Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention

Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera

Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention

Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.Peer reviewe

Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples

Microorganisms in flotation and minerals processing may significantly affect the grade and yield of metal concentrates. However, studying the phenomena requires working techniques to detach microorganisms and their DNA from mineral particles to which they strongly adhere. We developed a new method utilizing the competitive properties of anionic nanocellulose to block sorption of DNA to and detach microbial cells from mineral particles from ore processing. In general, up to one ng DNA mL−1 sample was obtained with the custom anionic nanocellulose method (CM) compared to DNA amounts below the Qubit assay's detection limit for extractions with a commercial kit (KIT). Similarly, 0.5–4 orders of magnitude more bacterial 16S and fungal 5.8S rRNA gene copies were detected by qPCR from CM treated samples compared to KIT extractions. A clear difference in the detected microbial community structure between CM and KIT extracted samples was also observed. Commercial kits optimized for mineral soils are easy to use and time efficient but may miss a considerable part of the microbial communities. A competing agent such as anionic nanocellulose may decrease the interaction between microorganisms or their DNA and minerals and provide a comprehensive view into the microbial communities in mineral processing environments.</p

Arkit boreaalisten metsäpuiden sienijuuristossa

Archaea were long thought to be a group of ancient bacteria, which mainly lived in extreme environments. Due to the development of DNA sequencing methods and molecular phylogenetic analyses, it was shown that the living organisms are in fact divided into three domains; the Archaea, Bacteria and the Eucarya. Since the beginning of the previous decade, it was shown that archaea generally inhabit moderate environments and that these non-extremophilic archaea are more ubiquitous than the extremophiles. Group 1 of non-extreme archaea affiliate with the phylum Crenarchaeota. The most commonly found soil archaea belong to the subgroup 1.1b. However, the Crenarchaeota found in the Fennoscandian boreal forest soil belong to the subgroup 1.1c. The organic top layer of the boreal forest soil, the humus, is dominated by ectomycorrhizal fungal hyphae. These colonise virtually all tree fine root tips in the humus layer and have been shown to harbour distinct bacterial populations different from those in the humus. The archaea have also been shown to colonise both boreal forest humus and the rhizospheres of plants. In this work, studies on the archaeal communities in the ectomycorrhizospheres of boreal forest trees were conducted in microcosms. Archaea belonging to the group 1.1c Crenarchaeota and Euryarchaeota of the genera Halobacterium and Methanolobus were detected. The archaea generally colonised fungal habitats, such as ectomycorrhizas and external mycelia, rather than the non-mycorrhizal fine roots of trees. The species of ectomycorrhizal fungus had a great impact on the archaeal community composition. A stable euryarchaeotal community was detected especially in the mycorrhizas, of most of the tested Scots pine colonising ectomycorrhizal fungi. The Crenarchaeota appeared more sporadically in these habitats, but had a greater diversity than the Euryarchaeota. P. involutus mycorrhizas had a higher diversity of 1.1c Crenarchaeota than the other ectomycorrhizal fungi. The detection level of archaea in the roots of boreal trees was generally low although archaea have been shown to associate with roots of different plants. However, alder showed a high diversity of 1.1c Crenarchaeota, exceeding that of any of the tested mycorrhizas. The archaeal 16S rRNA genes detected from the non-mycorrhizal roots were different from those of the P. involutus mycorrhizas. In the phylogenetic analyses, the archaeal 16S rRNA gene sequences obtained from non-mycorrhizal fine roots fell in a separate cluster within the group 1.1c Crenarchaeota than those from the mycorrhizas. When the roots of the differrent tree species were colonised by P. involutus, the diversity and frequency of the archaeal populations of the different tree species were more similar to each other. Both Cren- and Euryarchaeota were enriched in cultures to which C-1 substrates were added. The 1.1c Crenarchaeota grew anaerobically in mineral medium with CH4 and CO2 as the only available C sources, and in yeast extract media with CO2 and CH4 or H2. The crenarchaeotal diversity was higher in aerobic cultures on mineral medium with CH4 or CH3OH than in the anaerobic cultures. Ecological functions of the mycorrhizal 1.1c Crenarchaeota in both anaerobic and aerobic cycling of C-1 compounds were indicated. The phylogenetic analyses did not divide the detected Crenarchaeota into anaerobic and aerobic groups. This may suggest that the mycorrhizospheric crenarchaeotal communities consist of closely related groups of anaerobic and aerobic 1.1c Crenarchaeota, or the 1.1c Crenarchaeota may be facultatively anaerobic. Halobacteria were enriched in non-saline anaerobic yeast extract medium cultures in which CH4 was either added or produced, but were not detected in the aerobic cultures. They may potentially be involved in anaerobic CH4 cycling in ectomycorrhizas. The CH4 production of the mycorrhizal samples was over 10 times higher than for humus devoid of mycorrhizal hyphae, indicating a high CH4 production potential of the mycorrhizal metanogenic community. Autofluorescent methanogenic archaea were detected by microscopy and 16S rRNA gene sequences of the genus Methanolobus were obtained. The archaeal community depended on both tree species and the type of ectomycorrhizal fungus colonising the roots and the Cren- and Euryarchaeota may have different ecological functions in the different parts of the boreal forest tree rhizosphere and mycorrhizosphere. By employing the results of this study, it may be possible to isolate both 1.1c Crenarchaeota as well as non-halophilic halobacteria and aerotolerant methanogens from mycorrhizospheres. These archaea may be used as indicators for change in the boreal forest soil ecosystem due to different factors, such as exploitations of forests and the rise in global temperature. More information about the microbial populations with apparently low cell numbers but significant ecological impacts, such as the boreal forest soil methanogens, may be of crucial importance to counteract human impacts on such globally important ecosystems as the boreal forests.Arkéer i skogsträdens svamprötter Arkéerna antogs länge vara en uråldrig typ av bakterier som bebodde endast extrema miljöer (t.ex. heta källor, sjöar med hög salt halt). Med hjälp av DNA baserade metoder påvisades det dock att arkéerna tillhörde en helt egen grupp av organismer och att livsformerna på jorden kan indelas i tre domäner, nämnligen Archaea, Bacteria och Eucaryota. Sedan början av 1990-talet har man förutom i olika vatten och jord prov, funnit att arkéerna är allmänt spridda i olika vanliga miljöer och att de typer som typiskt hittas i finsk skogsjord skiljer sej åtskilligt från de arkéer som vanligen hittas i jord. I det organiska ytskiktet, humusen, i de boreala skogarna växer stora mänger svamphyfer. Dessa bildar symbiotiska förhållanden med skogsträdens rötter, så kallade mykorrhizor. Dessa har påvisats ha speciella bakteriefloror som skiljer sej från den i humusen. Också arkéer har påvisats leva både i skogshumus samt på växtrötter. I den här forskningen studerades arké-populationerna i boreala skogsträds ektomykorrhizosfär. Man fann att mykorrhizorna och svamphyferna i allmänhet har en större population av arkéer än de 'nakna' trädrötterna eller humus utan svamphyfer. Både svamparterna och trädarterna inverkar på bestånder av arkéer i rötterna och mykorrhizosfären. Mykorrhizornas arkéer skiljer sej från dem som hittas på rötterna, men rötternas bestånd av arkéer förändras då mykorrhizosfären i rötterna bildas. Förutom de crenarkeoter som vanligen hittas i finsk skogsjord hittades i de flesta mykorrhiza-prov också sekvenser av gener för ribosomalt RNA som tillhörde släktet Halobacterium, vilka i allmänhet lever i väldigt hög salthalt. Arkéer hittades också i både anaeroba och aeroba oldingar. I de anaeroba metan-producerande odlingarna hittades euryarkeoter av släktena Methanolobus (methan-producerande arkéer) och Halobacterium samt de crenarkeoter som typiskt hittas i finsk skogsjord. I de aeroba odlingarna matade med antingen metan eller formamid (en komponent av metancykeln) hittades bara crenarkeoter. Inga ekologiska funktioner har ännu påvisats för de arkéer som hittats i finsk skogsjord och i trädenas rötter och mykorrhizosfär, men dessa resultat indikerar att de kan ha en betydelse för metanets kretslop i både anaeroba och aeroba förhållanden. Man har ännu inte lyckats isolera dessa arkéer för att kunna studera deras fysiologi, men genom att tillämpa dessa reultat kan detta vara möjligt. Genom att få mera information om de här dåligt kända mikro-organismerna kunde de möjligen också få en användning som indikatororganismer för att registrera förändringar i skogsjordens ekosystem, förorsakade av olika faktorer, såsom intensivt skogsbruk men också den globala temperaturökningen. Mera information om viktiga mikrobgrupper med troligtvis låg populationstäthet men stor ekologisk betydelse, som t.ex. metanogenerna i skogsjorden, kan vara av stor betydelse för att kunna minska de miljöeffekter människan förorsakar dessa globalt viktiga ekosystem

Ni(II) Interactions in Boreal Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. Strains Isolated From an Acidic, Ombrotrophic Bog

The uptake of nickel [Ni(II)] by Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. strains isolated from a boreal bog was studied using batch experiments. All strains removed Ni(II) from the solution and the uptake efficiency was affected by the nutrient source, incubation temperature, time, and pH. As highest Ni uptake (with a maximum K-d of 1890 L/kg DW) was recorded for the Pseudomonas sp. strains, these bacteria were used in the following protein expression (SDS-PAGE and MALDI-TOFF), transmission electron microscopy (TEM) and EDS experiments. In addition, Freundlich and Langmuir sorption isotherms were determined. In the Ni(II) treated cells, dense crystalline intra-cellular accumulations were observed in TEM examinations, which were identified as Ni accumulations using EDS. SDS-PAGE and MALDI-TOFF spectra of Ni(II) treated cells showed several changes in the protein profiles, which can indicate active accumulation of Ni in these bacteria. Concurrently, we observed Ni(II) uptake to follow Freundlich and Langmuir isotherms, suggesting straight cellular biosorption in addition to the intra-cellular accumulation. The role of cellular (cell membrane and cell wall) functional groups involved in Ni(II) binding were therefore studied using Fourier transformation infrared spectroscopy. These analyses supported the potential role of the alcoholic hydroxyl, carboxyl and amine groups in Ni(II) binding in these bacteria, therefore suggesting two different Ni(II) uptake mechanisms; (i) intra-cellular accumulation [possibly connected to detoxification of Ni(II)], and (ii) straight biosorption on cell membrane/wall functional groups.Peer reviewe

Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater

Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of similar to 3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.Peer reviewe

The effects of indigenous microorganisms and water treatment with ion exchange resin on Cu-Ni flotation performance

Mineral processing utilizes large amounts of water and aims to reduce water consumption by recirculation and closing the water loops. This results in accumulation of chemical and biological contaminants in process water that may have adverse outcomes on the process performance. To optimize water quality suitable for each process step and plant, knowledge of both chemical and biological effects are needed as well as techniques to best remove the contaminants. This study focused on the consequences of microorganisms, enriched from the actual process earlier, on the flotation performance in the multi-metal Kevitsa mine in Northern Finland and the applicability of ion exchange for the removal of dissolved sulfur species and microorganisms from water. The increase of microbial load from the original 106 to added 107 16S rRNA copies mL−1 affected positively the flotation selectivity, especially in the case of nickel. Two tested water types, process water (PW) and final tailings water (FT), behaved slightly differently. In the Cu flotation phase added microorganisms did not affect the Cu recovery of FT but decreased significantly the recovery of Cu in PW. With equal Cu grade, the recovery was as high as approximately 25 percentage points lower. However, added microorganisms in both water types decreased notably the recovery of Ni in Cu concentrate (18 to 37 %-points). At the same time the amount of Ni recovered in the Ni concentrate increased by 18 to 33 %-points with added microorganisms. Visually the froth layer was higher and more stable in the Ni flotation in experiments with added microorganisms compared to experiments without added microorganisms. The concentrations of dissolved sulfate and thiosulfate ions were low in the studied waters compared to operations treating massive sulfide ores and did not significantly affect the flotation performance. For this reason, the IX water treatment was not required for these ions. However, the IX treatment proved to be effective in removing both sulfur species and microorganisms. The use of dissolved air flotation (DAF) was a successful pretreatment for ion exchange in removal of microorganisms. However, microorganisms are not usually taken into consideration when process performance or water cleaning techniques are designed and optimization could result generally in even better outcome

Microbial communities in a former pilot-scale uranium mine in Eastern Finland – Association with radium immobilization

The bacterial, fungal and archaeal communities were characterized in 17 top soil organic and mineral layer samples and in top sediment samples of the Paukkajanvaara area, a former pilot-scale uranium mine, located in Eno, Eastern Finland. using amplicon sequencing and qPCR. Soil and sediment samples were in addition analyzed for (Ra-226), radium sulfate (SO42-), nitrate (NO3-) and phosphate (PO43-) concentrations. New bacterial strains, representing Pseudomonas spp., were isolated from the mine and reference area and used in laboratory experiments on uptake and leaching of radium (Ra). The effect of these strains on the sulfate leaching from the soil samples was also tested in vitro. Between 6 x 10(6) and 5 x 10(8) copies g(-1) DW (dry weight) of bacterial 16S rRNA genes, 5 x 10(5)-1 x 10(8) copies g(-1) DW archaeal 16S rRNA genes and 1 x 10(5)-1 x 10(8) copies g(-1) DW fungal 5.8S rRNA genes were detected in the samples. A total of 814. 54 and 167 bacterial, archaeal and fungal genera. respectively, were identified. Proteobacteria, Euryarchaeota and Mortiriella were the dominant bacterial, archaeal and fungal phyla, respectively. All tested Pseudomonas spp. strains isolates from Paukkajanvaara removed Ra from the solution, but the amount of removed Ra depended on incubation conditions (temperature, time and nutrient broth). The highest removal of Ra (5320 L/kg DW) was observed by the Pseudomonas sp. strain T5-6-I at 37 degrees C. All Pseudomonas spp. strains decreased the release of Ra from soil with an average of 23% while simultaneously increasing the concentration of SO42- in the solution by 11%. As Pseudomonas spp. were frequent in both the sequence data and the cultures, these bacteria may play an important role in the immobilization of Ra in the Paukkajanvaara mine area. (C) 2019 The Authors. Published by Elsevier B.V.Peer reviewe