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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, 170(6-7), 288-295
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 1769-7123, Vol. 170, no 6-7, p. 288-295Article in journal, Letter (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2019
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)000491121700006 ()
Available from: 2018-09-10 Created: 2018-09-10 Last updated: 2019-10-31Bibliographically approved
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, 1-5, 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, p. 1-5, 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, 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
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-86412 (URN)10.1016/j.btre.2019.e00321 (DOI)2-s2.0-85063054023 (Scopus ID)
Available from: 2019-07-11 Created: 2019-07-11 Last updated: 2019-10-11Bibliographically approved
Broman, E., Asmala, E., Carstensen, J., Pinhassi, J. & Dopson, M. (2019). Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter. Frontiers in Microbiology, 10, 1-15, Article ID 2579.
Open this publication in new window or tab >>Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter
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2019 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, p. 1-15, article id 2579Article in journal (Refereed) Published
Abstract [en]

Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
16S rRNA gene, DOM, estuarial and coastal areas, DNA, water
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-90507 (URN)10.3389/fmicb.2019.02579 (DOI)000498524600001 ()31787958 (PubMedID)
Available from: 2019-12-12 Created: 2019-12-12 Last updated: 2019-12-12Bibliographically approved
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 ()2-s2.0-85068205987 (Scopus ID)
Available from: 2019-04-01 Created: 2019-04-01 Last updated: 2019-08-29Bibliographically approved
Ni, G., Harnawan, P., Seidel, L., Heijne, A. T., Sleutels, T., Buisman, C. J. N. & Dopson, M. (2019). Haloalkaliphilic microorganisms assist sulfide removal in a microbial electrolysis cell. Journal of Hazardous Materials, 363, 197-204
Open this publication in new window or tab >>Haloalkaliphilic microorganisms assist sulfide removal in a microbial electrolysis cell
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2019 (English)In: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 363, p. 197-204Article in journal (Refereed) Published
Abstract [en]

Several industrial processes produce toxic sulfide containing streams that are often scrubbed using caustic solutions. An alternative, cost effective sulfidetreatment method is bioelectrochemical sulfide removal. For the first time, a haloalkaliphilic sulfide-oxidizing microbial consortium was introduced to the anodic chamber of a microbial electrolysis cell operated at alkaline pH and with 1.0 M sodium ions. Under anode potential control, the highest sulfideremoval rate was 2.16 mM/day and chemical analysis supported that the electrical current generation was from the sulfide oxidation. Biotic operation produced a maximum current density of 3625 mA/m(2) compared to 210 mA/m2 while under abiotic operation. Furthermore, biotic electrical production was maintained for a longer period than for abiotic operation, potentially due to the passivation of the electrode by elemental sulfur during abiotic operation. The use of microorganisms reduced the energy input in this study compared to published electrochemical sulfide removal technologies. Sulfide-oxidizing populations dominated both the planktonic and electrode-attached communities with 16S rRNA gene sequences aligning within the genera Thioctikalivibrio, Thioalkaihnicrobium, and Desulfurivibrio. The dominance of the Desulfurivibrio-like population on the anode surface offered evidence for the first haloalkaliphilic bacterium able to couple electrons from sulfide oxidation to extracellular electron transfer to the anode.

Place, publisher, year, edition, pages
Elsevier, 2019
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-78859 (URN)10.1016/j.jhazmat.2018.09.049 (DOI)000449891900022 ()30308358 (PubMedID)2-s2.0-85054420208 (Scopus ID)
Note

Is included in the dissertation as a manuscript.

Available from: 2018-11-16 Created: 2018-11-16 Last updated: 2019-12-06Bibliographically 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 ()2-s2.0-85069474322 (Scopus ID)
Available from: 2019-08-01 Created: 2019-08-01 Last updated: 2019-08-29Bibliographically approved
Hogfors-Ronnholm, E., Lopez-Fernandez, M., Christel, S., Brambilla, D., Huntemann, M., Clum, A., . . . Dopson, M. (2019). Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Scientific Data, 6, 1-6, Article ID 207.
Open this publication in new window or tab >>Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
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2019 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 6, p. 1-6, article id 207Article in journal (Refereed) Published
Abstract [en]

Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-89865 (URN)10.1038/s41597-019-0222-3 (DOI)000490560100003 ()31619684 (PubMedID)
Available from: 2019-10-31 Created: 2019-10-31 Last updated: 2019-10-31Bibliographically 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. 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 (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2019
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)000480330600016 ()2-s2.0-85066994013 (Scopus ID)
Funder
Swedish Research Council, 2017-05186Swedish Research Council, 2014-4398Swedish Research Council Formas, 2017-00766
Available from: 2019-06-05 Created: 2019-06-05 Last updated: 2019-08-29Bibliographically approved
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 ()2-s2.0-85049948034 (Scopus ID)
Available from: 2018-07-18 Created: 2018-07-18 Last updated: 2019-08-29Bibliographically approved
Lopez-Fernandez, M., Broman, E., Simone, D., Bertilsson, S. & Dopson, M. (2019). Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters. mBio, 10(4), 1-6, Article ID e01470-19.
Open this publication in new window or tab >>Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
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2019 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 4, p. 1-6, article id e01470-19Article in journal (Refereed) Published
Abstract [en]

Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H-2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases." IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omits studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

Place, publisher, year, edition, pages
American Society of Microbiology, 2019
Keywords
deep biosphere, groundwaters, metatranscriptomes, protein-coding RNA, rRNA
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-88841 (URN)10.1128/mBio.01470-19 (DOI)000481617000077 ()31409677 (PubMedID)
Available from: 2019-08-29 Created: 2019-08-29 Last updated: 2019-08-29Bibliographically 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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