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Christel, S., Yu, C., Wu, X., Josefsson, S., Lillhonga, T., Högfors-Rönnholm, E., . . . Dopson, M. (2019). Comparison of Boreal Acid Sulfate Soil Microbial Communities in Oxidative and Reductive Environments [Letter to the editor]. Research in Microbiology
Open this publication in new window or tab >>Comparison of Boreal Acid Sulfate Soil Microbial Communities in Oxidative and Reductive Environments
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2019 (English)In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123Article in journal, Letter (Refereed) In press
Abstract [en]

Due to land uplift after the last ice age, previously stable Baltic Sea sulfidic sediments are becoming dry land. When these sediments are drained, the sulfide minerals are exposed to air and can release large amounts of metals and acid into the environment. This can cause severe ecological damage such as fish kills in rivers feeding the northern Baltic Sea. In this study, five sites were investigated for the occurrence of acid sulfate soils and their geochemistry and microbiology was identified. The pH and soil chemistry identified three of the areas as having classical acid sulfate soil characteristics and culture independent identification of 16S rRNA genes identified populations related to acidophilic bacteria capable of catalyzing sulfidic mineral dissolution, including species likely adapted to low temperature. These results were compared to an acid sulfate soil area that had been flooded for ten years and showed that the previously oxidized sulfidic materials had an increased pH compared to the unremediated oxidizied layers. In addition, the microbiology of the flooded soil had changed such that alkalinity producing ferric and sulfate reducing reactions had likely occurred. This suggested that flooding of acid sulfate soils mitigates their environmental impact.

Keywords
sulfide mineral; metal; sulfur; 16S rRNA gene; mitigation; wetland
National Category
Microbiology Earth and Related Environmental Sciences
Research subject
Natural Science, Environmental Science
Identifiers
urn:nbn:se:lnu:diva-77664 (URN)10.1016/j.resmic.2019.06.002 (DOI)
Available from: 2018-09-10 Created: 2018-09-10 Last updated: 2019-07-04
Buetti-Dinh, A., Galli, V., Bellenberg, S., Ilie, O., Herold, M., Christel, S., . . . Dopson, M. (2019). Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition. Biotechnology Reports, 22, Article ID e00321.
Open this publication in new window or tab >>Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition
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2019 (English)In: Biotechnology Reports, ISSN 0156-1383, E-ISSN 2215-017X, Vol. 22, article id e00321Article in journal (Refereed) Published
Abstract [en]

Background: Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases. Methods: The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles. Results: A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts. Conclusions: Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods. © 2019 The Author

Place, publisher, year, edition, pages
Elsevier B.V., 2019
Keywords
Acidophiles, Bacterial biofilm, Biomining, Convolutional neural networks, Deep learning, Microscopy imaging, sulfide, Acidithiobacillus caldus, Article, artificial neural network, bacterium, bacterium culture, biofilm, bioleaching, epifluorescence microscopy, high throughput screening, image analysis, Leptospirillum ferriphilum, microbial colonization, microscopy, nonhuman, performance, priority journal, Sulfobacillus thermosulfidooxidans, training
Identifiers
urn:nbn:se:lnu:diva-86412 (URN)10.1016/j.btre.2019.e00321 (DOI)2-s2.0-85063054023 (Scopus ID)
Note

Export Date: 22 May 2019; Article

Available from: 2019-07-11 Created: 2019-07-11 Last updated: 2019-07-11
Esparza, M., Jedlicki, E., González, C., Dopson, M. & Holmes, D. (2019). Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Frontiers in Microbiology, 10, 1-15, Article ID 603.
Open this publication in new window or tab >>Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans
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2019 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, p. 1-15, article id 603Article in journal (Refereed) Published
Abstract [en]

This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3-), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1 -5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-81537 (URN)10.3389/fmicb.2019.00603 (DOI)000463397000001 ()
Available from: 2019-04-01 Created: 2019-04-01 Last updated: 2019-04-18Bibliographically approved
Osorio, H., Mettert, E., Kiley, P., Dopson, M., Jedlicki, E. & Holmes, D. S. (2019). Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Frontiers in Microbiology, 10, 1-14, Article ID 1642.
Open this publication in new window or tab >>Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans
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2019 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, p. 1-14, article id 1642Article in journal (Refereed) Published
Abstract [en]

The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S](2+) iron-sulfur cluster. Under O-2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S](2+) center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O-2 stability could allow At. ferrooxidans to survive in environments with fluctuating O-2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
fumarate nitrate reductase, anaerobic regulation, transcriptional regulation, DNA binding, iron-sulfur cluster, biomining, microbial ecology
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-87057 (URN)10.3389/fmicb.2019.01642 (DOI)000476728500001 ()
Available from: 2019-08-01 Created: 2019-08-01 Last updated: 2019-08-01Bibliographically approved
Yu, C., Drake, H., Lopez-Fernandez, M., Whitehouse, M., Dopson, M. & Åström, M. E. (2019). Micro-scale isotopic variability of low-temperature pyrite in fractured crystalline bedrock ― A large Fe isotope fractionation between Fe(II)aq/pyrite and absence of Fe-S isotope co-variation [Letter to the editor]. Chemical Geology, 522, 192-207
Open this publication in new window or tab >>Micro-scale isotopic variability of low-temperature pyrite in fractured crystalline bedrock ― A large Fe isotope fractionation between Fe(II)aq/pyrite and absence of Fe-S isotope co-variation
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2019 (English)In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 522, p. 192-207Article in journal, Letter (Refereed) In press
Abstract [en]

This study assessed Fe-isotope ratio (56Fe/54Fe, expressed as δ56Fe relative to the IRMM-014 standard) variability and controls in pyrite that has among the largest reported S-isotope variability (maximum δ34S: 140‰). The pyrite occurs as fine-grained secondary crystals in fractures throughout the upper kilometer of granitoids of the Baltic Shield, and was analyzed here for δ56Fe by in situ secondary ion mass spectrometry (SIMS). Part of these pyrite crystals were picked from borehole instrumentation at depths of >400 m below sea level (m.b.s.l.), and thus are modern (known to have formed within 17 years) and can be compared with the δ56Fe of the source dissolved ferrous iron. The δ56Fe values of the modern pyrite crystals (−1.81‰ to +2.29‰) varied to a much greater extent than those of the groundwaters from which they formed (−0.48‰ to +0.13‰), providing strong field evidence for a large Fe isotope fractionation during the conversion of Fe(II)aq to FeS and ultimately to pyrite. Enrichment of 56Fe in pyrite relative to the groundwater was explained by equilibrium Fe(II)aq-FeS isotope fractionation, whereas depletion of 56Fe in pyrite relative to the groundwater was mainly the result of sulfidization of magnetite and kinetic isotopic fractionation during partial transformation of microsized FeS to pyrite. In many pyrite crystals, there is an increase in δ34S from crystal center to rim reflecting Rayleigh distillation processes (reservoir effects) caused by the development of closed-system conditions in the micro-environment near the growing crystals. A corresponding center-to-rim feature was not observed for the δ56Fe values. It is therefore unlikely that the groundwater near the growing pyrite crystals became progressively enriched in the heavy Fe isotope, in contrast to what has been found for the sulfur in sulfate. Other pyrite crystals formed following bacterial sulfate reduction in the time period of mid-Mesozoicum to Quaternary, had an almost identical Fe-isotope variability (total range: −1.50‰ to +2.76‰), frequency-distribution pattern, and relationship with δ34S as the recent pyrite formed on the borehole instrumentation. These features suggest that fundamental processes are operating and governing the Fe-isotope composition of pyrite crystals formed in fractured crystalline bedrock over large time scales.

Keywords
Pyrite, Iron isotopes, Equilibrium Fe-isotope fractionation, Magnetite sulfidization, Partial pyritization, Fractured crystalline bedrock
National Category
Earth and Related Environmental Sciences
Research subject
Natural Science, Environmental Science
Identifiers
urn:nbn:se:lnu:diva-84618 (URN)10.1016/j.chemgeo.2019.05.026 (DOI)
Available from: 2019-06-05 Created: 2019-06-05 Last updated: 2019-06-05
Broman, E., Li, L., Fridlund, J., Svensson, F., Legrand, C. & Dopson, M. (2019). Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure. Microbial Ecology (2), 288-303
Open this publication in new window or tab >>Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure
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2019 (English)In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, no 2, p. 288-303Article in journal (Refereed) Published
Abstract [en]

Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2 + NO3 in the sediment surface (0–1 cm) and iron in the underlying layer (1–2 cm). In addition, an increase in NO2 + NO3 was observed in the overlying benthic water in all amended and control incubations. The combination of NO2 + NO3 diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.

Place, publisher, year, edition, pages
Springer, 2019
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-76944 (URN)10.1007/s00248-018-1229-6 (DOI)000460479100002 ()
Available from: 2018-07-18 Created: 2018-07-18 Last updated: 2019-03-29Bibliographically approved
Ni, G., Simone, D., Palma, D., Broman, E., Wu, X., Turner, S. & Dopson, M. (2018). A novel inorganic sulfur compound metabolizing Ferroplasma-like population is suggested to mediate extracellular electron transfer. Frontiers in Microbiology, Article ID 2945.
Open this publication in new window or tab >>A novel inorganic sulfur compound metabolizing Ferroplasma-like population is suggested to mediate extracellular electron transfer
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2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, article id 2945Article in journal (Refereed) Published
Abstract [en]

Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbemineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-likepopulation had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylylsulfate released electrons and the extracellular electrontransfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganicsulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-78860 (URN)10.3389/fmicb.2018.02945 (DOI)000452119800001 ()
Available from: 2018-11-16 Created: 2018-11-16 Last updated: 2019-01-18Bibliographically approved
Bellenberg, S., Buetti-Dinh, A., Galli, V., Ilie, O., Herold, M., Christel, S., . . . Dopson, M. (2018). Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms. Applied and Environmental Microbiology, 84(20), Article ID UNSP e01835-18.
Open this publication in new window or tab >>Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms
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2018 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 84, no 20, article id UNSP e01835-18Article in journal (Refereed) Published
Abstract [en]

Industrial biomining processes are currently focused on metal sulfides and their dissolution, which is catalyzed by acidophilic iron(II)- and/or sulfur-oxidizing microorganisms. Cell attachment on metal sulfides is important for this process. Biofilm formation is necessary for seeding and persistence of the active microbial community in industrial biomining heaps and tank reactors, and it enhances metal release. In this study, we used a method for direct quantification of the mineral-attached cell population on pyrite or chalcopyrite particles in bioleaching experiments by coupling high-throughput, automated epifluorescence microscopy imaging of mineral particles with algorithms for image analysis and cell quantification, thus avoiding human bias in cell counting. The method was validated by quantifying cell attachment on pyrite and chalcopyrite surfaces with axenic cultures of Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. The method confirmed the high affinity of L. ferriphilum cells to colonize pyrite and chalcopyrite surfaces and indicated that biofilm dispersal occurs in mature pyrite batch cultures of this species. Deep neural networks were also applied to analyze biofilms of different microbial consortia. Recent analysis of the L. ferriphilum genome revealed the presence of a diffusible soluble factor (DSF) family quorum sensing system. The respective signal compounds are known as biofilm dispersal agents. Biofilm dispersal was confirmed to occur in batch cultures of L. ferriphilum and S. thermosulfidooxidans upon the addition of DSF family signal compounds. IMPORTANCE The presented method for the assessment of mineral colonization allows accurate relative comparisons of the microbial colonization of metal sulfide concentrate particles in a time-resolved manner. Quantitative assessment of the mineral colonization development is important for the compilation of improved mathematical models for metal sulfide dissolution. In addition, deep-learning algorithms proved that axenic or mixed cultures of the three species exhibited characteristic biofilm patterns and predicted the biofilm species composition. The method may be extended to the assessment of microbial colonization on other solid particles and may serve in the optimization of bioleaching processes in laboratory scale experiments with industrially relevant metal sulfide concentrates. Furthermore, the method was used to demonstrate that DSF quorum sensing signals directly influence colonization and dissolution of metal sulfides by mineral-oxidizing bacteria, such as L. ferriphilum and S. thermosulfidooxidans.

Place, publisher, year, edition, pages
American society for microbiology, 2018
Keywords
bioleaching, biofilm formation, biofilm dispersal, image analysis, microbe-mineral interaction, quorum sensing, diffusible soluble factor, biofilms, fluorescent image analysis, microbe-mineral interactions
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-78464 (URN)10.1128/AEM.01835-18 (DOI)000446206900020 ()30076195 (PubMedID)
Available from: 2018-10-24 Created: 2018-10-24 Last updated: 2019-07-09Bibliographically approved
Högfors-Rönnholm, E., Christel, S., Dalhem, K., Lillhonga, T., Engblom, S., Österholm, P. & Dopson, M. (2018). Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils. Science of the Total Environment, 625, 39-49
Open this publication in new window or tab >>Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils
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2018 (English)In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 625, p. 39-49Article in journal (Refereed) Published
Abstract [en]

Naturally occurring sulfide rich deposits are common along the northern Baltic Sea coast thatwhen exposed to air, release large amounts of acid and metals into receiving water bodies. This causes severe environmental implications for agriculture, forestry, and building of infrastructure. In this study, we investigated the efficiency of ultrafine-grained calcium carbonate and peat (both separately and in combination) to mitigate acid and metal release. The experiments were carried out aerobically that mimicked summer conditions when the groundwater level is low and acid sulfate soils are exposed to oxygen, and anaerobically that is similar to autumn to spring conditions. The ultrafine-grained calcium carbonate dissipated well in the soil and its effect alone and when mixed with peat raised the pH and reduced pyrite dissolution while peat alone was similar to the controls and did not halt metal and acid release. High throughput 16S rRNA gene sequencing identified populations most similar to characterized acidophiles in the control and peat treated incubations while the acidophilic like populations were altered in the calcium carbonate alone and calcium carbonate plus peat treated acid sulfate soils. Coupled with the geochemistry data, it was suggested that the acidophiles were inactivated by the high pH in the presence of calcium carbonate but catalyzed pyrite dissolution in the controls and peat incubations. In conclusion, the anaerobic conditions during winter would likely be sufficient to mitigate acid production and metal release from acid sulfate soils and in the summer, treatment with calcium carbonate was the best mitigation method. (c) 2017 Elsevier B.V. All rights reserved.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Mitigation, Pyrite, Iron, 16S rRNA, Compositional PCA
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-71751 (URN)10.1016/j.scitotenv.2017.12.287 (DOI)000426356600005 ()29287211 (PubMedID)
Available from: 2018-03-22 Created: 2018-03-22 Last updated: 2018-03-22Bibliographically approved
Lopez-Fernandez, M., Åström, M. E., Bertilsson, S. & Dopson, M. (2018). Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers. Frontiers in Microbiology, 9, Article ID 2880.
Open this publication in new window or tab >>Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers
2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 2880Article in journal (Refereed) Published
Abstract [en]

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 Aspo 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.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
16S rRNA gene, amplicon sequencing, deep subsurface, groundwaters, chemistry, microbial diversity
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-79095 (URN)10.3389/fmicb.2018.02880 (DOI)000451406100001 ()
Funder
Swedish Research Council, 2014-4398; 2012-3892; 2017-04422
Available from: 2018-12-06 Created: 2018-12-06 Last updated: 2019-02-27Bibliographically approved
Projects
Syntrofi och symbios för överlevnad och tillväxt i den djupa terrestra biosfären [202100-6271]; Linnaeus University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9622-3318

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