Comparative Genomics of Sigma Factors in Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments.

Extreme acidophiles from the class thrive in highly acidic environments where they rely on diverse regulatory mechanisms for adaptation. These mechanisms include sigma factors, transcription factors (TFs), and transcription factor binding sites (TFBS), which control essential pathways. Comparative genomics and bioinformatics analyses identified sigma factors and TFs in , showing similarities but key differences from reference neutrophiles.

QS molecules change the planktonic/mineral subpopulations distribution of moderately thermophilic leaching bacteria in pyrite and decrease leaching in chalcopyrite.

Biomining is a sustainable alternative to conventional mineral processing that uses acidophilic microorganisms to catalyze the extraction of valuable metals from sulfide minerals. Mixed microbial consortia composed of moderate thermophiles such as and some species improve metal extraction efficiency at higher temperatures compared to pure cultures of mesophiles. However, quorum sensing (QS), which regulates microbial interactions and likely influences bioleaching performance, has not been studied in these species.

Dissolution of mining waste and semi-selective solubilization of magnesium by "Fervidacidithiobacillus caldus".

Aim: Several raw materials are identified as critical to securing non-energy supplies for industrial value chains. Magnesium (Mg) is central to the global drive toward electrification and, as such, is both economically important and under high supply risk. This project evaluated a biologically mediated strategy to solubilize Mg-containing waste in the pursuit of valorizing waste streams and to inform on strategies for the winning of metals from the solubilized waste.

Toward the bioleaching of bauxite residue by Gluconobacter oxydans.

Aim: This project evaluated a biologically mediated strategy to solubilize several rare earth elements and critical raw materials, including scandium, from bauxite residue. This work seeks to expand on previous research on contact leaching with bauxite.

Methods And Results: In this study, Gluconobacter oxydans was shown to secrete mixed organic acids, including gluconic acid, which was superior to pure gluconic acid in the dissolution of bauxite residue, even at low molarities.

Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.

The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene).

Uranium Repartitioning during Microbial Driven Reductive Transformation of U(VI)-Sorbed Schwertmannite and Jarosite.

This study exposes U(VI)-sorbed schwertmannite and jarosite to biotic reductive incubations under field-relevant conditions and examines the changes in aqueous and solid-phase speciation of U, Fe, and S as well as associated microbial communities over 180 days. The chemical, X-ray absorption spectroscopy, X-ray diffraction, and microscopic data demonstrated that the U(VI)-sorbed schwertmannite underwent a rapid reductive dissolution and solid-phase transformation to goethite, during which the surface-sorbed U(VI) was partly reduced and mostly repartitioned to monomeric U(VI)/U(IV) complexes by carboxyl and phosphoryl ligands on biomass or organic substances. Furthermore, the microbial data suggest that these processes were likely driven by the consecutive developments of fermentative and sulfate- and iron- reducing microbial communities.

Ecological filtering drives rapid spatiotemporal dynamics in fish skin microbiomes.

Skin microbiomes provide vital functions, yet knowledge about the drivers and processes structuring their species assemblages is limited-especially for non-model organisms. In this study, fish skin microbiome was assessed by high throughput sequencing of amplicon sequence variants from metabarcoding of V3-V4 regions in the 16S rRNA gene on fish hosts subjected to the following experimental manipulations: (i) translocation between fresh and brackish water habitats to investigate the role of environment; (ii) treatment with an antibacterial disinfectant to reboot the microbiome and investigate community assembly and priority effects; and (iii) maintained alone or in pairs to study the role of social environment and inter-host dispersal of microbes. The results revealed that fish skin microbiomes harbour a highly dynamic microbial composition that was distinct from bacterioplankton communities in the ambient water.

Climate change induces shifts in coastal Baltic Sea surface water microorganism stress and photosynthesis gene expression.

The world's oceans are challenged by climate change linked warming with typically highly populated coastal areas being particularly susceptible to these effects. Many studies of climate change on the marine environment use large, short-term temperature manipulations that neglect factors such as long-term adaptation and seasonal cycles. In this study, a Baltic Sea 'heated' bay influenced by thermal discharge since the 1970s from a nuclear reactor (in relation to an unaffected nearby 'control' bay) was used to investigate how elevated temperature impacts surface water microbial communities and activities.

Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming.

Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked.

Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives.

Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits.

Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield.

Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the Äspö Hard Rock Laboratory, Sweden.

Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments.

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies.

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°C but have an optimum temperature for growth above 15°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.

Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities.

Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems.

A nationwide acid sulfate soil study - A rapid and cost-efficient approach for characterizing large-scale features.

Acid sulfate soils are sulfide-rich soils that pose a notable environmental risk as their strong acidity and low pH mobilizes metals from soil minerals leading to both acidification and metal contamination of the surrounding environment. In this study a rapid and cost-efficient approach was developed to resolve the main distribution patterns and geochemical features of acid sulfate soils throughout coastal plains stretching for some 2000 km in eastern, southern, and western Sweden. Of the investigated 126 field sites, 47 % had acid sulfate soils including 33 % active, 12 % potential, and 2 % pseudo acid sulfate soils.

Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield.

The deep terrestrial biosphere encompasses the life below the photosynthesis-fueled surface that perseveres in typically nutrient and energy depleted anoxic groundwaters. The composition and cycling of this vast dissolved organic matter (DOM) reservoir relevant to the global carbon cycle remains to be deciphered. Here we show that recent Baltic Sea-influenced to ancient pre-Holocene saline Fennoscandian Shield deep bedrock fracture waters carried DOM with a strong terrigenous signature and varying contributions from abiotic and biotic processes.

Long-Term Warming of Baltic Sea Coastal Waters Affects Bacterial Communities in Bottom Water and Sediments Differently.

Coastal marine ecosystems are some of the most diverse natural habitats while being highly vulnerable in the face of climate change. The combination of anthropogenic influence from land and ongoing climate change will likely have severe effects on the environment, but the precise response remains uncertain. This study compared an unaffected "control" Baltic Sea bay to a "heated" bay that has undergone artificial warming from cooling water release from a nuclear power plant for ~50 years.

Weakened resilience of benthic microbial communities in the face of climate change.

Increased ocean temperature associated with climate change is especially intensified in coastal areas and its influence on microbial communities and biogeochemical cycling is poorly understood. In this study, we sampled a Baltic Sea bay that has undergone 50 years of warmer temperatures similar to RCP5-8.5 predictions due to cooling water release from a nuclear power plant.

Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle.

Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus along with the extremely acidophilic genera , , , and .

Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.

The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance.

Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history.

Coastal aquatic systems suffer from nutrient enrichment, which results in accelerated eutrophication effects due to increased microbial metabolic rates. Climate change related prolonged warming will likely accelerate existing eutrophication effects, including low oxygen concentrations. However, how the interplay between these environmental changes will alter coastal ecosystems is poorly understood.

Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials.

Sediments along the Baltic Sea coast can contain considerable amounts of metal sulfides that if dredged and the spoils deposited such that they are exposed to air, can release high concentrations of acid and toxic metals into recipient water bodies. Two river estuaries in western Finland were dredged from 2013 to 2018 and the dredge spoils were deposited on land previously covered with agricultural limestone to buffer the pH and mitigate acid and metal release. In this study, the geochemistry and 16S rRNA gene amplicon based bacterial communities were investigated over time to explore whether the application of lime prevented a conversion of the dredge spoils into acid producing and metal releasing soil.

Vanadium removal from mining ditch water using commercial iron products and ferric groundwater treatment residual-based materials.

Removal of vanadium from liquid waste streams protects the environment from toxic vanadium species and promotes the recovery of the valuable metal. In this study, real mining ditch water was sampled from a closed vanadium mine (V-Fe-Ti oxide deposit, Finland) and used in sorption experiments at prevailing vanadium concentration (4.66-6.

Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.

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.