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Moss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1 week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss–cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients. [ABSTRACT FROM AUTHOR]

Emissions of biogenic volatile organic compounds (BVOCs) from natural ecosystems impact atmospheric chemistry as well as biological interactions and even soil biogeochemical processes. Plant litter emits substantial amounts of BVOCs. These emissions may contribute to total ecosystem emissions especially in the Arctic where the living plant biomass is low and the amount of litter is expected to increase as the deciduous shrubs expand in response to a warmer climate. Here, we incubated in the laboratory litter from the evergreen Cassiope tetragona and deciduous Salix spp. from a high arctic and a low arctic location. The 8-week-long incubation was conducted with temperature increasing from 5 °C to 26 °C, mimicking the transition from winter to summer. BVOC emissions from the decomposing litter were sampled weekly in adsorbent cartridges and analyzed using gas chromatography–mass spectrometry, and the bacterial community composition was investigated by sequencing of PCR amplified 16S rRNA gene fragments. Our results showed that litter from C. tetragona , which is a terpenoid storing species, had higher BVOC emission rates (mainly terpenoids) than the Salix litter, which does not have specialized BVOC storing compartments. The C. tetragona litter emissions were higher in the high arctic than the low arctic samples. The emission rates from the C. tetragona litter increased during the incubation period, whereas emission rates from the Salix litter decreased, suggesting that the emissions originated from different sources and/or processes. The bacterial community composition in the Salix litter, but not in the C. tetragona litter, changed in parallel with the changes in the BVOC emissions during the incubation period. Therefore, we suggest that bacteria may be more important for the BVOC emissions from decomposing Salix litter than C. tetragona litter. [ABSTRACT FROM AUTHOR]

N 2 O emission from soil is regulated by the more or less sporadic occurrence of anoxic voids within the otherwise oxic soil matrix. Differences in size and density of these voids makes the process highly variable at the microscale. In a search for situations where variation in N 2 O emission is at the mesoscale rather than at the microscale we selected a drained and nitrogen rich organic soil incline. N 2 O emission rate gradients were observed at the mesoscale (10 m range). Massive N 2 O emissions occurred at an interface that may be defined by upslope oxic conditions inducing mineralizing organic nitrogen nitrate production and downslope anoxic conditions inducing the conversion of nitrate into N 2 O. This N 2 O-producing interface probably contained many small anoxic volumes distributed in the aerated soil matrix. The interface moved uphill in the wet season and downhill in the dry season so the mesoscale pattern also had a clear temporal component. When scaled on a hectare basis, the site with such a hot spot emitted 73 kg N annually as N2O, indicating the magnitude of this activity. [ABSTRACT FROM AUTHOR]

Three novel Gram-positive, endospore-forming bacteria were isolated from a cold and alkaline environment. Phylogenetic analysis showed that the strains were almost identical, and that they were related to Natronobacillus azotifigens 24KS-1 (95.8% identity), Paraliobacillus quinghaiensis YIM-C158 (95.1%), Paraliobacillus ryukyuensis O15-7 (94.5%), and Halolactibacillus miurensis M23-1 (93.9%). The isolates produced amylase, α-galactosidase, β-galactosidase, and β-glucuronidase, and showed optimal growth at pH 10, at 20°C, and at 2-8% (w/v) NaCl. Major fatty acids were C (10.6-11.6%), anteiso-C (25.7-32.7%), C ω11 c (12.2-16.0%), and C (14.0-20.4%). The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and meso-diaminopimelic acid was found in the cell-wall peptidoglycan. The G+C content was 38.4%. DNA-DNA hybridization between strain GCM68 and H. miurensis M23-1 was 32.4%, while hybridization to N. azotifigens 24KS-1, Amphibacillus tropicus Z-7792, and Paraliobacillus ryukyuensis O15-7 was below 30%. The phylogenetic analysis and G+C content place strain GCM68 in relation to species belonging to Bacillus rRNA group 1, but phylogenetic and physiologic data combined with chemotaxonomic analyses support our proposal for a new genus, Alkalilactibacillus, gen. nov., with the novel species Alkalilactibacillus ikkensis, sp. nov. (type strain is GCM68 = DSM 19937 = LMG 24405). [ABSTRACT FROM AUTHOR]

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4°C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species. [ABSTRACT FROM AUTHOR]

Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha−1 year−1) and cattle manure (75 and 150 kg N ha−1 year−1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different. Also, these sites significantly differed from the control plot (no fertilizer treatment), whereas the patterns for low and high N-additions were barely separable from each other. Sequencing and phylogenetic analysis of 54 nirK clones revealed that the major part of the nirK-containing bacteria investigated belonged to a yet uncultivated cluster of denitrifying bacteria. [Copyright &y& Elsevier]

Investigates the genetic heterogeneity of nitrite reductase gene fragments from denitrifying prokaryotes in forested upland and wetland soils. Analysis of deduced amino acids; Destruction of stratospheric ozone; Reduction of nitrite into nitric oxide.

The extremophile bacterium Deinococcus radiodurans is characterized by its ability to survive and sustain its activity at high levels of radiation and is considered an organism that might survive in extraterrestrial environments. In the present work, we studied the combined effects of temperature and chlorine-containing salts, with focus on perchlorate salts which have been detected at high concentrations in Martian regolith, on D. radiodurans activity (CO2 production rates) and viability after incubation in liquid cultures for up to 30 days. Reduced CO2 production capacity and viability was observed at high perchlorate concentrations (up to 10% w/v) during incubation at 0 or 25 °C. Both the metabolic activity and viability were reduced as the perchlorate and chloride salt concentration increased and temperature decreased, and an interactive effect of temperature and salt concentration on the metabolic activity was found. These results indicate the ability of D. radiodurans to remain metabolically active and survive in low temperature environments rich in perchlorate. [ABSTRACT FROM AUTHOR]

Many Arctic regions are currently experiencing substantial summer and winter climate changes. Litter decomposition is a fundamental component of ecosystem carbon and nutrient cycles, with fungi being among the primary decomposers. To assess the impacts of seasonal climatic changes on litter fungal communities and their functioning, Betula glandulosa leaf litter was surface-incubated in two adjacent low Arctic sites with contrasting soil moisture regimes: dry shrub heath and wet sedge tundra at Disko Island, Greenland. At both sites, we investigated the impacts of factorial combinations of enhanced summer warming (using open-top chambers; OTCs) and deepened snow (using snow fences) on surface litter mass loss, chemistry and fungal decomposer communities after approximately 1 year. Enhanced summer warming significantly restricted litter mass loss by 32% in the dry and 17% in the wet site. Litter moisture content was significantly reduced by summer warming in the dry, but not in the wet site. Likewise, fungal total abundance and diversity were reduced by OTC warming at the dry site, while comparatively modest warming effects were observed in the wet site. These results suggest that increased evapotranspiration in the OTC plots lowered litter moisture content to the point where fungal decomposition activities became inhibited. In contrast, snow addition enhanced fungal abundance in both sites but did not significantly affect litter mass loss rates. Across sites, control plots only shared 15% of their fungal phylotypes, suggesting strong local controls on fungal decomposer community composition. Nevertheless, fungal community functioning (litter decomposition) was negatively affected by warming in both sites. We conclude that although buried soil organic matter decomposition is widely expected to increase with future summer warming, surface litter decay and nutrient turnover rates in both xeric and relatively moist tundra are likely to be significantly restricted by the evaporative drying associated with warmer air temperatures. [ABSTRACT FROM AUTHOR]

Simple Summary: Surface temperatures in the Arctic are rising more rapidly than elsewhere on Earth. Precipitation patterns in the region are also altering, with an increased incidence of heavy rainfall. However, the effects of warming and increased water availability on soil microbes—which have pivotal roles in nutrient cycling and greenhouse gas exchange—inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic are not well understood. Here, we warmed patterned ground soils on Svalbard with open top chambers and irrigated the soils twice each summer. After four years, a 1 °C rise in summertime near-surface soil temperature affected the exchange of the greenhouse gases carbon dioxide (CO2) and methane (CH4), with warmed soils emitting 44% more CO2, and consuming 78% more CH4, than soils that were not warmed. Warming also increased soil bacterial abundance by 32%, and, of the 40 most abundant bacterial taxa, led to both reductions and increases in the relative abundances of four taxa. Irrigation did not influence the measured variables. At the current rate of summertime warming in soils on Svalbard (0.8 °C per decade), we anticipate that these effects will become apparent in the natural environment by approximately the mid 2030s. 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. [ABSTRACT FROM AUTHOR]

Aims: Fungi play a central role in litter decomposition, a key process controlling the terrestrial carbon cycle and nutrient availability for plants and microorganisms. Climate change and elevated CO affect soil fungi, but the relative importance of the global change variables for litter decomposition is still uncertain. The main objective was therefore to assess the short-term litter decomposition and associated fungal community in a global change manipulated temperate heath ecosystem. Methods: The heath had been exposed to 6 years of warming, elevated atmospheric CO and an extended pre-summer drought. Litterbags with litter from heather ( Calluna vulgaris) and wavy-hair grass ( Deschampsia flexuosa) were incubated in the litter layer for 6 months, where after we analyzed the litter-associated fungal community, litter loss, CO respiration, and total content of carbon, nitrogen and phosphorus. Results: Elevated temperature tended to increase litter decomposition rates, whereas elevated CO had no effect on the process. The pre-summer drought treatment had a positive impact on litter decomposition, CO respiration and fungal abundance in the litterbags, although we observed no major changes in fungal community composition. Conclusions: The drought treatment during pre-summer had a legacy effect on litter decomposition as decomposition rates were positively affected later in the year. The community structure of litter-decomposing fungi was not affected by the drought treatment. Hence, the legacy effect was not mediated by a change in the fungal community structure. [ABSTRACT FROM AUTHOR]

• CO 2 fluxes increased with altitude below treeline, declining from treeline to summit. • There were no significant changes of CH 4 fluxes along the altitudinal gradient. • An uptake of atmospheric N 2 O was observed below the treeline. • N 2 O fluxes were controlled by specific nitrification and denitrification genes. • Microbial activities were driven by soil organic matter quantity and composition. Mountain ecosystems, contributing substantially to the global carbon (C) and nitrogen (N) biogeochemical cycles, are heavily impacted by global changes. Although soil respiration and microbial activities have been extensively studied at different elevation, little is known on the relationships between environmental drivers, microbial functions, and greenhouse gas fluxes (GHGs; carbon dioxide [CO 2 ], methane [CH 4 ] and nitrous oxide [N 2 O]) in soils of different elevation. Here, we measured how in situ GHG fluxes were linked to soil properties, soil organic matter (SOM) quantity and composition (the proportion of humic-like vs. protein-like OM), microbial biomass, enzyme activities and functional gene abundances in natural soils spanning an elevational gradient of ∼2400 m in Switzerland. Soil CO 2 fluxes did not significantly vary from low (lowland zone) to higher (montane and subalpine zones) elevation forests, but decreased significantly (P<0.001) from the treeline to the mountain summit. Multivariate analyses revealed that CO 2 fluxes were controlled by C-acquiring enzymatic activities which were mainly controlled by air mean annual temperature (MAT) and SOM quantity and composition. CH 4 fluxes were characterized by uptake of atmospheric CH 4 , but no trend was observed along the elevation. N 2 O fluxes were also dominated by uptake of atmospheric N 2 O. The flux rates remained stable with increasing elevation below the treeline, but decreased significantly (P<0.001) from the treeline to the summit. N 2 O fluxes were driven by specific nitrifying and denitrifying microbial genes (ammonia-oxidizing amo A and N 2 O-producing nor B), which were again controlled by SOM quantity and composition. Our study indicates the treeline as a demarcation point changing the patterns of CO 2 and N 2 O fluxes along the elevation, highlighting the importance of SOM quantity and composition in controlling microbial enzyme activities and GHG fluxes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background and aims: Soil microbial responses to global change can affect organic matter turnover and nutrient cycling thereby altering the overall ecosystem functioning. In a large-scale experiment, we investigated the impact of 5 years of climate change and elevated atmospheric CO on soil microorganisms and nutrient availability in a temperate heathland. Methods: The future climate was simulated by increased soil temperature (+0.3 °C), extended pre-summer drought (excluding 5-8 % of the annual precipitation) and elevated CO (+130 ppm) in a factorial design. Soil organic matter and nutrient pools were analysed and linked to microbial measures by quantitative PCR of bacteria and fungi, chloroform fumigation extraction, and substrate-induced respiration to assess their impact of climate change on nutrient availability. Results: Warming resulted in higher measures of fungi and bacteria, of microbial biomass and of microbial growth potential, however, this did not reduce the availability of nitrogen or phosphorus in the soil. Elevated CO did not directly affect the microbial measures or nutrient pools, whereas drought shifted the microbial community towards a higher fungal dominance. Conclusions: Although we were not able to show strong interactive effects of the global change factors, warming and drought changed both nutrient availability and microbial community composition in the heathland soil, which could alter the ecosystem carbon and nutrient flow in the long-term. [ABSTRACT FROM AUTHOR]

Pollution-induced community tolerance (PICT) constitutes a sensitive and ecologically relevant impact parameter in ecotoxicology. We report the development and application of a novel anaerobic [H]leucine incorporation assay and its comparison with the conventional aerobic [H]leucine incorporation assay for PICT detection in soil bacterial communities. Selection of bacterial communities was performed over 42 d in bulk soil microcosms (no plants) and in rice ( Oryza sativa) rhizosphere soil mesocosms. The following experimental treatments were imposed using a full factorial design: two soil types, two soil water regimes, and four Cu application rates (0, 30, 120, or 280 µg g). Bacterial communities in bulk soil microcosms exhibited similar Cu tolerance patterns when assessed by aerobic and anaerobic PICT assays, whereas aerobic microorganisms tended to be more strongly selected for Cu tolerance than anaerobic microorganisms in rhizosphere soil. Despite similar levels of water-extractable Cu, bacterial Cu tolerance was significantly higher in acid sulfate soil than in alluvial soil. Copper amendment selected for significant PICT development in soils subjected to alternate wetting and drying, but not in continuously flooded soils. Our results demonstrate that soil bacterial communities subjected to alternate wetting and drying may be more affected by Cu than bacterial communities subjected to continuous flooding. We conclude that the parallel use of anaerobic and aerobic [H]leucine PICT assays constitutes a valuable improvement over existing procedures for PICT detection in irrigated soils and other redox gradient environments such as sediments and wetlands. Environ. Toxicol. Chem. 2011; 30:588-595. © 2011 SETAC [ABSTRACT FROM AUTHOR]

The bacterial community of Zostera marina-inhabited bulk sediment vs. root-associated bacteria was investigated by terminal restriction fragment length polymorphism and sequencing, and the spatial extension of the oxygen loss from roots was determined by oxygen microsensors. Extensive oxygen loss was found in the tip region of the youngest roots, and most of the rhizoplane of Z. marina roots was thus anoxic. A significant difference between the bacterial communities associated with the roots and bulk sediment was found. No significant differences were found between differently aged root-bundles. Terminal restriction fragments (TRFs) assigned to sulfate-reducing Deltaproteobacteria showed a relative mean distribution of 12% and 23% of the PCR-amplified bacterial community in the bulk-sediment at the two sites, but only contributed <2% to the root-associated communities. TRFs assigned to Epsilonproteobacteria showed a relative mean distribution of between 5% and 11% in the root-associated communities of the youngest root bundle, in contrast to the bulk-sediment where this TRF only contributed <1.3%. TRFs assigned to Actinobacteria and Gammaproteobacteria also seemed important first root-colonizers, whereas TRFs assigned to Deltaproteobacteria became increasingly important in the root-associated community of the older root bundles. The presence of the roots thus apparently selects for a distinct bacterial community, stimulating the growth of potential symbiotic Epsilon- and Gammaproteobacteria and/or inhibiting the growth of sulfate-reducing Deltaproteobacteria. [ABSTRACT FROM AUTHOR]

Moss-associated nitrogen (N 2) fixation performed by epiphytic, N 2 -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 N 2 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 N 2 fixation in mosses over 8 weeks and assessed their nutrient loss (fixed N 2 , total dissolved N, ammonium, phosphate) during the FTCs. We expected lower nitrogenase activity in mosses exposed to more severe FTCs and different sensitivities of N 2 fixation towards FTCs along the climate gradient. However, no differences were found in N 2 fixation between mild and severe FTCs, but N 2 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 N 2 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. [Display omitted] • Nitrogen fixation by moss-associated cyanobacteria is strongly moisture dependent. • We assessed the effects of mild and severe freeze-thaw cycles (FTCs) on N fixation. • Activity was not consistently affected by FTCs across climates. • But substantial amounts of nutrients were lost from the moss after repeated FTCs. [ABSTRACT FROM AUTHOR]

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). 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. 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. 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. • Rhizosphere microbiome reduced plant biomass. • Soil nitrogen availability moderated microbiome effect on plant nutrient status. • Experimental design developed specifically for plant-microbiome studies. [ABSTRACT FROM AUTHOR]

Background: Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season. Results: The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted. Conclusions: We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate. [ABSTRACT FROM AUTHOR]

Soil microbial communities have remarkable capacities to cope with ceaseless environmental changes, but little is known about their adaptation potential when facing an unprecedented disturbance. We tested the effect of incremental dose of microwaving on soil bacteria as a model of unprecedented stress. 16S rRNA gene qPCR at both the DNA and cDNA levels was used to characterize the total (DNA) and transcriptionally active (cDNA) fractions of the bacterial community. Amplicon sequencing of 16S rRNA gene transcripts was performed to decipher tolerance ranges within the community using the concept of functional response groups (FRGs). Increasing microwaving doses resulted in 90% loss in total and transcriptionally active bacterial communities after 6.8 and 4.7 min, respectively. Four distinct FRGs with peculiar phylogenetic signatures were identified, revealing a link between taxonomy and increasing stress doses. FRG1, the most sensitive group, was dominated by Actinobacteria. FRG2 and FRG3, with intermediate tolerance, displayed prevalence of Proteobacteria, while FRG4, the most resistant group, was driven by Firmicutes. While the most sensitive FRGs showed predictable responses linked to changes in temperature and soil water content associated with microwaving, more tolerant FRG4 members exhibited a stochastic response nested within the Firmicutes phylum, potentially revealing bet-hedging strategists. The concept of FRGs based on 16S rRNA gene transcripts stood as an efficient tool for unraveling bacterial survival strategies and tolerance ranges triggered by incremental doses of an unprecedented stress, with regard to phylogeny linkages. [ABSTRACT FROM AUTHOR]

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. [ABSTRACT FROM AUTHOR]

This study investigates spatial-temporal trends in N 2 O 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 (NH 4 NO 3) as well as potassium nitrate (KNO 3). Soils in a laboratory experiment were incubated under both drained and flooded conditions. Continuous measurements from automatic chambers show that annual N 2 O fluxes were dominated by bursts over few weeks following N-fertilisation with peak emissions up to 60 g N-N 2 O ha−1 day−1. A two-month slope experiment with static chambers after KNO 3 -fertilisation with 90 kg N ha−1 showed N 2 O significant differences between the highest daily emission rates from the top and the bottom of the slope (134 ± 20 g N-N 2 O ha−1 and 336 ± 104 g N-N 2 O ha−1, respectively) which can be explained by NO 3 - transport downhill and flooded conditions favouring denitrification at the bottom of the slope. Incubation experiments indicate that denitrification is the main process controlling N 2 O emissions but also that nitrification can result in low N 2 O emission rates under drained conditions. It can be concluded that the reported N 2 O emissions from the coffee agroforestry systems are generally low, but may be underestimated, as both poorly drained depressions functioning as N 2 O hotspots as well as temporal N 2 O bursts need to be taken into account. • This study measures of N 2 O bursts from coffee production in Costa Rica. • N 2 O emissions are linked to fertilization and nitrate concentrations. • N 2 O budgets without including bursts underestimate the emission factor. • Local hydrology can result in hot spots of very high N 2 O emissions. • Contrasting soil types result in highly variable N 2 O emissions from coffee fields. [ABSTRACT FROM AUTHOR]

Copper has been intensively used in industry and agriculture since mid-18th century and is currently accumulating in soils. We investigated the diversity of potential active bacteria by 16S rRNA gene transcript amplicon sequencing in a temperate grassland soil subjected to century-long exposure to normal (~15mgkg-1), high (~450mgkg-1) or extremely high (~4500mgkg-1) copper levels. Results showed that bioavailable copper had pronounced impacts on the structure of the transcriptionally active bacterial community, overruling other environmental factors (e.g. season and pH). As copper concentration increased, bacterial richness and evenness were negatively impacted, while distinct communities with an enhanced relative abundance of Nitrospira and Acidobacteria members and a lower representation of Verrucomicrobia, Proteobacteria and Actinobacteria were selected. Our analysis showed the presence of six functional response groups (FRGs), each consisting of bacterial taxa with similar tolerance response to copper. Furthermore, the use of FRGs revealed that specific taxa like the genus Nitrospira and several Acidobacteria groups could accurately predict the copper legacy burden in our system, suggesting a potential promising role as bioindicators of copper contamination in soils. [ABSTRACT FROM AUTHOR]

Despite the critical ecological roles of microeukaryotes in terrestrial ecosystems, most descriptive studies of soil microbes published so far focused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in public repositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in order to investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factors impacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While most studies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this work represents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure and reference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronounced effect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publicly available metagenome data can provide valuable information on soil microeukaryotes for comparative purposes when handled appropriately, complementing the current view provided by ribosomal amplicon sequencing methods. [ABSTRACT FROM AUTHOR]

Abstract: In temperate regions, climate change is predicted to increase annual mean temperature and intensify the duration and frequency of summer droughts, which together with elevated atmospheric carbon dioxide (CO2) concentrations, may affect the exchange of nitrous oxide (N2O) and methane (CH4) between terrestrial ecosystems and the atmosphere. We report results from the CLIMAITE experiment, where the effects of these three climate change parameters were investigated solely and in all combinations in a temperate heathland. Field measurements of N2O and CH4 fluxes took place 1–2 years after the climate change manipulations were initiated. The soil was generally a net sink for atmospheric CH4. Elevated temperature (T) increased the CH4 uptake by on average 10 μg C m−2 h−1, corresponding to a rise in the uptake rate of about 20%. However, during winter elevated CO2 (CO2) reduced the CH4 uptake, which outweighed the positive effect of warming when analyzed across the study period. Emissions of N2O were generally low (<10 μg N m−2 h−1). As single experimental factors, elevated CO2, temperature and summer drought (D) had no major effect on the N2O fluxes, but the combination of CO2 and warming (TCO2) stimulated N2O emission, whereas the N2O emission ceased when CO2 was combined with drought (DCO2). We suggest that these N2O responses are related to increased rhizodeposition under elevated CO2 combined with increased and reduced nitrogen turnover rates caused by warming and drought, respectively. The N2O flux in the multifactor treatment TDCO2 was not different from the ambient control treatment. Overall, our study suggests that in the future, CH4 uptake may increase slightly, while N2O emission will remain unchanged in temperate ecosystems on well-aerated soils. However, we propose that continued exposure to altered climate could potentially change the greenhouse gas flux pattern in the investigated heathland. [Copyright &y& Elsevier]

Field-scale experiments simulating realistic future climate scenarios are important tools for investigating the effects of current and future climate changes on ecosystem functioning and biogeochemical cycling. We exposed a seminatural Danish heathland ecosystem to elevated atmospheric carbon dioxide (CO), warming, and extended summer drought in all combinations. Here, we report on the short-term responses of the nitrogen (N) cycle after 2 years of treatments. Elevated CO significantly affected aboveground stoichiometry by increasing the carbon to nitrogen (C/N) ratios in the leaves of both co-dominant species ( Calluna vulgaris and Deschampsia flexuosa), as well as the C/N ratios of Calluna flowers and by reducing the N concentration of Deschampsia litter. Belowground, elevated CO had only minor effects, whereas warming increased N turnover, as indicated by increased rates of microbial NH consumption, gross mineralization, potential nitrification, denitrification and NO emissions. Drought reduced belowground gross N mineralization and decreased fauna N mass and fauna N mineralization. Leaching was unaffected by treatments but was significantly higher across all treatments in the second year than in the much drier first year indicating that ecosystem N loss is highly sensitive to changes and variability in amount and timing of precipitation. Interactions between treatments were common and although some synergistic effects were observed, antagonism dominated the interactive responses in treatment combinations, i.e. responses were smaller in combinations than in single treatments. Nonetheless, increased C/N ratios of photosynthetic tissue in response to elevated CO, as well as drought-induced decreases in litter N production and fauna N mineralization prevailed in the full treatment combination. Overall, the simulated future climate scenario therefore lead to reduced N turnover, which could act to reduce the potential growth response of plants to elevated atmospheric CO concentration. [ABSTRACT FROM AUTHOR]

A line probe assay (GenoType MTBC) was evaluated for species differentiation within the Mycobacterium tuberculosis complex (MTBC). We included 387 MTBC isolates, 43 IS6110 low-copy MTBC isolates, 28 clinical specimens with varying microscopy grade, and 30 isolates of non-tuberculous mycobacteria. The assay was 100% specific and identified all 387 isolates and 98% of all IS6110 low-copy strains in concordance with the gold standard. The 2% discrepancy was caused by 1 isolate showing a faint restriction fragment length polymorphism (RFLP) pattern. The assay could provide specifies identification in 13 of 19 (68%) microscopy-positive specimens and 0 of 9 microscopy-negative specimens. To our surprise, the probe for M. africanum subtype I reacted with M. pinnipedii. This cross-reaction has not previously been reported. The assay was rapid, easy to perform and directly applicable in highly smear-positive specimens. We predict that the assay will enable enhanced surveillance of species-specific treatment outcome, which may change treatment regimens. [ABSTRACT FROM AUTHOR]

• Specialized microbiome transfers increased plant growth at higher salinities. • Rice field microbiome is better suited to support plant growth. • Halotolerant microbiome promoted similar network structures between salinities. • Plant growth at high salinities was linked to denser and more complex networks. • Potential keystone taxa tolerant to salinity were identified. 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 microbial community. [ABSTRACT FROM AUTHOR]

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery. [ABSTRACT FROM AUTHOR]

In a dry heathland ecosystem we manipulated temperature (warming), precipitation (drought) and atmospheric concentration of CO2 in a full-factorial experiment in order to investigate changes in below-ground biodiversity as a result of future climate change. We investigated the responses in community diversity of nematodes, enchytraeids, collembolans and oribatid mites at two and eight years of manipulations. We used a structural equation modelling (SEM) approach analyzing the three manipulations, soil moisture and temperature, and seven soil biological and chemical variables. The analysis revealed a persistent and positive effect of elevated CO2 on litter C:N ratio. After two years of treatment, the fungi to bacteria ratio was increased by warming, and the diversities within oribatid mites, collembolans and nematode groups were all affected by elevated CO2 mediated through increased litter C:N ratio. After eight years of treatment, however, the CO2-increased litter C:N ratio did not influence the diversity in any of the four fauna groups. The number of significant correlations between treatments, food source quality, and soil biota diversities was reduced from six to three after two and eight years, respectively. These results suggest a remarkable resilience within the soil biota against global climate change treatments in the long term. [ABSTRACT FROM AUTHOR]