Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Neubeck, Anna; Sun, Li; Müller, Bettina; Ivarsson, Magnus; Hoşgörmez, Hakan; Özcan, Doğacan; Broman, Curt; Schnürer, Anna

doi:10.1128/aem.03430-16

Cited by 26 publications

(29 citation statements)

References 62 publications

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“…This heterogeneity provides a wide variety of habitats for chemolithotrophs, as there is more substrate variability in addition to temperature and pressure gradients. “Window” sections of the deepest subsurface are accessible as uplifted ophiolites ( Neubeck et al, 2017 ; Rempfert et al, 2017 ). These environments provide information on deeper geology and interactions between these and microbial communities, though the degree to which these sites are reflective of the true deep subsurface varies according to local conditions.…”

Section: Earth’s Subsurface Habitat Typesmentioning

confidence: 99%

Low Energy Subsurface Environments as Extraterrestrial Analogs

2018

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Earth’s subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth’s low energy subsurface habitats.

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Section: Earth’s Subsurface Habitat Typesmentioning

confidence: 99%

Low Energy Subsurface Environments as Extraterrestrial Analogs

2018

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“…A high relative abundance of 16S ribosomal RNA (rRNA) genes closely related to known methanogens (up to 90% of the total archaeal population) coupled with detection of all key genes involved in hydrogenotrophic methanogenesis, acetoclastic methanogenesis, and formatotrophic methanogenesis in metagenomes from the Santa Elena Ophiolite, Costa Rica, reveals the putative importance of methanogens in this and potentially other environments undergoing active serpentinization [8]. Similarly, physiological inference based on homology of 16S rRNA genes suggests that organisms capable of H 2 oxidation, CO oxidation, and CH 4 cycling inhabit a serpentinizing seep in the Zambales Ophiolite, Philippines [18], and putative H 2 and CH 4 oxidizers have similarly been identified via homology of 16S rRNA genes in a serpentinite-hosted seep at the Chimaera Ophiolite, Turkey [19]. The isotopic signature of lipid biomarkers combined with metagenomic insights suggest that HCOO − serves as a source of electrons for sulfate reducers, but not methanogens, in the LCHF [20].…”

Section: Introductionmentioning

confidence: 99%

Physiological adaptations to serpentinization in the Samail Ophiolite, Oman

et al. 2019

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Hydration of ultramafic rock during the geologic process of serpentinization can generate reduced substrates that microorganisms may use to fuel their carbon and energy metabolisms. However, serpentinizing environments also place multiple constraints on microbial life by generating highly reduced hyperalkaline waters that are limited in dissolved inorganic carbon. To better understand how microbial life persists under these conditions, we performed geochemical measurements on waters from a serpentinizing environment and subjected planktonic microbial cells to metagenomic and physiological analyses. Metabolic potential inferred from metagenomes correlated with fluid type, and genes involved in anaerobic metabolisms were enriched in hyperalkaline waters. The abundance of planktonic cells and their rates of utilization of select single-carbon compounds were lower in hyperalkaline waters than alkaline waters. However, the ratios of substrate assimilation to dissimilation were higher in hyperalkaline waters than alkaline waters, which may represent adaptation to minimize energetic and physiologic stress imposed by highly reducing, carbon-limited conditions. Consistent with this hypothesis, estimated genome sizes and average oxidation states of carbon in inferred proteomes were lower in hyperalkaline waters than in alkaline waters. These data suggest that microorganisms inhabiting serpentinized waters exhibit a unique suite of physiological adaptations that allow for their persistence under these polyextremophilic conditions.

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“…Two recent reports indicated guanidine thiocyanate (GTC) solution promotes a stability in composition and diversity of human fecal microbial analysis at room temperature form 1 day to 1 week (Nishimoto et al, 2016; Hosomi et al, 2017). Guanidine isothiocyanate denatures RNase and DNase, inhibits the growth of bacteria (Chomczynski & Sacchi, 2006; Hisada, Endoh & Kuriki, 2015), and is widely used in DNA isolation (Stearns et al, 2015; Neubeck et al, 2017) and the preservation of human stool samples. However, this compound has not been applied for analysis of the plant rhizosphere microbiome to date.…”

Section: Introductionmentioning

confidence: 99%

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis

Sun

Wang

Guo

et al. 2019

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The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results demonstrated that GTC solution may provide a reliable alternative for the preservation of rhizosphere samples in the field.

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Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Cited by 26 publications

References 62 publications

Low Energy Subsurface Environments as Extraterrestrial Analogs

Low Energy Subsurface Environments as Extraterrestrial Analogs

Physiological adaptations to serpentinization in the Samail Ophiolite, Oman

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis

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