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Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations
Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). (Ctr Ecol & Evolut Microbial Model Syst EEMiS)
Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). (Ctr Ecol & Evolut Microbial Model Syst EEMiS)ORCID-id: 0000-0002-6887-6661
Uppsala University.
Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). (Ctr Ecol & Evolut Microbial Model Syst EEMiS)ORCID-id: 0000-0002-8779-6464
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2016 (Engelska)Ingår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 5, s. 1192-1203Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Ort, förlag, år, upplaga, sidor
2016. Vol. 10, nr 5, s. 1192-1203
Nationell ämneskategori
Mikrobiologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
URN: urn:nbn:se:lnu:diva-49416DOI: 10.1038/ismej.2015.185ISI: 000374377200016PubMedID: 26484735Scopus ID: 2-s2.0-84944910110OAI: oai:DiVA.org:lnu-49416DiVA, id: diva2:898785
Tillgänglig från: 2016-01-29 Skapad: 2016-01-29 Senast uppdaterad: 2018-10-24Bibliografiskt granskad
Ingår i avhandling
1. Structure and function of microbial communities in acid sulfate soil and the terrestrial deep biosphere
Öppna denna publikation i ny flik eller fönster >>Structure and function of microbial communities in acid sulfate soil and the terrestrial deep biosphere
2016 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

This thesis describes the use of different DNA sequencing technologies to investigate the structure and function of microbial communities in two extreme environments, boreal acid sulfate soil and the terrestrial deep biosphere.

The first of the two investigated environments was soils containing un-oxidized metal sulfides that are termed ‘potential acid sulfate soil’ (PASS) materials. If these materials are exposed to atmospheric oxygen by either natural phenomena (e.g., land uplift) or human activities (e.g., drainage) then the metal sulfides become oxidized and the PASS becomes acidic and is defined as an ‘acid sulfate soil’ (ASS). The resulting acid and metal release from metal sulfide oxidation can lead to severe environmental damage. Although acidophilic microorganisms capable of catalyzing acid and metal release have been identified from many sulfide mineral containing environments, the microbial community of boreal PASSs/ASSs remains unclear. This study investigated the physicochemical and microbial characteristics of PASSs and ASSs from the Risöfladan experimental field in Vasa, Finland. Sanger sequencing of 16S rRNA gene sequences of microorganisms present in the PASSs and ASSs were mostly assigned to acidophilic species and environmental clones previously identified from acid- and metal-contaminated environments. Enrichment cultures inoculated from the ASS demonstrated that the acidophilic microorganisms were responsible for catalyzing acid and metal release from PASSs/ASSs. Lastly, the study investigated how to mitigate metal sulfide oxidation and the concomitant formation of sulfuric acid by treating ASSs in situ with CaCO3 or Ca(OH)2 suspensions. The DNA sequencing still identified acidophilic microorganisms after the chemical treatments. However, the increased pH during and after treatment suggested that the activity of the acidophiles might be inhibited. This study was the first to identify the microbial community present in boreal PASSs/ASSs and suggested that treatment with basic compounds may inhibit microbial catalysis of metal sulfide dissolution.

The second studied environment was the deep, dark terrestrial subsurface that is suggested to be both extremely stable and highly oligotrophic. Despite the scarcity of carbon and energy sources, the deep biosphere is estimated to constitute up to 20% of the total biomass on earth and thus, represents the largest microbial ecosystem. However, due to the difficulties of accessing this environment and our inability to cultivate the indigenous microbial populations, details of the diversity and metabolism of these communities remain largely unexplored. This study was carried out at Äspö Hard Rock Laboratory, Sweden and utilized second-generation sequencing to identify the taxonomic composition and genetic potential of planktonic and biofilm populations. Community DNA sequencing of planktonic cells from three water types at varied age and depth (‘modern marine’, ‘undefined mixed’, and ‘old saline’) showed the existence of ultra-small cells capable of passing through a 0.22 μm filter that were phylogenetically distinct communities from the >0.22 μm fraction. The reduced cell size and/or genome size suggested a potential adaptation to the oligotrophic environment in the terrestrial deep biosphere. The identified planktonic communities were dominated by Proteobacteria, Candidate divisions, unclassified archaea, and unclassified bacteria. Functional analysis of the assembled genomes showed that the planktonic population from the shallow modern marine water demonstrated a predominantly anaerobic and heterotrophic lifestyle. In contrast, the deeper, old saline water was more closely aligned with the hypothesis of a hydrogen-driven deep biosphere. Metagenomic analysis of subsurface biofilms from ‘modern marine’ and ‘old saline’ water types suggested only a subset of populations were involved in initial biofilm formation. The identified biofilm populations from both water types were distinct from the planktonic community and were suggested to be dominated by hydrogen fed, chemolithoautotrophic and diazotrophic populations.

Ort, förlag, år, upplaga, sidor
Växjö: Linnaeus University Press, 2016. s. 146
Serie
Linnaeus University Dissertations ; 255/2016
Nyckelord
molecular phylogeny, acid sulfate soils, metal, acidophiles, deep biosphere, oligotrophy, biofilm formation, metagenome, binning, metabolism
Nationell ämneskategori
Ekologi
Forskningsämne
Ekologi, Mikrobiologi
Identifikatorer
urn:nbn:se:lnu:diva-52538 (URN)978-91-88357-22-9 (ISBN)
Disputation
2016-06-17, Hörsalen Fullriggaren, Landgången 4, Kalmar, 09:30 (Engelska)
Opponent
Handledare
Tillgänglig från: 2016-05-20 Skapad: 2016-05-17 Senast uppdaterad: 2018-10-24Bibliografiskt granskad

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