Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance

Stable nitrogen-cycling capacity in relation to fertilization and intercropping in a sub-boreal grassland

Grasslands are important in sub-boreal climate agricultural systems and are managed with various combinations of N fertilization and plant species. Ammonia-oxidizing and denitrifying microorganisms are key players in determining the fate of nitrogen (N) and thereby also the yield in grassland systems and their impact on gaseous N losses and leaching. We established a three-year field study in southern Finland with fertilizer treatment as a main-plot factor, including organic and synthetic fertilizers and plant species and mixtures thereof as the sub-plot factor. We quantified six genes encoding key N-cycling enzymes by quantitative PCR to determine the abundance of the communities involved in N-transformation processes and also included previously published data on crop yield, soil properties and the overall bacterial community composition. With the exception of ammonia oxidizing bacteria (AOB), which were primarily affected by fertilization, the abundances of all other N-cycling communities changed over time with either an increase or decrease from summer to autumn. Differences in gene abundances between plant species treatments and in fertilizer by plant species interactions were detected mainly in the beginning of the cropping season during the first year. The nirS-type denitrifiers and nosZII nitrous oxide reducers responded more to changes in soil properties than their functional counterpart nirK and nosZI communities. Using structural equation modeling, we show that the overall microbial community composition and diversity played an important role in mediating the management effects on crop yield, genetic potential for N retention and N2O sink capacity. However, a trade-off between the genetic potential for N retention and N2O sink capacity was detected, indicating the challenges in managing grasslands in a sustainable way.Peer reviewe

Temporal dynamics of microbial community in soil during phytoremediation field experiment

Oil‐shale chemical industry creates approximately 600 000 tons of thermally processed oil shale solid wastes (semi‐coke) every year in Estonia. A field phytoremediation and bioaugmentation experiment has been monitored for three years in the solid waste depository area of oil‐shale chemical industry. We found enhanced degradation rates of pollutants in plots with vegetation and added bacterial biomass. The concentration of volatile phenols had decreased almost by 100 %, and the concentration of oil products had decreased approximately 3 times in planted plots compared to the control plots. The degradation rates were the highest in the upper soil layer which has the highest root density. Vegetation also changed the microbial community structure in comparison with the control plots. In addition to the vegetation, properties of the substrate had an essential effect on the microbial community. Mikroorganizmų dirvožemyje kaita vykdant fitoatkūrimo lauko eksperimentą Santrauka Kasmet Estijoje naftos skalūnų chemijos pramonėje susidaro apytiksliai 600 000 t termiškai apdorotų naftos skalūnų kietųjų atliekų (pusiau kokso). Fitoatkūrimo ir biopapildymo lauko eksperimentas buvo vykdomas trejus metus naftos skalūnų chemijos pramonės kietųjų atliekų saugojimo zonoje. Pastebėta, kad padidėjo teršalų degradacijos greitis plotuose, kur yra augalijos, ir pridėta bakterinės biomasės. Lakiųjų fenolių koncentracija sumažėjo beveik 100 %, o naftos produktų koncentracija sumažėjo apytiksliai 3 kartus apsodintuose plotuose, palygti su kontroliniais plotais. Degradacijos greitis buvo didžiausias viršutinimame dirvožemio sluoksnyje, kuriame yra didžiausias šaknų tankis. Augalija taip pat pakeitė mikrobiologinės bendrijos struktūrą, palyginti su kontroliniais plotais. Be augalijos, dar ir substrato savybės turėjo didelės įtakos mikrobiologinei bendrijai. Reikšminiai žodžiai: naftos skalūnai, chemijos pramonės kietosios atliekos, biopapildymas, fitoatkūrimas, mikrobiologinė bendrija. Смена микроорганизмов в почве во время полевого эксперимента с применением фиторемедиации Резюме В химической промышленности по обработке нефтяных сланцев Эстонии ежегодно примерно 600 000 т составляют термически обработанные твердые отходы нефтяных сланцев. Эксперимент по полевой фиторемедиации и биодополнению проводился в течение трех лет на территории хранения твердых отходов химической промышленности по обработке нефтяных сланцев. Установлено, что скорость деградации загрязнителей увеличивается на площадях, где имеется растительность и добавлена бактерицидная биомасса. На засаженных площадях концентрация летучих фенолей уменьшилась почти в два раза, а нефтяных продуктов – приблизительно в 3 раза по сравнению с контрольными площадями. Скорость деградации была наибольшей в верхнем слое почвы, в котором больше всего корней. Растительность также изменила структуру микробиологического сообщества по сравнению с контрольными площадями. Кроме растительности, существенное воздействие на микробиологическое сообщество оказали также свойства субстрата. Ключевые слова: нефтяной сланец, твердые отходы химической промышленности, биодополнение, фиторемедиация, микробиологическое сообщество. First Published Online: 14 Oct 201

Stable nitrogen-cycling capacity in relation to fertilization and intercropping in a sub-boreal grassland

Grasslands are important in sub-boreal climate agricultural systems and are managed with various combinations of N fertilization and plant species. Ammonia-oxidizing and denitrifying microorganisms are key players in determining the fate of nitrogen (N) and thereby also the yield in grassland systems and their impact on gaseous N losses and leaching. We established a three-year field study in southern Finland with fertilizer treatment as a main-plot factor, including organic and synthetic fertilizers and plant species and mixtures thereof as the sub-plot factor. We quantified six genes encoding key N-cycling enzymes by quantitative PCR to determine the abundance of the communities involved in N-transformation processes and also included previously published data on crop yield, soil properties and the overall bacterial community composition. With the exception of ammonia oxidizing bacteria (AOB), which were primarily affected by fertilization, the abundances of all other N-cycling communities changed over time with either an increase or decrease from summer to autumn. Differences in gene abundances between plant species treatments and in fertilizer by plant species interactions were detected mainly in the beginning of the cropping season during the first year. The nirS-type denitrifiers and nosZII nitrous oxide reducers responded more to changes in soil properties than their functional counterpart nirK and nosZI communities. Using structural equation modeling, we show that the overall microbial community composition and diversity played an important role in mediating the management effects on crop yield, genetic potential for N retention and N2O sink capacity. However, a trade-off between the genetic potential for N retention and N2O sink capacity was detected, indicating the challenges in managing grasslands in a sustainable way.Peer reviewe

Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater

Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes

Disentangling the roles of plant functional diversity and plaint traits in regulating plant nitrogen accumulation and denitrification in freshwaters

1. There is a growing recognition that functional measures of diversity, based on quantification of functionally important species traits, are useful for explaining variation in ecosystem processes. However, the mechanisms linking functional diversity to different processes remain poorly understood, hindering development of a predictive framework for ecosystem functioning based on species traits.2. The current understanding of how the functional traits of aquatic plants (macrophytes) affect nitrogen (N) cycling by regulating microbial communities and their activity in freshwater habitats is particularly limited. Denitrifying bacteria are typically associated with the roots of both aquatic and terrestrial plants and denitrification is the main cause of loss of N from ecosystems. Disentangling the interplay between plants and microbial denitrifiers is key to understanding variation in rates of denitrification from local to landscape scales.3. In a mesocosm experiment, we varied the species richness (monocultures or two-species mixtures) and composition of macrophytes. We quantified effects of both macrophyte functional diversity, quantified as functional trait dissimilarity, and functional trait composition, quantified as community weighted mean trait values, on N removal in wetlands. We used structural equation modelling to disentangle the direct and indirect influences of traits on N accumulation in plant biomass, denitrification activity and abundance of key bacterial denitrification genes (nirS and nirK).4. Both functional diversity and functional trait composition regulated N removal, explaining 70%-94% variation in the underlying ecosystem processes. Increased macrophyte functional diversity increased plant N accumulation, and indirectly enhanced denitrification by increasing denitrification gene abundance. Among traits, greater plant relative growth rates, specific leaf area and above-ground biomass increased plant N accumulation. Denitrification activity increased with increasing below-ground biomass but decreased with increasing root diameter.5. These findings improve our understanding of N removal in freshwater wetlands dominated by macrophytes, and have broad ecological implications for wetland management targeting enhanced ecosystem services. Our results highlight the potential for optimizing denitrification and plant N accumulation in wetlands and thereby improving water purification by increasing macrophyte functional diversity and ensuring the presence of key traits in macrophyte assemblages

Bacterioplankton seasonality in deep high-mountain lakes

Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. Highmountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes

Bacterioplankton seasonality in deep high-mountain lakes

Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes

Microbial community changes in TNT spiked soil bioremediation trial using biostimulation, phytoremediation and bioaugmentation

Trinitrotoluene (TNT), a commonly used explosive for military and industrial applications, can cause serious environmental pollution. 28-day laboratory pot experiment was carried out applying bioaugmentation using laboratory selected bacterial strains as inoculum, biostimulation with molasses and cabbage leaf extract, and phytoremediation using rye and blue fenugreek to study the effect of these treatments on TNT removal and changes in soil microbial community responsible for contaminant degradation. Chemical analyses revealed significant decreases in TNT concentrations, including reduction of some of the TNT to its amino derivates during the 28-day tests. The combination of bioaugmentation-biostimulation approach coupled with rye cultivation had the most profound effect on TNT degradation. Although plants enhanced the total microbial community abundance, blue fenugreek cultivation did not significantly affect the TNT degradation rate. The results from molecular analyses suggested the survival and elevation of the introduced bacterial strains throughout the experiment. First published online: 15 Feb 201