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Streams are important sources of methane (CH4) to the atmosphere but magnitudes and regulation of stream CH4 fluxes remain uncertain. Stream CH4 can come from groundwater and/or produced in anoxic sediments. A fraction can be microbially oxidized to carbon dioxide (CO2) when passing redox gradients in soil, sediment, or water, while the fraction escaping oxidation is emitted to the atmosphere. The relative importance of the CH4 sources (groundwater inputs vs. sediment production) and the fraction oxidized is typically unknown, yet key for the regulation and magnitude of stream emissions. In this study, we followed the transport of CH4 from below‐stream soils to the stream water surface and to the atmosphere using a combination of CH4 concentration and stable carbon isotope gradient measurements, high resolution stream flux and discharge assessments, and inverse mass‐balance modeling. Sampling was done in multiple locations in the stream network of two independent catchments in Sweden to consider spatial variability. We show that the surface water, sub‐surface, and groundwater CH4 concentration, CH4 oxidation, and emission were highly variable in space. Our results indicate that the variability could be related to stream morphology and soil characteristics. Of the total CH4 input into the streams, roughly half of it was estimated to come from groundwater CH4 in both catchments (39% and 57%; the rest from sediment production), and most of the CH4 was oxidized (97%–99%) before emission to the atmosphere. Our results indicate that CH4 oxidation is a major sink for CH4 in the studied streams. Plain Language Summary: Streams emit a large amount of the greenhouse gas methane to the atmosphere. Sources of this methane can be groundwater and/or production in stream sediments. A part of the methane can be oxidized by microbes into carbon dioxide and the rest can evade to the atmosphere as methane. The relative magnitudes of the sources, oxidation, and emission are usually unknown but important for understanding the regulation of stream methane emissions. In this study in two stream networks of Sweden, inverse mass‐balance modeling was done using multiple measurements and we show that the sources of methane, its oxidation and emission were highly variable in space. About half of the methane in the streams was contributed by groundwater and the rest was estimated to be produced in the sediments. Most of the methane was oxidized in the streams and only a small fraction escaped to the atmosphere. Key Points: Large spatial variability in CH4 concentration, net inputs, oxidation and emission was observedRoughly half of the CH4 inputs in the streams were contributed by groundwater and the rest by sediment productionMost of the total potential stream CH4 input was oxidized before reaching the atmosphere [ABSTRACT FROM AUTHOR]

CO 2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO 2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

Four neurologic diseases affect dogs of the Lagotto Romagnolo (LR) breed, namely benign familial juvenile epilepsy (BFJE), vacuolar storage disease, and 2 forms of cerebellar cortical degeneration. Intraneuronal inclusion bodies in cerebellar Purkinje cells were first described in the BFJE phenotype. Upon further characterization of these diseases, similar inclusions were also noted in the brain of LRs used as controls. This study investigated the clinical, histologic, and electron microscopic findings in 23 LRs to determine the nature of their neuronal inclusions and whether the presence, distribution, or number of inclusions is associated with neurologic signs. Electron microscopy of the inclusions revealed a cytoplasmic aggregate without a limiting membrane. The inclusions appeared proteinaceous on histochemical staining and positive on phosphotungstic-acid-hematoxylin (PTAH) stain for proteins rich in basic amino acids. Markers of commonly known proteinopathies of humans (ubiquitin, p62, LC3, α-synuclein, and β-amyloid) were not detected in the inclusions when assessed by immunohistochemistry. The overall presence of inclusion bodies was not significantly associated with the dog's neurologic status. The results show an association between inclusions in the cerebral cortex and an absence of clinical neurologic disease in LRs. There was no significant difference in the quantitative inclusion body burden when compared in LRs with or without neurologic signs. Although PTAH-positive proteinaceous neuronal inclusions are a common finding in LRs regardless of neurologic signs, these inclusions may be a protective response when present in the cerebral cortex., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Uptake of elements into plants is an integral part of many environmental impact assessments. Typically, the plant uptake is determined using an empirical soil-to-plant transfer factor (CR). The elemental concentrations in plants are expected to vary with plant species and plant functional type (PFT), but also according to soil and element properties. Specifically, the uptake of essential elements is regulated, and likely less related to soil concentrations than the uptake of non-essential elements. In this study, the impact of PFT, species and environmental factors on the CR of mire plants was tested. The plants included in the study were four common boreal peatland species ( Andromeda polifolia, Vaccinium oxycoccus, Eriophorum vaginatum and Carex rostrata ) sampled from 40 minerogenic mires along an age gradient. The results show that while plant species and PFT (heathers and sedges) are the main determinants of the CR value, also environmental factors, such as peat C:N ratio, are important. Further, concentrations of essential elements in plants were only weakly correlated to peat concentrations, whereas the correlation was stronger for non-essential elements and elements utilized at trace amounts. The results of this study verify that CR values may vary substantially between peatland plant species and PFTs. Further, the results suggest that it is relevant to include effects of PFTs on CR and among-species variation in environmental impact assessments. This is because the PFT may have a large impact on the exposure pathways to humans, which could, for example, be berries or animal feed, and also due to the uncertainties of the composition of the future vegetation communities. Since CR varies systematically with several soil properties, there may be potential for adjusting the CR values for expected environmental changes, and thereby reduce the uncertainties of empirical CR values determined from a broad range of environmental conditions., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Author(s).)

Eutrophication increases the input of labile, algae-derived, organic matter (OM) into lake sediments. This potentially increases methane (CH 4 ) emissions from sediment to water through increased methane production rates and decreased methane oxidation efficiency in sediments. However, the effect of OM lability on the structure of methane oxidizing (methanotrophic) and methane producing (methanogenic) microbial communities in lake sediments is still understudied. We studied the vertical profiles of the sediment and porewater geochemistry and the microbial communities (16S rRNA gene amplicon sequencing) at five profundal stations of an oligo-mesotrophic, boreal lake (Lake Pääjärvi, Finland), varying in surface sediment OM sources (assessed via sediment C:N ratio). Porewater profiles of methane, dissolved inorganic carbon (DIC), acetate, iron, and sulfur suggested that sites with more autochthonous OM showed higher overall OM lability, which increased remineralization rates, leading to increased electron acceptor (EA) consumption and methane emissions from sediment to water. When OM lability increased, the abundance of anaerobic nitrite-reducing methanotrophs ( Candidatus Methylomirabilis) relative to aerobic methanotrophs ( Methylococcales ) in the methane oxidation layer of sediment surface decreased, suggesting that Methylococcales were more competitive than Ca . Methylomirabilis under decreasing redox conditions and increasing methane availability due to their more diverse metabolism (fermentation and anaerobic respiration) and lower affinity for methane. Furthermore, when OM lability increased, the abundance of methanotrophic community in the sediment surface layer, especially Ca . Methylomirabilis, relative to the methanogenic community decreased. We conclude that increasing input of labile OM, subsequently affecting the redox zonation of sediments, significantly modifies the methane producing and consuming microbial community of lake sediments. IMPORTANCE Lakes are important natural emitters of the greenhouse gas methane (CH 4 ). It has been shown that eutrophication, via increasing the input of labile organic matter (OM) into lake sediments and subsequently affecting the redox conditions, increases methane emissions from lake sediments through increased sediment methane production rates and decreased methane oxidation efficiency. However, the effect of organic matter lability on the structure of the methane-related microbial communities of lake sediments is not known. In this study, we show that, besides the activity, also the structure of lake sediment methane producing and consuming microbial community is significantly affected by changes in the sediment organic matter lability.

The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life., (© 2022. The Author(s).)

Although development of microbiota in childhood has been linked to chronic immune-related conditions, early childhood determinants of microbiota development have not been fully elucidated. We used 16S rRNA sequencing to analyse faecal and saliva samples from 83 children at four time-points during their first 2 years of life and from their mothers. Our findings confirm that gut microbiota in infants have low diversity and highlight that some properties are shared with the oral microbiota, although inter-individual differences are present. A considerable convergence in gut microbiota composition was noted across the first 2 years of life, towards a more diverse adult-like microbiota. Mode of delivery accounted for some of the inter-individual variation in early childhood, but with a pronounced attenuation over time. Our study extends previous research with further characterization of the major shift in gut microbiota composition during the first 2 years of life., (© 2022. The Author(s).)

Climate change-driven permafrost thaw has a strong influence on pan-Arctic regions, via, for example, the formation of thermokarst ponds. These ponds are hotspots of microbial carbon cycling and greenhouse gas production, and efforts have been put on disentangling the role of bacteria and archaea in recycling the increasing amounts of carbon arriving to the ponds from degrading watersheds. However, despite the well-established role of fungi in carbon cycling in the terrestrial environments, the interactions between permafrost thaw and fungal communities in Arctic freshwaters have remained unknown. We integrated data from 60 ponds in Arctic hydro-ecosystems, representing a gradient of permafrost integrity and spanning over five regions, namely Alaska, Greenland, Canada, Sweden, and Western Siberia. The results revealed that differences in pH and organic matter quality and availability were linked to distinct fungal community compositions and that a large fraction of the community represented unknown fungal phyla. Results display a 16%-19% decrease in fungal diversity, assessed by beta diversity, across ponds in landscapes with more degraded permafrost. At the same time, sites with similar carbon quality shared more species, aligning a shift in species composition with the quality and availability of terrestrial dissolved organic matter. We demonstrate that the degradation of permafrost has a strong negative impact on aquatic fungal diversity, likely via interactions with the carbon pool released from ancient deposits. This is expected to have implications for carbon cycling and climate feedback loops in the rapidly warming Arctic., (© 2021 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Background: Finnish community pharmacies have undergone digitalization during the past decade. The introduction of the electronic prescription has had a significant impact on pharmacy workflows, such as the dispensing process. This inevitably has significant sociotechnical implications. We examine the impact of digitalization on the dispensing process and the sociotechnical orientation of a pharmacy., Methods: We utilize data collected in customer service situations in Finnish community pharmacies at two points in time: in the traditional workflow, when electronic prescriptions were not in use, and in the new direct dispensing workflow, which is the usual delivery model in the case of electronic prescriptions. We analyze this data in terms of changes in workflow efficiency. We also draw on existing literature to build a conceptual model for digitalization in the pharmacy sector from a sociotechnical standpoint., Results: In the Finnish environment, the results, based on our study sample, show that with electronic prescriptions and the direct dispensing model, the delivery time for a single medication over the counter was reduced by 13%. The results also indicate that the process has become more predictable, as the variation in terms of the workflow lead time has decreased., Conclusions: The results indicate that the dispensing process has become more efficient in terms of time and throughput as well as more technically oriented and predictable. From a sociotechnical perspective, the results indicate that the technical subsystem has strengthened, and pharmacies have adapted to the new technology in the dispensing process., (© 2021. The Author(s).)

Thermokarst activity at permafrost sites releases considerable amounts of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing different stages of permafrost integrity. Surface water samples were taken from the ponds and, additionally, for most of the ponds also the detritus and sediment samples were taken. All the samples were extracted for total DNA, which was then amplified for the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling., (© 2021. The Author(s).)

Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales ) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales , Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH 4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH 4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O 2 and CH 4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Martin, Rissanen, Garcia, Mehrshad, Buck and Peura.)

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi ) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or "species"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium , and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium -associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia -associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs., (Copyright © 2021 Garcia et al.)

High levels of nitrogen originating from blasting operations, for example at mining sites or quarries, risk contaminating water bodies through leaching from waste rock dumps. Woodchip bioreactors can be a simple and cost-effective way of reducing nitrate concentrations in the leachate. In this study we investigated how bottle sedge, barley straw, and pine woodchips used as electron donors for denitrification influenced microbial community composition and nitrate removal in lab-scale bioreactors during 270 days. The reactors were operated to ensure that nitrate was never limiting and to achieve similar nitrate removal (%). Distinct bacterial communities developed due to the different substrates, as determined by sequencing of the 16S rRNA gene. Sedge and straw reactors shared more taxa with each other than with woodchips and throughout the experimental period, sedge and straw were more diverse than woodchips. Cellulose degrading bacteria like Fibrobacteres and Verrucomicrobia were detected in the substrates after 100-150 days of operation. Nitrate removal rates were highest in the sedge and straw reactors. After initial fluctuations, these reactors removed 5.1-6.3 g N m -3  water day -1 , which was 3.3-4.4 times more than in the woodchip reactors. This corresponded to 48%, 42%, and 44% nitrate removal for the sedge, straw, and woodchip reactors respectively. The functional communities were characterized by quantitative PCR and denitrification was the major nitrate removing process based on genetic potential and water chemistry, although sedge and straw developed a capacity for ammonification. Gene ratios suggested that denitrification was initially incomplete and terminating with nitrous oxide. An increase in abundances of nitrous oxide reducing capacity in all substrate types towards the end increased the potential for less emissions of the greenhouse gas nitrous oxide., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)

The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived, especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in clusters of orthologous groups (COG) categories L (replication, recombination and repair) and S (function unknown) were relatively high in metagenome-assembled genomes representing Methylococcales clearly thriving below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. By contrast, genes in COG category N (cell motility) were relatively high in metagenome-assembled genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface., (© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.)

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes., (© 2020 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

Aquatic N-fixation is generally associated with the growth and mass development of Cyanobacteria in nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data and nif gene clusters analysis. Groups with diazotrophic operons were functionally divergent and included Cholorobi , Geobacter , Desulfobacterales , Methylococcales , and Acidobacteria . In addition to nifH (a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within the Chlorobi population, the nitrogenase ( nifH ) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence of rnf genes (related to the expression of H + /Na + -translocating ferredoxin: NAD+ oxidoreductase) in Methylococcales and Desulfobacterales suggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes., (Copyright © 2020 Fernandez, Peura, Eiler, Linz, McMahon and Bertilsson.)

Early life determinants of the oral microbiota have not been thoroughly elucidated. We studied the association of birth and early childhood characteristics with oral microbiota composition using 16 S ribosomal RNA (rRNA) gene sequencing in a population-based Swedish cohort of 59 children sampled at 6, 12 and 24 months of age. Repeated-measurement regression models adjusted for potential confounders confirmed and expanded previous knowledge about the profound shift of oral microbiota composition in early life. These alterations included increased alpha diversity, decreased beta diversity and alteration of bacterial composition with changes in relative abundance of 14 of the 20 most common operational taxonomic units (OTUs). We also found that birth characteristics, breastfeeding and antibiotic use were associated with overall phyla distribution and/or with the relative abundance of specific OTUs. Further, we detected a novel link between morning salivary cortisol level, a physiological marker of neuroendocrine activity and stress, and overall phyla distribution as well as with decreased abundance of the most common OTU mapped to the Streptococcaceae family. In conclusion, a major part of the maturation of the oral microbiome occurs during the first two years of life, and this development may be influenced by early life circumstances.

Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage., (© FEMS 2019.)

Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae , one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off. IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes., (Copyright © 2019 Garcia et al.)

Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes. IMPORTANCE Despite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment., (Copyright © 2018 Bravo et al.)

Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community. IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics., (Copyright © 2018 Peura et al.)

Faecal calprotectin is a protein used as a diagnostic marker for inflammatory bowel diseases. We determined upper limits for normal calprotectin values for neonatal, 6, 12 and 24 months old children using a turbidimetric immunoassay in a cohort of Swedish children. The advantage of the method is that opposite to previously used enzyme-linked immunosorbent assay (ELISA) method, it enables measuring single samples, and thus, shortens the analysis time significantly. There were 72 samples (41.7% female) collected neonatally, 63 samples (34.9% female) at 6 months, 60 samples (40.0% female) at 12 months and 51 samples (43.1% female) at 24 months. The upper limits for normal values were 233, 615, 136 and 57 µg mg -1 for infants aged 0, 6, 12 and 24 months, respectively.

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

The role of anaerobic CH4 oxidation in controlling lake sediment CH4 emissions remains unclear. Therefore, we tested how relevant EAs (SO42-, NO3-, Fe3+, Mn4+, O2) affect CH4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe3+ and Mn4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH4-oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3.4% and 0.5% of archaeal and bacterial 16S rRNA genes, respectively), likely due to the low environmental stability associated with shallow depths. Consequently, the potential anaerobic CH4 oxidation (0-2.1 nmol g-1dry weight (DW)d-1) was not enhanced by the addition of EAs, nor important in consuming the produced CH4 (0.6-82.5 nmol g-1DWd-1). Instead, the increased EA availability suppressed CH4 production via the outcompetition of methanogens by anaerobically respiring bacteria and via the increased protection of organic matter from microbial degradation induced by Fe3+ and Mn4+. Future studies could particularly assess whether anaerobic CH4 oxidation has any ecological relevance in reducing CH4 emissions from the numerous CH4-emitting shallow lakes in boreal and tundra landscapes., (© FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions.

Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as ε-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.

Although complex cooccurrence patterns have been described for microbes in natural communities, these patterns have scarcely been interpreted in the context of ecosystem functioning and stability. Here we constructed networks from species cooccurrences between pairs of microorganisms which were extracted from five individual aquatic time series, including a dystrophic and a eutrophic lake as well as an open ocean site. The resulting networks exhibited higher clustering coefficients, shorter path lengths, and higher average node degrees and levels of betweenness than those of random networks. Moreover, simulations demonstrated that taxa with a large number of cooccurrences and placement at convergence positions in the network, so-called "hubs" and "bottlenecks," confer resistance against random removal of "taxa." Accordingly, we refer to cooccurrences at convergence positions as system-relevant interdependencies, as they, like hubs and bottlenecks, determine network topology. These topology features of the cooccurrence networks point toward microbial community dynamics being resistant over time and thus could provide indicators for the state of ecosystem stability., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Background: Asthma and allergies are common and cause substantial burden in symptoms and suffering, hospitalizations and medication costs. However, despite the high prevalence, asthma burden has already decreased in Finland in 2000s., Objective: We carried out an asthma barometer survey in all Finnish pharmacies to study changes in asthma severity and control, and use of health care services from 2001 to 2010., Methods: Asthma severity, comorbid allergic conditions, and use of medication and health care services were assessed in subjects who purchased asthma or allergy medication from the pharmacies all across the country during one week in 2001 and again in 2010. In 2001, 3,062 patients (mean age, 49 years), and in 2010, 1,114 patients (mean age, 51 years) participated., Results: In 2001 90% and in 2010 73% of the respondents reported physician-diagnosed asthma and were entitled to special reimbursement for their drug costs, i.e., they needed regular maintenance treatment. In 2001, 10% of the asthmatics regarded their disease as severe, compared with 4% in 2010, while the figures for mild asthma were 45% and 62%, respectively (p < 0.001). The proportion of patients needing emergency care during the last year decreased from 34% (2001) to 14% (2010) (p < 0.001) and the need for hospitalizations from 18% to 6% (p < 0.001). Smoking reduced from 24% to 18% among asthmatics ( p = 0.002). In 2010, risk factors for severe asthma were older age, comorbid atopic eczema, and food allergy., Conclusion: During ten years, self-reported asthma severity has reduced and disease control improved in Finland.

Electronic prescriptions affect pharmacy workflows. In this study, we measure the workflow efficiency in pharmacies in 2006 and 2012: both, in traditional workflow when electronic prescription was not in use, and in new direct delivery workflow, which is the mandated workflow model in the case of electronic prescriptions.

Background: In an automated dose dispensing (ADD) service, medicines are packed in unit-dose bags according to administration times. When the service is initiated, the patient's medication list is reconciled and the medication is reviewed on the basis of this list., Objective: The aim of this national study was to investigate how the medication list was reconciled, what type of medication review was conducted, and what changes were made to the patient's medications when the ADD service is initiated., Setting: Primary care in Finland., Method: All patients enrolled in the service during a 3-week period in autumn 2010 were included in the study. All community pharmacies (n = 267) purchasing unit-dose bags from Espoonlahti Pharmacy documented the actions taken in the ADD initiation process using a structured data collection sheet., Main Outcome Measure: Information sources needed in medication reconciliation, the type of medication review conducted and changes made to patients' medications., Results: Documentation was completed for 147 out of 325 new ADD users resulting 45 % as a response rate. More than one source was needed for 63 % of the patients in medication reconciliation. The most common sources used were nursing staff (72 % of the patients) and an existing medication list (71 %). Some type of medication review, most commonly a prescription review, was conducted for the majority of the patients (96 %), usually in multi-professional collaboration. Treatment-related changes were made for 43 % of the patients and technical changes were made for 93 % of the patients., Conclusion: The medication list was incomplete for more than half of the patients. Some type of medication review was conducted for most of the patients. Both treatment-related changes and technical changes were made on patients' medications during the initiation process. The start-up process of the ADD service needs further development to ensure a standard procedure and optimum use of resources.

The recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS) of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters.

Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.

This commentary describes the development and evidence-base of the Comprehensive Medication Review (CMR) procedure for community and hospital settings in Finland. The development was coordinated by a national steering group. The group collaborated with 26 experienced pharmacists who developed and tested CMR procedures during a 1.5 year accreditation training for CMR. The development consisted of: (1) a literature review and inventory of medication review procedures in different countries; (2) the creation of potential procedures and related documentation; (3) integration of potential procedures into a national standard procedure; and (4) piloting the standard procedure in practice settings. The resulting comprehensive medication review procedure requires access to a patient's clinical information, an in-home patient interview and a case conference with the collaborating physician. This procedure covers the four main dimensions critical for safe and appropriate geriatric pharmacotherapy: aging and safety; co-morbidities; polypharmacy; and adherence. The CMR measures and documentation build on these dimensions.