| 1. |
- Lopez-Fernandez, Margarita, et al.
(författare)
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Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers
- 2018
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The continental deep biosphere is suggested to contain a substantial fraction of the earth’s total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the Äspö Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a “modern marine (MM)” signature, (ii) a “thoroughly mixed (TM)” water containing groundwaters of several origins, and (iii) deep “old saline (OS)” waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by “geogases” such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.
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| 2. |
- Lopez-Fernandez, Margarita, et al.
(författare)
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Effect of U(VI) aqueous speciation on the binding of uranium by the cell surface of Rhodotorula mucilaginosa, a natural yeast isolate from bentonites
- 2018
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Ingår i: Chemosphere. - : Elsevier. - 0045-6535 .- 1879-1298. ; 199, s. 351-360
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Tidskriftsartikel (refereegranskat)abstract
- This study presents the effect of aqueous uranium speciation (U-hydroxides and U-hydroxo-carbonates) on the interaction of this radionuclide with the cells of the yeast Rhodotorula mucigilanosa BII-R8. This strain was isolated from Spanish bentonites considered as reference materials for the engineered barrier components of the future deep geological repository of radioactive waste. X-ray absorption and infrared spectroscopy showed that the aqueous uranium speciation has no effect on the uranium binding process by this yeast strain. The cells bind mobile uranium species (U-hydroxides and U-hydroxo-carbonates) from solution via a time-dependent process initiated by the adsorption of uranium species to carboxyl groups. This leads to the subsequent involvement of organic phosphate groups forming uranium complexes with a local coordination similar to that of the uranyl mineral phase meta-autunite. Scanning transmission electron microscopy with high angle annular dark field analysis showed uranium accumulations at the cell surface associated with phosphorus containing ligands. Moreover, the effect of uranium mobile species on the cell viability and metabolic activity was examined by means of flow cytometry techniques, revealing that the cell metabolism is more affected by higher concentrations of uranium than the cell viability. The results obtained in this work provide new insights on the interaction of uranium with bentonite natural yeast from genus Rhodotorula under deep geological repository relevant conditions. (C) 2018 The Authors. Published by Elsevier Ltd.
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| 3. |
- Lopez-Fernandez, Margarita, et al.
(författare)
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Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling
- 2018
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 94:8
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Tidskriftsartikel (refereegranskat)abstract
- The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligo trophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modem marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligo trophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoauto trophic deep biosphere.
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| 4. |
- Lopez-Fernandez, Margarita, et al.
(författare)
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Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
- 2018
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Ingår i: mBio. - : American Society of Microbiology. - 2161-2129 .- 2150-7511. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Aspo Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as "modern marine," and an "old saline" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available. IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Aspo Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbonfed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 165 rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.
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| 5. |
- Lopez-Fernandez, Margarita, et al.
(författare)
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Microbial community changes induced by uranyl nitrate in bentonite clay microcosms
- 2018
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Ingår i: Applied Clay Science. - : Elsevier. - 0169-1317 .- 1872-9053. ; 160, s. 206-216
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Tidskriftsartikel (refereegranskat)abstract
- Deep geological repository (DGR) is one of the internationally accepted options to dispose radioactive wastes. Bentonite formations from Almeria, Spain, were selected as reference material for artificial barriers for the future Spanish repository. However, the safety of this long-term disposal could be compromised not only by physicochemical factors but also by microbial processes. The highly radioactive waste must be safely stored at least for 100,000 years for the radioactivity to decrease to similar levels to those of natural uranium. To simulate a scenario where the mobilization of radionuclides from the repository to the host formations may occur, long-term microcosms were studied. After being exposed to uranyl nitrate for 5 months, the response of the bentonite microbial community to the addition of this radionuclide was evaluated. High throughput 16S rRNA gene sequencing revealed that the structure of the microbial community after the uranyl nitrate treatment differs to that of the control microcosms. The microbial diversity was dominated by Firmicutes and Proteobacteria. Moreover, after the uranyl nitrate treatment OTUs annotated as Paracoccus and Bacillus were highly enriched. The mineralogy of bentonites was not affected by the uranyl nitrate treatment as was demonstrated by X-ray diffraction analysis. In addition, the study of uranium-bacteria interaction revealed the ability of isolates to biomineralize uranium as uranium phosphate mineral phases. Thus, the changes induced by the release of uranium in the microbial population may also affect the mobility of this radionuclide, making it less mobile and therefore less harmful for this environment.
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| 6. |
- Ni, Gaofeng, et al.
(författare)
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Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells
- 2018
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the 'cyanate' degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.
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