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The history of Greenland is marked by repeated waves of Paleo-Inuit immigration from North America. From the 10th to 15th century, Norse settlers immigrated from Europe and flourished in southwest Greenland with the introduction of domestic livestock. The different Inuit and Norse cultures created middens by dumping and accumulating domestic waste. Today, animal bones, excrements, mollusc shells and other artefacts associated with past human occupation are a valuable resource for archaeologists to study these past societies’ diets, habits, life and death. However, these archaeological features might also represent unique microbial reservoirs of organisms from mixed origins within an organic rich matrix. A latent source of microbes, that is currently exposed to climate change. Drastic increase in temperature observed in Greenland leads midden material to be carried away by enlarged melting water from snowdrifts. Rising sea levels and loss of sea ice also accelerates the erosion of middens that are most often situated along the coast and might be washed out into the sea. This raises the question whether these sites represent a disease emergence threat. Especially that the increase in plant production in West Greenland is opening for the development of sheep farming in the Nuuk area, exactly where sheep farms were situated during the Norse era and abandoned for the past 500 years. In the VEO project, we aim to evaluate if ancient Arctic settlements are possible hot-spots for pathogenic agents, and if potential pathogens may spread to the surrounding environment. Using metagenomics, we compared the microbial communities of middens from different age and location in West and South Greenland (Paleo-Inuit, Norse and Modern Inuit middens) to pristine surrounding soils. We found that even after hundreds of years, the middens harbor a distinctive microbial signature enriched in host-associated and/or pathogenic bacteria belonging to Clostridium an

The notion of life outside Earths boundaries has captivated man's imagination for centuries. In the recent years many exoplanets have been located and studied, but there is a chance we may not need to look further than our own solar system neighbourhood to uncover a biologically liveable environment. At first glance, the low temperatures, water deficit and radiation pressure, makes Mars an unlikely candidate for habitation, but the persistence of Earths biology has shown us that life can be pushed to the limit, and persist. For any life to survive on Mars, it is crucial that it can withstand the extreme UV radiation environment, especially the UVC radiation, present on the planet. In this study Chroococcidiopsis cubana show extreme tolerance towards UVC radiation compared to Nostoc sp. NHVL1, as the CO2 consumption pr. day of NHVL1 is halved more than five-fold with increasing UVC radiation compared to C. cubana. Furthermore, 745 J m-2 of monochromatic UVC radiation did not affect the activity of C. cubana and after a flux of 22.356 J m-2 there was still significant biological activity. It was also revealed that evolutionary adaptions for C. cubana towards UVC radiation seems possible over short timespans, as the possible mutant C. cubana C50 had a 38.2% higher CO2 consumption pr. day than its parental strain C. cubana, after experiencing a flux of 22.356 J m-2. The study also finds that both elevated CO2 and perchlorate has a negative synergistic effect in combination with increasing UVC radiation exposure, and the transcription of the ScyA gene increases with increasing UVC flux. Even though C. cubana is not able to survive for longer periods in the present UV environment, it presents as an interesting candidate for further research, and could be a candidate in evolutionary studies focussing on the bacteria's potential to evolve to survive the barren red plains of Mars.

This study investigates spatial-temporal trends in N2O emissions from coffee production systems in Costa Rica with a focus on the effects of nitrogen fertilisation, topography and soil type. This is done by combining (i) multi-year continuous dynamic chamber measurements from sites with different fertilisation levels, (ii) static chamber measurements taken along a typical sloping coffee field and (iii) measurements from a laboratory incubation experiment with nutrient addition to different soil types. In the field and in the laboratory, additions included standard NPK fertiliser, ammonium nitrate (NH4NO3) as well as potassium nitrate (KNO3). Soils in a laboratory experiment were incubated under both drained and flooded conditions. Continuous measurements from automatic chambers show that annual N2O fluxes were dominated by bursts over few weeks following N-fertilisation with peak emissions up to 60 g N-N2O ha−1 day−1. A two-month slope experiment with static chambers after KNO3-fertilisation with 90 kg N ha−1 showed N2O significant differences between the highest daily emission rates from the top and the bottom of the slope (134 ± 20 g N-N2O ha−1 and 336 ± 104 g N-N2O ha−1, respectively) which can be explained by NO3- transport downhill and flooded conditions favouring denitrification at the bottom of the slope. Incubation experiments indicate that denitrification is the main process controlling N2O emissions but also that nitrification can result in low N2O emission rates under drained conditions. It can be concluded that the reported N2O emissions from the coffee agroforestry systems are generally low, but may be underestimated, as both poorly drained depressions functioning as N2O hotspots as well as temporal N2O bursts need to be taken into account., This study investigates spatial-temporal trends in N2O emissions from coffee production systems in Costa Rica with a focus on the effects of nitrogen fertilisation, topography and soil type. This is done by combining (i) multi-year continuous dynamic chamber measurements from sites with different fertilisation levels, (ii) static chamber measurements taken along a typical sloping coffee field and (iii) measurements from a laboratory incubation experiment with nutrient addition to different soil types. In the field and in the laboratory, additions included standard NPK fertiliser, ammonium nitrate (NH4NO3) as well as potassium nitrate (KNO3). Soils in a laboratory experiment were incubated under both drained and flooded conditions. Continuous measurements from automatic chambers show that annual N2O fluxes were dominated by bursts over few weeks following N-fertilisation with peak emissions up to 60 g N-N2O ha−1 day−1. A two-month slope experiment with static chambers after KNO3-fertilisation with 90 kg N ha−1 showed N2O significant differences between the highest daily emission rates from the top and the bottom of the slope (134 ± 20 g N-N2O ha−1 and 336 ± 104 g N-N2O ha−1, respectively) which can be explained by NO3- transport downhill and flooded conditions favouring denitrification at the bottom of the slope. Incubation experiments indicate that denitrification is the main process controlling N2O emissions but also that nitrification can result in low N2O emission rates under drained conditions. It can be concluded that the reported N2O emissions from the coffee agroforestry systems are generally low, but may be underestimated, as both poorly drained depressions functioning as N2O hotspots as well as temporal N2O bursts ne

The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly understood. Here, in a four-year experiment on Svalbard, we warmed patterned ground soil with open top chambers and biannually irrigated the soil to predict the responses of its microbial community to rising temperatures and precipitation. A 1 °C rise in summertime soil temperature caused 44% and 78% increases in CO2 efflux and CH 4 consumption, respectively, and a 32% increase in the frequency of bacterial 16S ribosomal RNA genes. Bacterial alpha diversity was unaffected by the treatments, but, of the 40 most frequent bacterial taxa, warming caused 44-45% reductions in the relative abundances of a Sphingomonas sp. and Ferruginibacter sp. and 33-91% increases in those of a Phenylobacterium sp. and a member of the Acetobacteraceae. Warming did not influence the frequency of fungal internal transcribed spacer 2 copies, and irrigation had no effects on the measured variables. Our study suggests rapid changes to the activities and abundances of microbes, and particularly bacteria, in High Arctic patterned ground soils as they warm. At current rates of soil warming on Svalbard (0.8 °C per decade), we anticipate that similar effects to those reported here will manifest themselves in the natural environment by approximately the mid 2030s.

Tropical mountain cloud forests (TMCF) harbour a high bryophyte (mosses and liverworts) biomass and diversity. Furthermore, the high air humidity makes these forests well suited for bryophyte-associated nitrogen (N2) fixation by cyanobacteria, providing a potentially important source of N input to the ecosystem. However, few studies have assessed bryophyte-associated N input in these ecosystems, and these have focused on epiphytic bryophytes, whereas abundant ground-covering bryophytes have not been included. In this study, we quantified N2 fixation rates associated with bryophytes, focusing on ground-covering mosses in a neotropical mountain cloud forest. Furthermore, we identified the effects of climate change (higher temperature 10 vs. 20° and lower bryophyte moisture level 50% vs. 100%) on N2 fixation across bryophyte species and groups (mosses and liverworts). Nitrogen fixation rates associated with ground-covering moss species were up to 2 kg N ha−1 year−1, which is comparable to other N inputs (e.g. N deposition) in tropical cloud forests. Furthermore, changes in temperature showed little effect on N2 fixation, but low moisture levels significantly suppressed N2 fixation activity. We found low N2 fixation activity associated with the investigated liverworts. Our results demonstrate the importance of ground-covering, moss-associated N2 fixation as a N source in tropical cloud forests and suggest that predicted future declines in precipitation in these systems will reduce N inputs from bryophyte-associated cyanobacteria. Read the free Plain Language Summary for this article on the Journal blog.

Global warming is most pronounced in the Arctic region. Greenhouse gas (GHG) release from Arctic soils increase due to global warming. By this, the Arctic may change from currently being a carbon sink to a future source. To improve accurate predictions of future GHG release from Arctic soils, it is important to unravel factors controlling both the microbial community structure and activity. Soil microbial activity is important for Arctic greenhouse gas production, but depends on soil conditions such as salinity being increased by calcium (Ca) and decreased by amorphous silica (Si) potentially enhancing water availability. In the Arctic, climate changes may alter salinity by changing Si and Ca concentrations upon permafrost thaw as a result of global warming with Si potentially decreasing and Ca potentially increasing salinity. Here, we show that higher Si concentration increased and higher Ca concentrations decreased the microbial CO2 production for both a salt-poor and a salt-rich soil from Greenland. In the salt-rich soil, Si amendment increased CO2 production and the abundance of gram-negative bacteria. However, the bacterial community became dominated by spore-forming gram-positive Firmicutes and Actinobacteria. The CO2 release from soils was directly affected by the abundance of bacteria and fungi, and their community structure. Our results highlight the importance of the soil Si and Ca concentration on organic carbon turnover by strongly changing microbial abundance and community structure, with consequences for CO2 release in the Arctic. Consequently, Ca and Si and their relation to Arctic soil microbial community structure has to be considered when estimating pan-Arctic carbon budgets.

The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly understood. Here, in a four-year experiment on Svalbard, we warmed patterned ground soil with open top chambers and biannually irrigated the soil to predict the responses of its microbial community to rising temperatures and precipitation. A 1 °C rise in summertime soil temperature caused 44% and 78% increases in CO2 efflux and CH4 consumption, respectively, and a 32% increase in the frequency of bacterial 16S ribosomal RNA genes. Bacterial alpha diversity was unaffected by the treatments, but, of the 40 most frequent bacterial taxa, warming caused 44–45% reductions in the relative abundances of a Sphingomonas sp. and Ferruginibacter sp. and 33–91% increases in those of a Phenylobacterium sp. and a member of the Acetobacteraceae. Warming did not influence the frequency of fungal internal transcribed spacer 2 copies, and irrigation had no effects on the measured variables. Our study suggests rapid changes to the activities and abundances of microbes, and particularly bacteria, in High Arctic patterned ground soils as they warm. At current rates of soil warming on Svalbard (0.8 °C per decade), we anticipate that similar effects to those reported here will manifest themselves in the natural environment by approximately the mid 2030s.

Across the Sahel sub-region, most childhood malaria infections occur during the rainy season. To prevent both uncomplicated and severe malaria in children, The World Health Organization recommends seasonal malaria chemoprevention for children aged 0-5 years. SMC is an intermittent distribution of the antimalarial drugs, sulfadoxine-pyrimethamine (SP), and amodiaquine (AQ) when the malarial transmission is high. Albeit effective, large-scale use of SMC treatments in children can lead to antimalarial drug resistance in the main malaria parasite, Plasmodium falciparum, and render this crucial strategy ineffective. Resistance to the drug SP is already prominent in areas of Africa. Consequently, treatment with another drug combination, dihydroartemisinin-piperaquine (DHA-PQ), has been suggested as an alternative. Antimalarial drug resistance can be monitored by detecting molecular markers of drugs resistance, particularly Single Nucleotide Polymorphisms (SNPs), and copy number variations (CNV) of specific genes of P. falciparum associated with antimalarial drug resistance. Assessing these SNPs and CNV before and after SMC could give an insight into the impact of the prophylactic strategy on the prevalence and selection of antimalarial drug resistance in P. falciparum. This project will determine and compare the prevalence of SNPs and CNV in specific P. falciparum genes in infections of children of different age groups from Mali who have received either SP-AQ or DHAPQ. After DNA extraction of the P. falciparum positive blood samples from Mali, the samples will be examined by PCR followed by targeted amplicon sequencing using an in-house developed nextgeneration sequencing platform (Illumina MiSeq platform) for the prevalence of SNPs in an array of genes that have been associated with SP, AQ, DHA, and PQ resistance. Additionally, a qPCR methodology will be applied to determine gene copy numbers of spec

Moss-associated nitrogen (N2) fixation performed by epiphytic, N2-fixing bacteria (diazotrophs) contributes significantly to ecosystem N input in pristine habitats. While we have some understanding of the effects of climate warming on moss-associated N2 fixation, we lack data on effects of freeze-thaw cycles (FTCs) on diazotroph activity, although increased frequency of FTCs is predicted. We collected the widespread moss Pleurozium schreberi along a climate gradient (temperate, boreal, arctic) and exposed moss and associated diazotrophs to severe (20 °C difference, cycling between +10 and −10 °C) and mild (6 °C difference, ±3 °C) diurnal FTCs. We measured N2 fixation in mosses over 8 weeks and assessed their nutrient loss (fixed N2, total dissolved N, ammonium, phosphate) during the FTCs. We expected lower nitrogenase activity in mosses exposed to more severe FTCs and different sensitivities of N2 fixation towards FTCs along the climate gradient. However, no differences were found in N2 fixation between mild and severe FTCs, but N2 fixation in mosses from the temperate heath was less susceptible to FTCs than those from colder sites, suggesting adapted temperate diazotroph communities. Mosses lost little N, most at constant, positive temperatures, while more phosphate was lost from mosses exposed to FTCs, depending on the positioning along the climate gradient, mirroring nutrient demand and limitation. Our results show that moss-associated N2 fixation is less susceptible towards FTCs than expected but nutrient loss from moss carpets can increase following FTCs, with consequences for nutrient pools and fluxes.

Aims: Microorganisms play a dichotomous role in the soil nitrogen cycle through mineralization and immobilization. We aimed to understand how nitrogen availability modifies the effect of microorganisms on plant growth. We hypothesized that soil microorganisms would increase plant biomass following amendment with a substrate rich in organic nitrogen (net mineralization), be neutral when adding inorganic nitrogen, and decrease biomass when adding organic nitrogen-limited substrate (nitrogen competition). Method: Barley (Hordeum vulgare L., cv. Evergreen) was exposed to either i) limited, organically bound nitrogen, ii) organically bound nitrogen or iii) inorganic nitrogen. In these amendments, we assessed the differences in plant biomass and physiology between plants with or without soil microbiome addition. Results: The soil microbiome reduced shoot biomass equally (12%) across all nitrogen amendments. However, nitrogen availability did modulate the effect of the soil microbiome on plant physiological parameters associated with nitrogen deficiency. Conclusions: The results indicate that the net negative effect of complex microbiomes on shoot biomass is independent of nitrogen availability. Thus, microbiome addition was deleterious to biomass even in a nutrient-stress-free environment. We suggest that strategies for improving plant growth through manipulation of microorganisms should not exclusively focus on beneficial and pathogenic microorganisms, but also include minimizing plant metabolic costs of microbiome interactions.

The root microbiota is crucial for plant productivity and stress tolerance. Still, our understanding of the factors that structure these microbial communities is limited, and we lack a theoretical framework to predict their assemblage and interactions. Here, we used rice as a model system to explore the hypothesis that microbiomes from specific environments enhance plant tolerance to salinity. We used 16S rRNA sequencing to track salinity-induced changes in microbiomes of plants inoculated with either a rice field microbiome, or a halotolerant microbiome, compared to only the seed microbiome. We found that, at salinities higher than 1.1 % plant growth was severely impeded. Nevertheless, at 0.11 % and 0.35 % salinity, plants inoculated with rice field and halotolerant microbiomes displayed enhanced shoot and root biomass, when compared to plants surviving only with the seed microbiome. Rice field microbiome had the highest plant growth-promoting effect and was the only treatment that promoted growth at 0.35 % salinity. The salinity effects on bacterial composition and alpha diversity were more pronounced for plants that relied only on the seed microbiome. The root-associated compartments harboured distinct microbiomes, but salinity explained most of the variation observed. Rice plants interacted with the rice field and halotolerant microbiomes to shape rhizosphere microbial community composition and the co-occurrence patterns, supporting plant growth at higher salinity. Assemblages of the halotolerant microbiome promoted similar network structures between the different salinity treatments, when compared to the other inoculations. Moreover, salinity responsive and keystone bacteria were taxonomically diverse and responded in guilds of taxa to the salinity levels. We conclude that both specialized inoculations differ greatly in how they influence the plant microbiome and that plant growth at higher salinity levels was associated with a denser and more complex root m

Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with 14C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at −4°C, while no degradation was detected at −18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.

To understand and manipulate the interactions between plants and microorganisms, sterile seeds are a necessity. The seed microbiome (inside and surface microorganisms) is unknown for most plant species and seed-borne microorganisms can persist and transfer to the seedling and rhizosphere, thereby obscuring the effects that purposely introduced microorganisms have on plants. This necessitates that these unidentified, seed-borne microorganisms are removed before seeds are used for studies on plant–microbiome interactions. Unfortunately, there is no single, standardized protocol for seed sterilization, hampering progress in experimental plant growth promotion and our study shows that commonly applied sterilization protocols for barley grains using H2O2, NaClO, and AgNO3 yielded insufficient sterilization. We therefore developed a sterilization protocol with AgNO3 by testing several concentrations of AgNO3 and added two additional steps: Soaking the grains in water before the sterilization and rinsing with salt water (1% (w/w) NaCl) after the sterilization. The most efficient sterilization protocol was to soak the grains, sterilize with 10% (w/w) AgNO3, and to rinse with salt water. By following those three steps, 97% of the grains had no culturable, viable microorganism after 21 days based on microscopic inspection. The protocol left small quantities of AgNO3 residue on the grain, maintained germination percentage similar to unsterilized grains, and plant biomass was unaltered. Hence, our protocol using AgNO3 can be used successfully for experiments on plant–microbiome interactions.