Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities

The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.     

Effects of mercury on the activity and community composition of soil ammonia oxidizers

Purpose  

Experiments were conducted to examine the effects of mercury (Hg) on soil nitrification activities and the microbial communities of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA).     

Influence of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on ammonia-oxidizing bacteria and archaea in rhizosphere and bulk soil

In agricultural plant production nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are used to retard the microbial nitrification process of fertilized ammonium to enhance the nitrogen supply for cultivated crops and to reduce nitrogen losses from the production system. Besides the well-known ammonia-oxidizing bacteria (AOB) it is known for a few years that also ammonia-oxidizing archaea (AOA) are able to perform the first step in nitrification, hence being also a target for a nitrification inhibitor. However, so far no information are available concerning the effectiveness of DMPP and its extent towards AOB and AOA, neither in bulk soil nor in the root-rhizosphere complex. We investigated in a field experiment performed according to agricultural practice the effect of DMPP on the abundance of AOB and AOA two, four and eight weeks after fertilization. We observed impaired abundances of AOB but not of AOA in both soil compartments that were still visible eight weeks after application, possibly indicating a reduced effectiveness of the nitrification inhibitor in our study.     

Nitrogen impacts on atrazine-degrading Arthrobacter strain and bacterial community structure in soil microcosms

The objective of this study was to investigate the impacts of exogenous nitrogen on a microbial community inoculated with the atrazine-degrading Arthrobacter sp. in soil amended with a high concentration of atrazine. Inoculated and uninoculated microcosms for biodegradation tests were constructed. Atrazine degradation capacity of the strain DAT1 and the strain's atrazine-metabolic potential and survival were assessed. The relative abundance of the strain DAT1 and the bacterial community structure in soils were characterized using quantitative PCR in combination with terminal restriction fragment length polymorphism. Atrazine degradation by the strain DAT1 and the strain's atrazine-metabolic potential and survival were not affected by addition of a medium level of nitrate, but these processes were inhibited by addition of a high level of nitrate. Microbial community structure changed in both inoculated and uninoculated microcosms, dependent on the level of added nitrate. Bioaugmentation with the strain DAT1 could be a very efficient biotechnology for bioremediation of soils with high concentrations of atrazine.     

Effects of submerged macrophytes on the abundance and community composition of ammonia-oxidizing prokaryotes in a eutrophic lake

Abundances and community compositions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in unvegetated sediment and the rhizosphere sediments of three submerged macrophytes (Ceratophyllum demersum, Vallisneria spinulosa, and Potamogeton crispus) were investigated in a large, eutrophic freshwater lake, Lake Taihu. Abundances of archaeal ammonia monooxygenase alpha-subunit (amoA) gene (from 6.56?×?10⁶ copies to 1.06?×?10⁷ copies per gram of dry sediment) were higher than those of bacterial amoA (from 6.13?×?10⁵ to 3.21?×?10⁶ copies per gram of dry sediment) in all samples. Submerged macrophytes exhibited no significant effect on the abundance and diversity of archaeal amoA gene. C. demersum and V. spinulosa increased the abundance and diversity of bacterial amoA gene in their rhizosphere sediment. However, the diversity of bacterial amoA gene in the rhizosphere sediments of P. crispus was decreased. The data obtained in this study would be helpful to elucidate the roles of submerged macrophytes involved in the nitrogen cycling of eutrophic lake ecosystems.     

Nitrifying community analysis in a single submerged attached-growth bioreactor for treatment of high-ammonia waste stream.

This study investigated the nitrifying community structure in a single-stage submerged attached-growth bioreactor (SAGB) that successfully achieved stable nitrogen removal over nitrite of a high-strength ammonia wastewater. The reactor was operated with intermittent aeration and external carbon addition (methanol). With influent ammonia and total Kjeldahl nitrogen ranging from 537 to 968 mg/L and 643 to 1510 mg/L, respectively, 85% nitrogen removal was obtained, and effluent was dominated by nitrite (NO2-/NOx > 0.95). Nitrifying community analysis using fluorescence in situ hybridization (FISH), with a hierarchical set of probes targeting known ammonia-oxidizing bacteria (AOB) within beta-proteobacteria, showed that the AOB community of the biofilter consists almost entirely of members of the Nitrosomonas europaea/eutropha and the Nitrosococcus mobilis lineages. Image analysis of FISH pictures was used to quantify the identified AOB, and it was estimated that Nitrosomonas europaea/eutropha-like AOB accounted for 4.3% of the total volume of the biofilm, while Nitrosococcus mobilis-like AOB made up 1.2%; these numbers summed up to a total AOB fraction of 5.5% of the total volume on the biofilm. Nitrite-oxidizing bacteria (NOB) were not detectable in the biofilm samples with probes for either Nitrospira sp. or Nitrobacter sp., which indicated that NOB were either absent from the biofilters or present in numbers below the detection limit of FISH (< 0.1% of the total biofilm). Nitrite oxidizers were likely outcompeted from the system because of the free ammonia inhibition and the possibility that the aeration period (from intermittent aeration) was not sufficiently long for the NOB to be released from the competition for oxygen with heterotrophs and AOB. The nitrogen removal via nitrite in a SAGB reactor described in this study is applicable for high-ammonia-strength wastewater treatment, such as centrate or industrial wastes.     

Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation

Background, aim, and scope

The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession.

Methods

The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement viadischarging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats? ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing.

Results and discussion

The pollutants removal performances became stable in the four reactors after 2 months?? operation, with ammonia nitrogen and permanganate index (COD_Mn) removal efficiencies of 84.41?C94.21% and 69.66?C76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats?. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche.

Conclusion

Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.     

Effects of a sulfonylurea herbicide on the soil bacterial community

Sulfonylurea herbicides are widely used on a wide range of crops to control weeds. Chevalier® OnePass herbicide is a sulfonylurea herbicide intensively used on cereal crops in Algeria. No information is yet available about the biodegradation of this herbicide or about its effect on the bacterial community of the soil. In this study, we collected an untreated soil sample, and another sample was collected 1 month after treatment with the herbicide. Using a high-resolution melting DNA technique, we have shown that treatment with Chevalier® OnePass herbicide only slightly changed the composition of the whole bacterial community. Two hundred fifty-nine macroscopically different clones were isolated from the untreated and treated soil under both aerobic and microaerobic conditions. The strains were identified by sequencing a conserved fragment of the 16S rRNA gene. The phylogenetic trees constructed using the sequencing results confirmed that the bacterial populations were similar in the two soil samples. Species belonging to the Lysinibacillus, Bacillus, Pseudomonas, and Paenibacillus genera were the most abundant species found. Surprisingly, we found that among ten strains isolated from the treated soil, only six were resistant to the herbicide. Furthermore, bacterial overlay experiments showed that only one resistant strain (related to Stenotrophomonas maltophilia) allowed all the sensitive strains tested to grow in the presence of the herbicide. The other resistant strains allowed only certain sensitive strains to grow. On the basis of these results, we propose that there must be several biodegradation pathways for this sulfonylurea herbicide.     

污泥好氧颗粒化过程中氨氧化菌群结构的演替与分析

为了揭示颗粒污泥形成过程中氨氧化菌(AOB)群落结构的演替规律,利用变性梯度凝胶电泳(DGGE)、克隆测序和实时定量聚合酶链式反应(real-time PCR)等分子生物学技术对AOB群落的演替进行了研究。DGGE结果表明,污泥接种驯化期,AOB群结构的变化较为剧烈,在外加选择压的作用下,种群多样性迅速下降;但随着污泥颗粒化的完成而趋于稳定。测序结果表明,接种污泥中的大多数亚硝化单胞菌属因可快速适应工艺的淘洗过程而被保留在系统内,而亚硝化螺菌属逐渐被淘汰。real-time PCR结果表明,在经历了运行初期的淘洗后,AOB含量随着污泥浓度的提高而逐渐增长;但污泥的氨氧化活性随着污泥浓度的增长而降低。     

Role of cosubstrate and bioaccessibility played in the enhanced anaerobic biodegradation of organochlorine pesticides (OCPs) in a paddy soil by nitrate and methyl-β-cyclodextrin amendments

The present study was conducted to investigate the anaerobic biodegradation potential of biostimulation by nitrate (KNO₃) and methyl-β-cyclodextrin (MCD) addition on an aged organochlorine pesticide (OCP)-contaminated paddy soil. After 180 days of incubation, total OCP biodegradation was highest in soil receiving the addition of nitrate and MCD simultaneously and then followed by nitrate addition, MCD addition, and control. The highest biodegradation of chlordanes, hexachlorocyclohexanes, endosulfans, and total OCPs was 74.3, 63.5, 51.2, and 65.1 %, respectively. Meanwhile, MCD addition significantly increased OCP bioaccessibility (p?<?0.05) evaluated by Tenax TA extraction and a three-compartment model method. Moreover, the addition of nitrate and MCD also obtained the highest values of soil microbial activities, including soil microbial biomass carbon and nitrogen, ATP production, denitrifying bacteria count, and nitrate reductase activity. Such similar trend between OCP biodegradation and soil-denitrifying activities suggests a close relationship between OCP biodegradation and N cycling and the indirect/direct involvement of soil microorganisms, especially denitrifying microorganisms in the anaerobic biodegradation of OCPs.     

Influence of microbial and synthetic surfactant on the biodegradation of atrazine

The present study reports the effect of surfactants (rhamnolipids and triton X-100) on biodegradation of atrazine herbicide by strain A6, belonging to the genus Acinetobacter. The strain A6 was able to degrade nearly 80 % of the 250-ppm atrazine after 6 days of growth. The bacterium degraded atrazine by de-alkylation process. Bacterial cell surface hydrophobicity as well as atrazine solubility increased in the presence of surfactant. However, addition of surfactant to the mineral salt media reduced the rate and extent of atrazine degradation by decreasing the bioavailability of herbicide. On the contrary, addition of surfactant to atrazine-contaminated soil increased the rate and extent of biodegradation by increasing the bioavailability of herbicide. As compared to triton X-100, rhamnolipids were more efficient in enhancing microbial degradation of atrazine as a significant amount of atrazine was removed from the soil by rhamnolipids. Surfactants added for the purpose of hastening microbial degradation may have an unintended inhibitory effect on herbicide degradation depending upon contiguous condition, thus highlighting the fact that surfactant must be judiciously used in bioremediation of herbicides.     

Behaviour of simazine in soil amended with the final residue of the olive-oil extraction process

Addition of organic wastes to agricultural soils is becoming a common practice as a disposal strategy and to improve the physical and chemical soil properties. However, in order to optimise the use of organic wastes as soil amendments, their effect on the behaviour of other compounds that are also used in agriculture, such as pesticides, needs to be assessed. In this work, we have investigated the effects of the addition of the final solid residue of the new technology of olive-oil extraction (extracted alperujo or solid olive-mill waste, SOMW2) on the sorption, degradation and leaching of the herbicide simazine in a sandy loam soil. The results are compared with those of a previous study, where the intermediary by-product of the olive-oil processing technology (unextracted alperujo or SOMW1) was applied to the same soil. The soil was amended in the laboratory with SOMW2 at two different rates (5% and 10% w/w). Simazine sorption isotherms showed a great increase in herbicide sorption after SOMW2 addition to soil. SOMW2 addition also increased sorption irreversibility. Incubation studies revealed reduced biodegradation of simazine in the soil amended with SOMW2 compared to the unamended soil. Breakthrough curves of simazine in handpacked soil columns showed that SOMW2 addition retarded the vertical movement of the herbicide through the soil and greatly reduced the amount of herbicide available for leaching. Interestingly, the results were quantitatively different from those obtained for the intermediary by-product SOMW1, illustrating the importance of the specific characteristics of the organic amendment in determining its effect on pesticide behaviour.     

Adsorption studies of the herbicide simazine in agricultural soils of the Aconcagua valley, central Chile

Simazine is a s-triazine herbicide that has been applied worldwide for agriculture. This herbicide is the second most commonly detected pesticide in surface and groundwater in the United States, Europe and Australia. In this study, simazine adsorption behaviour was studied in two agricultural soils of the Aconcagua valley, central Chile. The two studied soils were soil A (loam, 8.5% organic matter content) and soil B (clay-loam, 3.5% organic matter content). Three times higher simazine adsorption capacity was observed in soil A (68.03 mg kg⁻¹) compared to soil B (22.03 mg kg⁻¹). The simazine adsorption distribution coefficients (K_d) were 9.32 L kg⁻¹ for soil A and 7.74 L kg⁻¹ for soil B. The simazine adsorption enthalpy in soil A was −21.0 kJ mol⁻¹ while in soil B the adsorption enthalpy value was −11.5 kJ mol⁻¹. These results indicate that simazine adsorption process in these soils is exothermic, governing H bonds the adsorption process of simazine in both the loam and clay-loam soils. These results and the potentiometric profiles of both soils, suggest that simazine adsorption in soil A is mainly governed by simazine–organic matter interactions and in soil B by simazine–clay interactions. The understanding of simazine sorption–desorption processes is essential to determine the pesticide fate and availability in soil for pest control, biodegradation, runoff and leaching.     

Impact of carbon source on nitrous oxide emission from anoxic/oxic biological nitrogen removal process and identification of its emission sources

Wastewater treatment is an important source of nitrous oxide (N₂O), which is a strong greenhouse gas and dominate ozone-depleting substance. The purpose of this study was to evaluate the effect of carbon source on N₂O emission from anoxic/oxic biological nitrogen removal process. The mechanisms of N₂O emission were also studied. Long-term experiments were operated to evaluate the effect of three different carbon sources (i.e., glucose, sodium acetate, and soluble starch) on N₂O emission characteristics. And batch experiments, in the presence or absence of specific inhibitors, were carried out to identify the sources of N₂O emission. The ammonia-oxidizing bacteria (AOB) and denitrifiers community compositions under different circumstances were also analyzed based on which the underlying mechanisms of N₂O emission were elucidated. The conversion ratios of N₂O in reactors with glucose, sodium acetate, and soluble starch were 5.3 %, 8.8 %, and 2.8 %, respectively. The primary process responsible for N₂O emission was nitrifier denitrification by Nitrosomonas-like AOB, while denitrification by heterotrophic denitrifiers acted as the sink. Reactor with sodium acetate showed the highest N₂O emission, together with the highest nitrogen and phosphate removal ratios. Carbon source has a significant impact on N₂O emission quantity and relatively minor effect on its production mechanism.     

Biodegradation of atrazine by Rhodococcus sp. BCH2 to N-isopropylammelide with subsequent assessment of toxicity of biodegraded metabolites

Atrazine is a persistent organic pollutant in the environment which affects not only terrestrial and aquatic biota but also human health. Since its removal from the environment is needed, atrazine biodegradation is achieved in the present study using the bacterium Rhodococcus sp. BCH2 isolated from soil, long-term treated with atrazine. The bacterium was capable of degrading about 75 % atrazine in liquid medium having pH 7 under aerobic and dark condition within 7 days. The degradation ability of the bacterium at various temperatures (20–60 °C), pH (range 3–11), carbon (glucose, fructose, sucrose, starch, lactose, and maltose), and nitrogen (ammonium molybdate, sodium nitrate, potassium nitrate, and urea) sources were studied for triumph optimum atrazine degradation. The results indicate that atrazine degradation at higher concentrations (100 ppm) was pH and temperature dependent. However, glucose and potassium nitrate were optimum carbon and nitrogen source, respectively. Atrazine biodegradation analysis was carried out by using high-performance thin-layer chromatography (HPTLC), Fourier transform infrared spectroscopy (FTIR), and liquid chromatography quadrupole time-of-flight (LC/Q-TOF-MS) techniques. LC/Q-TOF-MS analysis revealed formation of various intermediate metabolites including hydroxyatrazine, N-isopropylammelide, deisopropylhydroxyatrazine, deethylatrazine, deisopropylatrazine, and deisopropyldeethylatrazine which was helpful to propose biochemical degradation pathway of atrazine. Furthermore, the toxicological studies of atrazine and its biodegraded metabolites were executed on earthworm Eisenia foetida as a model organism with respect to enzymatic (SOD and Catalase) antioxidant defense mechanism and lipid peroxidation studies. These results suggest innocuous degradation of atrazine by Rhodococcus sp. BCH2 in nontoxic form. Therefore the Rhodococcus sp.BCH2 could prove a valuable source for the eco-friendly biodegradation of atrazine pesticide.     

Laboratory study on leachability of five herbicides in South Australian soils

Abstract

Norflurazon, oxadiazon, oxyfluorfen, trifluralin and simazine are herbicides widely used in the vineyards of the Barossa Valley, South Australia. The leaching behaviour of norflurazon, oxadiazon, oxyfluorfen and trifluralin was investigated on four key soils in the Barossa Valley. Leaching potential on packed soil columns and actual mobility using intact soil columns were investigated. On the packed soil columns, norflurazon was the most leachable herbicide. More of the herbicides were detected in the leachates from the sandy soils (Mountadam and Nuriootpa) than from the clayey soils (Lyndoch and Tanunda). Organic matter is generally low in soils in the Barossa region. Porosity and saturated conductivity significantly affect herbicide movement and in the sandy Mountadam and Nuriootpa soils, the water flux is greater than for the higher clay content Lyndoch and Tanunda soils. Increasing the time interval between herbicide application and the incidence of “rainfall”; reduced the amounts of herbicides found in the leachates. The use of intact soil columns and including simazine for comparison showed that both norflurazon and simazine were present in the leachates. Simazine was the first herbicide to appear in leachates. Sectioning of the intact soil columns after leaching clearly demonstrated that norflurazon and simazine reached the bottom of the soil columns for all soils studied. Greater amounts of norflurazon were retained in the soil columns compared with simazine. The other herbicides were mostly retained in the initial sections of the soil columns.     

Effect of biochar on nitrous oxide emission and its potential mechanisms

Extensive use of biochar to mitigate nitrous oxide (N₂O) emission is limited by the lack of understanding on the exact mechanisms altering N₂O emission from biochar-amended soil. Biochars produced from rice straw and dairy manure at 350 and 500 °C by oxygen-limited pyrolysis were used to investigate their influence on N₂O emission. A quadratic effect of biochar levels was observed on the N₂O emissions. The potential mechanisms were explored by terminal restriction fragment length polymorphism (T-RFLP) and real-time polymerase chain reaction (qPCR). A lower relative abundance of bacteria, which included ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), was observed at 4% biochar application rate. Reduced copy numbers of the ammonia monooxygenase gene amoA and the nitrite reductase gene nirS coincided with decreased N₂O emissions. Therefore, biochar may potentially alter N₂O emission by affecting ammonia-oxidizing and denitrification bacteria, which is determined by the application rate of biochar in soil.

Implications:Biochar research has received increased interest in recent years because of the potential beneficial effects of biochar on soil properties. Recent research shows that biochar can alter the rates of nitrogen cycling in soil systems by influencing nitrification and denitrification, which are key sources of the greenhouse gas nitrous oxide (N₂O). However, there are still some controversial data. The purpose of this research was to (1) examine how applications of different dose of biochar to soil affect emission of N₂O and (2) improve the understanding of the underlying mechanisms.     

Laboratory study on leachability of five herbicides in South Australian soils

Norflurazon, oxadiazon, oxyfluorfen, trifluralin and simazine are herbicides widely used in the vineyards of the Barossa Valley, South Australia. The leaching behaviour of norflurazon, oxadiazon, oxyfluorfen and trifluralin was investigated on four key soils in the Barossa Valley. Leaching potential on packed soil columns and actual mobility using intact soil columns were investigated. On the packed soil columns, norflurazon was the most leachable herbicide. More of the herbicides were detected in the leachates from the sandy soils (Mountadam and Nuriootpa) than from the clayey soils (Lyndoch and Tanunda). Organic matter is generally low in soils in the Barossa region. Porosity and saturated conductivity significantly affect herbicide movement and in the sandy Mountadam and Nuriootpa soils, the water flux is greater than for the higher clay content Lyndoch and Tanunda soils. Increasing the time interval between herbicide application and the incidence of "rainfall" reduced the amounts of herbicides found in the leachates. The use of intact soil columns and including simazine for comparison showed that both norflurazon and simazine were present in the leachates. Simazine was the first herbicide to appear in leachates. Sectioning of the intact soil columns after leaching clearly demonstrated that norflurazon and simazine reached the bottom of the soil columns for all soils studied. Greater amounts of norflurazon were retained in the soil columns compared with simazine. The other herbicides were mostly retained in the initial sections of the soil columns.     

Atrazine biodegradation by Arthrobacter strain DAT1: effect of glucose supplementation and change of the soil microbial community

The objective of this study was to investigate the impact of glucose supplementation on the soil microbiota inoculated with the atrazine-degrading Arthrobacter strain DAT1. Soil microcosms with different treatments were constructed for biodegradation tests. The impact of glucose supplementation on atrazine degradation capacity of the strain DAT1 and the strain’s survival and growth were assessed. The densities of the 16S rRNA gene and the atrazine-metabolic trzN gene were determined using quantitative PCR. The growth of the strain DAT1 and the bacterial community structure were characterized using terminal restriction fragment length polymorphism. Glucose supplementation could affect atrazine degradation by the strain DAT1 and the strain’s trzN gene density and growth. The density of the16S rRNA gene decreased during the incubation period. Glucose supplementation could alter the bacterial community structure during the bioaugmentation process. Glucose supplementation could promote the growth of the autochthonous soil degraders that harbored novel functional genes transforming atrazine. Further study will be necessary in order to elucidate the impact of exogenous carbon on autochthonous and inoculated degraders. This study could add some new insights on atrazine bioremediation.