.F.); (A.M.)
- Faculty of Food Science and Nutrition, University of Iceland, 102 Reykjavík, Iceland
- Agricultural University of Iceland, 112 Reykjavík, Iceland
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Nicholls HCG, Rolfe SA, Mallinson HEH, Hjort M, Spence MJ, Bonte M, Thornton SF. Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1223-1238. [PMID: 34350568 PMCID: PMC8724112 DOI: 10.1007/s11356-021-15606-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Microbes in aquifers are present suspended in groundwater or attached to the aquifer sediment. Groundwater is often sampled at gasoline ether oxygenate (GEO)-impacted sites to assess the potential biodegradation of organic constituents. However, the distribution of GEO-degrading microorganisms between the groundwater and aquifer sediment must be understood to interpret this potential. In this study, the distribution of ethyl tert-butyl ether (ETBE)-degrading organisms and ETBE biodegradation potential was investigated in laboratory microcosm studies and mixed groundwater-aquifer sediment samples obtained from pumped monitoring wells at ETBE-impacted sites. ETBE biodegradation potential (as determined by quantification of the ethB gene) was detected predominantly in the attached microbial communities and was below detection limit in the groundwater communities. The copy number of ethB genes varied with borehole purge volume at the field sites. Members of the Comamonadaceae and Gammaproteobacteria families were identified as responders for ETBE biodegradation. However, the detection of the ethB gene is a more appropriate function-based indicator of ETBE biodegradation potential than taxonomic analysis of the microbial community. The study shows that a mixed groundwater-aquifer sediment (slurry) sample collected from monitoring wells after minimal purging can be used to assess the aquifer ETBE biodegradation potential at ETBE-release sites using this function-based concept.
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Affiliation(s)
- Henry C G Nicholls
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK
| | - Stephen A Rolfe
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, S10 2TN, Sheffield, UK
| | - Helen E H Mallinson
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK
| | - Markus Hjort
- Concawe, Boulevard du Souverain 165, 1160, Brussels, Belgium
| | - Michael J Spence
- Concawe, Boulevard du Souverain 165, 1160, Brussels, Belgium
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham, NG12 5GG, UK
| | - Matthijs Bonte
- Concawe, Boulevard du Souverain 165, 1160, Brussels, Belgium
- Shell Global Solutions International B.V., Rijswijk, 2288GK, The Netherlands
- Ministry of Infrastructure and Water Management, The Hague, The Netherlands
| | - Steven F Thornton
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK.
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Bergsten P, Vannier P, Klonowski AM, Knobloch S, Gudmundsson MT, Jackson MD, Marteinsson VT. Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland. Front Microbiol 2021; 12:728977. [PMID: 34659155 PMCID: PMC8513691 DOI: 10.3389/fmicb.2021.728977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/30/2021] [Indexed: 01/04/2023] Open
Abstract
The island of Surtsey was formed in 1963–1967 on the offshore Icelandic volcanic rift zone. It offers a unique opportunity to study the subsurface biosphere in newly formed oceanic crust and an associated hydrothermal-seawater system, whose maximum temperature is currently above 120°C at about 100m below surface. Here, we present new insights into the diversity, distribution, and abundance of microorganisms in the subsurface of the island, 50years after its creation. Samples, including basaltic tuff drill cores and associated fluids acquired at successive depths as well as surface fumes from fumaroles, were collected during expedition 5059 of the International Continental Scientific Drilling Program specifically designed to collect microbiological samples. Results of this microbial survey are investigated with 16S rRNA gene amplicon sequencing and scanning electron microscopy. To distinguish endemic microbial taxa of subsurface rocks from potential contaminants present in the drilling fluid, we use both methodological and computational strategies. Our 16S rRNA gene analysis results expose diverse and distinct microbial communities in the drill cores and the borehole fluid samples, which harbor thermophiles in high abundance. Whereas some taxonomic lineages detected across these habitats remain uncharacterized (e.g., Acetothermiia, Ammonifexales), our results highlight potential residents of the subsurface that could be identified at lower taxonomic rank such as Thermaerobacter, BRH-c8a (Desulfallas-Sporotomaculum), Thioalkalimicrobium, and Sulfurospirillum. Microscopy images reveal possible biotic structures attached to the basaltic substrate. Finally, microbial colonization of the newly formed basaltic crust and the metabolic potential are discussed on the basis of the data.
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Affiliation(s)
- Pauline Bergsten
- Exploration & Utilization of Genetic Resources, Matís, Reykjavík, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Pauline Vannier
- Exploration & Utilization of Genetic Resources, Matís, Reykjavík, Iceland
| | | | - Stephen Knobloch
- Exploration & Utilization of Genetic Resources, Matís, Reykjavík, Iceland
| | | | - Marie Dolores Jackson
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, United States
| | - Viggó Thor Marteinsson
- Exploration & Utilization of Genetic Resources, Matís, Reykjavík, Iceland.,Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
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Orsi WD. Ecology and evolution of seafloor and subseafloor microbial communities. Nat Rev Microbiol 2018; 16:671-683. [DOI: 10.1038/s41579-018-0046-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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