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The abundance and taxonomic composition of ammonia‐oxidizing archaea (AOA) were assessed in paddy soils that had received more than 50 years of fertilization with and without inorganic N. The inorganic N fertilized treatments were: NPK and NPK + CO (nitrogen (N), phosphorus (P), potassium (K) and compost (CO)). The treatments without inorganic N were: CO, PK and control (unfertilized soils). Quantitative PCR (qPCR) analysis of the archaeal amoA gene showed no significant changes in AOA abundance following the long‐term application of inorganic N fertilizers. However, subsequent analysis of amoA gene sequencing data showed that inorganic N application significantly changed the AOA community composition and alpha diversity indices. Edge principal components analysis (PCA) showed varying contributions of distinct AOA lineages in separating samples according to the fertilization treatment. Addition of inorganic N favoured an increase in the abundance of AOA lineages belonging to Nitrososphaera, and the treatments without inorganic N additions formed a separate cluster dominated by Nitrosotalea lineage. The distinct response of the two AOA lineages points towards different community organization of soil AOA and strongly supports the concept of habitat partitioning in paddy soil ecosystems. Highlights: Lineages of AOA responded differently to different N management practices.Long‐term N fertilization selectively enriched AOA lineages, with C:N ratio a factor associated with such changesInorganic N favoured Nitrososphaera lineage abundanceRegardless of fertilizer status, Nitrosotalea lineage was dominant in the absence of inorganic N fertilization. [ABSTRACT FROM AUTHOR]

Silicon (Si) is widely used in improving crop yield, but effect of its application on soil bacterial community composition is poorly known. Quantitative PCR and high-throughput sequencing targeting the bacterial 16S rRNA gene were employed to characterize the bacterial community composition of long-term fertilized paddy soils treated with nitrogen (N), phosphorus (P), potassium (K), and Si (NPK + Si), with NPK or not fertilized (control). The NPK + Si fertilization significantly increased the urease and dehydrogenase activity. The relative abundance of Actinobacteria was significantly higher in the NPK + Si soil than in other two soils. Linear discriminant analysis (LDA) and effect size (LEfSe) analysis demonstrated that Actinobacteria and its associated taxonomic groups were significantly more abundant in the NPK + Si-treated plots. The bacterial community composition of the NPK + Si soil was significantly different from those of NPK and control soils as shown by the ordination plot. According to distance-based regression analysis, variation in bacterial community composition was related to available SiO2 and P2O5 concentrations. Functional profiles predicted from 16S rRNA abundance data showed that the NPK + Si plots were more enriched by genes coding enzymes related to plant growth promotion compared to NPK and control plots. [ABSTRACT FROM AUTHOR]

Biochar has shown great potential as an amendment to improve soil quality and promote plant growth, as well as to adsorb pollutants from water. However, information about the effect of biochar on the wastewater treatment efficiency in horizontal subsurface flow (HSSF) constructed wetlands (CWs) is still scarce. In this study, we assessed the effect of biochar amendment on the purification efficiency of pretreated municipal wastewater in planted ( Typha latifolia ) experimental horizontal subsurface flow filters filled with lightweight expanded clay aggregates (LECA). The addition of wood-derived biochar (10% v/v) to LECA significantly increased plant biomass production and enhanced the wastewater treatment efficiency of the planted filters. Both the aboveground plant biomass and belowground plant biomass were higher (1.9- and 1.5-fold, respectively) in the filters of the LBP (LECA + biochar + plants) treatments compared to the LP (LECA + plants) filters. The water pH was significantly lower in the planted filters (LBP < LP < LB-LECA + biochar). The efficiencies of TN and TP removal from wastewater were highest in the LBP filters (20.0% and 22.5%, respectively), followed by the LP (13.7% and 16.2%, respectively) and LB (9.5% and 15.6%, respectively) filters. More N and P were incorporated into the plant biomass from wastewater in the presence of biochar in the filter medium. The study results confirm that biochar can be an advantageous supplement for planted HSSF CWs to enhance the treatment efficiency of these systems. [ABSTRACT FROM AUTHOR]

Abstract: The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values. [ABSTRACT FROM AUTHOR]

Abstract: The two alder species, black alder (Alnus glutinosa (L.) Gaertn.) and grey alder (Alnus incana (L.) Moench) are known to be pioneer species in the succession of new land areas, and important tree species in renewable biomass production, the restoration of post-mining sites and riparian forest ecosystems. We analyzed the influence of soil physico-chemical characteristics (soil water content, pHKCl, total N, soluble P, organic matter content, C and N ratio, and elemental content) on bacterial community structure based on pyrosequencing analysis of the 16S rRNA gene V2 and partly V3 region in two black and two grey alder stand soils with different management histories. The analyses revealed clear differences in all the measured chemical characteristics of studied soils. All the studied stands also had distinct soil bacterial communities, and the number of shared species was low. In all stands species from phylum Proteobacteria were dominant, and the next phyla by percentage were Bacteroidetes and Actinobacteria. At the family level, Chitinophagaceae and Bradyrhizobiaceae species dominated. The obtained bacterial community Inverted Simpson''s diversity indices showed no difference between the studied sites. The alder species did not affect soil bacterial community structure. Distance-based regression analysis indicated that soil pH value, water content, soluble phosphorus concentration and also total boron, cadmium, and aluminium content were related to the variation of soil bacterial community structure in alder stand soils. The results of this study emphasize the importance of soil geomorphological properties in addition to soil physical and chemical characteristics in the formation of soil bacterial community structure during restoration of exhausted open mining areas, management of abandoned agricultural lands, and short rotation forests with different alder species. [Copyright &y& Elsevier]

A long-term field experiment was carried out to estimate the efficiency of bioaugmentation in combination with phytoremediation for oil shale chemical industry solid waste dump area remediation. Soil samples for microbiological and chemical analysis were collected during 3 years after bacterial biomass application. Microbial communities in soil samples were analysed using both culture-based and molecular methods. The survival of the introduced bacterial strains was confirmed by cultivation-based Box-PCR genomic fingerprints and denaturing gradient gel electrophoresis fingerprinting of the 16S rRNA and lmPH genes. The introduced bacterial strains as well as corresponding catabolic genes were recovered several years after biomass application, predominantly from the rhizosphere of birches. Soil samples from bioaugmented plots showed an elevated potential for degradation of phenolic compounds even 40 months after treatment. Based on our results we can conclude that the introduced Pseudomonas strains both survived, and their metabolic traits have persisted at the contaminated site over a long period of time. [ABSTRACT FROM AUTHOR]

Abstract: The effect of secondary-treated wastewater irrigation of a short-rotation willow coppice on soil microbial parameters was evaluated twice in 3 years using microbiological and biochemical properties. The soil metabolically active microbial biomass, basal respiration, N-mineralization, potential nitrification, alkaline and acid phosphatase and dehydrogenase activities were measured. The microbial community metabolic profile was determined with Biolog EcoPlates and bacterial community structure was assessed using denaturing gradient gel electrophoresis. After 2 years, a significant increase had occurred in soil microbial biomass, respiration and nitrogen mineralization activity both in the irrigated and in the non-treated plots. Wastewater irrigation increased the soil potassium concentration and enhanced the activity of alkaline phosphatase. Plant growth and irrigation affected the nitrogen mineralization activity—the increase was twice as high in the control plots as in the irrigated plots after 2 years. Potential nitrification, acid phosphatase activity and microbial community metabolic activity did not differ significantly (P >0.05) between the control and the irrigated plots during the study. The comparison of soil profiles indicated that the observed increases in the soil microbiological parameters were allocated to the upper 10cm. The establishment of willow plants on the fields affected the microbial community structure, with an increased diversity and higher similarity among the planted plots after 2 years. From our results we conclude that the willow coppice affected the soil bacterial community structure and had a positive effect on soil biological activity. Irrigation with pre-treated wastewater affected soil chemical and biochemical properties. [Copyright &y& Elsevier]

Abstract: A set of soil microbiological and biochemical properties was used to assess the influence of agricultural practices such as rotation, usage of pesticides, and fertilizers on the three most widespread soil types (Calcaric Regosols, Calcaric Cambisols and Stagnic Luvisols) in the fields of horticultural farms throughout Estonia. Microbial biomass, dehydrogenase and alkaline phosphatase activity were significantly higher in Calcaric Regosols, whereas measured soil chemical parameters showed practically no difference among soil types. Multivariate exploratory analysis of soil biochemical and microbiological parameters clearly distinguished soils with different management practices when the effect of soil type was taken into account in data analysis. Activity of dehydrogenase, potential nitrification, N-mineralisation, and microbial biomass contributed most strongly to the differentiation of soils from differently managed fields. Soils managed according to organic farming principles were generally characterized by elevated microbiological parameter values, but at the same time the variation of those parameters among soils from these fields was also highest. The application of organic manure positively affected microbial biomass, N-mineralisation, potential nitrification, dehydrogenase and acidic phosphatase activity. Data analysis indicated that the amount of mineral nitrogen fertilizers added over time has a stronger effect on microbial biomass than the amount added in a given year. Legume-based crop rotation increased soil respiration and microbial biomass. [Copyright &y& Elsevier]

Abstract: Earthworm communities in the soil of flooded (coastal and floodplain grasslands) and non-flooded (boreo-nemoral) meadows were studied. The average number of species in coastal and floodplain meadows was low, earthworm communities of boreo-nemoral meadows were diverse and the average number of species was high. Specific composition of earthworm communities varied between the three types of meadows. Earthworm communities of flooded meadows possess specific characteristics being low in both numbers and species due to periodical anaerobic conditions during over flooding and negative effect of sea water in coastal meadows. [Copyright &y& Elsevier]

We studied an experimental horizontal subsurface-flow planted sand filter in Kodijärve, Estonia. We measured the microbial biomass, nitrogen immobilization, potential nitrification, soil respiration, multiple carbon source utilization patterns of the microbial consortia of the soil samples, the carbon, nitrogen, and phosphorus content of the soil samples, the water quality and physicochemical indicators in water sampling wells as well as emissions of CO2, N2, NO2, and CH4 from the two beds (the dry bed and the wet bed) in the wetland. The potential nitrification of the upper layer of the dry bed could not be attributed primarily to autotrophic nitrification, or the nitrifying bacteria in this layer could be facultative heterotrophs, whereas autotrophic nitrification is predominant in the upper layer of the wet bed. It also was found that changing aeration conditions in the lower layer of the dry bed have resulted in a lower diversity of the microbial community and led to a relative depletion of easily degradable soil carbon resources. [ABSTRACT FROM AUTHOR]

Microbial community structure was assessed in a horizontal subsurface flow planted sand filter treating domestic wastewater with molecular and culture-based methods. The diversity and spatial distribution of the microbial community was investigated using a PCR-DGGE (eubacterial and archaeal primers, ammonia-oxidizing bacteria, and ammonium monooxygenase specific primers), and spread plate and MPN counts. Significant differences were found in the spatial distribution of the microbial community structure. Data analysis revealed that different components of the microbial community possessed different spatial distribution patterns within the filter bed and depending on community type, relationships with soil chemical, and microbiological parameters varied. The most important spatial pattern in microbial community structure within the constructed wetland was related to the depth gradient, followed by differences between inflow and outflow. A comparison of a number of heterotrophic bacteria between inlet and outlet pipes as well as between two sampling depths showed no significant differences. In addition, the variation of the abundance of ammonia-oxidizing bacteria demonstrated no clear spatial pattern. [ABSTRACT FROM AUTHOR]

The composition (% relative abundance) of diatom assemblages from soft bottom sediments was studied at 75 sites situated in 46 rivers, brooks, and ditches in the islands of Hiiumaa and Saaremaa and in the lowland of West Estonia. Although the total number of recorded taxa was 205, the studied diatom assemblages consisted of 54, 55, 48, and 50 constant species in the drainage basin of Moonsund, the Gulf of Riga, Hiiumaa, and Saaremaa, respectively. The habitats of the dominating taxa were heterogenous and the most widespread species were Achnanthidium minutissimum, Martyana martyi, Meridion circulare, Cocconeis placentula, Planothidium lanceolatum, and Amphora pediculus. The Shannon–Weaver diversity (H′) index varied from 2.09 to 4.63. Multivariate analyses were used to identify the environmental variables governing the composition and structure of the benthic diatom assemblage. Principal Component Analysis (PCA) and Redundancy Analysis (RDA), based on 56 most abundant taxa, indicated differences in the composition and structure of diatom assemblages between different drainage basins as well as between the upper and lower stream courses. In the headwaters there prevailed small epipsammic diatoms (Martyana, Planothidium, Staurosira, Staurosirella). Different motile epipelic species from the genera Amphora, Navicula, Nitzschia, etc. were distributed abundantly in the lower courses of the streams. There was a positive correlation between order of the stream site and trophic level of water (R=0.35; p<0.05). Along a river system, the increasing order of the stream was accompanied by higher trophic level of water. [ABSTRACT FROM AUTHOR]

In this study, the effect of seed treatment with Achromobacter xylosoxidans AUM54 and glycolipid-type biosurfactants produced by this bacterial strain to suppress Ralstonia solanacearum, which causes bacterial wilt in tomato plants, was investigated. Applying biosurfactant in combination with the biosurfactant-producing bacteria reduced the R. solanacearum population on the tomato seed surface by 44% and reduced the seed infection percentage by 87%. In addition, these treatments induced resistance in tomato plants against this pathogen, evidenced by the increased activities of defence-related enzymes, such as phenylalanine ammonia-lyase, polyphenol oxidase, and peroxidase, and reduced the percentage of disease severity (DS). [ABSTRACT FROM AUTHOR]

Highlights • Bacterial diversity and community response was investigated in response to phosphate availability in soil. • Phosphorus limitation influenced the structural and functional diversity of bacteria. • Genus Massilia and Geobacter were significantly abundant in P limited soils. • Enzymes related to phosphorus cycling were induced in P limited soils. Abstract The effects of phosphorus (P) availability on soil microbial community and its functional responses have not been widely explored till date. The present study involved high throughput sequencing of 16S rRNA to investigate the bacterial community structure, size and function in long-term fertilized paddy soils that received P fertilizers (+ P) and compared with soils without P fertilizer (− P) application. Data analysis revealed that changes in P availability in the soil significantly influenced the phylogenetic composition of bacterial communities and their functional profiles. The populations of bacterial phyla Verrucomicrobia, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria were significantly induced in (− P) treatment when compared with (+ P). The bacterial genus Geobacter reported to use high-affinity P transporter during P limitation and Massilia known as a prominent P solubilizer were significantly more abundant in (− P) soils. The functional profile analysis demonstrated (− P) soils were characterized by more abundant enzymes related to P cycling. The present study enabled us to characterize the dominant indigenous microbiome of (− P) soils and also provided a better insight into the ecological and evolutionary responses of microbes in P limited soils. [ABSTRACT FROM AUTHOR]

Background and Aims The response of subarctic grassland's below-ground to soil warming is key to understanding this ecosystem's adaptation to future climate. Functionally different below-ground plant organs can respond differently to changes in soil temperature (T s). We aimed to understand the below-ground adaptation mechanisms by analysing the dynamics and chemistry of fine roots and rhizomes in relation to plant community composition and soil chemistry, along with the duration and magnitude of soil warming. Methods We investigated the effects of the duration [medium-term warming (MTW; 11 years) and long-term warming (LTW; > 60 years)] and magnitude (0–8.4 °C) of soil warming on below-ground plant biomass (BPB), fine root biomass (FRB) and rhizome biomass (RHB) in geothermally warmed subarctic grasslands. We evaluated the changes in BPB, FRB and RHB and the corresponding carbon (C) and nitrogen (N) pools in the context of ambient, T s < +2 °C and T s > +2 °C scenarios. Key Results BPB decreased exponentially in response to an increase in T s under MTW, whereas FRB declined under both MTW and LTW. The proportion of rhizomes increased and the C–N ratio in rhizomes decreased under LTW. The C and N pools in BPB in highly warmed plots under MTW were 50 % less than in the ambient plots, whereas under LTW, C and N pools in warmed plots were similar to those in non-warmed plots. Approximately 78 % of the variation in FRB, RHB, and C and N concentration and pools in fine roots and rhizomes was explained by the duration and magnitude of soil warming, soil chemistry, plant community functional composition, and above-ground biomass. Plant's below-ground biomass, chemistry and pools were related to a shift in the grassland's plant community composition – the abundance of ferns increased and BPB decreased towards higher T s under MTW, while the recovery of below-ground C and N pools under LTW was related to a higher plant diversity. Conclusion Our results indicate that plant community-level adaptation of below ground to soil warming occurs over long periods. We provide insight into the potential adaptation phases of subarctic grasslands. [ABSTRACT FROM AUTHOR]

Methane (CH 4) emissions generated from waste management facilities represent a serious global warming concern. The objective of this study was to monitor a fully instrumented biocover capable of abating fugitive CH 4 emissions from a closed landfill located at Kudjape, Saaremaa Island, Estonia. This investigation documented the alteration in the emission of CH 4 , carbon dioxide, and temperature fluctuation for a monitoring period of 10 years after the implementation of biocover. The fine fraction reclaimed from landfill mining along with natural mineral soil and sewage sludge compost in a proportion of 3:1:1 was used as a biocover substrate. CH 4 emissions were monitored at the surface and from three locations at a regular depth of 25 cm up to 2 m inside the biocover layer. The measurements recorded from three gas monitoring wells present different scenarios of a typical landfill due to the heterogenous nature of waste and non-homogeneous distribution of landfill gas load to the methane-oxidation layer, namely, a) desired situation where a permanent reduction in CH 4 concentration took place over time; b) hot-spot with an extremely high concentration of CH 4 albeit consistent decrease over the years; c) a location with minimal initial concentration of CH 4. Multivariate analysis showed that the CH 4 concentration dynamics and parameters reflecting the CH 4 oxidation process activity were different in biocover across the landfill. Based on data analysis results, the CH 4 oxidation process stabilizes in biocover in 5–6 years after establishing the cover. [ABSTRACT FROM AUTHOR]

Northern peatlands constitute a significant source of atmospheric methane ( CH4). However, management of undisturbed peatlands, as well as the restoration of disturbed peatlands, will alter the exchange of CH4 with the atmosphere. The aim of this systematic review and meta-analysis was to collate and analyze published studies to improve our understanding of the factors that control CH4 emissions and the impacts of management on the gas flux from northern (latitude 40° to 70°N) peatlands. The analysis includes a total of 87 studies reporting measurements of CH4 emissions taken at 186 sites covering different countries, peatland types, and management systems. Results show that CH4 emissions from natural northern peatlands are highly variable with a 95% CI of 7.6-15.7 g C m−2 year−1 for the mean and 3.3-6.3 g C m−2 year−1 for the median. The overall annual average (mean ± SD) is 12 ± 21 g C m−2 year−1 with the highest emissions from fen ecosystems. Methane emissions from natural peatlands are mainly controlled by water table ( WT) depth, plant community composition, and soil pH. Although mean annual air temperature is not a good predictor of CH4 emissions by itself, the interaction between temperature, plant community cover, WT depth, and soil pH is important. According to short-term forecasts of climate change, these complex interactions will be the main determinant of CH4 emissions from northern peatlands. Drainage significantly ( p < .05) reduces CH4 emissions to the atmosphere, on average by 84%. Restoration of drained peatlands by rewetting or vegetation/rewetting increases CH4 emissions on average by 46% compared to the original premanagement CH4 fluxes. However, to fully evaluate the net effect of management practice on the greenhouse gas balance from high latitude peatlands, both net ecosystem exchange ( NEE) and carbon exports need to be considered. [ABSTRACT FROM AUTHOR]

This study examined physiochemical conditions and prokaryotic community structure (the bacterial and archaeal 16S rRNA genes and mcrA gene abundances and proportions), and evaluated the effect of reed canary grass cultivation and mineral fertilisation on these factors, in the 60 cm thick residual peat layer of experimental plots located on an abandoned peat extraction area. The archaeal proportion was 0.67–39.56% in the prokaryotic community and the methanogens proportion was 0.01–1.77% in the archaeal community. When bacterial abundance was higher in the top 20 cm of peat, the archaea were more abundant in the 20–60 cm layer and methanogens in the 40–60 cm layer of the residual peat. The bacterial abundance was significantly increased, but archaeal abundance was not affected by cultivation. The fertiliser application had a slight effect on peat properties and on archaeal and methanogen abundances in the deeper layer of cultivated peat. The CH4 emission was positively related to mcrA abundance in the 20–60 cm of the bare peat, while in case of reed canary grass cultivation these two parameters were not correlated. Reed canary grass cultivation mitigated CH4 emission, although methanogen abundance remained approximately the same or even increased in different layers of residual peat under cultivated sites over time. This study supports the outlook of using abandoned peat extraction areas to produce reed canary grass for energy purposes as an advisable land-use practice from the perspective of atmospheric impact in peatland-rich Northern Europe. [ABSTRACT FROM AUTHOR]

In previous studies, hydrated oil shale ash has demonstrated outstanding phosphorus removal. However, long-term efficiency in field conditions and the impact on greenhouse gas emissions was unknown. From November 2011 to October 2012 we measured purification of pretreated municipal wastewater and greenhouse gas fluxes in an experimental 5-cell horizontal subsurface flow filter filled with oil shale ash and well-mineralized peat in different proportions. The cell with 60 cm peat (HF1) removed 63% of the inflow total phosphorus (TP; median 22.0 mg P L −1 ), whereas in cells with oil-shale ash HF2 (10 cm ash layer on 50 cm peat), HF3 (20 + 40 cm), HF4 (30 + 30 cm) and HF5 (60 cm ash), the TP removal efficiency was 70, 87, 98.6, and 99%, respectively. HFs 1–3 lost P removal capacity after 4 months, whereas in HFs 4–5 it remained throughout the experiment. HFs 4–5 increased the pH value and Ca 2+ concentration in outflow. The oil shale ash cells showed lower CO 2 emissions than the cells with peat. CH 4 emissions were highest in HF2 and HF3 and N 2 O emissions in HF5. During the snowmelt a peak in N 2 O emission was observed. The estimated NH 3 fluxes from HFs 3–5 accounted for 15–23% of the TN removal. During the long-term use of oil shale ash under open-air conditions, atmospheric CO 2 binding did not affect P removal capacity. The current study serves a good knowledge for the development of ecologically sustainable filter systems for wastewater treatment. [ABSTRACT FROM AUTHOR]

The impacts of site-specific characteristics, such as wetland type, water regime, and soil chemical parameters, on the abundance of denitrifying genes encoding nitrite ( nirS and nirK ) and nitrous oxide ( nosZ ) reductases, and their proportions in a bacterial community were investigated in a river diversion wetland complex using quantitative real time polymerase chain reaction. The water regimes of the wetlands had the greatest effect on all denitrification gene parameter values, except nirK abundance. While the proportion of nirS genes dominated other targeted genes, and their abundance and proportion in bacterial community was highest in constantly flooded areas, nosZ and nirK gene proportions were highest in occasionally flooded areas. Environmental factors had different effects on the abundances and proportions of nirS , nirK , and nosZ genes. The abundance of the nirS gene and ratio of nirK and nirS genes were affected by soil pH, and nirK gene proportions in the bacterial community were related to the NO 3 -N concentration in soil; however, the nature of these relationships varied in different wetlands and transitional areas, respectively. This finding suggests that microbes related to denitrification in soils of different wetland types do not respond similarly to the same environmental variables. [ABSTRACT FROM AUTHOR]

During the World Wars large quantities of phenylarsenic chemical warfare agents (CWAs) were dumped in the Baltic Sea. Many transformation products of these chemicals have been identified, but the pathways that produce the found chemicals has not been investigated. Here we studied the biotic and abiotic transformation of phenylarsenic CWAs under oxic and anoxic conditions and investigated how the sediment bacterial communities are affected by CWA exposure. By chemical analysis we were able to identify seventeen CWA-related phenylarsenicals, four of which (methylphenylarsinic acid (MPAA), phenylthioarsinic acid (PTAA), phenyldithioarsinic acid (PDTAA) and diphenyldithioarsinic acid (DPDTAA)) have not been reported for marine sediments before. For the first time PTAA was verified from environmental samples. We also observed equilibrium reactions between the found transformation products, which may explain the occurrence of the chemicals. 16S rRNA-analysis showed that bacterial communities in sediments are affected by exposure to phenylarsenic CWAs. We observed increases in the amounts of arsenic-resistant and sulphur-metabolising bacteria. Different transformation products were found in biotic and abiotic samples, which suggests that bacteria participate in the transformation of phenylarsenic CWAs. We propose that methylated phenylarsenicals are produced in microbial metabolism and that chemical reactions with microbially produced sulphur species form sulphur-containing transformation products. [Display omitted] • First study on differences in biotic and abiotic transformation of sea-dumped CWAs. • New transformation products (MPAA, PTAA, PDTAA, DPDTAA) were detected in sediment. • PTAA was identified from environmental samples for the first time. • Phenylarsenic CWA exposure modified bacterial community structure. • Microbes participate in the transformation by methylation and H 2 S-production. [ABSTRACT FROM AUTHOR]

Soil biodiversity constitutes the biological pillars of ecosystem services provided by soils worldwide. Soil life is threatened by intense agricultural management and shifts in climatic conditions as two important global change drivers which are not often jointly studied under field conditions. We addressed the effects of experimental short-term drought over the wheat growing season on soil organisms and ecosystem functions under organic and conventional farming in a Swiss long term trial. Our results suggest that activity and community metrics are suitable indicators for drought stress while microbial communities primarily responded to agricultural practices. Importantly, we found a significant loss of multiple pairwise positive and negative relationships between soil biota and process-related variables in response to conventional farming, but not in response to experimental drought. These results suggest a considerable weakening of the contribution of soil biota to ecosystem functions under long-term conventional agriculture. Independent of the farming system, experimental and seasonal (ambient) drought conditions directly affected soil biota and activity. A higher soil water content during early and intermediate stages of the growing season and a high number of significant relationships between soil biota to ecosystem functions suggest that organic farming provides a buffer against drought effects. [ABSTRACT FROM AUTHOR]

Abstract: The study examined the variability in 16S ribosomal RNA (16S rRNA) and tetracycline resistance tetA gene quantification from environmental samples in relation to modifications in quantitative polymerase chain reaction (qPCR) workflow and subsequent data evaluation and analysis. We analysed three types of soil samples using two DNA extraction methods, two qPCR chemistries (SYBR green, LUX™), and qPCR reaction kits from different manufacturers. To improve data quality, we employed a three-step amplification outlier removal approach prior to gene quantification calculations. We compared three variants of target gene enumerations and four variants of functional tetA gene normalisations against 16S rRNA genes. Results reveal that modifications in qPCR workflow steps significantly influence the gene quantification results from environmental samples. Primary factors affecting qPCR amplification efficiency included the variability of the target amplicon and the qPCR chemistry; the quality of the resulting datasets also had an impact. Although LUX™ qPCR has shown promise for environmental samples, SYBR green qPCR yielded considerably better-quality datasets and higher, more stable amplification efficiency values. Gene enumeration data of outlier-removed and unmodified sample sets showed minor differences for good-quality datasets (i.e., amplifications with SYBR green), but differed by up to 40% among lower-quality datasets. Different DNA extraction methods yielded varying amounts and purities of extracted microbial community DNA from environmental samples, with as much as an order of magnitude variation in gene copy numbers. Target gene normalisations yielded stable results on good-quality data, regardless of the DNA extraction method or qPCR chemistry used. Even though qPCR is regarded as a precise method with low detection limit, technical variability in the qPCR workflow tends to overestimate or effectively mask minute changes in community. [Copyright &y& Elsevier]

The article focuses on a research that assesses the spring-arrival timing of 42 migratory bird species in Estonia from 1957 to 1996. It evaluates the divisions of migratory birds, the climatic factors that influence their spring-arrival timing, and the trends in their spring-arrival timing in connection with climate change. Results show that there are two general clusters and six sub-clusters of species during the spring arrival of migratory birds: 23 are short-distance migrants while 19 are long-distance migrants. It discusses the relationship of the short-distance migrants' first arrival dates to the seasonal winter North Atlantic Oscillation (NAO) index and other climatic variables. It adds that long-distance migrants' first arrival dates are weakly correlated with climatic factors.

The aim of the current article is to give an overview about microbial communities and their functioning but also about factors affecting microbial activity in the three most common types (surface flow and two types of sub-surface flow) of constructed wetlands. The paper reviews the community composition and structural diversity of the microbial biomass, analyzing different aspects of microbial activity with respect to wastewater properties, specific wetland type, and environmental parameters. A brief introduction about the application of different novel molecular techniques for the assessment of microbial communities in constructed wetlands is also given. Microbially mediated processes in constructed wetlands are mainly dependent on hydraulic conditions, wastewater properties, including substrate and nutrient quality and availability, filter material or soil type, plants, and different environmental factors. Microbial biomass is within similar ranges in both horizontal and vertical subsurface flow and surface flow constructed wetlands. Stratification of the biomass but also a stratified structural pattern of the bacterial community can be seen in subsurface flow systems. Microbial biomass C/N ratio is higher in horizontal flow systems compared to vertical flow systems, indicating the structural differences in microbial communities between those two constructed wetland types. The total activity of the microbial community is in the same range, but heterotrophic growth is higher in the subsurface (vertical flow) system compared to the surface flow systems. Available species-specific data about microbial communities in different types of wetlands is scarce and therefore it is impossible make any general conclusions about the dynamics of microbial community structure in wetlands, its relationship to removal processes and operational parameters. [Copyright &y& Elsevier]

The depth distribution of photosynthetic pigments and benthic marine diatoms was investigated in late spring at three different sites on the Swedish west coast. At each site, sediment cores were taken at six depths (7-35 m) by scuba divers. It was hypothesized that (1) living benthic diatoms constitute a substantial part of the benthic microflora even at depths where the light levels are<1% of the surface irradiance, and (2) the changing light environment along the depth gradient will be reflected in (a) the composition of diatom assemblages, and (b) different pigment ratios. Sediment microalgal communities were analysed using epifluorescence microscopy (to study live cells), light microscopy and scanning electron microscopy (diatom preparations), and HPLC (photosynthetic pigments). Pigments were calculated as concentrations (mg m-2) and as ratios relative to chlorophylla. Hypothesis (1) was accepted. At 20 m, the irradiance was 0.2% of surface irradiance and at 7 m, 1%. Living (epifluorescent) benthic diatoms were found down to 20 m at all sites. The cell counts corroborated the diatom pigment concentrations, decreasing with depth from 7 to 25 m, levelling out between 25 and 35 m. There were significant positive correlations between chlorophyllaand living (epifluorescent) benthic diatoms and between the diatom pigment fucoxanthin and chlorophylla. Hypothesis (2) was only partly accepted because it could not be shown that light was the main environmental factor. A principal component analysis on diatom species showed that pelagic forms characterized the deeper locations (25-35 m), and epipelic-epipsammic taxa the shallower sites (7-20 m). Redundancy analyses showed a significant relationship between diatom taxa and environmental factors - temperature, salinity, and light intensities explained 57% of diatom taxa variations. [ABSTRACT FROM AUTHOR]

Drought and agricultural management influence soil microorganisms with unknown consequences for the functioning of agroecosystems. We simulated drought periods in organic (biodynamic) and conventional wheat fields and monitored effects on soil water content, microorganisms and crops. Above the wilting point, water content and microbial respiration were higher under biodynamic than conventional farming. Highest bacterial and fungal abundances were found in biodynamically managed soils, and distinct microbial communities characterised the farming systems. Most biological soil quality parameters and crop yields were only marginally affected by the experimental drought, except for arbuscular mycorrhizal fungi (AMF), which increased in abundance under the experimental drought in both farming systems. AMF were further strongly promoted by biodynamic farming resulting in almost three times higher AMF abundance under experimental drought in the biodynamic compared with the conventional farming system. Our data suggest an improved water storage capacity under biodynamic farming and confirms positive effects of biodynamic farming on biological soil quality. The interactive effects of the farming system and drought may further be investigated under more substantial droughts. Given the importance of AMF for the plant's water supply, more in-depth studies on AMF may help to clarify their role for yields under conditions predicted by future climate scenarios. [ABSTRACT FROM AUTHOR]

Cover crops play an increasingly important role in improving soil quality, reducing agricultural inputs and improving environmental sustainability. The main objectives of this critical global review and systematic analysis were to assess cover crop practices in the context of their impacts on nitrogen leaching, net greenhouse gas balances (NGHGB) and crop productivity. Only studies that investigated the impacts of cover crops and measured one or a combination of nitrogen leaching, soil organic carbon (SOC), nitrous oxide (N2O), grain yield and nitrogen in grain of primary crop, and had a control treatment were included in the analysis. Long‐term studies were uncommon, with most data coming from studies lasting 2–3 years. The literature search resulted in 106 studies carried out at 372 sites and covering different countries, climatic zones and management. Our analysis demonstrates that cover crops significantly (p < 0.001) decreased N leaching and significantly (p < 0.001) increased SOC sequestration without having significant (p > 0.05) effects on direct N2O emissions. Cover crops could mitigate the NGHGB by 2.06 ± 2.10 Mg CO2‐eq ha−1 year−1. One of the potential disadvantages of cover crops identified was the reduction in grain yield of the primary crop by ≈4%, compared to the control treatment. This drawback could be avoided by selecting mixed cover crops with a range of legumes and non‐legumes, which increased the yield by ≈13%. These advantages of cover crops justify their widespread adoption. However, management practices in relation to cover crops will need to be adapted to specific soil, management and regional climatic conditions. [ABSTRACT FROM AUTHOR]

Wastewater treatment systems receiving municipal wastewater are major dissemination nodes of antibiotic resistance genes (ARGs) between anthropogenic and natural environments. This study examined the fate of antibiotic resistome and class 1–3 integron-integrase genes in photobioreactors that were treating municipal wastewater diluted (70/30) with lake or tap water for the algal biomass production. A combined approach of metagenomic and quantitative (qPCR) analysis was undertaken. Municipal wastewater treatment in the photobioreactors led to reduced antibiotic resistome proportion, number of ARG subtypes, and abundances of individual ARGs in the bacterial community. The ARGs and intI1 gene abundances and relative abundances in the discharges of the photobioreactors were either comparable or lower than the respective values in the effluents of conventional wastewater treatment plants. The reduction of the resistome proved to be strongly related to the changes in the bacterial community composition during the wastewater treatment process as it was responding to rising pH levels caused by intense algal growth. Several bacterial genera (e.g., Azoarcus, Dechloromonas, and Sulfuritalea ) were recognized as potential hosts of multiple antibiotic resistance types. Although the lake water contributed a diverse and abundant resistome and intI genes profile to the treatment system, it proved to be considerably more beneficial for wastewater dilution than the tap water. The diversity (number of detected resistance types and subtypes) and proportion of the antibiotic resistome, the amount of plasmid borne integron-integrase gene reads, and the abundances and relative abundances of the majority of quantified ARGs ( aadA , sul1 , tetQ, tetW , qnrS , ermB , blaOXA2 -type) and intI1 gene as well as the amount of multi-resistance determinants were significantly lower in the discharges of photobioreactors where lake water was used to dilute wastewater. [ABSTRACT FROM AUTHOR]

• Ag nanoparticles affect wastewater antibiotic resistome in constructed wetland. • Elevated Ag resulted in higher antibiotic resistance gene discharge via effluent. • Elevated Ag increased pathogens in biofilm and effluent of vertical flow filter. Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag+ in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO 3 -treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1 , in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation. [Display omitted] [ABSTRACT FROM AUTHOR]

Objectives To profile the seminal microbiome applying next generation sequencing. Methods Semen samples of 67 men were involved in the study (21 men with and 46 men without prostatitis). Seminal microbiomes were profiled applying the method that uses combinatorial sequence tags attached to polymerase chain reaction primers that amplify the ribosomal ribonucleic acid V6 region. Amplified polymerase chain reaction products were sequenced using an Illumina paired-end protocol on HiSeq2000 platform. Results The most abundant phylum in semen was Firmicutes, comprising nearly half of the sequences found (median 41.7%, quartiles 28.5-47.2%) followed by Bacteroidetes, Proteobacteria and Actinobacteria. The counts of lactobacilli were higher in healthy men than prostatitis patients (27% [20.2-34.6%] vs 20.2% [4.9-25.0%]; P = 0.05), especially for Lactobacillus iners. Proteobacteria comprised higher proportions in prostatitis patients than healthy men. The species richness was higher in prostatitis patients than healthy men (inverted Simpson index 13.5 ± 5.8 vs 10.3 ± 4.0). Conclusions The semen of chronic prostatitis patients contains fewer health-supporting lactobacilli, and has higher species diversity than that of healthy men. Firmicutes (especially lactobacilli), Bacteroidetes, Proteobacteria and Actinobacteria comprise the highest proportion of seminal microbiome. [ABSTRACT FROM AUTHOR]

Soil fertilization with animal manure or its digestate may facilitate an important antibiotic resistance dissemination route from anthropogenic sources to the environment. This study examines the effect of mineral fertilizer (NH 4 NO 3 ), cattle slurry and cattle slurry digestate amendment on the abundance and proportion dynamics of five antibiotic resistance genes (ARGs) and two classes of integron-integrase genes ( intI1 and intI2 ) in agricultural grassland soil. Fertilization was performed thrice throughout one vegetation period. The targeted ARGs ( sul1 , tetA , blaCTX-M , blaOXA2 and qnrS ) encode resistance to several major antibiotic classes used in veterinary medicine such as sulfonamides, tetracycline, cephalosporins, penicillin and fluoroquinolones, respectively. The non-fertilized grassland soil contained a stable background of tetA , blaCTX-M and sul1 genes. The type of applied fertilizer significantly affected ARGs and integron-integrase genes abundances and proportions in the bacterial community (p < 0.001 in both cases), explaining 67.04% of the abundance and 42.95% of the proportion variations in the grassland soil. Both cattle slurry and cattle slurry digestate proved to be considerable sources of ARGs, especially sul1 , as well as integron-integrases. Sul1 , intI1 and intI2 levels in grassland soil were elevated in response to each organic fertilizer's application event, but this increase was followed by a stage of decrease, suggesting that microbes possessing these genes were predominantly entrained into soil via cattle slurry or its digestate application and had somewhat limited survival potential in a soil environment. However, the abundance of these three target genes did not decrease to a background level by the end of the study period. TetA was most abundant in mineral fertilizer treated soil and blaCTX-M in cattle slurry digestate amended soil. Despite significantly different abundances, the abundance dynamics of bacteria possessing these genes were similar (p < 0.05 in all cases) in different treatments and resembled the dynamics of the whole bacterial community abundance in each soil treatment. [ABSTRACT FROM AUTHOR]

Silver nanoparticles (AgNPs) threaten human and ecosystem health, and are among the most widely used engineered nanomaterials that reach wastewater during production, usage, and disposal phases. This study evaluated the effect of a 100-fold increase in collargol (protein-coated AgNP) and Ag+ ions concentrations in municipal wastewater on the microbial community composition of the filter material biofilms (FMB) and the purification efficiency of the hybrid treatment system consisting of vertical (VF) and horizontal (HF) subsurface flow filters. We found that increased amounts of collargol and AgNO 3 in wastewater had a modest effect on the prokaryotic community composition in FMB and did not significantly affect the performance of the studied system. Regardless of how Ag was introduced, 99.9% of it was removed by the system. AgNPs and AgNO 3 concentrations did not significantly affect the purification efficiency of the system. AgNO 3 induced a higher increase in the genetic potential of certain Ag resistance mechanisms in VFs than collargol; however, the increase in Ag resistance potential was similar for both substances in HF. Hence, the microbial community composition in biofilms of vertical and horizontal flow filters is largely resistant, resilient, or functionally redundant in response to AgNPs addition in the form of collargol. [Display omitted] • Collargol and AgNO 3 in wastewater modestly affected the prokaryotic community composition. • Collargol and AgNO 3 did not significantly affect the performance of the hybrid wastewater treatment system. • Genetic potential of certain Ag resistance mechanisms in VFs was higher with AgNO 3 than with collargol. • Microbial communities are resilient to collargol addition in vertical and horizontal flow filter biofilms. [ABSTRACT FROM AUTHOR]

Artificial pulsing of water table is often used in horizontal subsurface flow (HSSF) constructed wetlands (CW) to enhance removal of BOD, COD, NH 4 and total N utilization by bacteria. In 2008–2010 and during the experimental session in October–November 2012 we studied the impact of a fluctuating water table on the water purification efficiency and GHG emissions in the 216 m 2 HSSF bed of a hybrid CW commissioned in 2002 in Paistu, Estonia. For comparison, water purification data from a previous study ( Öövel et al., 2007 ) have been used. Isotopologue studies have been conducted in order to distinguish between denitrification and nitrification as source processes of N 2 O. Short-term (one month) and short-range (up to 35 cm) fluctuations in the water table enhanced CO 2 and N 2 O emission whereas the median values varied from 0.5 to 246 μg CH 4 -C m −2 h −1 and 1.5 to 8.3 μg N 2 O-N m −2 h −1 , respectively. There was a significant ( p < 0.05) negative correlation between water table depth and CO 2 ( R 2 = 0.53) and N 2 O ( R 2 = 0.35) emissions. Due to the plant cover disturbance in the outflow section of the HSSF bed, CH 4 emission did not show any significant difference between the high and low water table phase, and the correlation between water table depth and CH 4 emission was positive. The impact of pulsing water table on water purification was minor: high water table enhanced the TOC removal and inhibited the TN removal, whereas the TP concentrations showed remarkable variations but no significant differences between the inflow and outflow values. Likewise, pH and dissolved O 2 values, and NH 4 + -N removal were not significantly influenced by water table manipulations. The value of δ 15 N bulk N 2 O, δ 18 O-N 2 O and site preference (SP) of N 2 O in water samples varied from −2 to 32 ‰, between 41 and 78 ‰, and from 15 to 41 ‰, respectively. There was a significant positive correlation between the δ 18 O-N 2 O vs SP N 2 O values ( R 2 = 0.77). This correlation, the range of isotopologue values and relatively low N 2 O emission corroborate that the main source of N 2 O fluxes in the studied HSSF CW bed is denitrification. [ABSTRACT FROM AUTHOR]

The biological nitrogen cycle is complex, and the origin of different nitrogen compounds and factors driving the transformation processes in different environments are not completely understood as new bacterial pathways and genes associated with nitrogen metabolism are discovered. In this study, the impact of water regime, soil type and chemical parameters on the genetic potential of nitrous oxide reduction and anaerobic ammonium oxidation (ANAMMOX) of the soils and sediments of a created riverine wetland complex was determined by quantifying the proportions of nitrous oxide reductase encoding nosZ gene clades I and II, and the ANAMMOX-specific 16S rRNA gene, respectively. The ANAMMOX-specific bacterial community structure was profiled using high-throughput sequencing of the 16S rRNA gene. The results of the study showed that bacterial 16S rRNA gene abundances were higher in the organic rich sediments of permanently flooded areas of freshwater marshes. The proportions of nosZ clade I and II genes (0.56–4.59% and 0.48–3.01%, respectively) were quite equally represented in the microbial communities of the studied soils. Both proportions of nosZ genes in the soil were dependent on hydrological conditions at the site, showing higher values in occasionally flooded areas than in the permanently flooded sites of two freshwater marshes in the study area. The proportion of clade I of the nosZ gene was related to NH 4 –N, C/N, P, K, and Ca concentrations in the soil, while proportions of the clade II showed a relationship with soil Mg content. Both nosZ gene clades’ proportions were positively correlated with the nirK gene proportion in the microbial community, while a negative relationship was detected between the proportions of nosZ clade I and nirS genes. The ANAMMOX-specific 16S rRNA gene proportion was between 0.00005% and 0.084% in the studied soils and sediments. Significantly higher ANAMMOX potential was detected in the soils and sediments of the inflow areas of freshwater marshes. An analysis of 16S rRNA gene fragments identified members of three ANAMMOX-specific bacterial genera ( Candidatus Brocadia , Candidatus Scalindua , and Candidatus Kuenenia ) from the soils of the study area. The results indicated that the ANAMMOX genetic potential was lower than the potential of N 2 emission via denitrification in the studied soils. In addition, the current study revealed that the nirS gene can be related to both N 2 producing processes in wetland soils, since the strong positive correlation between the ANAMMOX-specific 16S rRNA and nirS gene proportions in the bacterial communities of the studied wetland complex soils was detected. [ABSTRACT FROM AUTHOR]

The genital tract microbiome is tightly associated with reproductive health. Although many research studies have been performed on the vaginal microbiome, current knowledge of the male microbiome is scarce, and parallel studies examining couples are extremely rare. In this work, we aimed to compare seminal and vaginal microbiomes in couples and to assess the influence of sexual intercourse on vaginal microbiome. The study included 23 couples. Microbiomes of semen and vaginal fluid (pre- and post–intercourse) were profiled using Illumina HiSeq2000 sequencing of the V6 region of 16S rRNA gene. Seminal communities were significantly more diverse, but with lower total bacterial concentrations than those of the vagina. Gardnerella vaginalis was predominant in half of the women whose partners had significant leukocytospermia, but only in one of 17 women who had a partner without leukocytospermia. There was significant decrease in the relative abundance of Lactobacillus crispatus after intercourse, and high concordance between semen and vaginal samples. Our data support the hypothesis that semen and vaginal microbiomes are in association, inasmuch as the predominance of G. vaginalis in female partners was significantly related to inflammation in male genital tracts. [ABSTRACT FROM AUTHOR]

Known as biogeochemical hotspots in landscapes, riparian buffer zones exhibit considerable potential concerning mitigation of groundwater contaminants such as nitrate, but may in return enhance the risk for indirect N2O emission. Here we aim to assess and to compare two riparian gray alder forests in terms of gaseous N2O and N2 fluxes and dissolved N2O, N2, and NO3- in the near-surface groundwater. We further determine for the first time isotopologue ratios of N2O dissolved in the riparian groundwater in order to support our assumption that it mainly originated from denitrification. The study sites, both situated in Estonia, northeastern Europe, receive contrasting N loads from adjacent uphill arable land. Whereas N2O emissions were rather small at both sites, average gaseous N2-to-N2O ratios inferred from closed-chamber measurements and He-O laboratory incubations were almost four times smaller for the heavily loaded site. In contrast, groundwater parameters were less variable among sites and between landscape positions. Campaign-based average 15N site preferences of N2O (SP) in riparian groundwater ranged between 11 and 44 o. Besides the strong prevalence of N2 emission over N2O fluxes and the correlation pattern between isotopologue and water quality data, this comparatively large range highlights the importance of denitrification and N2O reduction in both riparian gray alder stands. [ABSTRACT FROM AUTHOR]

Wader populations have been declining worldwide, providing a fundamental question as to which environmental factors limit population growth. Many studies have focused on the effects of habitat change on wader populations as a result of climate change, agricultural intensification or abandonment of arable land. However, there are few studies investigating the relationship between wader distribution/abundance and prey abundance. This study focused on the relationship between breeding wader abundance, habitat characteristics and prey abundance on different types of coastal and floodplain grasslands. The study was carried out in the Matsalu Bay area, Western Estonia between 2001 and 2005. Results showed that most wader species were strongly related to habitat flooding type but not to plant species richness or evenness or mean vegetation coverage. Abundance of epigeic earthworms at a site was positively correlated with wader species diversity and abundance, as well as at the individual species level for abundance of Northern Lapwing Vanellus vanellus, Black-tailed Godwit Limosa limosa and Redshank Tringa totanus. Endogeic earthworm abundance was not significantly related to total wader abundance, although for some species there was a weak negative relationship. We conclude that epigeic earthworms are an important food source for most wader species on Matsalu grasslands and endogeic earthworms are not likely to be utilised as a prey source. Wader abundance was most strongly related to flooding as a determinate factor for breeding habitat characteristics and with epigeic earthworms as a food source. These factors are important environmental variables influencing local abundance and distribution of coastal waders. [ABSTRACT FROM AUTHOR]

Abstract: A literature analysis of 158 papers published in international peer-reviewed journals indexed by the Thomson Reuters Web of Knowledge from 1994 to 2013 showed that CO2 C emission was significantly lower in free water surface (FWS) constructed wetlands (CW) than in subsurface flow (SF) CWs (median values from 95.8 to 137.0mgm−2 h−1, respectively). In vertical subsurface flow (VSSF) CWs the CH4 C emission was significantly lower than in horizontal subsurface flow (HSSF) CWs (median values 3.0, 6.4, and 4.0mgm−2 h−1, respectively). There were no significant differences in N2O N emission in various CW types (median for FWS, VSSF and HSSF CWs: 0.09, 0.12, and 0.13mgm−2 h−1 correspondingly). The highest value of emission factor (EF) of CH4 ((CH4 C/inflow TOCin)*100%) was found for FWS CWs (median 18.0%), followed by HSSF CWs (3.8%), and VSSF CWs (1.28%). Median values of N2O EFs ((N2O N/inflow TNin)*100%) differed significantly in all three CW types: 0.34% for HSSF, 0.11% for FWS, and 0.018% for VSSF CWs. We found a significant correlation between TOCin and CH4 C emission and between the TNin and N2O N emission values for all of the types of CWs we studied. Hybrid CWs (e.g., the subsequent combination of VSSF, HSSF and FWS CWs) are beneficial from the point of view of both water purification and minimization of greenhouse gas (GHG) emissions. Likewise, intermittent loading in VSSF CWs and macrophyte harvesting in HSSF and FWS CWs can mitigate GHG emissions. [Copyright &y& Elsevier]

The residues from human environments often contain antibiotics and antibiotic resistance genes ( ARGs) that can contaminate natural environments; the clearest consequence of that is the selection of antibiotic-resistant bacteria. The Baltic Sea is the second largest isolated brackish water reservoir on Earth, serving as a drainage area for people in 14 countries, which differ from one another in antibiotic use and sewage treatment policies. The aim of this study was to characterize the bacterioplankton structure and quantify ARGs ( tetA, tetB, tetM, ermB, sul1, blaSHV, and ampC) within the bacterioplankton community of the Baltic Sea. Quantitative polymerase chain reaction was applied to quantify ARGs from four different sampling sites of the Baltic Sea over 2 years, and the bacterial communities were profiled sequencing the V6 region of the 16S r RNA gene on Illumina Hi Seq2000. The results revealed that all the resistance genes targeted in the study were detectable from the Baltic Sea bacterioplankton. The percentage of tetA, tetB, tetM, ermB, and sul1 genes in the sea bacterial community varied between 0.0077% and 0.1089%, 0.0003% and 0.0019%, 0.0001% and 0.0105%, 0% and 0.0136%, and 0.0001% and 0.0438%, respectively. The most numerous ARG detected was the tetA gene and this gene also had the highest proportion in the whole microbial community. A strong association between bacterioplankton ARGs' abundance data and community phylogenetic composition was found, implying that the abundance of most of the studied ARGs in the Baltic Sea is determined by fluctuations in its bacterial community structure. [ABSTRACT FROM AUTHOR]

Abstract: Municipal wastewater treatment is one of the pathways by which antibiotic resistance genes from anthropogenic sources are introduced into natural ecosystems. This study examined the abundance and proportion dynamics of seven antibiotic resistance genes in the wetland media biofilm and in the influent and effluent of parallel horizontal subsurface flow mesocosm cells of a newly established hybrid constructed wetland treating municipal wastewater. The targeted genes (tetA, tetB, tetM, ermB, sul1, ampC, and qnrS) encode resistance to major antibiotic classes such as tetracyclines, macrolides, sulfonamides, penicillins, and fluoroquinolones, respectively. All targeted antibiotic resistance genes were detectable in the tested mesocosm environments, with the tetA, sul1, and qnrS genes being the most abundant in the mesocosm effluents. After initial fluctuation in the microbial community, target gene abundances and proportions stabilized in the wetland media biofilm. The abundance of 16S rRNA and antibiotic resistance genes, and the proportion of antibiotic resistance genes in the microbial community, were reduced during the wastewater treatment by the constructed wetland. The concentration of antibiotic resistance genes in the system effluent was similar to conventional wastewater treatment facilities; however, the mesocosms reduced sulfonamide resistance encoding sul1 concentrations more effectively than some traditional wastewater treatment options. The concentrations of antibiotic resistance genes in the wetland media biofilm and in effluent were affected by system operation parameters, especially time and temperature. The results also revealed a relationship between antibiotic resistance genes abundance and the removal efficiencies of NO2–N, NH4–N, and organic matter. Correlation analysis between the abundance of individual antibiotic resistance genes in the mesocosms influent, effluent and wetland media biofilm indicated that depending on antibiotic resistance gene type the microbes carrying these genes interact differently with microbial communities already present on the wetland media. [Copyright &y& Elsevier]

Abstract: The coastal waters of the Baltic Sea are constantly threatened by oil spills, due to the extensive transportation of oil products across the sea. To characterise the hydrocarbon-degrading bacterial community of this marine area, microcosm experiments on diesel fuel, crude oil and shale oil were performed. Analysis of these microcosms, using alkane monooxygenase (alkB) and 16S rRNA marker genes in PCR-DGGE experiments, demonstrated that substrate type and concentration strongly influence species composition and the occurrence of alkB genes in respective oil degrading bacterial communities. Gammaproteobacteria (particularly the genus Pseudomonas) and Alphaproteobacteria were dominant in all microcosms treated with oils. All alkB genes carried by bacterial isolates (40 strains), and 8 of the 11 major DGGE bands from the microcosms, had more than 95% sequence identity with the alkB genes of Pseudomonas fluorescens. However, the closest relatives of the majority of sequences (54 sequences from 79) of the alkB gene library from initially collected seawater DNA were Actinobacteria. alkB gene expression, induced by hexadecane, was recorded in isolated bacterial strains. Thus, complementary culture dependent and independent methods provided a more accurate picture about the complex seawater microbial communities of the Baltic Sea. [Copyright &y& Elsevier]

Abstract: We studied the dechlorination of hexachlorobenzene (HCB) in wetland mesocosm (MC) trials filled with sediment (well mineralized homogenized peat mixed with mud) from a wastewater treatment wetland located in a floodplain: three MCs were planted with common reed (Phragmites australis) and another three with broad-leaved cattail (Typha latifolia). According to the rootzone development we distinguished between the upper (0–10 cm from the soil surface) and lower layers (20–30 cm). Over 36 days, the initial measured concentration of HCB was reduced to 61%, 51%, 42% and 40% in the lower layer without roots of Phragmites, in the lower layer with roots of Typha, in the upper layer with roots of Typha, and in the upper layer with roots of Phragmites respectively. The 90% degradation time (DT90) of the initial measured HCB can be calculated as 192, 121, 110 and 92 days (d) respectively. PeCB, 1, 2, 3, 4-, 1, 2, 3, 5- and 1, 2, 4, 5-TeCB, and 1, 2, 3-, 1, 2, 4- and 1, 3, 5-TCB were the main dechlorination products detected in MC sediment samples. The dechlorination rates of HCB were higher in sediment layers with well-developed root zones. According to the DT50 of 28–58 days and DT90 of 92–192 days, HCB can be considered to be a less persistent organic pollutant in constructed wetlands. [Copyright &y& Elsevier]

The aim of this study is to estimate emissions of greenhouse gases CO, CH and NO, and the effects of drainage and peat extraction on these processes, in Estonian transitional fens and ombrotrophic bogs. Closed-chamber-based sampling lasted from January to December 2009 in nine peatlands in Estonia, covering areas with different land-use practices: natural (four study sites), drained (six sites), abandoned peat mining (five sites) and active peat mining areas (five sites). Median values of soil CO efflux were 1,509, 1,921, 2,845 and 1,741 kg CO-C ha year from natural, drained, abandoned and active mining areas, respectively. Emission of CH-C (median values) was 85.2, 23.7, 0.07 and 0.12 kg ha year, and NO-N −0.05, −0.01, 0.18 and 0.19 kg ha year, respectively. There were significantly higher emissions of CO and NO from abandoned and active peat mining areas, whereas CH emissions were significantly higher in natural and drained areas. Significant Spearman rank correlation was found between soil temperature and CO flux at all sites, and CH flux with high water level at natural and drained areas. Significant increase in CH flux was detected for groundwater levels above 30 cm. [ABSTRACT FROM AUTHOR]

Abstract: There is little understanding of the pathways of hexachlorobenzene (HCB) removal in treatment wetlands. The aim of this research was to evaluate HCB dechlorination as affected by common reed (Phragmites australis) and broad-leaved cattail (Typha latifolia) applications in neutralized and enriched with nutrients peat with high, low and nil HCB concentration (300, 15, and 0μg/g, respectively). After 10 weeks of the experiment, HCB removal was 49.4–67.2% in High-HCB peat, and 57.6–74.8% in Low-HCB peat. The mean removal of HCB was 53.5% in the unvegetated and 68.7% in the vegetated microcosm wetlands. The amount of HCB metabolites showed that dechlorination rates in Low-HCB microcosms were higher than in High-HCB microcosms, which were mainly attributed to the lower phytotoxicity and higher dissolved organic carbon (DOC) content than that of Low-HCB. Although HCB uptake by plants was <0.1% of the initial concentration, in both High-HCB and Low-HCB peats vegetated with Typha and Phragmites, enhanced HCB dechlorination rate was found. This was probably because the roots and its exudates enhanced dechlorination process. Microbial degradation was the predominating process in HCB removal. The following dechlorinated metabolites of HCB were detectable from the water, macrophytes and peat samples: PeCB, 1,2,3,4-, 1,2,3,5- and 1,2,4,5-TeCB, 1,2,3-, 1,2,4- and 1,3,5-TCB. [Copyright &y& Elsevier]

Limited nutrient acquisition from soil is a key process limiting productivity in boreal forest. We investigated short-root morphological adaptations and rhizosphere effect in relation to site conditions in interaction with tree mineral nutrition. We studied seven young (8- to 14-year-old) silver birch ( Betula pendula Roth.) stands on abandoned agricultural land in Estonia. Soil pH varied from 3.8 to 7.0, and soil N % from 0.07 to 0.26%. Tree nutrient (NPK) status was expressed by leaf nutrient concentrations. Leaf N correlated negatively with short-root specific length and area. Summed activity (SA) and metabolic diversity of bacteria (by BIOLOG Ecoplate™), bacterial community diversity (by DGGE) and pH were determined for rhizosphere (R) and bulk soil (S) to reveal the extent of the rhizosphere effect . Bacterial activity in rhizosphere was 1.4-4.7 times higher than in bulk soil. Ratio SA/SA indicating root support to the rhizosphere bacterial communities decreased with increasing bulk soil pH; however, when bulk soil pH was ≥5, the decrease in SA/SA was insignificant, i.e. the rhizosphere effect stayed at a stable level. Diversity of bacterial community was 6% higher in bulk soil than in rhizosphere. Rhizosphere acidification occurred in studied stands when bulk soil pH ≥ 5. Short-root N % correlated positively with SA/SA. We concluded that tree N-nutritional status was related to short-root morphological parameters but not to studied microbiological characteristics in the soil of young silver birch stands. [ABSTRACT FROM AUTHOR]

Abstract: Mining activities create wastelands that require reclamation. The relief of abandoned opencast oil shale mining area is rugged, and the mining spoil is extremely stony and alkaline (pH 8), with low N and organic content. Planting of fast-growing deciduous tree species such as silver birch (Betula pendula) on post-mining area is the best means to accelerate the development of a new forest ecosystem in such harsh conditions. A chronosequence of silver birch stands (1, 2, 3, 5, 29, 40 years old) was investigated to reveal changes in bulk soil (S) and rhizosphere (R) properties, in rhizosphere effect on bacterial activity and diversity, and in fine-root morphological adaptations in relation to stand development. The rhizosphere effect on bacterial activity was measured as a rhizosphere/soil (R/S) ratio and on species diversity as a similarity (%) between rhizosphere and bulk soil bacterial communities. Bacterial species diversity was determined by denaturing gradient gel electrophoresis (DGGE) technique and was expressed as Shannon diversity index. Biolog EcoPlates were used to determine the summed activity of cultivable bacteria in rhizosphere and bulk soil. Short-root morphological parameters were measured using WinRHIZO™ Pro. Soil pH and available P concentration decreased logarithmically, and N% and organic matter concentration increased linearly with increasing stand age. During the first 30 years of stand development SIR increased an order, from 0.18 to 1.90mgCg−1. Bulk soil bacterial diversity increased logarithmically with stand age. The bacterial diversity was higher in rhizosphere than in bulk soil. Rhizosphere effect on bacterial activity was low a year after planting, increased more than two times in the next 2 years, and decreased thereafter rapidly with stand age. Rhizosphere effect, indicating plant support to rhizosphere microbial communities, was highest when soil conditions were still poor, but trees had already overcome the transplant shock. All short-root morphological parameters showed certain trends with age. Specific short-root length varied between 56 and 313mg−1 and decreased logarithmically with stand age and soil improvement. The fastest changes in short-root morphology, rhizosphere effect, and soil pH occurred during the early development of silver birch stands – in the first 5 years; P nutrition and N use efficiency improved simultaneously. Rhizosphere effect and short-root morphological adaptation have an important role in soil and stand development on oil shale post-mining area, and silver birch is a promising tree species for reclamation of alkaline mining spoil. [Copyright &y& Elsevier]

The article explores the relationship of atmospheric circulation types (CT) and the arrival of migratory birds in Estonia during spring. The 1958-2002 spring migration phenology of 42 bird species in Estonia's Tartu and Kuressaare was analyzed to obtain the first arrival dates and later compared it to CT of COST 733 catalog 1.2, domain 05. The authors conclude that spring arrival of migratory birds in western and eastern Estonia is affected by weather conditions and climate change.