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It is well documented that microbial biomass increases during winter in cold mountain or tundra ecosystems, but the cause and mechanism of such accumulation is unclear. Results from a grassland in Iceland demonstrated that the microbial biomass carbon (MBC, measured by the fumigation-extraction method) increased in winter, while microbial DNA content remained constant. We thus hypothesized that this accumulation of microbial biomass during the cold season is driven by the decrease in temperature, that increases the carbon storage of individual cells, but not by an increase in microbial cell numbers.To test this hypothesis, we conducted a laboratory incubation experiment with soils from a grassland in Iceland sampled before the onset of winter in early October (around 9 °C). We then exposed the soils to decreasing temperatures (0.5 °C, 3 °C, 6 °C and 9 °C) over five months. We analyzed microbial biomass carbon (MBC) and quantified the DNA content. Over the course of five months, we found higher MBC values at cool temperatures compared to warm conditions. As expected, cooling did not affect the DNA content, leading to a significantly higher MBC to DNA ratio when soils were incubated at 0.5 °C compared to 9 °C. This indicates that numbers of microbial cells did not change across temperatures, but that microbes at lower temperatures stored more carbon. We also found similar patterns in soils collected at different time points in the field. Furthermore, we estimated microbial DNA production, i.e., growth rates, by measuring the incorporation of 18O from labelled water into DNA. We observed lower microbial growth rates under field conditions in winter, indicating that increasing biomass carbon was not due to increased growth and that growth and turnover was balanced at all temperatures. Instead, we suggest that carbon uptake (which was decreased at lower temperatures) was less affected by cold temperatures than growth, so that microbial carbon could accumulate. We also verified this pattern in growth and carbon uptake rates with decreasing temperatures in the laboratory incubation experiment.Decreasing growth (cell division) and turnover rates with decreasing temperatures, at a lower but sustained carbon uptake rate, suggest that the cell size of soil microorganisms may increase when exposed to cooling. We will show and discuss first results from measurements with a suspended microchannel resonator (SMR), that, together with microscopic imaging allows to assess the mass (size) of individual cells of microorganisms at different temperatures.

Objectives A carrier prototype by Aerocom® (Schwäbisch Gmünd, Germany) for pneumatic tube systems (PTS) is able to transport 9 blood tubes which are automatically fixed by closing the lid. In this study, we examined the influence of the transport on blood sample quality using the carrier prototype comparing to courier transport and a conventional carrier (AD160, Aerocom®). Methods Triplicate blood samples sets (1 lithium heparin, 1 EDTA, 1 sodium citrate) of 35 probands were split among the transportation methods: 1. courier, 2. conventional carrier, and 3. carrier prototype. After transport 51 measurands from clinical chemistry, hematology and coagulation were measured and compared. Results Overall, 49 of the investigated 51 measurands showed a good concordance among the three transport types, especially between the conventional carrier and the carrier prototype. Focusing on well-known hemolysis sensitive measurands, potassium showed no statistically significant differences. However, between courier and both carrier types lactate dehydrogenase (LDH) and free hemoglobin (fHb) showed statistically significant shifts, whereas the clinical impact of the identified differences was neglectable. The median concentration of fHb, for example, was 0.29 g/L (18 µmol/L), 0.31 g/L (19 µmol/L) and 0.32 g/L (20 µmol/L) for courier transport, conventional carrier and carrier prototype, respectively. These differences cannot be resolved analytically since the minimal difference (MD) for fHb is 0.052 g/L (3.23 µmol/L), at this concentration. Conclusions The carrier prototype by Aerocom® is suitable for transportation of diagnostic blood samples. The overall workflow is improved by decreasing hands-on-time on the ward and laboratory while minimizing the risk of incorrectly packed carriers.

BackgroundThe soil alpine microbiome is dependent on season and elevation, yet there is limited understanding of how complex communities are differentially shaped by abiotic and biotic factors. Here we investigated the spring-to-summer dynamics of soil microbiomes in alpine grasslands, focussing on soil food web interactions. To this end, we conducted a survey along altitudinal transects in three mountains in the Alps, in spring at snowmelt and in the following summer, recorded vegetation and topographic, climatic and edaphic parameters for 158 soil samples. By using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified by nutrition guilds.ResultsOur results show: (i) that biotic interactions could explain more variation of the microbial communities than topographic and edaphic variables, more for consumers than for preys, and this effect was stronger in summer than in spring; (ii) a seasonal dynamic in biotic interactions: the consumers’ pressure on preys increases from spring to summer, resulting in a higher diversity and evenness of preys.ConclusionIn alpine grasslands, consumers effectively contribute to maintain the diverse soil bacterial and fungal community essential for ecosystem functioning.

In temperate regions, climate warming alters temperature and precipitation regimes. During winter, a decline in insulating snow cover changes the soil environment, where especially frost exposure can have severe implications for soil microorganisms and subsequently for soil nutrient dynamics. Here, we investigated winter climate change responses in European beech forests soil microbiome. Nine study sites with each three treatments (snow exclusion, insolation, and ambient) were investigated. Long-term adaptation to average climate was explored by comparing across sites. Triplicated treatment plots were used to evaluate short-term (one single winter) responses. Community profiles of bacteria, archaea and fungi were created using amplicon sequencing. Correlations between the microbiome, vegetation and soil physicochemical properties were found. We identify core members of the forest-microbiome and link them to key processes, for example, mycorrhizal symbiont and specialized beech wood degraders (fungi) and nitrogen cycling (bacteria, archaea). For bacteria, the shift of the microbiome composition due to short-term soil temperature manipulations in winter was similar to the community differences observed between long-term relatively cold to warm conditions. The results suggest a strong link between the changes in the microbiomes and changes in environmental processes, for example, nitrogen dynamics, driven by variations in winter climate.

Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.

Climatic warming has been hypothesized to accelerate organic matter decomposition by soil microorganisms and thereby enhance carbon (C) release to the atmosphere. However, the long-term consequences of soil warming on belowground biota interactions are poorly understood. Here we investigate how geothermal warming by 6 degrees C for more than 50 years affects soil microbiota. Using metatranscriptomics we obtained comprehensive profiles of the prokaryotic, eukaryotic and viral players of the soil microbial food web. When compared to ambient soil temperature conditions, we found pronounced differences in taxa abundances within and between trophic modules of the soil food web. Specifically, we observed a 'trophic downgrading' at elevated temperature, with soil fauna decreasing in abundance, while predatory bacteria and viruses became relatively more abundant. We propose that the drivers for this shift are previously observed decreases in microbial biomass and soil organic carbon, and the increase in soil bulk density (decrease in soil porosity) at elevated temperature. We conclude that a trophic downgrading may have important implications for soil carbon sequestration and nutrient dynamics in a warming world.

How soil microorganisms respond to global warming is a key question in microbial ecology and eminently relevant for soil ecosystems, the terrestrial carbon cycle, and the climate system. However, physiological responses of soil microorganisms – key to infer future soil-climate feedbacks – are poorly understood.We here make use of the longest lasting in situ soil warming experiment worldwide, ForHot, in which an Icelandic subarctic grassland site has been exposed to natural geothermal soil warming for more than 50 years. Using a metatranscriptomics approach, allowing the comprehensive study of the entire active soil microbial community and their functions by analysing expressed genes, we revealed key physiological responses of soil Bacteria to medium- (8 years) and long-term (>50 years) soil warming of +6 °C.Irrespective of the duration of warming, we observed a community-wide upregulation of central (carbohydrate) metabolisms and cell replication and a downregulation of the bacterial protein biosynthesis machinery in the warmed soils. This coincided with a decrease of microbial biomass, a decrease of total and biomass-specific RNA content, and lower soil substrate concentrations in the warmed soils. We conclude that higher biochemical reaction rates, caused by higher temperatures, allow soil Bacteria to reduce their cellular number of ribosomes, the macromolecular complexes carrying out protein biosynthesis. To further test this we revisited the site and conducted a short-term warming experiment (6 weeks, +6 °C), which supported our conclusion.The downregulation of the protein biosynthesis machinery (i.e., the reduction of ribosomes) liberates energy and matter, leading to a resource re-allocation, and allows soil Bacteria to maintain high metabolic activities and cell division rates even after decades of warming.

How soil microorganisms respond to global warming is key to infer future soil-climate feedbacks, yet poorly understood. Here we applied metatranscriptomics to investigate microbial physiological responses to medium- (8 years) and long-term (>50 years) subarctic grassland soil warming of +6 °C. Besides indications for a community-wide upregulation of central metabolisms and cell replication we observed a downregulation of the protein biosynthesis machinery in the warmed soils, coinciding with a lower microbial biomass, RNA, and soil substrate content. We conclude that permanently accelerated reaction rates at higher temperatures and reduced substrate concentrations results in a cellular reduction of ribosomes, the macromolecular complexes carrying out protein biosynthesis. Later efforts to test this, including a short-term warming experiment (6 weeks, +6 °C), further supported our conclusion. Downsizing the protein biosynthesis machinery facilitates liberation of energy and matter, allowing microorganisms to maintain high metabolic activities and cell division rates even after decades of warming.

Fungi play a crucial role in terrestrial Arctic ecosystems as symbionts of vascular plants and nutrient recyclers in soil, with many species persistently or temporarily inhabiting the phyllosphere of the vegetation. In this study we apply high-throughput sequencing to investigate the mycobiome of 172 samples of fresh (current year) and aged (3 year old) needles of Picea glauca from three sites over a distance of 500 km in Alaska (USA). We analysed Illumina-generated ITS2 sequences to relate mycobiome data with phenotypic tree traits, measures of genetic variation and climate variables obtained from long-term monitoring of the sites. Alpha-diversity declined with increasing environmental stress/climate harshness. Fungal communities differed in richness and taxonomic composition between sites, with a pronounced difference in the relative abundance of OTUs assigned to species of the rust genus Chrysomyxa , plant pathogens which seem to have been in an outbreak at two sites at the time of sampling. Beside climate parameters, needle age was the second strongest explanatory variable of the mycobiome composition, whereas we found no effect of tree genetic variation, indicating that environmental and tree trait specific variables mainly determined individual white spruce mycobiomes at Alaska's treelines.

The diversity of dark-spored myxomycetes in forest ground litter and soil from four study plots across a fire chronosequence in Nizhne-Svirskiy Nature Reserve (northwest of Russia) was assessed by a DNA metabarcoding approach. The history of fire disturbances and the season of sampling influenced the composition of myxomycete assemblages. Several species showed substrate preferences different from what is known from fruiting body records. A high abundance of nivicolous species in the majority of the samples suggests that this ecological group constitutes a common element of soil microbial communities in lowland taiga forests. Four species are reported for the Leningrad region for the first time. Our results support the hypothesis that amoebae populations of myxomycetes may have much wider ecological niches than indicated by records of fructifications, and further environmental studies may provide valuable new insights on myxomycete ecology and distribution.

We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.

Microbial physiological responses to long-term warming are poorly understood. Here we applied metatranscriptomics to investigate how microorganisms react to medium-term (8 years) and long-term (>5 decades) subarctic grassland soil warming of +6 °C. Decades, but not years, of warming induced changes in relative abundances of eukaryotic, prokaryotic, and viral transcripts and reduced functional richness. However, irrespective of the duration of warming, we observed a community-wide upregulation of central (carbon) metabolisms and cell replication in the warmed soils, whereas essential energy metabolism and protein biosynthesis complexes and pathways were downregulated. This coincided with a decrease of microbial biomass and lower soil substrate concentrations (e.g. dissolved organic carbon and phosphorus). We conclude that permanently accelerated reaction rates at higher temperatures facilitate a downregulation of energy metabolism and protein biosynthesis, potentially freeing energy and matter for substrate acquisition and growth. This resource allocation seems to be a common response in microorganisms and allows sustaining high metabolic activities and replication rates even after decades of soil warming.

Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.

Future increases in temperature and cloud cover will alter plant growth and decomposition of the large carbon pools stored in Arctic soils. A better understanding of interactions between above- and belowground processes and communities of plants and microorganisms is essential for predicting Arctic ecosystem responses to climate change. We measured ecosystem CO2 fluxes during the growing season for seven years in a dwarf-shrub tundra in West Greenland manipulated with warming and shading and experiencing a natural larvae outbreak. Vegetation composition, soil fungal community composition, microbial activity, and nutrient availability were analyzed after six years of treatment. Warming and shading altered the plant community, reduced plant CO2 uptake, and changed fungal community composition. Ecosystem carbon accumulation decreased during the growing season by 61% in shaded plots and 51% in warmed plots. Also, plant recovery was reduced in both manipulations following the larvae outbreak during the fifth treatment year. The reduced plant recovery in manipulated plots following the larvae outbreak suggests that climate change may increase tundra ecosystem sensitivity to disturbances. Also, plant community changes mediated via reduced light and reduced water availability due to increased temperature can strongly lower the carbon sink strength of tundra ecosystems.

Introduction The diagnosis of diabetes mellitus is based on suitable cut-off values of specific biomarkers, such as the concentration of glucose in plasma. The German Diabetes Association has very recently published a clinical practice guideline on the definition, classification and diagnosis of diabetes mellitus that recommends measurements of plasma glucose concentration have an imprecision defined as a minimal difference (MD) of at a fasting plasma glucose concentration of 7.0 mmol/L. To obtain reliable values for the MD, we investigated long-term and short-term measurement uncertainty. Methods The imprecision was determined by two approaches: (1) a long-term dataset with imprecision based on the Guideline of the German Medical Association on Quality Assurance in Medical Laboratory Examinations (Rili-BAEK), in a medical laboratory operating 24/7, using internal quality control (IQC) data for four concentrations during a 10-year period; and (2) a detailed short-term dataset with imprecision assessed by hourly measurements of control materials. These datasets were used to calculate the MD cut-off (MDcut-off) as: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\text{MD}}_{\text{cut-off}} = k \times {\text{SD}} $$\end{document}MDcut-off=k×SD = 2 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \times {\text{SD}} $$\end{document}×SD, where SD is the standard deviation and k = 2 represents a confidence level of 95%. Results The MDcut-off of ≤ 0.7 mmol/L at a fasting plasma glucose concentration of 7.0 mmol/L (MDcut-off 7.0) for the long-term and the short-term approaches were 0.44 and 0.40 mmol/L, respectively. The MDcut-off 7.0 from both approaches was therefore below the recommended value of 0.7 mmol/L. It was noted that the variability in performance within and between instruments can be covered by reporting the long-term MDcut-off 7.0 across all connected instruments. In this study, stable results for the MDcut-off 7.0 were obtained after 1 year. Conclusion Imprecision as measured by IQC data is remarkably stable over many years of operation. Current imprecision assessment usually focuses on only single instruments, whereas clinicians perceive the measurement as the result of the combined analytical performance of all instruments used for a certain assay. In the clinical setting, the MD may be a more useful measure of imprecision, and we suggest deriving the MDcut-off combined from all instruments and control cycles that are used in the patient care setting for a given analyte. Electronic supplementary material The online version of this article (10.1007/s13300-019-00740-w) contains supplementary material, which is available to authorized users.

Plant-associated mycobiomes in extreme habitats are understudied and poorly understood. - We analysed Illumina-generated ITS1 sequences from the needle mycobiome of white spruce (Picea glauca) at the northern treeline in Alaska (USA). Sequences were obtained from the same DNA that was used for tree genotyping. In the present study, fungal metabarcoding and tree microsatellite data were compared for the first time. - In general, neighbouring trees shared more fungal taxa with each other than trees growing in further distance. Mycobiomes correlated strongly with phenological host traits and local habitat characteristics contrasting a dense forest stand with an open treeline site. Genetic similarity between trees did not influence fungal composition and no significant correlation existed between needle mycobiome and tree genotype. - Our results suggest the pronounced influence of local habitat conditions and phenotypic tree traits on needle-inhabiting fungi. By contrast, the tree genetic identity cannot be benchmarked as a dominant driver for needle-inhabiting mycobiomes, at least not for white spruce in this extreme environment.

Among soil-inhabiting protists, myxomycetes stand out by their macroscopic fructifications which have allowed studies on their ecology and distribution for more than two hundred years. One of the most distinct ecological guilds in myxomycetes are the nivicolous or “snowbank” myxomycete species, which produce fruit bodies at the edge of melting snowbanks in spring. Relationship between the occurrence of fructifications and myxamoebae remain unknown. In this study we used modern molecular techniques, by direct DNA amplification from soil extracts (NGS metabarcoding) to compare the distribution of soil-inhabiting myxamoebae found in 2016 with fructifications from the same sites collected over the course of four years (2013, 2015–17) along an elevational transect in the northern German Alps. A coherent community composition between fructification and soil myxamoebae, though with species-specific differences in relative abundance, was revealed. Although patterns varied among species, myxamoebae were found at both low and high elevations, whereas fruit bodies were mainly found at higher elevations, likely explained by the presence of a stable and long-lasting snow cover. In addition, a year to year comparison of fructification records support the hypothesis that the abundance of fructifications strongly depends on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.

International audience; Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α-and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.

Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.