| 1. |
- Lorenz, Henning, Dr. 1972-, et al.
(författare)
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COSC-2 – drilling the basal décollement and underlying margin of palaeocontinent Baltica in the Paleozoic Caledonide Orogen of Scandinavia
- 2022
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Ingår i: Scientific Drilling. - Göttingen : Copernicus Publications. - 1816-8957 .- 1816-3459. ; 30, s. 43-57
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Tidskriftsartikel (refereegranskat)abstract
- Abstract.The Collisional Orogeny in the Scandinavian Caledonides (COSC) scientific drilling project aims to characterise the structure and orogenic processes involved in a major collisional mountain belt by multidisciplinary geoscientific research. Located in western central Sweden, the project has drilled two fully cored deep boreholes into the bedrock of the deeply eroded Early Paleozoic Caledonide Orogen. COSC-1 (2014) drilled a subduction-related allochthon and the associated thrust zone. COSC-2 (2020, this paper) extends this section deeper through the underlying nappes (Lower Allochthon), the main Caledonian décollement, and the upper kilometre of basement rocks. COSC-2 targets include the characterisation of orogen-scale detachments, the impact of orogenesis on the basement below the detachment, and the Early Paleozoic palaeoenvironment on the outer margin of palaeocontinent Baltica. This is complemented by research on heat flow, groundwater flow, and the characterisation of the microbial community in the present hard rock environment of the relict mountain belt. COSC-2 successfully, and within budget, recovered a continuous drill core to 2276 m depth. The retrieved geological section is partially different from the expected geological section with respect to the depth to the main décollement and the expected rock types. Although the intensity of synsedimentary deformation in the rocks in the upper part of the drill core might impede the analysis of the Early Paleozoic palaeoenvironment, the superb quality of the drill core and the borehole will facilitate research on the remaining targets and beyond. Protocols for sampling in the hard rock environment and subsequent sample preservation were established for geomicrobiological research and rock mechanical testing. For the former, a sparse sample series along the entire drill core was taken, while the target of the latter was the décollement. COSC-2 was surveyed by a comprehensive post-drilling downhole logging campaign and a combined borehole/land seismic survey in autumn 2021. This paper provides an overview of the COSC-2 (International Continental Scientific Drilling Project – ICDP 5054_2_A and 5054_2_B boreholes) operations and preliminary results. It will be complemented by a detailed operational report and data publication.
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| 2. |
- Abromaitis, V., et al.
(författare)
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Effect of shear stress and carbon surface roughness on bioregeneration and performance of suspended versus attached biomass in metoprolol-loaded biological activated carbon systems
- 2017
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Ingår i: Chemical Engineering Journal. - : Elsevier. - 1385-8947 .- 1873-3212. ; 317, s. 503-511
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Tidskriftsartikel (refereegranskat)abstract
- The bioregeneration of activated carbon (AC) in biological activated carbon (BAC) systems is limited by sorption-desorption hysteresis and transport between the adsorbent and biomass. In this study, we investigated these limitations and whether a biofilm covering the AC surface is required. Consequently, BAC reactors were operated at different shear stress and AC surface smoothness, since this may affect biofilm formation. The experiments were carried out in BAC and blank reactors treating synthetic wastewater containing the pharmaceutical metoprolol. After start-up, all reactors removed metoprolol completely; however, after 840 h the removal dropped due to saturation of the AC. In the blank reactors, the removal dropped to 0% while in the BAC reactors removal recovered to >99%, due to increased biological activity. During the initial phase, the metoprolol was adsorbed, rather than biodegraded. At the end, the AC from the BAC reactors had higher pore volume and sorption capacity than from the blank reactors, showing that the AC had been bioregenerated. At high shear (G = 25 s(-1)), the rough AC granules (R-a = 13 mu m) were covered with a 50-400 gm thick biofilm and the total protein content of the biofilm was 2.6 mg/gAC, while at lower shear (G = 8.8 s(-1)) the rough AC granules were only partly covered. The biofilm formation at lower shear (G = 8.8 s(-1)) on smooth AC granules (R-a = 1.6 mu m) was negligible. However, due to the presence of suspended biomass the reactor performance or bioregeneration were not reduced. This showed that direct contact between the AC and biomass was not essential in mixed BAC systems. The microbial analyses of the suspended biomass and the biofilm on AC surface indicated that metoprolol was mainly biodegraded in suspension. (C) 2017 Elsevier B.V. All rights reserved.
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| 3. |
- Barragan, Carlos Eduardo, et al.
(författare)
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Isolation of Arsenic Resistant and Arsenopyrite Oxidizing Acidithiobacillus Species from pH Neutral Colombian Mine Effluents
- 2020
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Ingår i: Geomicrobiology Journal. - : Taylor & Francis Group. - 0149-0451 .- 1521-0529. ; 37:7, s. 682-689
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Tidskriftsartikel (refereegranskat)abstract
- Inactive mines provide a great source of bacterial diversity for studying acidophilic communities and their biotechnological applications, but prospecting of these anthropogenic environments in Colombia has been limited. Conventional microbiological methods were used to isolate acidophilic bacterial strains from effluents emanating from the Colombian gold mine 'El Zancudo' (Titiribi, Antioquia). Despite the drainage waters having circumneutral pH, all of the isolated strains were phylogenetically related to the extreme acidophile Acidithiobacillus genus. However, based upon 16S rRNA gene sequences the mesophilic sulfur-oxidizing indigenous strains could not be assigned to a species. Pure cultures were selected by screening in medium with soluble inorganic arsenic (III) and their mineral-oxidative activity was evaluated at 30 degrees C in Erlenmeyer flasks with arsenopyrite ore under rotary shaking conditions. The indigenous strains were able to catalyze arsenopyrite oxidation in a mixed culture with a pulp density of 10%, maintaining their growth in the presence of >80 mM leached arsenic. This research provides information regarding the isolation of arsenic resistant bacterial communities from neutral effluents from El Zancudo mine and the possibility of the isolated strains to be useful in the biooxidation pretreatment of refractory gold-bearing arsenopyrite ores and concentrates.
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| 4. |
- Barragan, Carlos Eduardo, et al.
(författare)
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RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite
- 2021
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Ingår i: Extremophiles. - : Springer. - 1431-0651 .- 1433-4909. ; 25, s. 143-158
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Tidskriftsartikel (refereegranskat)abstract
- Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.
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| 5. |
- Bellenberg, Sören, et al.
(författare)
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Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms
- 2018
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Ingår i: Applied and Environmental Microbiology. - : American society for microbiology. - 0099-2240 .- 1098-5336. ; 84:20
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Bellenberg, Sören, et al.
(författare)
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Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Bioleaching of metal sulfide ores involves acidophilic microbes that catalyze the chemical dissolution of the metal sulfide bond that is enhanced by attached and planktonic cell mediated oxidation of iron(II)-ions and inorganic sulfur compounds. Leptospirillum spp. often predominate in sulfide mineral-containing environments, including bioheaps for copper recovery from chalcopyrite, as they are effective primary mineral colonizers and oxidize iron(II)-ions efficiently. In this study, we demonstrated a functional diffusible signal factor interspecies quorum sensing signaling mechanism in Leptospirillum ferriphilum and Leptospirillum ferrooxidans that produces (Z)-11-methyl-2-dodecenoic acid when grown with pyrite as energy source. In addition, pure diffusible signal factor and extracts from supernatants of pyrite grown Leptospirillum spp. inhibited biological iron oxidation in various species, and that pyrite grown Leptospirillum cells were less affected than iron grown cells to self inhibition. Finally, transcriptional analyses for the inhibition of iron-grown L. ferriphilum cells due to diffusible signal factor was compared with the response to exposure of cells to N- acyl-homoserine-lactone type quorum sensing signal compounds. The data suggested that Leptospirillum spp. diffusible signal factor production is a strategy for niche protection and defense against other microbes and it is proposed that this may be exploited to inhibit unwanted acidophile species.
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| 7. |
- Bellenberg, Sören, et al.
(författare)
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Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery
- 2021
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Vanadium - a transition metal - is found in the ferrous-ferric mineral, magnetite. Vanadium has many industrial applications, such as in the production of high-strength low-alloy steels, and its increasing global industrial consumption requires new primary sources. Bioleaching is a biotechnological process for microbially catalyzed dissolution of minerals and wastes for metal recovery such as biogenic organic acid dissolution of bauxite residues. In this study, 16S rRNA gene amplicon sequencing was used to identify microorganisms in Nordic mining environments influenced by vanadium containing sources. These data identified gene sequences that aligned to the Gluconobacter genus that produce gluconic acid. Several strategies for magnetite dissolution were tested including oxidative and reductive bioleaching by acidophilic microbes along with dissimilatory reduction by Shewanella spp. that did not yield significant metal release. In addition, abiotic dissolution of the magnetite was tested with gluconic and oxalic acids, and yielded 3.99 and 81.31% iron release as a proxy for vanadium release, respectively. As a proof of principle, leaching via gluconic acid production by Gluconobacter oxydans resulted in a maximum yield of 9.8% of the available iron and 3.3% of the vanadium. Addition of an increased concentration of glucose as electron donor for gluconic acid production alone, or in combination with calcium carbonate to buffer the pH, increased the rate of iron dissolution and final vanadium recoveries. These data suggest a strategy of biogenic organic acid mediated vanadium recovery from magnetite and point the way to testing additional microbial species to optimize the recovery.
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| 8. |
- Berggren, Hanna
(författare)
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Consequences of Environmental Variation for Fish and Their Skin Associated Microbial Communities
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Environmental conditions that vary in space and time influence the distribution, abundance, diversity and evolution of individuals, populations, species and communities. This thesis explores how environmental variation affects diversity at different levels of biological organization, and across a wide range of spatiotemporal scales, by studying fish and their associated microbiomes. The specific aims were to investigate i) effects of coarse- and fine-scale environmental variation for the performance of fish populations and individuals, and ii) ecological drivers impacting the structure and dynamics of microbial communities associated with fish hosts.For the first aim, I studied effects of environmental variation both within and between local habitats, by comparing populations of spawning migrating pike and monitor sun-basking behaviour of carp individuals. Results revealed that natal spawning site fidelity can promote evolution of local adaptations and population differentiation on relatively fine spatial scales in relation to the species dispersal capacity. I also demonstrated that fish can actively thermo-regulate and attain body temperatures in excess of the surrounding water by sun-basking, and that this translates into faster growth. Homing and sun-basking behaviour thus are important drivers of phenotypic diversity among and within populations and can also - as it turned out - influence the microbial communities associated with fish skin.For the second aim, I used a mixture of observational and experimental approaches to characterize and identify sources of variation in microbial communities associated with fish skin of perch, roach and carp. An important finding was that fish skin microbiomes are highly dynamic biodiversity hotspots. Results further suggested that variation in the assembly, composition, spatial structure, and temporal shifts of these microbiomes are influenced by stochastic events in combination with ecological filtering imposed by environment and host phenotype, most notably behaviour. A key conclusion that emerges from this thesis is that diversity at one level of biological organisation seems to support and increase diversity at a higher hierarchical level of organisation. My thesis thus adds to the knowledge, and contribute new understanding and insight into, how environmental heterogeneity and the complex interplay between different species and hierarchical levels generate and maintain biodiversity.
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| 9. |
- Broman, Elias, 1985-, et al.
(författare)
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Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments
- 2017
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society Publishing. - 0962-8452 .- 1471-2954. ; 284:1864
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Tidskriftsartikel (refereegranskat)abstract
- An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.
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| 10. |
- Broman, Elias, 1985-, et al.
(författare)
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Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 10, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 11. |
- Broman, Elias, 1985-, et al.
(författare)
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Eutrophication induced early stage hypoxic ‘dead zone’ sediment releases nitrate and stimulates growth of archaea
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In the Baltic Sea, two annual algal blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water column, 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, referred to as ‘dead zones’). These zones prevent the establishment of benthic communities and result in fish mortality. The aim of the study was to determine how the sediment chemistry and microbial community composition changed due to phytoplankton biomass degradation by adding cyanobacterial or diatom biomass to sediment cores from an all-year round oxic coastal Baltic Sea bay. After biomass addition, some typical anaerobic microbial processes were observed 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 water phase in all incubations (including controls without addition of phytoplankton biomass). The combination of NO2-+NO3- diffusion from the sediment plus nitrification of the available NH4+ could not account for this increase. Potential nitrogen sources that could at least partially explain this discrepancy included microbial nitrogen fixation and cycling of nitrogen compounds from deeper layers of the sediment. Based on 16S rRNA gene sequences, the addition of diatom biomass caused minor changes in the relative abundance of microbial community members while cyanobacterial biomass caused a large increase in ferrous iron-oxidizing archaea. Considering that OTUs sharing lineages with acidophilic microorganisms were present, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling in oxic sediments and early microbial community changes in the sediment surface due to sinking phytoplankton before major hypoxia events occur. The release of nitrate into the water could potentially enhance algal blooms and facilitate the development of ‘dead zones’.
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| 12. |
- Broman, Elias, 1985-, et al.
(författare)
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Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor
- 2017
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Ingår i: Biodegradation. - : Springer. - 0923-9820 .- 1572-9729. ; 28:4, s. 287-301
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Tidskriftsartikel (refereegranskat)abstract
- Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH < 3) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8 °C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.
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| 13. |
- Broman, Elias, 1985-, et al.
(författare)
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Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.
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| 14. |
- Broman, Elias, 1985-, et al.
(författare)
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Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.
- 2017
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5:1, s. 96-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.RESULTS: Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.CONCLUSIONS: These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.
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| 15. |
- Broman, Elias, 1985-, et al.
(författare)
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Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure
- 2019
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Ingår i: Microbial Ecology. - : Springer. - 0095-3628 .- 1432-184X. ; 77:2, s. 288-303
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 16. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition
- 2019
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Ingår i: Biotechnology Reports. - : Elsevier. - 2215-017X. ; 22, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- 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
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| 17. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
- 2020
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Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 21:1, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. Methods: We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. Results: The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. Conclusions: The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.
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| 18. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Systems biology of acidophile biofilms for efficient metal extraction
- 2020
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 7:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput "omics" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.
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| 19. |
- Christel, Stephan, et al.
(författare)
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Comparison of Boreal Acid Sulfate Soil Microbial Communities in Oxidative and Reductive Environments
- 2019
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Ingår i: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 170:6-7, s. 288-295
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 20. |
- Christel, Stephan
(författare)
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Function and Adaptation of Acidophiles in Natural and Applied Communities
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Acidophiles are organisms that have evolved to grow optimally at high concentrations of protons. Members of this group are found in all three domains of life, although most of them belong to the Archaea and Bacteria. As their energy demand is often met chemolithotrophically by the oxidation of basic ions and molecules such as Fe2+, H2, and sulfur compounds, they are often found in environments marked by the natural or anthropogenic exposure of sulfide minerals. Nonetheless, organoheterotrophic growth is also common, especially at higher temperatures. Beside their remarkable resistance to proton attack, acidophiles are resistant to a multitude of other environmental factors, including toxic heavy metals, high temperatures, and oxidative stress. This allows them to thrive in environments with high metal concentrations and makes them ideal for application in so-called biomining technologies.The first study of this thesis investigated the iron-oxidizer Acidithiobacillus ferrivorans that is highly relevant for boreal biomining. Several unresolved nodes of its sulfur metabolism were elucidated with the help of RNA transcript sequencing analysis. A model was proposed for the oxidation of the inorganic sulfur compound tetrathionate. In a second paper, this species’ transcriptional response to growth at low temperature was explored and revealed that At. ferrivorans increases expression of only very few known cold-stress genes, underlining its strong adaptation to cold environments.Another set of studies focused on the environmentally friendly metal winning technology of bioleaching. One of the most important iron-oxidizers in many biomining operations is Leptospirillum ferriphilum. Despite its significance, only a draft genome sequence was available for its type strain.Therefore, in the third paper of this thesis we published a high quality, closed genome sequence of this strain for future use as a reference, revealing a previously unidentified nitrogen fixation system and improving annotation of genes relevant in biomining environments. In addition, RNA transcript and protein patterns during L. ferriphilum’s growth on ferrous iron and in bioleaching culture were used to identify key traits that aid its survival in extremely acidic, metal-rich environments. The biomining of copper from chalcopyrite is plagued by a slow dissolution rate, which can reportedly be circumvented by low redox potentials. As conventional redox control is impossible in heap leaching, paper four explored the possibility of using differentially efficient iron oxidizers to influence this parameter. The facultative heterotrophic Sulfobacillus thermosulfidooxidans was identified as maintaining a redox potential of ~550 mV vs Ag/AgCl, favorable for chalcopyrite dissolution,while L. ferriphilum caused the potential to raise far above this critical value. RNA transcript analysis was used to identify genomic features that may contribute to this behavior.Lastly, six fields in Northern Sweden were examined for the presence of acid sulfate soils in the fifth paper. The study revealed three acid sulfate soils. The presence of acidophiles that likely catalyze the production of acid in the soil was confirmed by community 16S gene amplicon analysis. One site that was flooded in a remediation attempt and is therefore anoxic still exhibited similar bacteria, however, these now likely grow via ferric iron reduction. This process consumes protons and could explain the observed rise in pH at this site.This thesis examines acidophiles in pure culture, as well as natural and designed communities. Key metabolic traits involved in the adaptation to their habitats were elucidated, and their application in mining operations was discussed. Special attention was paid to acidophiles in chalcopyrite bioleaching and in cold environments, including environmental acid sulfate soils in Northern Sweden.
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| 21. |
- Christel, Stephan, et al.
(författare)
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Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT
- 2018
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Ingår i: Applied and Environmental Microbiology. - : American society for microbiology. - 0099-2240 .- 1098-5336. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilumT applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as substrate and bioleaching cultures containing chalcopyrite (CuFeS2). Leptospirillum ferriphilumT adaptations to growth on chalcopyrite included a possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, expression and translation of genes responsible for chemotaxis and motility were enhanced.
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| 22. |
- Christel, Stephan, et al.
(författare)
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Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching
- 2018
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidicores that provides a more environmentally friendly alternative to many traditional metal extractionmethods, such as roasting or smelting. Industrial interest increases steadily and today, circa 15-20%of the world’s copper production can be traced back to this method. However, bioleaching of theworld’s most abundant copper mineral chalcopyrite suffers from low dissolution rates, oftenattributed to passivating layers, which need to be overcome to use this technology to its full potential.To prevent these passivating layers from forming, leaching needs to occur at a lowoxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult andcostly. As an alternative, selected weak iron-oxidizers could be employed that are incapable ofscavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onsetof bioleaching, but not high enough to allow for the occurrence of passivation. In this study, wereport that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications.Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole ironoxidizer exhibited significantly lower redox potentials and higher release of copper compared tocommunities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic responseto single and co-culture of these two iron oxidizers was studied and revealed a greatly decreasednumber of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured inthe presence of L. ferriphilum. This allowed for the identification of genes potentially responsible forS. thermosulfidooxidans’ weaker iron oxidation to be studied in the future, as well as underlined theneed for mechanisms to control the microbial population in bioleaching heaps
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| 23. |
- Dopson, Mark, 1970-, et al.
(författare)
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Biomining Microorganisms : Diversity and Modus Operandi
- 2023
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Ingår i: Biomining Technologies. - Cham : Springer. - 9783031053825 - 9783031053818 ; , s. 89-110
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Bokkapitel (refereegranskat)abstract
- Consortia of biomining microorganisms catalyze metal sulfide dissolution for extraction and recovery of metals such as gold and copper by regenerating the ferric iron oxidant along with metabolizing the resultant elemental and reduced inorganic sulfur compounds. These microorganisms are from the Bacteria and Archaea domains with the Bacteria having generally lower growth temperatures while the Archaea comprise mostly moderate and extreme thermophilic species. All microorganisms used in current biomining operations are able to grow at acidic pH values along with metal tolerance systems that allow them to survive the multiple extreme conditions in leaching liquors. The bacterial and archaeal ferrous iron oxidation systems differ while their reduced inorganic sulfur compound metabolisms contain enzyme pathways that are similar but not identical between the two domains. In addition, dissolution of non-sulfidic ores such as oxyhydroxide minerals, and electronic wastes, can also be mediated via biogenic acidolysis and complexation or by microbial Fe-reducing activity. Recent advances in “omics” technologies have aided in identifying new acidophilic biomining species and future studies will continue to elucidate their modus operandi to aid in increasing rates of mineral dissolution.
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| 24. |
- Dopson, Mark, 1970-, et al.
(författare)
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Eurypsychrophilic acidophiles : From (meta)genomes to low-temperature biotechnologies
- 2023
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 14
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Forskningsöversikt (refereegranskat)abstract
- Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4 degrees C but have an optimum temperature for growth above 15 degrees C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, "Ferrovum myxofaciens," and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of "omics" techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15 degrees C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
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| 25. |
- Dopson, Mark, 1970-
(författare)
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Physiological and phylogenetic diversity of acidophilic bacteria
- 2016
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Ingår i: Acidophiles. - : Caister Academic Press. - 9781910190333 - 9781910190340 ; , s. 79-92
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Bokkapitel (refereegranskat)abstract
- Acidophilic bacteria can be found in natural and anthropogenic acidic environments such as acid sulfate soils and biomining operations. These environments range in temperatures from below zero where low temperature adapted, acidophilic bacteria accelerate metal and acid release from sulfide minerals, through mesophilic environments, to hot solfataric fields containing Hydrogenobaculum acidophilum with a temperature optimum of 65°C. Acidophilic bacteria have been isolated from the Actinobacteria, Aquificae, Firmicutes, Nitropsora, Proteobacteria, and Verrucomicrobia phyla, and are capable of oxidizing both inorganic and organic electron donors coupled to the reduction of oxygen or ferric iron, though no extremely acidophilic bacteria are known to ferment organic substrates. Acidophilic bacteria also exhibit a range of carbon metabolisms, from obligate autotrophs such as Leptospirillum spp., facultative autotrophs such as Sulfobacillus spp. that can both fix carbon dioxide (CO2) or assimilate organic carbon, to obligate heterotrophs such as Alicyclobacillus tolerans. This chapter summarizes present knowledge of the physiological and phylogenetic diversity of acidophilic bacteria and highlights differences in growth characteristics between the various species.
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