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Biological soil crusts (BSCs) are key components of polar ecosystems. These complex communities are important for terrestrial polar habitats as they include major primary producers that fix nitrogen, prevent soil erosion and can be regarded as indicators for climate change. To study the genus richness of microalgae and Cyanobacteria in BSCs, two different methodologies were employed and the outcomes were compared: morphological identification using light microscopy and the annotation of ribosomal sequences taken from metatranscriptomes. The analyzed samples were collected from Ny-Ålesund, Svalbard, Norway, and the Juan Carlos I Antarctic Base, Livingston Island, Antarctica. This study focused on the following taxonomic groups: Klebsormidiophyceae, Chlorophyceae, Trebouxiophyceae, Xanthophyceae and Cyanobacteria. In total, combining both approaches, 143 and 103 genera were identified in the Arctic and Antarctic samples, respectively. Furthermore, both techniques concordantly determined 15 taxa in the Arctic and 7 taxa in the Antarctic BSC. In general, the molecular analysis indicated a higher microalgal and cyanobacterial genus richness (about 11 times higher) than the morphological approach. In terms of eukaryotic algae, the two sampling sites displayed comparable genus counts while the cyanobacterial genus richness was much higher in the BSC from Ny-Ålesund. For the first time, the presence of the genera Chloroidium, Ankistrodesmus and Dunaliella in polar regions was determined by the metatranscriptomic analysis. Overall, these findings illustrate that only the combination of morphological and molecular techniques, in contrast to one single approach, reveals higher genus richness for complex communities such as polar BSCs.

There has been a gradual increase in 16S deep sequencing studies on infectious disease materials. Management of bacterial DNA contamination is a major challenge in such diagnostics, particularly in low biomass samples. In this article, we investigate patterns of microbial DNA contamination in targeted 16S rRNA amplicon sequencing (16S deep sequencing) and demonstrate how this can be used to filter background bacterial DNA in diagnostic microbiology. We also investigate the importance of sequencing depth. We first determined the patterns of contamination by performing repeat 16S deep sequencing of negative and positive extraction controls. This process identified a few bacterial species dominating across all replicates but also a high intersample variability among low abundance contaminant species in replicates split before PCR amplification. Replicates split after PCR amplification yielded almost identical sequencing results. On the basis of these observations, we suggest using the abundance of the most dominant contaminant species to define a threshold in each clinical sample from where identifications with lower abundances possibly represent contamination. We evaluated this approach by sequencing of a diluted, staggered mock community and of bile samples from 41 patients with acute cholangitis and noninfectious bile duct stenosis. All clinical samples were sequenced twice using different sequencing depths. We were able to demonstrate the following: (i) The high intersample variability between sequencing replicates is caused by events occurring before or during the PCR amplification step. (ii) Knowledge about the most dominant contaminant species can be used to establish sample-specific cutoffs for reliable identifications. (iii) Below the level of the most abundant contaminant, it rapidly becomes very demanding to reliably discriminate between background and true findings. (iv) Adequate sequencing depth can be claimed only when the analysis also picks up background contamination. IMPORTANCE There has been a gradual increase in 16S deep sequencing studies on infectious disease materials. Management of bacterial DNA contamination is a major challenge in such diagnostics, particularly in low biomass samples. Reporting a contaminant species as a relevant pathogen may cause unnecessary antibiotic treatment or even falsely classify a noninfectious condition as a bacterial infection. Yet, there are few studies on how to filter contamination in clinical microbiology. Here, we demonstrate that sequencing of extraction controls will not reveal the full spectrum of contaminants that could occur in the associated clinical samples. Only the most abundant contaminant species were consistently detected, and we present how this can be used to set sample specific thresholds for reliable identifications. We believe this work can facilitate the implementation of 16S deep sequencing in diagnostic laboratories. The new data we provide on the patterns of microbial DNA contamination is also important for microbiome research.

Biological soil crusts (BSCs) occur in arid and semi-arid regions worldwide including the Polar Regions. They are important ecosystem engineers, and their composition and areal coverage should be understood before assessing key current functional questions such as their role in biogeochemical nutrient cycles and possible climate change scenarios. Our aim was to investigate the variability of BSCs from Arctic Svalbard and the Antarctic Island, Livingston, using vegetation surveys based on classification by functional group. An additional aim was to describe the structure of BSCs and represent a classification system that can be used in future studies to provide a fast and efficient way to define vegetation type and areal coverage. Firstly, this study demonstrates huge areas occupied by BSCs in Arctic Svalbard, with up to 90 % of soil surface covered, dominated by bryophytes and cyanobacteria, and showing an unexpectedly high variability in many areas. Livingston Island has lower percentage coverage, up to 55 %, but is dominated by lichens. Our findings show that both Polar Regions have varied BSC coverage, within the sites and between them, especially considering their harsh climates and latitudinal positions. Secondly, we have classified the BSCs of both areas into a system that describes the dominant functional groups and local geography, creating a simple scheme that allows easy identification of the prevailing vegetation type. Our results represent the first contribution to the description of BSCs based on their functional group composition in Polar Regions.

Biological soil crusts (BSCs) are amalgamations of autotrophic, heterotrophic and saprotrophic organisms. In the Polar Regions, these unique communities occupy essential ecological functions such as primary production, nitrogen fixation and ecosystem engineering. Here, we present the first molecular survey of BSCs from the Arctic and Antarctica focused on both eukaryotes and prokaryotes as well as passive and active biodiversity. Considering sequence abundance, Bryophyta is among the most abundant taxa in all analyzed BSCs suggesting that they were in a late successional stage. In terms of algal and cyanobacterial biodiversity, the genera Chloromonas, Coccomyxa, Elliptochloris and Nostoc were identified in all samples regardless of origin confirming their ubiquitous distribution. For the first time, we found the chrysophyte Spumella to be common in polar BSCs as it was present in all analyzed samples. Co-occurrence analysis revealed the presence of sulfur metabolizing microbes indicating that BSCs also play an important role for the sulfur cycle. In general, phototrophs were most abundant within the BSCs but there was also a diverse community of heterotrophs and saprotrophs. Our results show that BSCs are unique microecosystems in polar environments with an unexpectedly high biodiversity.

We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hyper-variable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (ca. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new generation sequencing primers. In mountain grasslands soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 OTUs at 97% similarity threshold from 26 samples, with ca. 50,000 sequences per site, and only 8% of non-cercozoan sequences. We could contribute to a further increase of the diversity of Cercozoa, since only 43% of the OTUs were 97-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.

Malnutrition linked to noncommunicable diseases presents major health problems across Europe. The World Health Organisation encourages countries to conduct national dietary surveys to obtain data to inform public health policies designed to prevent noncommunicable diseases. Data on 27334 participants aged 19-64y were harmonised and pooled across national dietary survey datasets from 12 countries across the WHO European Region. Weighted mean nutrient intakes were age-standardised using the Eurostat 2013 European Standard Population. Associations between country-level Gross Domestic Product (GDP) and key nutrients and nutrient densities were investigated using linear regression. The potential mitigating influence of participant-level educational status was explored. Higher GDP was positively associated with total sugar intake (5·0% energy for each 10% increase in GDP, 95% CI 0·6, 9·3). Scandinavian countries had the highest vitamin D intakes. Participants with higher educational status had better nutritional intakes, particularly within lower GDP countries. A 10% higher GDP was associated with lower total fat intakes (-0·2% energy, 95% CI -0·3, -0·1) and higher daily total folate intakes (14μg, 95% CI 12, 16) in higher educated individuals. Lower income countries and lower education groups had poorer diet, particularly for micronutrients. We demonstrate for the first time that higher educational status appeared to have a mitigating effect on poorer diet in lower income countries. It illustrates the feasibility and value of harmonising national dietary survey data to inform European policy regarding access to healthy diets, particularly in disadvantaged groups. It specifically highlights the need for strong policies supporting nutritional intakes, prioritising lower education groups and lower income countries.

Subglacial meltwater channels beneath the Antarctic Ice Sheet have been reported, but the nature and distribution of these meltwater pathways are unclear. Remote sensing observations reveal persistent channelized features beneath the Filchner–Ronne Ice Shelf in West Antarctica, suggesting widespread channelized flow driven by melting. Meltwater generated beneath the Antarctic Ice Sheet exerts a strong influence on the speed of ice flow, in particular for major ice streams 1 , 2 . The subglacial meltwater also influences ocean circulation beneath ice shelves, initiating meltwater plumes that entrain warmer ocean water and cause high rates of melting 3 . However, despite its importance, the nature of the hydrological system beneath the grounded ice sheet remains poorly characterized. Here we present evidence, from satellite and airborne remote sensing, for large channels beneath the floating Filchner–Ronne Ice Shelf in West Antarctica, which we propose provide a means for investigating the hydrological system beneath the grounded ice sheet. We observe features on the surface of the ice shelf from satellite imagery and, using radar measurements, show that they correspond with channels beneath the ice shelf. We also show that the sub-ice-shelf channels are aligned with locations where the outflow of subglacial meltwater has been predicted. This agreement indicates that the sub-ice-shelf channels are formed by meltwater plumes, initiated by subglacial water exiting the upstream grounded ice sheet in a focused (channelized) manner. The existence of a channelized hydrological system has implications for the behaviour and dynamics of ice sheets and ice shelves near the grounding lines of ice streams in Antarctica.

The World Health Organisation encourages countries to conduct national dietary surveys to obtain data to inform public health policies designed to prevent NCDs (3). Higher GDP was positively associated with total sugar intake (5.0% energy for each 10% increase in GDP, 95% CI 0.6%, 9.3%). Scandinavian countries had the highest vitamin D intakes and Central and Eastern European countries generally had lower total folate intakes.

The bed of the West Antarctic ice sheet is, in places, more than 1.5 km below sea level. Radio-echo sounding data from the Weddell Sea sector of Antarctica reveal a large subglacial basin immediately upstream of the ice sheet’s grounding line, with a steep reverse gradient and a smooth floor. The bed of the West Antarctic Ice Sheet is, in places, more than 1.5 km below sea level 1 , 2 . It has been suggested that a positive ice-loss feedback may occur when an ice sheet’s grounding line retreats across a deepening bed 1 , 2 , 3 . Applied to the West Antarctic Ice Sheet, this process could potentially raise global sea level 4 by more than 3 m. Hitherto, attention has focussed on changes at the Siple Coast 5 , 6 , 7 and Amundsen Sea embayment 8 , 9 , 10 sectors of West Antarctica. Here, we present radio-echo sounding information from the ice sheet’s third sector, the Weddell Sea embayment, that reveals a large subglacial basin immediately upstream of the grounding line. The reverse bed slope is steep, with about 400 m of decline over 40 km. The basin floor is smooth and flat, with little small-scale topography that would delay retreat, indicating that it has been covered with marine sediment 5 , 11 and was previously deglaciated. Upstream of the basin, well-defined glacially carved fjords with bars at their mouths testify to the position of a former ice margin about 200 km inland from the present margin. Evidence so far suggests that the Weddell Sea sector of the West Antarctic Ice Sheet has been stable, but in the light of our data we propose that the region could be near a physical threshold of substantial change.

The Institute Ice Stream (IIS) rests on a reverse-sloping bed, extending >150 km upstream into the ~1.8 km deep Robin Subglacial Basin, placing it at the threshold of marine ice-sheet instability. Understanding IIS vulnerability has focused on the effect of grounding-line melting, which is forecast to increase significantly this century. Changes to ice-flow dynamics are also important to IIS stability, yet little is known about them. Here we reveal that the trunk of the IIS occurs downstream of the intersection of three discrete subglacial features; a large ‘active’ subglacial lake, a newly-discovered sharp transition to a zone of weak basal sediments and a major tectonic rift. The border of IIS trunk flow is confined by the sediment on one side, and by a transition between basal melting and freezing at the border with the Bungenstock Ice Rise. By showing how basal sediment and water dictate present-day flow of IIS, we reveal that ice-sheet stability here is dependent on this unusual arrangement.