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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]

The tree root-mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments., The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium ( EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics., Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure., We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root-mycorrhiza-bacteria continuum along climate and soil C : N gradients. [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]

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]

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 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]

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 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 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]

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]

Root studies are increasingly prominent and increasing amount of root trait data improve our understanding of ecosystem functioning and retention in the context of rapid global changes. We aimed 1) to analyze ectomycorrhizal (EcM) fungus specific morphology of absorptive roots in lab experiments in comparison to same fungus colonized root traits in field study sites along latitudinal gradient in European boreal forests 2) to compare the response of fine roots in manipulative studies and along climate gradient to describe the universal trends in root traits and to raise hypotheses about general mechanisms in fine root system adaptation of forest trees in global change. Root traits from climate manipulation experiments, manipulated by CO2 concentration, relative air humidity and soil warming in forest ecosystems and the data for different tree species along natural gradient encompassing different climate and forest zones in Northern Europe were analyzed.The fungal colonization was the main driver of absorptive root tip morphology in lab as well as in manipulation and gradient studies, while fungus-specific effect on root morphology along environmental gradients varied significantly. We envisage a role of trilateral relation between the morphological traits of absorptive fine roots, exploration types of colonising EcM fungi and rhizosphere and bulk soil bacterial community structure. A significant change in absorptive fine root biomass in all experiments and for all studied tree species coincided with changes in absorptive root morphology, being longer and thinner root tips with higher root tissue density in poor/treated sites. These changes were associated with significant shifts in community structure of dominating EcM fungi as well as soil and rhizosphere bacterial communities. We suggest a multidimensional concept of absorptive fine root foraging and adaptation strategies involving both qualitative and quantitative changes in root-mycorhizosphere along environmental gradients and in climate experiments. [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]

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]

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]

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]

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]

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]

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]

Highlights: [•] The response of the forest carbon cycle to rising humidity is still largely unknown. [•] Elevated air humidity reduced soil respiration at FAHM experiment. [•] Humidification caused an increase in below-ground biomass of the understory. [•] Microbial activity increased in humidified plots. [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: 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]

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]

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]

Abstract: The abundance and diversity of invertebrate communities (annelids and epigeic fauna) in three types of cultivated soils were studied. Soil biota communities in the three most widespread soil types in Estonia (Calcaric Regosols, Calcaric Cambisols and Stagnic Luvisols) are influenced by environmental conditions, the factors connected to soil texture including moisture, organic matter content and pH being the most essential, and by the intensity of agricultural practice. Potentially high biological activity and low intensity of agricultural human activity of Calcaric Regosols occurs in parameters of communities of organisms not sensitive to soil which dries off, i.e. epigeic fauna living on the soil surface and preferring dry and warm habitat; temporarily dried off soil is not a suitable habitat for Oligochaeta. Both groups of Oligochaeta (earthworms, enchytraeids) appear to prefer Calcaric Cambisols where soil moisture conditions are more stable. The abundance of invertebrate communities is the highest and the diversity is the lowest in Stagnic Luvisols. Some trends occurred in community characteristics along the soil surface following a hypothetical gradient; the number of carabids per trap and diversity of spiders decreased from the edge to the centre of the field. The results presented here on spatial variability in distribution of soil organisms are preliminary. [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]