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Beaver RC, Neufeld JD. Microbial ecology of the deep terrestrial subsurface. THE ISME JOURNAL 2024; 18:wrae091. [PMID: 38780093 PMCID: PMC11170664 DOI: 10.1093/ismejo/wrae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/04/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.
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Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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2
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Nuppunen-Puputti M, Kietäväinen R, Kukkonen I, Bomberg M. Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater. Front Microbiol 2023; 14:1054084. [PMID: 36819068 PMCID: PMC9932282 DOI: 10.3389/fmicb.2023.1054084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of ∼3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.
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Affiliation(s)
- Maija Nuppunen-Puputti
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland,*Correspondence: Maija Nuppunen-Puputti,
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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Rock Surface Fungi in Deep Continental Biosphere-Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap. Microorganisms 2020; 9:microorganisms9010064. [PMID: 33383728 PMCID: PMC7824546 DOI: 10.3390/microorganisms9010064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/16/2023] Open
Abstract
Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.
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Quemener M, Mara P, Schubotz F, Beaudoin D, Li W, Pachiadaki M, Sehein TR, Sylvan JB, Li J, Barbier G, Edgcomb V, Burgaud G. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ Microbiol 2020; 22:3950-3967. [PMID: 32743889 DOI: 10.1111/1462-2920.15181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023]
Abstract
The lithified oceanic crust, lower crust gabbros in particular, has remained largely unexplored by microbiologists. Recently, evidence for heterogeneously distributed viable and transcriptionally active autotrophic and heterotrophic microbial populations within low-biomass communities was found down to 750 m below the seafloor at the Atlantis Bank Gabbro Massif, Indian Ocean. Here, we report on the diversity, activity and adaptations of fungal communities in the deep oceanic crust from ~10 to 780 mbsf by combining metabarcoding analyses with mid/high-throughput culturing approaches. Metabarcoding along with culturing indicate a low diversity of viable fungi, mostly affiliated to ubiquitous (terrestrial and aquatic environments) taxa. Ecophysiological analyses coupled with metatranscriptomics point to viable and transcriptionally active fungal populations engaged in cell division, translation, protein modifications and other vital cellular processes. Transcript data suggest possible adaptations for surviving in the nutrient-poor, lithified deep biosphere that include the recycling of organic matter. These active communities appear strongly influenced by the presence of cracks and veins in the rocks where fluids and resulting rock alteration create micro-niches.
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Affiliation(s)
- Maxence Quemener
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Florence Schubotz
- MARUM-Center for Marine Environmental Sciences, University Bremen, Leobener Strasse 8, Bremen, 28359, Germany
| | - David Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Maria Pachiadaki
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Taylor R Sehein
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, 77845, USA
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Georges Barbier
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Gaëtan Burgaud
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
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Ivarsson M, Drake H, Bengtson S, Rasmussen B. A Cryptic Alternative for the Evolution of Hyphae. Bioessays 2020; 42:e1900183. [DOI: 10.1002/bies.201900183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/03/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Magnus Ivarsson
- Department of BiologyUniversity of Southern Denmark Campusvej 55 Odense M DK 5230 Denmark
- Department of PaleobiologySwedish Museum of Natural History Box 50007 Stockholm SE‐104 05 Sweden
| | - Henrik Drake
- Department of Biology and Environmental ScienceLinnaeus University Kalmar 391 82 Sweden
| | - Stefan Bengtson
- Department of PaleobiologySwedish Museum of Natural History Box 50007 Stockholm SE‐104 05 Sweden
| | - Birger Rasmussen
- School of Earth SciencesThe University of Western Australia Nedlands WA 6009 Australia
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Exceptional Preservation of Fungi as H2-Bearing Fluid Inclusions in an Early Quaternary Paleo-Hydrothermal System at Cape Vani, Milos, Greece. MINERALS 2019. [DOI: 10.3390/min9120749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The production of H2 in hydrothermal systems and subsurface settings is almost exclusively assumed a result of abiotic processes, particularly serpentinization of ultramafic rocks. The origin of H2 in environments not hosted in ultramafic rocks is, as a rule, unjustifiably linked to abiotic processes. Additionally, multiple microbiological processes among both prokaryotes and eukaryotes are known to involve H2-production, of which anaerobic fungi have been put forward as a potential source of H2 in subsurface environments, which is still unconfirmed. Here, we report fungal remains exceptionally preserved as fluid inclusions in hydrothermal quartz from feeder quartz-barite veins from the Cape Vani Fe-Ba-Mn ore on the Greek island of Milos. The inclusions possess filamentous or near-spheroidal morphologies interpreted as remains of fungal hyphae and spores, respectively. They were characterized by microthermometry, Raman spectroscopy, and staining of exposed inclusions with WGA-FITC under fluorescence microscopy. The spheroidal aqueous inclusions interpreted as fungal spores are unique by their coating of Mn-oxide birnessite, and gas phase H2. A biological origin of the H2 resulting from anaerobic fungal respiration is suggested. We propose that biologically produced H2 by micro-eukaryotes is an unrecognized source of H2 in hydrothermal systems that may support communities of H2-dependent prokaryotes.
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McMahon S, Ivarsson M. A New Frontier for Palaeobiology: Earth's Vast Deep Biosphere. Bioessays 2019; 41:e1900052. [PMID: 31241200 DOI: 10.1002/bies.201900052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/29/2019] [Indexed: 11/11/2022]
Abstract
Diverse micro-organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars.
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Affiliation(s)
- Sean McMahon
- School of Geosciences, University of Edinburgh, Edinburgh, EH8 9XP, UK.,UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Magnus Ivarsson
- Department of Biology, University of Southern Denmark, DK-5230, Odense, Denmark.,Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, SE-104 05, Sweden
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Ivarsson M, Bengtson S, Drake H, Francis W. Fungi in Deep Subsurface Environments. ADVANCES IN APPLIED MICROBIOLOGY 2018; 102:83-116. [PMID: 29680127 DOI: 10.1016/bs.aambs.2017.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.
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Affiliation(s)
- Magnus Ivarsson
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark; Swedish Museum of Natural History, Stockholm, Sweden.
| | | | | | - Warren Francis
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
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11
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12
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Biegańska MJ, Rzewuska M, Dąbrowska I, Malewska-Biel B, Ostrzeszewicz M, Dworecka-Kaszak B. Mixed Infection of Respiratory Tract in a Dog Caused by Rhodotorula mucilaginosa and Trichosporon jirovecii: A Case Report. Mycopathologia 2017; 183:637-644. [PMID: 29196923 PMCID: PMC5958165 DOI: 10.1007/s11046-017-0227-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
This report describes the isolation of two environmental fungi: Rhodotorula mucilaginosa and Trichosporon jirovecii accompanied by Pseudomonas aeruginosa and Escherichia coli from a dog with bronchotracheitis. All microorganisms were isolated routinely from a mucopurulent discharge, obtained during bronchoscopy from laryngotracheal area. The initial identification of yeasts was confirmed by API Candida and by molecular analysis of internal transcribed spacer region. Administered antimicrobial treatment with Marbofloxacin and Canizol has brought the improvement in the dogs’ health status. The final results of control mycological culture were negative. Most probably underlying hypothyroidism and the use of steroids were the factors predisposing this patient to opportunistic infection of mixed aetiology. As far as we are concerned, this is the first case of dogs’ respiratory tract infection caused by R. mucilaginosa and T. jirovecii.
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Affiliation(s)
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Iwona Dąbrowska
- Department of Preclinical Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Bożena Malewska-Biel
- Department of Small Animal Diseases with Clinic, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Ostrzeszewicz
- Department of Small Animal Diseases with Clinic, Warsaw University of Life Sciences, Warsaw, Poland
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13
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Drake H, Ivarsson M, Bengtson S, Heim C, Siljeström S, Whitehouse MJ, Broman C, Belivanova V, Åström ME. Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures. Nat Commun 2017; 8:55. [PMID: 28676652 PMCID: PMC5496868 DOI: 10.1038/s41467-017-00094-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/31/2017] [Indexed: 11/08/2022] Open
Abstract
The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (-740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.Deep subsurface microorganisms play an important role in nutrient cycling, yet little is known about deep continental fungal communities. Here, the authors show organically preserved and partly mineralized fungi at 740 m depth, and find evidence of an anaerobic fungi and sulfate reducing bacteria consortium.
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Affiliation(s)
- Henrik Drake
- Department of Biology and Environmental Science, Linnæus University, Kalmar, 39182, Sweden.
| | - Magnus Ivarsson
- Department of Palaeobiology and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50 007, Stockholm, 10405, Sweden
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50 007, Stockholm, 10405, Sweden
| | - Christine Heim
- Geoscience Centre Göttingen of the Georg-August University (Department of Geobiology), Goldschmidtstr. 3, Göttingen, 37077, Germany
| | - Sandra Siljeström
- Department of Surfaces, Chemistry and Materials, SP Technical Research Institute of Sweden, P.O. Box 857, Borås, 50115, Sweden
| | - Martin J Whitehouse
- Department of Geosciences and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50007, Stockholm, 10405, Sweden
| | - Curt Broman
- Department of Geological Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Veneta Belivanova
- Department of Palaeobiology and Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, P.O. Box 50 007, Stockholm, 10405, Sweden
| | - Mats E Åström
- Department of Biology and Environmental Science, Linnæus University, Kalmar, 39182, Sweden
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Lategan MJ, Klare W, Kidd S, Hose GC, Nevalainen H. The unicellular fungal tool RhoTox for risk assessments in groundwater systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 132:18-25. [PMID: 27258820 DOI: 10.1016/j.ecoenv.2016.05.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
The recent inclusion of yeasts in environmental monitoring recognizes their ecological significance and sensitivity to toxicants. Here we present a robust and simple two-step toxicity assay and demonstrate the sensitivity of an ubiquitous groundwater yeast, Rhodotorula minuta, to a range of metals and metalloids. The test species was sensitive to copper with a 24h EC50 of 35µg Cu/L, followed in order of decreasing sensitivity by zinc, chromium (VI) and arsenic (EC50 4.40mg As (III)/L). The strain demonstrated an unexpected tolerance to chromium (VI), having an EC50 value (3.45mg Cr (VI)/L) similar to that of arsenic. The inclusion of a unicellular, microbial test-species into the suite of existing multicellular test species for toxicity evaluation is a key step towards strengthening the assessment of risk for groundwater ecosystems.
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Affiliation(s)
- Maria Josie Lategan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2019, Australia.
| | - William Klare
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2019, Australia
| | - Sarah Kidd
- National Mycology Reference Centre, SA Pathology, South Australia 5000, Australia
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, NSW 2019, Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2019, Australia
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Nawaz A, Purahong W, Lehmann R, Herrmann M, Küsel K, Totsche KU, Buscot F, Wubet T. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities. Front Microbiol 2016; 7:666. [PMID: 27242696 PMCID: PMC4860458 DOI: 10.3389/fmicb.2016.00666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/21/2016] [Indexed: 11/13/2022] Open
Abstract
Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis.
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Affiliation(s)
- Ali Nawaz
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; Department of Biology, University of LeipzigLeipzig, Germany
| | - Witoon Purahong
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology Halle (Saale), Germany
| | - Robert Lehmann
- Institute of Geosciences, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Kirsten Küsel
- Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Kai U Totsche
- Institute of Geosciences, Friedrich Schiller University Jena Jena, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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16
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Miettinen H, Kietäväinen R, Sohlberg E, Numminen M, Ahonen L, Itävaara M. Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland. Front Microbiol 2015; 6:1203. [PMID: 26579109 PMCID: PMC4626562 DOI: 10.3389/fmicb.2015.01203] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/15/2015] [Indexed: 02/01/2023] Open
Abstract
Pyhäsalmi mine in central Finland provides an excellent opportunity to study microbial and geochemical processes in a deep subsurface crystalline rock environment through near-vertical drill holes that reach to a depth of more than two kilometers below the surface. However, microbial sampling was challenging in this high-pressure environment. Nucleic acid yields obtained were extremely low when compared to the cell counts detected (1.4 × 10(4) cells mL(-1)) in water. The water for nucleic acid analysis went through high decompression (60-130 bar) during sampling, whereas water samples for detection of cell counts by microscopy could be collected with slow decompression. No clear cells could be identified in water that went through high decompression. The high-pressure decompression may have damaged part of the cells and the nucleic acids escaped through the filter. The microbial diversity was analyzed from two drill holes by pyrosequencing amplicons of the bacterial and archaeal 16S rRNA genes and from the fungal ITS regions from both DNA and RNA fractions. The identified prokaryotic diversity was low, dominated by Firmicute, Beta- and Gammaproteobacteria species that are common in deep subsurface environments. The archaeal diversity consisted mainly of Methanobacteriales. Ascomycota dominated the fungal diversity and fungi were discovered to be active and to produce ribosomes in the deep oligotrophic biosphere. The deep fluids from the Pyhäsalmi mine shared several features with other deep Precambrian continental subsurface environments including saline, Ca-dominated water and stable isotope compositions positioning left from the meteoric water line. The dissolved gas phase was dominated by nitrogen but the gas composition clearly differed from that of atmospheric air. Despite carbon-poor conditions indicated by the lack of carbon-rich fracture fillings and only minor amounts of dissolved carbon detected in formation waters, some methane was found in the drill holes. No dramatic differences in gas compositions were observed between different gas sampling methods tested. For simple characterization of gas composition the most convenient way to collect samples is from free flowing fluid. However, compared to a pressurized method a relative decrease in the least soluble gases may appear.
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Affiliation(s)
- Hanna Miettinen
- Valtion Teknillinen Tutkimuskeskus Technical Research Centre of Finland Ltd.Espoo, Finland
| | | | - Elina Sohlberg
- Valtion Teknillinen Tutkimuskeskus Technical Research Centre of Finland Ltd.Espoo, Finland
| | - Mikko Numminen
- Pyhäsalmi Mine Oy, First Quantum Minerals Ltd.Pyhäsalmi, Finland
| | | | - Merja Itävaara
- Valtion Teknillinen Tutkimuskeskus Technical Research Centre of Finland Ltd.Espoo, Finland
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Kietäväinen R, Purkamo L. The origin, source, and cycling of methane in deep crystalline rock biosphere. Front Microbiol 2015; 6:725. [PMID: 26236303 PMCID: PMC4505394 DOI: 10.3389/fmicb.2015.00725] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/02/2015] [Indexed: 11/13/2022] Open
Abstract
The emerging interest in using stable bedrock formations for industrial purposes, e.g., nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical, and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source, and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites.
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Affiliation(s)
| | - Lotta Purkamo
- VTT Technical Research Centre of Finland Espoo, Finland
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Sohlberg E, Bomberg M, Miettinen H, Nyyssönen M, Salavirta H, Vikman M, Itävaara M. Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland. Front Microbiol 2015; 6:573. [PMID: 26106376 PMCID: PMC4460562 DOI: 10.3389/fmicb.2015.00573] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/25/2015] [Indexed: 11/23/2022] Open
Abstract
The diversity and functional role of fungi, one of the ecologically most important groups of eukaryotic microorganisms, remains largely unknown in deep biosphere environments. In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths. Results showed that fungi were present in fracture zones at all depths and fungal diversity was higher than expected. Most of the observed fungal sequences belonged to the phylum Ascomycota. Phyla Basidiomycota and Chytridiomycota were only represented as a minor part of the fungal community. Dominating fungal classes in the deep bedrock aquifers were Sordariomycetes, Eurotiomycetes, and Dothideomycetes from the Ascomycota phylum and classes Microbotryomycetes and Tremellomycetes from the Basidiomycota phylum, which are the most frequently detected fungal taxa reported also from deep sea environments. In addition some fungal sequences represented potentially novel fungal species. Active fungi were detected in most of the fracture zones, which proves that fungi are able to maintain cellular activity in these oligotrophic conditions. Possible roles of fungi and their origin in deep bedrock groundwater can only be speculated in the light of current knowledge but some species may be specifically adapted to deep subsurface environment and may play important roles in the utilization and recycling of nutrients and thus sustaining the deep subsurface microbial community.
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Bengtson S, Ivarsson M, Astolfo A, Belivanova V, Broman C, Marone F, Stampanoni M. Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts. GEOBIOLOGY 2014; 12:489-96. [PMID: 25214186 DOI: 10.1111/gbi.12100] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 08/13/2014] [Indexed: 05/26/2023]
Abstract
The deep biosphere of the subseafloor crust is believed to contain a significant part of Earth's biomass, but because of the difficulties of directly observing the living organisms, its composition and ecology are poorly known. We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). Fungal hyphae provide the framework on which prokaryote-like organisms are suspended like cobwebs and iron-oxidizing bacteria form microstromatolites (Frutexites). The spatial inter-relationships show that the organisms were living at the same time in an integrated fashion, suggesting symbiotic interdependence. The community is contemporaneous with secondary mineralizations of calcite partly filling the cavities. The fungal hyphae frequently extend into the calcite, indicating that they were able to bore into the substrate through mineral dissolution. A symbiotic relationship with chemoautotrophs, as inferred for the observed consortium, may be a pre-requisite for the eukaryotic colonization of crustal rocks. Fossils thus open a window to the extant as well as the ancient deep biosphere.
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Affiliation(s)
- S Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm, Sweden
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Epidemiology of Rhodotorula: an emerging pathogen. Interdiscip Perspect Infect Dis 2012; 2012:465717. [PMID: 23091485 PMCID: PMC3469092 DOI: 10.1155/2012/465717] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/07/2012] [Indexed: 11/17/2022] Open
Abstract
This is an updated paper focusing on the general epidemiological aspects of Rhodotorula in humans, animals, and the environment. Previously considered nonpathogenic, Rhodotorula species have emerged as opportunistic pathogens that have the ability to colonise and infect susceptible patients. Rhodotorula species are ubiquitous saprophytic yeasts that can be recovered from many environmental sources. Several authors describe the isolation of this fungus from different ecosystems, including sites with unfavourable conditions. Compared to R. mucilaginosa, R. glutinis and R. minuta are less frequently isolated from natural environments. Among the few references to the pathogenicity of Rhodotorula spp. in animals, there are several reports of an outbreak of skin infections in chickens and sea animals and lung infections and otitis in sheep and cattle. Most of the cases of infection due to Rhodotorula in humans were fungemia associated with central venous catheter (CVC) use. The most common underlying diseases included solid and haematologic malignancies in patients who were receiving corticosteroids and cytotoxic drugs, the presence of CVC, and the use of broad-spectrum antibiotics. Unlike fungemia, some of the other localised infections caused by Rhodotorula, including meningeal, skin, ocular, peritoneal, and prosthetic joint infections, are not necessarily linked to the use of CVCs or immunosuppression.
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Smith RJ, Jeffries TC, Roudnew B, Fitch AJ, Seymour JR, Delpin MW, Newton K, Brown MH, Mitchell JG. Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems. Environ Microbiol 2011; 14:240-53. [DOI: 10.1111/j.1462-2920.2011.02614.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Borgonie G, García-Moyano A, Litthauer D, Bert W, Bester A, van Heerden E, Möller C, Erasmus M, Onstott TC. Nematoda from the terrestrial deep subsurface of South Africa. Nature 2011; 474:79-82. [DOI: 10.1038/nature09974] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 03/01/2011] [Indexed: 11/09/2022]
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Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate. Appl Environ Microbiol 2008; 74:3959-68. [PMID: 18469120 DOI: 10.1128/aem.02820-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sediment-associated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of the Basidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellate Heteromita globosa (Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 10(2) to 10(3) cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.
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Essén SA, Johnsson A, Bylund D, Pedersen K, Lundström US. Siderophore production by Pseudomonas stutzeri under aerobic and anaerobic conditions. Appl Environ Microbiol 2007; 73:5857-64. [PMID: 17675442 PMCID: PMC2074896 DOI: 10.1128/aem.00072-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The siderophore production of the facultative anaerobe Pseudomonas stutzeri, strain CCUG 36651, grown under both aerobic and anaerobic conditions, was investigated by liquid chromatography and mass spectrometry. The bacterial strain has been isolated at a 626-m depth at the Aspö Hard Rock Laboratory, where experiments concerning the geological disposal of nuclear waste are performed. In bacterial culture extracts, the iron in the siderophore complexes was replaced by gallium to facilitate siderophore identification by mass spectrometry. P. stutzeri was shown to produce ferrioxamine E (nocardamine) as the main siderophore together with ferrioxamine G and two cyclic ferrioxamines having molecular masses 14 and 28 atomic mass units lower than that of ferrioxamine E, suggested to be ferrioxamine D(2) and ferrioxamine X(1), respectively. In contrast, no siderophores were observed from anaerobically grown P. stutzeri. None of the siderophores produced by aerobically grown P. stutzeri were found in anaerobic natural water samples from the Aspö Hard Rock Laboratory.
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Affiliation(s)
- Sofia A Essén
- Department of Natural Sciences, Mid Sweden University, SE-851 70 Sundsvall, Sweden
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