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Sample records for rhizosphere denitrifier activity

  1. Evidence that elevated CO2 levels can indirectly increase rhizosphere denitrifier activity

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ritchie, K.; Stark, J. M.; Bugbee, B.

    1997-01-01

    We examined the influence of elevated CO2 concentration on denitrifier enzyme activity in wheat rhizoplanes by using controlled environments and solution culture techniques. Potential denitrification activity was from 3 to 24 times higher on roots that were grown under an elevated CO2 concentration of 1,000 micromoles of CO2 mol-1 than on roots grown under ambient levels of CO2. Nitrogen loss, as determined by a nitrogen mass balance, increased with elevated CO2 levels in the shoot environment and with a high NO3- concentration in the rooting zone. These results indicated that aerial CO2 concentration can play a role in rhizosphere denitrifier activity.

  2. Denitrifying bacteria in bulk and maize-rhizospheric soil: diversity and N2O-reducing abilities.

    PubMed

    Chèneby, D; Perrez, S; Devroe, C; Hallet, S; Couton, Y; Bizouard, F; Iuretig, G; Germon, J C; Philippot, L

    2004-07-01

    The aim of this study was to determine the effect of the rhizosphere of maize on the diversity of denitrifying bacteria. Community structure comparison was performed by constructing a collection of isolates recovered from bulk and maize planted soil. A total of 3240 nitrate-reducing isolates were obtained and 188 of these isolates were identified as denitrifiers based on their ability to reduce nitrate to N2O or N2. 16S rDNA fragments amplified from the denitrifying isolates were analysed by restriction fragment length polymorphism. Isolates were grouped according to their restriction patterns, and 16S rDNA of representatives from each group were sequenced. A plant dependent enrichment of Agrobacterium-related denitrifiers has been observed resulting in a modification of the structure of the denitrifying community between planted and bulk soil. In addition, the predominant isolates in the rhizosphere soil were not able to reduce N2O while dominant isolates in the bulk soil evolve N2 as a denitrification product. PMID:15381970

  3. Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates.

    PubMed

    Henry, S; Texier, S; Hallet, S; Bru, D; Dambreville, C; Chèneby, D; Bizouard, F; Germon, J C; Philippot, L

    2008-11-01

    To determine to which extent root-derived carbon contributes to the effects of plants on nitrate reducers and denitrifiers, four solutions containing different proportions of sugar, organic acids and amino acids mimicking maize root exudates were added daily to soil microcosms at a concentration of 150 microg C g(-1) of soil. Water-amended soils were used as controls. After 1 month, the size and structure of the nitrate reducer and denitrifier communities were analysed using the narG and napA, and the nirK, nirS and nosZ genes as molecular markers respectively. Addition of artificial root exudates (ARE) did not strongly affect the structure or the density of nitrate reducer and denitrifier communities whereas potential nitrate reductase and denitrification activities were stimulated by the addition of root exudates. An effect of ARE composition was also observed on N(2)O production with an N(2)O:(N(2)O + N(2)) ratio of 0.3 in microcosms amended with ARE containing 80% of sugar and of 1 in microcosms amended with ARE containing 40% of sugar. Our study indicated that ARE stimulated nitrate reduction or denitrification activity with increases in the range of those observed with the whole plant. Furthermore, we demonstrated that the composition of the ARE affected the nature of the end-product of denitrification and could thus have a putative impact on greenhouse gas emissions.

  4. The role of plant type and salinity in the selection for the denitrifying community structure in the rhizosphere of wetland vegetation.

    PubMed

    Bañeras, Luís; Ruiz-Rueda, Olaya; López-Flores, Rocío; Quintana, Xavier D; Hallin, Sara

    2012-06-01

    Coastal wetlands, as transient links from terrestrial to marine environments, are important for nitrogen removal by denitrification. Denitrification strongly depends on both the presence of emergent plants and the denitrifier communities selected by different plant species. In this study, the effects of vegetation and habitat heterogeneity on the community of denitrifying bacteria were investigated in nine coastal wetlands in two preserved areas of Spain. Sampling locations were selected to cover a range of salinity (0.81 to 31.3 mS/cm) and nitrate concentrations (0.1 to 303 μM NO3-), allowing the evaluation of environmental variables that select for denitrifier communities in the rhizosphere of Phragmites sp., Ruppia sp., and Paspalum sp. Potential nitrate reduction rates were found to be dependent on the sampling time and plant species and related to the denitrifier community structure, which was assessed by terminal restriction fragment length polymorphism analysis of the functional genes nirS, nirK and nosZ. The results showed that denitrifier community structure was also governed by plant species and salinity, with significant influences of other variables, such as sampling time and location. Ruppia sp. and Phragmites sp. selected for certain communities, whereas this was not the case for Paspalum sp. The plant species effect was strongest on nirK-type denitrifiers, whereas water carbon content was a significant factor defining the structure of the nosZ-harboring community. The differences recognized using the three functional gene markers indicated that different drivers act on denitrifying populations capable of complete denitrification, compared to the overall denitrifier community. This finding may have implications for emissions of the greenhouse gas nitrous oxide. PMID:22847270

  5. [Dynamics of soil enzyme activity and nutrient content in intercropped cotton rhizosphere and non-rhizosphere].

    PubMed

    Meng, Yali; Wang, Liguo; Zhou, Zhiguo; Wang, Ying; Zhang, Lizhen; Bian, Haiyun; Zhang, Siping; Chen, Binglin

    2005-11-01

    The study with high yield cotton-wheat double cropping system showed that soil urease, invertase, protease and catalase activities in intercropped cotton field had the same changing trends with those in mono-cultured cotton field, but were significantly higher in intercropped than in mono-cultured cotton rhizosphere and non-rhizosphere at all development stages of cotton. During the intergrowth period of wheat and cotton, soil nutrient contents in intercropped cotton rhizosphere and non-rhizosphere were lower than or had little difference with those in mono-cultured cotton rhizosphere and non-rhizosphere, but became significantly higher after wheat harvested. The changing trends of soil nutrient contents in intercropped cotton field had little difference from those in mono-cultured cotton field, but the nutrient absorption peak appeared late. The soil enzyme activities and nutrient contents were generally higher in rhizosphere than in non-rhizosphere of both intercropped and mono-cultured cotton. Soil nutrient contents had significant (P < 0.05, n = 32) or very significant (P < 0.01, n = 32) correlation with the activities of soil urease, invertase and protease, but had little correlation with soil catalase activity.

  6. Removal of pharmaceutically active compounds in nitrifying-denitrifying plants.

    PubMed

    Suárez, S; Ramil, M; Omil, F; Lema, J M

    2005-01-01

    The behaviour of nine pharmaceutically active compounds (PhACs) of different diagnostic groups is studied during a nitrifying-denitrifying process in an activated sludge system. The compounds selected cover a wide range of frequently used substances such as anti-epileptics (carbamazepine), tranquillisers (diazepam), anti-depressants (fluoxetine and citalopram), anti-inflammatories (ibuprofen, naproxen and diclofenac) and estrogens (estradiol and ethinylestradiol). The main objective of this research is to investigate the effect of acclimation of biomass on the removal rates of these compounds, either by maintaining a high sludge retention time or at long-term operation. The removal rates achieved for nitrogen and carbon in the experimental unit exceed 90% and were not affected by the addition of PhACs. Carbamazepine, diazepam and diclofenac were only removed to a small extent. On the other hand, higher removal rates have been observed for naproxen and ibuprofen (68% and 82%), respectively. PMID:16312946

  7. [Effects of successive cropping Rehmannia glutinosa on rhizosphere soil microbial flora and enzyme activities].

    PubMed

    Chen, Hui; Hao, Hui-Rong; Xiong, Jun; Qi, Xiao-Hui; Zhang, Chong-Yi; Lin, Wen-Xiong

    2007-12-01

    With the soils cropped Rehmannia glutinosa for one and two years as test materials, this paper studied the variations of microbial flora and enzyme activities in rhizosphere. The results showed that with increasing year of cropping, the numbers of bacteria and fungi in rihzosphere had a slight decrease. In the soil successively cropped R. glutinosa for two years, the number of actinomycetes in rihzosphere was 4 times higher, the ammonifier, aerobic azotobacter, sulphate reducer, denitrifier, and anaerobic cellulose-decomposer increased by 25.99, 45.39, 11.43, 1.36, and 1.43 folds, respectively, while aerobic cellulose-decomposer reduced by 86.74%, compared with those in the soil cropped R. glutinosa for one year. The root exudates of successively cropped R. glutinosa increased the activities of urease, polyhphenol oxidase, sucrase, protease and cellulase in rhizosphere by 62.87%, 9.43%, 47.91%, 139.62% and 31.33%, respectively, but inhibited the activity of catalase. The findings suggested that successive cropping R. glutinosa would destroy the balance of rhizosphere soil microbial flora.

  8. Concurrent activity of anammox and denitrifying bacteria in the Black Sea

    PubMed Central

    Kirkpatrick, John B.; Fuchsman, Clara A.; Yakushev, Evgeniy; Staley, James T.; Murray, James W.

    2012-01-01

    After the discovery of ANaerobic AMMonium OXidation (anammox) in the environment, the role of heterotrophic denitrification as the main marine pathway for fixed N loss has been questioned. A 3 part, 15 month time series investigating nitrite reductase (nirS) mRNA transcripts at a single location in the Black Sea was conducted in order to better understand the activity of anammox and denitrifying bacteria. Here we show that both of these groups were active, as well as being concurrent in the lower suboxic zone over this time span. Their distributions, however, differed in that only expression of denitrification-type nirS was seen in the upper suboxic zone, where geochemistry was variable. Depth profiles covering the suboxic zone showed that the four groups of anammox-type sequences were expressed consistently in the lower suboxic zone, and were consistent with anammox 16 S rDNA gene profiles. By contrast, denitrifier-type nirS sequence groups were mixed; some groups exhibited consistent expression in the lower suboxic zone, while others appeared less consistent. Co-occurrence of both anammox and denitrifier expression was common and ongoing. Both types of transcripts were also found in samples with low concentrations of sulfide (>2 μM). Six major groups of denitrifier-type nirS transcripts were identified, and several groups of denitrifier-type nirS transcripts were closely related to sequences from the Baltic Sea. An increase in denitrifier-type nirS transcript diversity and depth range in October 2007 corresponded to a small increase in mixed layer net community productivity (NCP) as measured by O2/Ar gas ratios, as well as to an increase in N2 concentrations in the suboxic zone. Taken together, the variations in expression patterns between anammox and denitrification provide one possible explanation as to how near instantaneous rate measurements, such as isotope spike experiments, may regularly detect anammox activity but underreport denitrification. PMID

  9. Concurrent activity of anammox and denitrifying bacteria in the Black Sea.

    PubMed

    Kirkpatrick, John B; Fuchsman, Clara A; Yakushev, Evgeniy; Staley, James T; Murray, James W

    2012-01-01

    After the discovery of ANaerobic AMMonium OXidation (anammox) in the environment, the role of heterotrophic denitrification as the main marine pathway for fixed N loss has been questioned. A 3 part, 15 month time series investigating nitrite reductase (nirS) mRNA transcripts at a single location in the Black Sea was conducted in order to better understand the activity of anammox and denitrifying bacteria. Here we show that both of these groups were active, as well as being concurrent in the lower suboxic zone over this time span. Their distributions, however, differed in that only expression of denitrification-type nirS was seen in the upper suboxic zone, where geochemistry was variable. Depth profiles covering the suboxic zone showed that the four groups of anammox-type sequences were expressed consistently in the lower suboxic zone, and were consistent with anammox 16 S rDNA gene profiles. By contrast, denitrifier-type nirS sequence groups were mixed; some groups exhibited consistent expression in the lower suboxic zone, while others appeared less consistent. Co-occurrence of both anammox and denitrifier expression was common and ongoing. Both types of transcripts were also found in samples with low concentrations of sulfide (>2 μM). Six major groups of denitrifier-type nirS transcripts were identified, and several groups of denitrifier-type nirS transcripts were closely related to sequences from the Baltic Sea. An increase in denitrifier-type nirS transcript diversity and depth range in October 2007 corresponded to a small increase in mixed layer net community productivity (NCP) as measured by O(2)/Ar gas ratios, as well as to an increase in N(2) concentrations in the suboxic zone. Taken together, the variations in expression patterns between anammox and denitrification provide one possible explanation as to how near instantaneous rate measurements, such as isotope spike experiments, may regularly detect anammox activity but underreport denitrification. PMID

  10. Antibacterial Activity of Gamma-irradiated Chitosan Against Denitrifying Bacteria

    NASA Astrophysics Data System (ADS)

    Vilcáez, Javier; Watanabe, Tomohide

    2010-11-01

    In order to find an environmentally benign substitute to hazardous inhibitory agents, the inhibitory effect of γ-irradiated chitosans against a mixed culture of denitrifying bacteria was experimentally evaluated. Unlike other studies using pure aerobic cultures, the observed effect was not a complete inhibition but a transient inhibition reflected by prolonged lag phases and reduced growth rates. Raw chitosan under acid conditions (pH 6.3) exerted the strongest inhibition followed by the 100 kGy and 500 kGy irradiated chitosans respectively. Therefore because the molecular weight of chitosan decreases with the degree of γ-irradiation, the inhibitory properties of chitosan due to its high molecular weight were more relevant than the inhibitory properties gained due to the modification of the surface charge and/or chemical structure by γ-irradiation. High dosage of γ-irradiated appeared to increase the growth of mixed denitrifying bacteria in acid pH media. However, in neutral pH media, high dosage of γ-irradiation appeared to enhance the inhibitory effect of chitosan.

  11. [Effects of metolachlor on biological activities in celery rhizophere and non-rhizosphere soil].

    PubMed

    Chen, Bo; Xu, Dongmei; Liu, Guangshen; Liu, Weiping

    2006-05-01

    The study with rhizobag showed that in celery rhizophere and non-rhizosphere soil, metolachlor had a certain inhibitory effect on catalase activity, but stimulated dehydrogenase activity. Generally, the enzyme activities in rhizosphere soil were higher than those in non-rhizosphere soil. After 45 days of metolachlor treatment, the numbers of bacteria and fungi in rhizosphere soil were higher than those in non-rhizosphere soil, and the R/S was 1.76 to approximately 2. 51. The numbers of actinomycetes were relatively stable, and the rhizosphere effect was not significant. The degradation rate of metolachlor in rhizosphere and nonrhizosphere soil was 0. 0217 and 0.0176, and the corresponding half-live was 31.9 and 39.4 days, respectively. The degradation of metolachlor was enhanced greatly in rhizosphere soil.

  12. Effect of temperature on denitrifying methanotrophic activity of 'Candidatus Methylomirabilis oxyfera'.

    PubMed

    Kampman, Christel; Piai, Laura; Hendrickx, Tim L G; Temmink, Hardy; Zeeman, Grietje; Buisman, Cees J N

    2014-01-01

    The activity of denitrifying methanotrophic bacteria at 11-30 °C was assessed in short-term experiments. The aim was to determine the feasibility of applying denitrifying methanotrophic bacteria in low-temperature anaerobic wastewater treatment. This study showed that biomass enriched at 21 °C had an optimum temperature of 20-25 °C and that activity dropped as temperature was increased to 30 °C. Biomass enriched at 30 °C had an optimum temperature of 25-30 °C. These results indicated that biomass from low-temperature inocula adjusted to the enrichment temperature and that low-temperature enrichment is suitable for applications in low-temperature wastewater treatment. Biomass growth at ≤20 °C still needs to be studied. PMID:25429458

  13. Effect of temperature on denitrifying methanotrophic activity of 'Candidatus Methylomirabilis oxyfera'.

    PubMed

    Kampman, Christel; Piai, Laura; Hendrickx, Tim L G; Temmink, Hardy; Zeeman, Grietje; Buisman, Cees J N

    2014-01-01

    The activity of denitrifying methanotrophic bacteria at 11-30 °C was assessed in short-term experiments. The aim was to determine the feasibility of applying denitrifying methanotrophic bacteria in low-temperature anaerobic wastewater treatment. This study showed that biomass enriched at 21 °C had an optimum temperature of 20-25 °C and that activity dropped as temperature was increased to 30 °C. Biomass enriched at 30 °C had an optimum temperature of 25-30 °C. These results indicated that biomass from low-temperature inocula adjusted to the enrichment temperature and that low-temperature enrichment is suitable for applications in low-temperature wastewater treatment. Biomass growth at ≤20 °C still needs to be studied.

  14. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils.

  15. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

  16. Community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms.

    PubMed

    Satoh, Hisashi; Yamakawa, Takeshi; Kindaichi, Tomonori; Ito, Tsukasa; Okabe, Satoshi

    2006-07-01

    The bacterial community structure, in situ spatial distributions and activities of nitrifying and denitrifying bacteria in biofilms treating industrial wastewater were investigated by combination of the 16S rRNA gene clone analysis, fluorescence in situ hybridization (FISH) and microelectrodes. These results were compared with the nitrogen removal capacity of the industrial wastewater treatment plant (IWTP). Both nitrification and denitrification occurred in the primary denitrification (PD) tank and denitrification occurred in the secondary denitrification (SD) tank. In contrast, nitrification and denitrification rates were very low in the nitrification (N) tank. 16S rRNA gene clone sequence analysis revealed that the bacteria affiliated with Alphaproteobacteria, followed by Betaproteobacteria, were numerically important microbial groups in three tanks. The many clones affiliated with Alphaproteobacteria were closely related to the denitrifying bacteria (e.g., Hyphomicrobium spp., Rhodopseudomonas palustris, and Rhodobacter spp.). In addition, Methylophilus leisingeri affiliated with Betaproteobacteria, which favorably utilized methanol, was detected only in the SD-tank to which methanol was added. Nitrosomonas europaea and Nitrosomonas marina were detected as the ammonia-oxidizing bacteria affiliated with Betaproteobacteria throughout this plant, although the dominant species of them was different among three tanks. Nitrifying bacteria were mainly detected in the upper parts of the PD-biofilm whereas their populations were low in the upper parts of the N-biofilm. The presence of denitrifying bacteria affiliated with Hyphomicrobium spp. in SD- and N-biofilms was verified by FISH analysis. Microelectrode measurements showed that the nitrifying bacteria present in the N- and PD-biofilms were active and the bacteria present in the SD-biofilm could denitrify. PMID:16477661

  17. Spatial distribution of enzyme activities in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Razavi, Bahar S.; Zarebanadkouki, Mohsen; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2015-04-01

    The rhizosphere, the tiny zone of soil surrounding roots, certainly represents one of the most dynamic habitat and interfaces on Earth. Activities of enzymes produced by both plant roots and microbes are the primary biological drivers of organic matter decomposition and nutrient cycling. That is why there is an urgent need in spatially explicit methods for the determination of the rhizosphere extension and enzyme distribution. Recently, zymography as a new technique based on diffusion of enzymes through the 1 mm gel plate for analysis has been introduced (Spohn & Kuzyakov, 2013). We developed the zymography technique to visualize the enzyme activities with a higher spatial resolution. For the first time, we aimed at quantitative imaging of enzyme activities as a function of distance from the root tip and the root surface in the soil. We visualized the two dimensional distribution of the activity of three enzymes: β-glucosidase, phosphatase and leucine amino peptidase in the rhizosphere of maize using fluorogenically labelled substrates. Spatial-resolution of fluorescent images was improved by direct application of a substrate saturated membrane to the soil-root system. The newly-developed direct zymography visualized heterogeneity of enzyme activities along the roots. The activity of all enzymes was the highest at the apical parts of individual roots. Across the roots, the enzyme activities were higher at immediate vicinity of the roots (1.5 mm) and gradually decreased towards the bulk soil. Spatial patterns of enzyme activities as a function of distance from the root surface were enzyme specific, with highest extension for phosphatase. We conclude that improved zymography is promising in situ technique to analyze, visualize and quantify spatial distribution of enzyme activities in the rhizosphere hotspots. References Spohn, M., Kuzyakov, Y., 2013. Phosphorus mineralization can be driven by microbial need for carbon. Soil Biology & Biochemistry 61: 69-75

  18. Metabolic Profiles and Genetic Diversity of Denitrifying Communities in Activated Sludge after Addition of Methanol or Ethanol†

    PubMed Central

    Hallin, Sara; Throbäck, Ingela Noredal; Dicksved, Johan; Pell, Mikael

    2006-01-01

    External carbon sources can enhance denitrification rates and thus improve nitrogen removal in wastewater treatment plants. The effects of adding methanol and ethanol on the genetic and metabolic diversity of denitrifying communities in activated sludge were compared using a pilot-scale plant with two parallel lines. A full-scale plant receiving the same municipal wastewater, but without external carbon source addition, was the reference. Metabolic profiles obtained from potential denitrification rates with 10 electron donors showed that the denitrifying communities altered their preferences for certain compounds after supplementation with methanol or ethanol and that methanol had the greater impact. Clone libraries of nirK and nirS genes, encoding the two different nitrite reductases in denitrifiers, revealed that methanol also increased the diversity of denitrifiers of the nirS type, which indicates that denitrifiers favored by methanol were on the rise in the community. This suggests that there might be a niche differentiation between nirS and nirK genotypes during activated sludge processes. The composition of nirS genotypes also varied greatly among all samples, whereas the nirK communities were more stable. The latter was confirmed by denaturing gradient gel electrophoresis of nirK communities on all sampling occasions. Our results support earlier hypotheses that the compositions of denitrifier communities change during predenitrification processes when external carbon sources are added, although no severe effect could be observed from an operational point of view. PMID:16885297

  19. Long-term effect of temperature on N2O emission from the denitrifying activated sludge.

    PubMed

    Wang, Xiaojun; Yang, Xiaoru; Zhang, Zhaoji; Ye, Xin; Kao, Chih Ming; Chen, Shaohua

    2014-03-01

    The long-term effect of various temperature (4°C, 12°C, 20°C, 25°C and 34°C) on nitrous oxide (N2O) emission from lab-scale denitrifying activated sludge was studied in terms of activation energy, abundance of functional gene nosZ and its transcription. Results showed that temperature had a positive effect on N2O emissions as well as the maximum biomass-specific reduction rates of N2O and NO3(-), ranging from 0.006% to 0.681% of (N2O + N2), 17.3-116.2 and 5.2-66.2 mg N g(-1) VSS h(-1), respectively. The activation energies (Ea) for N2O and NO3(-) reduction of 44.1 kJ mol(-1) and 54.9 kJ mol(-1), shed light on differences in denitrifying rate variation. The maximum NO3(-) reduction rates were more sensitive to temperature variation than the corresponding N2O reduction rates under long-term acclimation. As a result, the ratio between N2O and NO3(-) reduction rates declined to 1.87 at 34°C from 3.31 at 4°C, suggesting great potential capacity for N2O losses at high temperature. The copy numbers of denitrifiers as nosZ gene (×10(8) copies mL(-1)) and total bacteria as 16S rRNA gene (×10(10) copies mL(-1)) did not show obvious relationship with temperature, having relative abundance of 0.42% on average. The transcriptional regulation of nosZ gene, in the range of 10(8)-10(5) copies mL(-1), was affected by reductase activity, substrate concentration as well as its duration. The active nosZ gene expression was accompanied with low reductase capacity, high dissolved N2O and the duration of N2O accumulation. These results provide insights into activation energy and gene expression responsible for N2O emission.

  20. Quantity-activity relationship of denitrifying bacteria and environmental scaling in streams of a forested watershed

    USGS Publications Warehouse

    O'Connor, B.L.; Hondzo, Miki; Dobraca, D.; LaPara, T.M.; Finlay, J.A.; Brezonik, P.L.

    2006-01-01

    The spatial variability of subreach denitrification rates in streams was evaluated with respect to controlling environmental conditions, molecular examination of denitrifying bacteria, and dimensional analysis. Denitrification activities ranged from 0 and 800 ng-N gsed-1 d-1 with large variations observed within short distances (<50 m) along stream reaches. A log-normal probability distribution described the range in denitrification activities and was used to define low (16% of the probability distributibn), medium (68%), and high (16%) denitrification potential groups. Denitrifying bacteria were quantified using a competitive polymerase chain reaction (cPCR) technique that amplified the nirK gene that encodes for nitrite reductase. Results showed a range of nirK quantities from 103 to 107 gene-copy-number gsed.-1 A nonparametric statistical test showed no significant difference in nirK quantifies among stream reaches, but revealed that samples with a high denitrification potential had significantly higher nirK quantities. Denitrification activity was positively correlated with nirK quantities with scatter in the data that can be attributed to varying environmental conditions along stream reaches. Dimensional analysis was used to evaluate denitrification activities according to environmental variables that describe fluid-flow properties, nitrate and organic material quantities, and dissolved oxygen flux. Buckingham's pi theorem was used to generate dimensionless groupings and field data were used to determine scaling parameters. The resulting expressions between dimensionless NO3- flux and dimensionless groupings of environmental variables showed consistent scaling, which indicates that the subreach variability in denitrification rates can be predicted by the controlling physical, chemical, and microbiological conditions. Copyright 2006 by the American Geophysical Union.

  1. Quantity-activity relationship of denitrifying bacteria and environmental scaling in streams of a forested watershed

    NASA Astrophysics Data System (ADS)

    O'Connor, Ben L.; Hondzo, Miki; Dobraca, Dina; Lapara, Timothy M.; Finlay, Jacques C.; Brezonik, Patrick L.

    2006-12-01

    The spatial variability of subreach denitrification rates in streams was evaluated with respect to controlling environmental conditions, molecular examination of denitrifying bacteria, and dimensional analysis. Denitrification activities ranged from 0 and 800 ng-N gsed-1 d-1 with large variations observed within short distances (<50 m) along stream reaches. A log-normal probability distribution described the range in denitrification activities and was used to define low (16% of the probability distribution), medium (68%), and high (16%) denitrification potential groups. Denitrifying bacteria were quantified using a competitive polymerase chain reaction (cPCR) technique that amplified the nirK gene that encodes for nitrite reductase. Results showed a range of nirK quantities from 103 to 107 gene-copy-number gsed-1. A nonparametric statistical test showed no significant difference in nirK quantities among stream reaches, but revealed that samples with a high denitrification potential had significantly higher nirK quantities. Denitrification activity was positively correlated with nirK quantities with scatter in the data that can be attributed to varying environmental conditions along stream reaches. Dimensional analysis was used to evaluate denitrification activities according to environmental variables that describe fluid-flow properties, nitrate and organic material quantities, and dissolved oxygen flux. Buckingham's pi theorem was used to generate dimensionless groupings and field data were used to determine scaling parameters. The resulting expressions between dimensionless NO3- flux and dimensionless groupings of environmental variables showed consistent scaling, which indicates that the subreach variability in denitrification rates can be predicted by the controlling physical, chemical, and microbiological conditions.

  2. Effect of Bacteria and Amoebae on Rhizosphere Phosphatase Activity

    PubMed Central

    Gould, W. Douglas; Coleman, David C.; Rubink, Amy J.

    1979-01-01

    The contributions of various components of soil microflora and microfauna to rhizosphere phosphatase activity were determined with hydroponic cultures. Three treatments were employed: (i) plants alone (Bouteloua gracilis (H.B.K.) Lag. ex Steud.) (ii) plants plus bacteria (Pseudomonas sp.), and (iii) plants plus bacteria plus amoebae (Acanthamoeba sp.). No alkaline phosphatase was detected, but an appreciable amount of acid phosphatase activity (120 to 500 nmol of p-nitrophenylphosphate hydrolyzed per h per plant) was found in the root culture solutions. The presence of bacteria or bacteria and amoebae increased the amount of acid phosphatase in solution, and properties of additional activity were identical to properties of plant acid phosphatase. The presence of bacteria or bacteria and amoebae increased both solution and root phosphatase activities at most initial phosphate concentrations. PMID:16345390

  3. Reduced nitrate leaching and enhanced denitrifier activity and efficiency in organically fertilized soils.

    PubMed

    Kramer, Sasha B; Reganold, John P; Glover, Jerry D; Bohannan, Brendan J M; Mooney, Harold A

    2006-03-21

    Conventional agriculture has improved in crop yield but at large costs to the environment, particularly off-site pollution from mineral N fertilizers. In response to environmental concerns, organic agriculture has become an increasingly popular option. One component of organic agriculture that remains in question is whether it can reduce agricultural N losses to groundwater and the atmosphere relative to conventional agriculture. Here we report reduced N pollution from organic and integrated farming systems compared with a conventional farming system. We evaluated differences in denitrification potential and a suite of other soil biological and chemical properties in soil samples taken from organic, integrated, and conventional treatments in an experimental apple orchard. Organically farmed soils exhibited higher potential denitrification rates, greater denitrification efficiency, higher organic matter, and greater microbial activity than conventionally farmed soils. The observed differences in denitrifier function were then assessed under field conditions after fertilization. N(2)O emissions were not significantly different among treatments; however, N(2) emissions were highest in organic plots. Annual nitrate leaching was 4.4-5.6 times higher in conventional plots than in organic plots, with the integrated plots in between. This study demonstrates that organic and integrated fertilization practices support more active and efficient denitrifier communities, shift the balance of N(2) emissions and nitrate losses, and reduce environmentally damaging nitrate losses. Although this study specifically examines a perennial orchard system, the ecological and biogeochemical processes we evaluated are present in all agroecosystems, and the reductions in nitrate loss in this study could also be achievable in other cropping systems. PMID:16537377

  4. Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen

    PubMed Central

    Palmer, Katharina; Köpp, Julia; Gebauer, Gerhard; Horn, Marcus A.

    2016-01-01

    Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities vmax were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting

  5. Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen.

    PubMed

    Palmer, Katharina; Köpp, Julia; Gebauer, Gerhard; Horn, Marcus A

    2016-01-01

    Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities v max were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting

  6. Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen.

    PubMed

    Palmer, Katharina; Köpp, Julia; Gebauer, Gerhard; Horn, Marcus A

    2016-01-01

    Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities v max were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting

  7. Comparison of aerobic denitrifying activity among three cultural species with various carbon sources.

    PubMed

    Otani, Y; Hasegawa, K; Hanaki, K

    2004-01-01

    Abilities of three aerobic denitrifiers such as Alcaligenes faecalis, Microvirgula aerodenitrificans and Paracoccus pantotrophus were compared from the viewpoints of nitrate removal efficiency and organic matter utilization. First, the effect of carbon source was investigated. Although nitrate reduction was observed in all strains under aerobic conditions, a change of carbon source considerably affected the denitrification ability. In the case of P. pantotrophus, nitrate and nitrite were completely removed in three days under sodium acetate or leucine as a carbon source. In the case of A. faecalis, sufficient nitrate removal was observed only when sodium acetate or ethanol was added. P. pantotrophus and A. faecalis showed a higher ability of nitrate removal than that of M. aerodenitrificans. Therefore, P. pantotrophus was selected in order to investigate the effects of concentration and repetitive addition of carbon. Sodium acetate was used as a sole carbon source. Nitrate was not reduced when the carbon concentration was below 500 mgC/L. However, when carbon source was added repeatedly, nitrate was reduced under 100 mgC/L after the optical density of the bacterium reached above 1.0. This result indicated that a high enough level of bacterial density was necessary to express aerobic denitrification activity. PMID:15566182

  8. Spatial variations in denitrification activity in wetland sediments explained by hydrology and denitrifying community structure.

    PubMed

    Kjellin, Johan; Hallin, Sara; Wörman, Anders

    2007-12-01

    We determined spatial variations in potential denitrification activity and the controlling hydrological as well as biochemical processes in the sediments of a Swedish treatment wetland. Hydrological processes, including water residence times, were analyzed using a 2D depth-averaged flow model and the denitrifier community structure was analyzed using denaturing gradient gel electrophoreses (DGGE) of nosZ genes, encoding nitrous oxide reductase. In addition, we provide a theoretical basis for evaluation of denitrification rates useful in nitrate-limited conditions. The results demonstrate that potential denitrification rates differed significantly between the sampling locations (CV=0.34). The variations were best described by concentration of nitrogen in sediments and water residence time. DGGE analyses indicated that a few key populations dominated and that the community diversity increased with decreasing nutrient levels and increasing water residence times. Moreover, we found that denitrification rates in terms of Menten and first-order kinetics can be evaluated by fitting a mathematical expression, comparing denitrification and other nitrogen-transforming processes to measured product formation in nitrate-limited experiments.

  9. [Effects of growing time on Panax ginseng rhizosphere soil microbial activity and biomass].

    PubMed

    Xiao, Chun-ping; Yang, Li-min; Ma, Feng-min

    2014-12-01

    Using the field sampling and indoor soil cultivation methods, the dynamic of ginseng rhizosphere soil microbial activity and biomass with three cultivated ages was studied to provide a theory basis for illustrating mechanism of continuous cropping obstacles of ginseng. The results showed that ginseng rhizosphere soil microbial activity and biomass accumulation were inhibited observably by growing time. The soil respiration, soil cellulose decomposition and soil nitrification of ginseng rhizosphere soil microorganism were inhibited significantly (P <0.05), in contrast to the control soil uncultivated ginseng (R0). And the inhibition was gradual augmentation with the number of growing years. The soil microbial activity of 3a ginseng soil (R3) was the lowest, and its activity of soil respiration, soil cellulose decomposition, soil ammonification and soil nitrification was lower than that in R0 with 56.31%, 86.71% and 90. 53% , respectively. The soil ammonification of ginseng rhizosphere soil microbial was significantly promoted compared with R0. The promotion was improved during the early growing time, while the promotion was decreased with the number of growing years. The soil ammonification of R1, R2 and R3 were lower than that in R0 with 32.43%, 80.54% and 66.64% separately. The SMB-C and SMB-N in ginseng rhizosphere soil had a decreased tendency with the number of growing years. The SMB-C difference among 3 cultivated ages was significant, while the SMB-N was not. The SMB of R3 was the lowest. Compared with R0, the SMB-C and the SMB-N were significantly reduced 77.30% and 69.36%. It was considered by integrated analysis that the leading factor of continuous cropping obstacle in ginseng was the changes of the rhizosphere soil microbial species, number and activity as well as the micro-ecological imbalance of rhizosphere soil caused by the accumulation of ginseng rhizosphere secretions.

  10. Impact of transgenic cotton varieties on activity of enzymes in their rhizosphere.

    PubMed

    Mina, Usha; Chaudhary, Anita

    2012-06-01

    The impact of five Bacillus thuringiensis (Bt) cotton varieties and their respective isogenic non-Bt(NBt) isolines (ANKUR-2534, MECH-6304, RCH-317, ANKUR-651 and MECH-6301) was assessed on the key soil enzymes i.e., dehydrogenase, alkaline phosphatase and urease in their rhizosphere at four growth stages of the crop, namely vegetative, flowering, bolling and harvesting. These varieties were grown on farmer's field in villages 22 miles and 24 miles of Ganganagar District of Rajasthan State in India. Results showed that dehydrogenase, alkaline phosphatase and urease activities were higher in rhizosphere of Bt isolines as compared to NBt isolines of all the varieties. Except phosphatase, differences in dehydrogenase and urease activities in rhizosphere of Bt and NBt isolines of all five varieties were significant (P < 0.05). Maximum enhancement in the three enzymes activities was observed in MECH-6304 Bt isoline rhizosphere. Maximum and minimum activities of dehydrogenase and urease were observed in MECH-6304 and RCH-317 Bt isolines, respectively, whereas phosphatase activity was maximum and minimum in MECH-6304 and ANKUR-651 Bt isolines, respectively. Maximum dehydrogenase and urease activities were observed at boll formation and minimum at flowering and harvesting stage, respectively, while maximum phosphatase activity was observed at vegetative stage and minimum at harvesting stage. In conclusion, all the studied Bt isolines of cotton varieties showed no adverse effect on dehydrogenase, alkaline phosphatase and urease activities in the rhizosphere.

  11. Phosphate solubilization potential and phosphatase activity of rhizospheric trichoderma spp.

    PubMed

    Anil, Kapri; Lakshmi, Tewari

    2010-07-01

    Trichoderma sp., a well known biological control agent against several phytopathogens, was tested for its phosphate (P) solubilizing potential. Fourteen strains of Trichoderma sp. were isolated from the forest tree rhizospheres of pinus, deodar, bamboo, guava and oak on Trichoderma selective medium. The isolates were tested for their in-vitro P-solubilizing potential using National Botanical Research Institute Phosphate (NBRIP) broth containing tricalcium phosphate (TCP) as the sole P source, and compared with a standard culture of T. harzianum. All the cultures were found to solubilize TCP but with varying potential. The isolate DRT-1 showed maximum amount of soluble phosphate (404.07 εg.ml(-1)), followed by the standard culture of T. harzianum (386.42 εg.ml(-1)) after 96 h of incubation at 30±1(0)C. Extra-cellular acid and alkaline phosphatases of the fungus were induced only in the presence of insoluble phosphorus source (TCP). High extra-cellular alkaline phosphatase activity was recorded for the isolate DRT-1 (14.50 U.ml(-1)) followed by the standard culture (13.41 U.ml(-1)) at 72h. The cultures showed much lesser acid phosphatase activities. Under glasshouse conditions, Trichoderma sp. inoculation increased chickpea (Cicer arietinum) growth parameters including shoot length, root length, fresh and dry weight of shoot as well as roots, in P-deficient soil containing only bound phosphate (TCP). Shoot weight was increased by 23% and 33% by inoculation with the isolate DRT-1 in the soil amended with 100 and 200 mg TCP kg(-1) soil, respectively, after 60 d of sowing. The study explores high P-solubilizing potential of Trichoderma sp., which can be exploited for the solubilization of fixed phosphates present in the soil, thereby enhancing soil fertility and plant growth.

  12. Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

    2014-01-01

    While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. PMID:25058658

  13. Anaerobic Activation of p-Cymene in Denitrifying Betaproteobacteria: Methyl Group Hydroxylation versus Addition to Fumarate

    PubMed Central

    Strijkstra, Annemieke; Trautwein, Kathleen; Jarling, René; Wöhlbrand, Lars; Dörries, Marvin; Reinhardt, Richard; Drozdowska, Marta; Golding, Bernard T.; Wilkes, Heinz

    2014-01-01

    The betaproteobacteria “Aromatoleum aromaticum” pCyN1 and “Thauera” sp. strain pCyN2 anaerobically degrade the plant-derived aromatic hydrocarbon p-cymene (4-isopropyltoluene) under nitrate-reducing conditions. Metabolite analysis of p-cymene-adapted “A. aromaticum” pCyN1 cells demonstrated the specific formation of 4-isopropylbenzyl alcohol and 4-isopropylbenzaldehyde, whereas with “Thauera” sp. pCyN2, exclusively 4-isopropylbenzylsuccinate and tentatively identified (4-isopropylphenyl)itaconate were observed. 4-Isopropylbenzoate in contrast was detected with both strains. Proteogenomic investigation of p-cymene- versus succinate-adapted cells of the two strains revealed distinct protein profiles agreeing with the different metabolites formed from p-cymene. “A. aromaticum” pCyN1 specifically produced (i) a putative p-cymene dehydrogenase (CmdABC) expected to hydroxylate the benzylic methyl group of p-cymene, (ii) two dehydrogenases putatively oxidizing 4-isopropylbenzyl alcohol (Iod) and 4-isopropylbenzaldehyde (Iad), and (iii) the putative 4-isopropylbenzoate-coenzyme A (CoA) ligase (Ibl). The p-cymene-specific protein profile of “Thauera” sp. pCyN2, on the other hand, encompassed proteins homologous to subunits of toluene-activating benzylsuccinate synthase (termed [4-isopropylbenzyl]succinate synthase IbsABCDEF; identified subunits, IbsAE) and protein homologs of the benzylsuccinate β-oxidation (Bbs) pathway (termed BisABCDEFGH; all identified except for BisEF). This study reveals that two related denitrifying bacteria employ fundamentally different peripheral degradation routes for one and the same substrate, p-cymene, with the two pathways apparently converging at the level of 4-isopropylbenzoyl-CoA. PMID:25261521

  14. Relationship between Nitrite Reduction and Active Phosphate Uptake in the Phosphate-Accumulating Denitrifier Pseudomonas sp. Strain JR 12

    PubMed Central

    Barak, Yoram; van Rijn, Jaap

    2000-01-01

    Phosphate uptake by the phosphate-accumulating denitrifier Pseudomonas sp. JR12 was examined with different combinations of electron and carbon donors and electron acceptors. Phosphate uptake in acetate-supplemented cells took place with either oxygen or nitrate but did not take place when nitrite served as the final electron acceptor. Furthermore, nitrite reduction rates by this denitrifier were shown to be significantly reduced in the presence of phosphate. Phosphate uptake assays in the presence of the H+-ATPase inhibitor N,N′-dicyclohexylcarbodiimide (DCCD), in the presence of the uncoupler carbonyl cyanide 3-chlorophenylhydrazone (CCCP), or with osmotic shock-treated cells indicated that phosphate transport over the cytoplasmic membrane of this bacterium was mediated by primary and secondary transport systems. By examining the redox transitions of whole cells at 553 nm we found that phosphate addition caused a significant oxidation of a c-type cytochrome. Based on these findings, we propose that this c-type cytochrome serves as an intermediate in the electron transfer to both nitrite reductase and the site responsible for active phosphate transport. In previous studies with this bacterium we found that the oxidation state of this c-type cytochrome was significantly higher in acetate-supplemented, nitrite-respiring cells (incapable of phosphate uptake) than in phosphate-accumulating cells incubated with different combinations of electron donors and acceptors. Based on the latter finding and results obtained in the present study it is suggested that phosphate uptake in this bacterium is subjected to a redox control of the active phosphate transport site. By means of this mechanism an explanation is provided for the observed absence of phosphate uptake in the presence of nitrite and inhibition of nitrite reduction by phosphate in this organism. The implications of these findings regarding denitrifying, phosphate removal wastewater plants is discussed. PMID

  15. Isolation, identification, and algicidal activity of aerobic denitrifying bacterium R11 and its effect on Microcystis aeruginosa.

    PubMed

    Su, Jun-feng; Shao, Si-cheng; Huang, Ting-lin; Ma, Fang; Zhang, Kai; Wen, Gang; Zheng, Sheng-chen

    2016-01-01

    Recently, algicidal bacteria have attracted attention as possible agents for the inhibition of algal water blooms. In this study, an aerobic denitrifying bacterium, R11, with high algicidal activity against the toxic Microcystis aeruginosa was isolated from lake sediments. Based on its physiological characteristics and 16S rRNA gene sequence, it was identified as Raoultella, indicating that the bacterium R11 has a good denitrifying ability at 30 °C and can reduce the concentration of nitrate-N completely within 36 h. Additionally, different algicidal characteristics against Microcystis aeruginosa were tested. The results showed that the initial bacterial cell density and algal cell densities strongly influence the removal rates of chlorophyll a. Algicidal activity increased with an increase in the bacterial cell density. With densities of bacterial culture at over 2.4 × 10(5) cell/mL, algicidal activity of up to 80% was obtained in 4 days. We have demonstrated that, with the low initial algal cell density (OD680 less than 0.220), the algicidal activity reached was higher than 90% after 6 days. PMID:27232395

  16. pH-driven shifts in overall and transcriptionally active denitrifiers control gaseous product stoichiometry in growth experiments with extracted bacteria from soil

    PubMed Central

    Brenzinger, Kristof; Dörsch, Peter; Braker, Gesche

    2015-01-01

    Soil pH is a strong regulator for activity as well as for size and composition of denitrifier communities. Low pH not only lowers overall denitrification rates but also influences denitrification kinetics and gaseous product stoichiometry. N2O reductase is particularly sensitive to low pH which seems to impair its activity post-transcriptionally, leading to higher net N2O production. Little is known about how complex soil denitrifier communities respond to pH change and whether their ability to maintain denitrification over a wider pH range relies on phenotypic redundancy. In the present study, we followed the abundance and composition of an overall and transcriptionally active denitrifier community extracted from a farmed organic soil in Sweden (pHH2O = 7.1) when exposed to pH 5.4 and drifting back to pH 6.6. The soil was previously shown to retain much of its functioning (low N2O/N2 ratios) over a wide pH range, suggesting a high functional versatility of the underlying community. We found that denitrifier community composition, abundance and transcription changed throughout incubation concomitant with pH change in the medium, allowing for complete reduction of nitrate to N2 with little accumulation of intermediates. When exposed to pH 5.4, the denitrifier community was able to grow but reduced N2O to N2 only when near-neutral pH was reestablished by the alkalizing metabolic activity of an acid-tolerant part of the community. The genotypes proliferating under these conditions differed from those dominant in the control experiment run at neutral pH. Denitrifiers of the nirS-type appeared to be severely suppressed by low pH and nirK-type and nosZ-containing denitrifiers showed strongly reduced transcriptional activity and growth, even after restoration of neutral pH. Our study suggests that low pH episodes alter transcriptionally active populations which shape denitrifier communities and determine their gas kinetics. PMID:26441895

  17. Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere.

    PubMed Central

    Kragelund, L; Hosbond, C; Nybroe, O

    1997-01-01

    The purpose of this study was to determine the metabolic activity of Pseudomonas fluorescens DF57 in the barley rhizosphere and to assess whether sufficient phosphate was available to the bacterium. Hence, two DF57 reporter strains carrying chromosomal luxAB gene fusions were introduced into the rhizosphere. Strain DF57-40E7 expressed luxAB constitutively, making bioluminescence dependent upon the metabolic activity of the cells under defined assay conditions. The DF57-P2 reporter strain responded to phosphate limitation, and the luxAB gene fusion was controlled by a promoter containing regulatory sequences characteristic of members of the phosphate (Pho) regulon. DF57 generally had higher metabolic activity in a gnotobiotic rhizosphere than in the corresponding bulk soil. Within the rhizosphere the distribution of metabolic activity along the root differed between the rhizosphere soil and the rhizoplane, suggesting that growth conditions may differ between these two habitats. The DF57-P2 reporter strain encountered phosphate limitation in a gnotobiotic rhizosphere but not in a natural rhizosphere. This difference in phosphate availability seemed to be due to the indigenous microbial population, as DF57-P2 did not report phosphate limitation when established in the rhizosphere of plants in sterilized soil amended with indigenous microorganisms. PMID:9406412

  18. Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii.

    PubMed

    Martineau, Christine; Mauffrey, Florian; Villemur, Richard

    2015-08-01

    Hyphomicrobium spp. are commonly identified as major players in denitrification systems supplied with methanol as a carbon source. However, denitrifying Hyphomicrobium species are poorly characterized, and very few studies have provided information on the genetic and physiological aspects of denitrification in pure cultures of these bacteria. This is a comparative study of three denitrifying Hyphomicrobium species, H. denitrificans ATCC 51888, H. zavarzinii ZV622, and a newly described species, H. nitrativorans NL23, which was isolated from a denitrification system treating seawater. Whole-genome sequence analyses revealed that although they share numerous orthologous genes, these three species differ greatly in their nitrate reductases, with gene clusters encoding a periplasmic nitrate reductase (Nap) in H. nitrativorans, a membrane-bound nitrate reductase (Nar) in H. denitrificans, and one Nap and two Nar enzymes in H. zavarzinii. Concurrently with these differences observed at the genetic level, important differences in the denitrification capacities of these Hyphomicrobium species were determined. H. nitrativorans grew and denitrified at higher nitrate and NaCl concentrations than did the two other species, without significant nitrite accumulation. Significant increases in the relative gene expression levels of the nitrate (napA) and nitrite (nirK) reductase genes were also noted for H. nitrativorans at higher nitrate and NaCl concentrations. Oxygen was also found to be a strong regulator of denitrification gene expression in both H. nitrativorans and H. zavarzinii, although individual genes responded differently in these two species. Taken together, the results presented in this study highlight the potential of H. nitrativorans as an efficient and adaptable bacterium that is able to perform complete denitrification under various conditions. PMID:25979892

  19. Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii

    PubMed Central

    Martineau, Christine; Mauffrey, Florian

    2015-01-01

    Hyphomicrobium spp. are commonly identified as major players in denitrification systems supplied with methanol as a carbon source. However, denitrifying Hyphomicrobium species are poorly characterized, and very few studies have provided information on the genetic and physiological aspects of denitrification in pure cultures of these bacteria. This is a comparative study of three denitrifying Hyphomicrobium species, H. denitrificans ATCC 51888, H. zavarzinii ZV622, and a newly described species, H. nitrativorans NL23, which was isolated from a denitrification system treating seawater. Whole-genome sequence analyses revealed that although they share numerous orthologous genes, these three species differ greatly in their nitrate reductases, with gene clusters encoding a periplasmic nitrate reductase (Nap) in H. nitrativorans, a membrane-bound nitrate reductase (Nar) in H. denitrificans, and one Nap and two Nar enzymes in H. zavarzinii. Concurrently with these differences observed at the genetic level, important differences in the denitrification capacities of these Hyphomicrobium species were determined. H. nitrativorans grew and denitrified at higher nitrate and NaCl concentrations than did the two other species, without significant nitrite accumulation. Significant increases in the relative gene expression levels of the nitrate (napA) and nitrite (nirK) reductase genes were also noted for H. nitrativorans at higher nitrate and NaCl concentrations. Oxygen was also found to be a strong regulator of denitrification gene expression in both H. nitrativorans and H. zavarzinii, although individual genes responded differently in these two species. Taken together, the results presented in this study highlight the potential of H. nitrativorans as an efficient and adaptable bacterium that is able to perform complete denitrification under various conditions. PMID:25979892

  20. Regulation of rhizosphere acidification by photosynthetic activity in cowpea (Vigna unguiculata L. walp.) seedlings.

    PubMed

    Rao, Theertham P; Yano, Katsuya; Iijima, Morio; Yamauchi, Akira; Tatsumi, Jiro

    2002-02-01

    In contrast to cereals or other crops, legumes are known to acidify the rhizosphere even when supplied with nitrates. This phenomenon has been attributed to N2 fixation allowing excess uptake of cations over anions; however, as we have found previously, the exposure of the shoot to illumination can cause rhizosphere acidification in the absence of N2 fixation in cowpea (Vigna unguiculata L. Walp). In this study, we examined whether the light-induced acidification can relate to photosynthetic activity and corresponding alterations in cation-anion uptake ratios. The changes of rhizosphere pH along the root axis were visualized using a pH indicator agar gel. The intensity of pH changes (alkalization/acidification) in the rhizosphere was expressed in proton fluxes, which were obtained by processing the images of the pH indicator agar gel. The uptake of cations and anions was measured in nutrient solution. The rhizosphere was alkalinized in the dark but acidified with exposure of the shoots to light. The extent of light-induced acidification was increased with leaf size and intensity of illumination on the shoot, and completely stopped with the application of photosynthesis inhibitor. Although the uptake of cations was significantly lower than that of anions, the rhizosphere was acidified by light exposure. Proton pump inhibitors N,N'-dicyclohexyl carbodimide and vanadate could not stop the light-induced acidification. The results indicate that light-induced acidification in cowpea seedlings is regulated by photosynthetic activity, but is not due to excess uptake of cations. PMID:12099352

  1. Effect of recycle-to-influent ratio on activities of nitrifiers and denitrifiers in a combined UASB-activated sludge reactor system.

    PubMed

    Huang, Ju-Sheng; Chou, Hsin-Hsien; Chen, Chih-Ming; Chiang, Chun-Mao

    2007-06-01

    A laboratory study using a combined upflow anaerobic sludge bed (UASB)-activated sludge (AS) reactor system was undertaken to explore the effect of recycle-to-influent ratio (R(e)=1, 2, and 3) on the activities of nitrifiers and denitrifiers. Suspended-solids pre-settled piggery wastewater was used as the substrate-feed wastewater. At the R(e) of 1-3, the combined reactor system achieved efficient removal of COD (96-97%), TKN (100%) and total nitrogen TN (54-77%). Methanogenesis occurred with nearly-complete denitrification in the UASB reactor, whereas complete nitrification took place in the AS reactor. A higher R(e) (i.e., accompanied with a shorter solids retention time) resulted in a larger amount of high-activity denitrifiers and thereby achieved a higher TN removal efficiency. Compact granules and a high biomass concentration in the UASB reactor were observed. At the R(e) of 1-3, the maximum specific reaction rate of nitrifiers (0.45-0.49 NH(4)(+)-NmgVSS(-1)d(-1)) and the specific nitrification rates of mixed culture (0.18-0.22mg NH(4)(+)-NmgVSS(-1)d(-1)) in the AS reactor varied slightly; whereas the maximum specific reaction rate of denitrifiers (0.18-0.27mg NO(x)(-)-NmgVSS(-1)d(-1)) and the specific denitrification and COD removal rates of mixed culture (0.025-0.050mg NO(x)(-)-NmgVSS(-1)d(-1); 0.24-0.31mgCODmgVSS(-1)d(-1)) in the UASB reactor increased with increasing R(e). The primary finding of the study is that the combined UASB-AS reactor system should be operated at a higher R(e) to maintain high-activity denitrifiers to remove organic materials and nitrogen from piggery wastewater.

  2. [Effects of allelopathic rice on rhizosphere microbial flora and enzyme activity].

    PubMed

    Hu, Kaihui; Luo, Qingguo; Wang, Shihua; Lin, Xuan; Lin, Wenxiong

    2006-06-01

    This paper studied the dynamics of microbial flora and enzyme activity in the rhizosphere of allelopathic rice PI312777 (PI) and non-allelopathic rice Lemont (LE) at the growth stage of 3 - 7 leaves. The results showed that in the rhizosphere of PI, the amounts of bacteria, actinomycetes and azotobacter were 11.2% - 28.3%, 40% - 78.6% and 111.5% - 173.9%, respectively, while that of fungi was lower, with the maximum being 25.5% of that in the rhizosphere of LE, suggesting that allelopathic rice PI promoted the growth of bacteria, actinomycetes and azotobacter, but inhibited that of fungi. Further analysis on the physiological groups of microbial flora showed that PI favored the growth of ammonifier, aerobic azotobacter, aerobic cellulose - decomposer, sulphate - reducer, nitrite - bacteria and nitrate - bacteria, among which, ammonifier and aerobic azotobacter increased by 53.7% and 57.6%, respectively, while inhibited the growth of desulphate bacteria and denitrifyier. Moreover, PI increased the activities of urease, phosphatase and sucrase, but decreased the catalase activity in its rhizosphere.

  3. Community composition and activity of anaerobic ammonium oxidation bacteria in the rhizosphere of salt-marsh grass Spartina alterniflora.

    PubMed

    Zheng, Yanling; Hou, Lijun; Liu, Min; Yin, Guoyu; Gao, Juan; Jiang, Xiaofen; Lin, Xianbiao; Li, Xiaofei; Yu, Chendi; Wang, Rong

    2016-09-01

    Anaerobic ammonium oxidation (anammox) as an important nitrogen removal pathway has been investigated in intertidal marshes. However, the rhizosphere-driven anammox process in these ecosystems is largely overlooked so far. In this study, the community dynamics and activities of anammox bacteria in the rhizosphere and non-rhizosphere sediments of salt-marsh grass Spartina alterniflora (a widely distributed plant in estuaries and intertidal ecosystems) were investigated using clone library analysis, quantitative PCR assay, and isotope-tracing technique. Phylogenetic analysis showed that anammox bacterial diversity was higher in the non-rhizosphere sediments (Scalindua and Kuenenia) compared with the rhizosphere zone (only Scalindua genus). Higher abundance of anammox bacteria was detected in the rhizosphere (6.46 × 10(6)-1.56 × 10(7) copies g(-1)), which was about 1.5-fold higher in comparison with that in the non-rhizosphere zone (4.22 × 10(6)-1.12 × 10(7) copies g(-1)). Nitrogen isotope-tracing experiments indicated that the anammox process in the rhizosphere contributed to 12-14 % N2 generation with rates of 0.43-1.58 nmol N g(-1) h(-1), while anammox activity in the non-rhizosphere zone contributed to only 4-7 % N2 production with significantly lower activities (0.28-0.83 nmol N g(-1) h(-1)). Overall, we propose that the rhizosphere microenvironment in intertidal marshes might provide a favorable niche for anammox bacteria and thus plays an important role in nitrogen cycling. PMID:27225476

  4. Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary.

    PubMed

    Francis, Christopher A; O'Mullan, Gregory D; Cornwell, Jeffrey C; Ward, Bess B

    2013-01-01

    Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd 1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96-123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity.

  5. Rhizosphere bacterial community composition responds to arbuscular mycorrhiza, but not to reductions in microbial activity induced by foliar cutting.

    PubMed

    Vestergård, Mette; Henry, Frédéric; Rangel-Castro, Juan Ignacio; Michelsen, Anders; Prosser, James I; Christensen, Søren

    2008-04-01

    Differences in bacterial community composition (BCC) between bulk and rhizosphere soil and between rhizospheres of different plant species are assumed to be strongly governed by quantitative and qualitative rhizodeposit differences. However, data on the relationship between rhizodeposit amounts and BCC are lacking. Other soil microorganisms, e.g. arbuscular mycorrhizal fungi (AMF), may also influence BCC. We simulated foliar herbivory (cutting) to reduce belowground carbon allocation and rhizodeposition of pea plants grown either with or without AMF. This reduced soil respiration, rhizosphere microbial biomass and bacteriovorous protozoan abundance, whereas none of these were affected by AMF. After labelling plants with (13)CO(2), root and rhizosphere soil (13)C enrichment of cut plants were reduced to a higher extent (24-46%) than shoot (13)C enrichment (10-24%). AMF did not affect (13)C enrichment. Despite these clear indications of reduced rhizosphere carbon-input, denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes PCR-amplified targeting DNA and RNA from rhizosphere soil did not reveal any effects of cutting on banding patterns. In contrast, AMF induced consistent differences in both DNA- and RNA-based DGGE profiles. These results show that a reduction in rhizosphere microbial activity is not necessarily accompanied by changes in BCC, whereas AMF presence inhibits proliferation of some bacterial taxa while stimulating others.

  6. Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments

    PubMed Central

    Thomas, François; Giblin, Anne E.; Cardon, Zoe G.; Sievert, Stefan M.

    2014-01-01

    Salt marshes are highly productive ecosystems hosting an intense sulfur (S) cycle, yet little is known about S-oxidizing microorganisms in these ecosystems. Here, we studied the diversity and transcriptional activity of S-oxidizers in salt marsh sediments colonized by the plant Spartina alterniflora, and assessed variations with sediment depth and small-scale compartments within the rhizosphere. We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB). Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT)-qPCR assays. We identified a diverse assemblage of S-oxidizers, with Chromatiales and Thiotrichales being dominant. The detection of transcripts from S-oxidizers was mostly confined to the upper 5 cm sediments, following the expected distribution of root biomass. A common pool of species dominated by Gammaproteobacteria transcribed S-oxidation genes across roots, rhizosphere, and surrounding sediment compartments, with rdsrAB transcripts prevailing over soxB. However, the root environment fine-tuned the abundance and transcriptional activity of the S-oxidizing community. In particular, the global transcription of soxB was higher on the roots compared to mix and rhizosphere samples. Furthermore, the contribution of Epsilonproteobacteria-related S-oxidizers tended to increase on Spartina roots compared to surrounding sediments. These data shed light on the under-studied oxidative part of the sulfur cycle in salt marsh sediments and indicate small-scale heterogeneities are important factors shaping abundance and potential activity of S-oxidizers in the rhizosphere. PMID:25009538

  7. Assessing the activity and diversity of fumarate-fed denitrifying bacteria by performing field single-well push-pull tests.

    PubMed

    Kim, Jin-Hoon; Ha, Chul-Yoon; Oa, Seong-Wook; Lee, Jin-Woo; Park, Sun-Hwa; Kwon, Soo-Youl; Kim, Sungpyo; Kim, Young

    2011-01-01

    In situ biological denitrification has been proposed as an important metabolic activity in the remediation of nitrate-contaminated groundwater. In this study, the effects of fumarate, an electron donor for biological denitrification, on the in situ denitrifying activity were determined by using three types of single-well push-pull tests; transport, biostimulation and activity tests. During the tests, changes in microbial community composition were also investigated using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes. Transport test demonstrated that non-reactive tracer and biologically reactive solutes behaved similarly. A biostimulation test was conducted to stimulate the denitrifying activities of native microorganisms, which were monitored by detecting the simultaneous production of CO(2) and drastic degradations of both nitrate and fumarate after the injection of fumarate as an electron donor and/or carbon source, with nitrate as an electron acceptor. A phylogenetic analysis suggested that the taxonomic affiliation of the dominant species before biostimulation was γ-Proteobacteria, including Acinetobacter species and Pseudomonas fluorescens, while the dominant species after biostimulation were affiliated with β-Proteobacteria, cytophaga-Flavobacterium-Bacteroides and high G+C gram-positive bacteria. These results suggest that the analyses of groundwater samples using a combination of single well push pull tests with DGGE can be applied to investigate the activity, diversity and composition shift of denitrifying bacteria in a nitrate-contaminated aquifer.

  8. Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands.

    PubMed

    Le Roux, Xavier; Schmid, Bernhard; Poly, Franck; Barnard, Romain L; Niklaus, Pascal A; Guillaumaud, Nadine; Habekost, Maike; Oelmann, Yvonne; Philippot, Laurent; Salles, Joana Falcao; Schloter, Michael; Steinbeiss, Sibylle; Weigelt, Alexandra

    2013-01-01

    Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes

  9. Rhizosphere priming: a nutrient perspective

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizosphere priming is the change in decomposition of soil organic matter (SOM) caused by root activity. Rhizosphere priming plays a crucial role in soil carbon (C) dynamics and their response to global climate change. Rhizosphere priming may be affected by soil nutrient availability, but rhizospher...

  10. Pyruvic Oxime Nitrification and Copper and Nickel Resistance by a Cupriavidus pauculus, an Active Heterotrophic Nitrifier-Denitrifier

    PubMed Central

    Linchangco, Richard

    2014-01-01

    Heterotrophic nitrifiers synthesize nitrogenous gasses when nitrifying ammonium ion. A Cupriavidus pauculus, previously thought an Alcaligenes sp. and noted as an active heterotrophic nitrifier-denitrifier, was examined for its ability to produce nitrogen gas (N2) and nitrous oxide (N2O) while heterotrophically nitrifying the organic substrate pyruvic oxime [CH3–C(NOH)–COOH]. Neither N2 nor N2O were produced. Nucleotide and phylogenetic analyses indicated that the organism is a member of a genus (Cupriavidus) known for its resistance to metals and its metabolism of xenobiotics. The microbe (a Cupriavidus pauculus designated as C. pauculus strain UM1) was examined for its ability to perform heterotrophic nitrification in the presence of Cu2+ and Ni2+ and to metabolize the xenobiotic phenol. The bacterium heterotrophically nitrified well when either 1 mM Cu2+ or 0.5 mM Ni2+ was present in either enriched or minimal medium. The organism also used phenol as a sole carbon source in either the presence or absence of 1 mM Cu2+ or 0.5 mM Ni2+. The ability of this isolate to perform a number of different metabolisms, its noteworthy resistance to copper and nickel, and its potential use as a bioremediation agent are discussed. PMID:25580463

  11. [Characteristics of soil denitrifying enzyme activity in riparian zones with different land use types in Chongming Island, Shanghai of China].

    PubMed

    Chen, Gang-Liang; Li, Jian-Hua; Yang, Chang-Ming

    2013-10-01

    By using acetylene inhibition method, this paper studied the soil denitrifying enzyme activity (DEA) and its affecting factors in the riparian zone with different land use types (cropland riparian, forested riparian, and grassy riparian zones) in Chongming Island, Shanghai of China. The riparian soil DEA was (0.69 +/- 0.11)--(134.93 +/- 33.72) microg N x kg(-1) x h(-1), which differed obviously among different land types, with a decreasing trend of forested riparian zone > cropland riparian zone > grassy riparian zone. The soil DEA was significantly (P < 0.05) higher in 0-10 cm in 10-30, 30-50, and 50-70 cm layers. There were significant positive relationships between soil DEA and soil TOC, TN, and NO(3-)-N (P < 0.01). Land use change mainly altered the soil natural structure and soil physical and chemical properties, decreased the accumulation of soil organic carbon, and affected the soil nitrogen transformation, and thus, inhibited the occurrence of riparian soil denitrification.

  12. [Effects of bio-mulching on rhizosphere soil microbial population, enzyme activity and tree growth in poplar plantation].

    PubMed

    Liu, Jiu-Jun; Fang, Sheng-Zuo; Xie, Bao-Dong; Hao, Juan-Juan

    2008-06-01

    Coriaria nepalensis, Pteridium aquilinum var. latiuscukum, Imperata cylindrical var. major, and Quercus fabric were used as mulching materials to study their effects on the rhizosphere soil microbial population and enzyme activity and the tree growth in poplar plantation. The results showed that after mulching with test materials, the populations of both bacteria and fungi in rhizosphere soil were more than those of the control. Of the mulching materials, I. cylindrical and Q. fabric had the best effect, with the numbers of bacteria and fungi being 23.56 and 1.43 times higher than the control, respectively. The bacterial and fungal populations in rhizosphere soil increased with increasing mulching amount. When the mulching amount was 7.5 kg m(-2), the numbers of bacteria and fungi in rhizosphere soil were 0.5 and 5.14 times higher than the control, respectively. Under bio-mulching, the bacterial and fungal populations in rhizosphere soil had a similar annual variation trend, which was accorded with the annual fluctuation of soil temperature and got to the maximum in July and the minimum in December. The urease and phosphatase activities in rhizosphere soil also increased with increasing mulching amount. As for the effects of different mulching materials on the enzyme activities, they were in the order of C. nepalensis > P. aquilinum > I. cylindrical > Q. fabric. The annual variation of urease and phosphatase activities in rhizosphere soil was similar to that of bacterial and fungal populations, being the highest in July and the lowest in December. Bio-mulching promoted the tree height, DBH, and biomass of poplar trees significantly.

  13. Effects of glyphosate and foliar amendments on activity of microorganisms in the soybean rhizosphere.

    PubMed

    Means, Nathan E; Kremer, Robert J; Ramsier, Clifford

    2007-02-01

    A field study was conducted to determine the effects of glyphosate on microbial activity in the rhizosphere of glyphosate-resistant (GR) soybean and to evaluate interactions with foliar amendments. Glyphosate at 0.84 kg ae ha(-1) was applied GR soybean at the V4-V5 development stages. Check treatments included a conventional herbicide tank mix (2003 study only) and no herbicides (hand-weeded). Ten days after herbicide application, a commercially available biostimulant and a urea solution (21.0% N) were applied to soybean foliage at 33.5 mL ha(-1) and 9.2 kg ha(-1), respectively. Soil and plant samples were taken 0, 5, 10, 15, 20 and 25 days after herbicide application then assayed for enzyme and respiration activities. Soil respiration and enzyme activity increased with glyphosate and foliar amendment applications during the 2002 growing season; however, similar increases were not observed in 2003. Contrasting cumulative rainfall between 2002 and 2003 likely accounted for differences in soil microbial activities. Increases in soil microbial activity in 2002 suggest that adequate soil water and glyphosate application acted together to increase microbial activity. Our study suggests that general soil microbial properties including those involving C and N transformations are not sensitive enough to detect effects of glyphosate on rhizosphere microbial activity. Measurements of soil-plant-microbe relationships including specific microbial groups (i.e., root-associated Fusarium spp.) are likely better indicators of impacts of glyphosate on soil microbial ecology.

  14. [Microbial activity and functional diversity in rhizosphere of cucumber under different subsurface drip irrigation scheduling].

    PubMed

    Li, Hua; He, Hong-Jun; Li, Teng-Fei; Zhang, Zi-Kun

    2014-08-01

    The effects of subsurface drip irrigation scheduling on microbial activity and functional diversity in rhizosphere of cucumber in solar greenhouse were studied in this paper. The results showed that the soil microbial biomass C and N, basal respiration, metabolic quotient and values of AWCD, Shannon and McIntosh indexes were increased at first and then decreased with the increase of irrigation water amount. The values of microbial C and N, basal respiration and metabolic quotient in I2 treatments were significantly higher than those in I1 treatments at the 0.8E(p) irrigation level. The numbers of bacteria, actinomyces and nitrogen-fixing bacteria, and the activities of urease, phosphatase, sucrase, catalase and polyhenoloxidase were significantly higher in the 0.8E(p) treatment than in the other treatments. The numbers of bacteria and nitrogen-fixing bacteria, the activities of urease, phosphatase and sucrase in I2 treatments were significantly higher than in I1 treatment, the actinomyces number and activities of catalase and polyhenoloxidase had no significant difference between I1 and I2 treatments, however, the fungi number in I2 treatments were significantly lower than in I2 treaments at the 0.8E(p) irrigation level. The microbial activity and functional diversity in rhizosphere of cucumber were strengthened in the I20.8E(p) treatment, meanwhile, the soil microflora was improved and the soil enzymes activities were enhanced, therefore, the cucumber growth was promoted as well.

  15. Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study investigated the activities of ß-glucosidase (C cycling, ß-glucosaminidase (C and N cycling), acid phosphatase (P cycling) and arylsulfatase (S cycling) under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall f...

  16. Microbial respiration and kinetics of extracellular enzymes activities through rhizosphere and detritusphere at agricultural site

    NASA Astrophysics Data System (ADS)

    Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2014-05-01

    Rhizosphere and detritusphere are soil microsites with very high resource availability for microorganisms affecting their biomass, composition and functions. In the rhizosphere low molecular compounds occur with root exudates and low available polymeric compounds, as belowground plant senescence. In detritusphere the substrate for decomposition is mainly a polymeric material of low availability. We hypothesized that microorganisms adapted to contrasting quality and availability of substrates in the rhizosphere and detritusphere are strongly different in affinity of hydrolytic enzymes responsible for decomposition of organic compounds. According to common ecological principles easily available substrates are quickly consumed by microorganisms with enzymes of low substrate affinity (i.e. r-strategists). The slow-growing K-strategists with enzymes of high substrate affinity are better adapted for growth on substrates of low availability. Estimation of affinity of enzyme systems to the substrate is based on Michaelis-Menten kinetics, reflecting the dependency of decomposition rates on substrate amount. As enzymes-mediated reactions are substrate-dependent, we further hypothesized that the largest differences in hydrolytic activity between the rhizosphere and detritusphere occur at substrate saturation and that these differences are smoothed with increasing limitation of substrate. Affected by substrate limitation, microbial species follow a certain adaptation strategy. To achieve different depth gradients of substrate availability 12 plots on an agricultural field were established in the north-west of Göttingen, Germany: 1) 4 plots planted with maize, reflecting lower substrate availability with depth; 2) 4 unplanted plots with maize litter input (0.8 kg m-2 dry maize residues), corresponding to detritusphere; 3) 4 bare fallow plots as control. Maize litter was grubbed homogenously into the soil at the first 5 cm to ensure comparable conditions for the herbivore and

  17. Effect of salinity tolerant PDH45 transgenic rice on physicochemical properties, enzymatic activities and microbial communities of rhizosphere soils

    PubMed Central

    Sahoo, Ranjan Kumar; Tuteja, Narendra

    2013-01-01

    The effect of genetically modified (GM) plants on environment is now major concern worldwide. The plant roots of rhizosphere soil interact with variety of bacteria which could be influenced by the transgene in GM plants. The antibiotic resistance genes in GM plants may be transferred to soil microbes. In this study we have examined the effect of overexpression of salinity tolerant pea DNA helicase 45 (PDH45) gene on microbes and enzymatic activities in the rhizosphere soil of transgenic rice IR64 in presence and absence of salt stress in two different rhizospheric soils (New Delhi and Odisha, India). The diversity of the microbial community and soil enzymes viz., dehydrogenase, alkaline phosphatase, urease and nitrate reductase was assessed. The results revealed that there was no significant effect of transgene expression on rhizosphere soil of the rice plants. The isolated bacteria were phenotyped both in absence and presence of salt and no significant changes were found in their phenotypic characters as well as in their population. Overall, the overexpression of PDH45 in rice did not cause detectable changes in the microbial population, soil enzymatic activities and functional diversity of the rhizosphere soil microbial community. PMID:23733066

  18. Elevated atmospheric CO2 affected photosynthetic products in wheat seedlings and biological activity in rhizosphere soil under cadmium stress.

    PubMed

    Jia, Xia; Liu, Tuo; Zhao, Yonghua; He, Yunhua; Yang, Mingyan

    2016-01-01

    The objective of this study was to investigate the effects of elevated CO2 (700 ± 23 μmol mol(-1)) on photosynthetic products in wheat seedlings and on organic compounds and biological activity in rhizosphere soil under cadmium (Cd) stress. Elevated CO2 was associated with decreased quantities of reducing sugars, starch, and soluble amino acids, and with increased quantities of soluble sugars, total sugars, and soluble proteins in wheat seedlings under Cd stress. The contents of total soluble sugars, total free amino acids, total soluble phenolic acids, and total organic acids in the rhizosphere soil under Cd stress were improved by elevated CO2. Compared to Cd stress alone, the activity of amylase, phenol oxidase, urease, L-asparaginase, β-glucosidase, neutral phosphatase, and fluorescein diacetate increased under elevated CO2 in combination with Cd stress; only cellulase activity decreased. Bacterial abundance in rhizosphere soil was stimulated by elevated CO2 at low Cd concentrations (1.31-5.31 mg Cd kg(-1) dry soil). Actinomycetes, total microbial abundance, and fungi decreased under the combined conditions at 5.31-10.31 mg Cd kg(-1) dry soil. In conclusion, increased production of soluble sugars, total sugars, and proteins in wheat seedlings under elevated CO2 + Cd stress led to greater quantities of organic compounds in the rhizosphere soil relative to seedlings grown under Cd stress only. Elevated CO2 concentrations could moderate the effects of heavy metal pollution on enzyme activity and microorganism abundance in rhizosphere soils, thus improving soil fertility and the microecological rhizosphere environment of wheat under Cd stress.

  19. Increased Activity of Rhizosphere and Hyphosphere Enzymes under Elevated CO2 in a Loblolly Pine Stand

    NASA Astrophysics Data System (ADS)

    Meier, I.; Phillips, R.

    2012-12-01

    The stimulatory effect of elevated atmospheric CO2 under global climate change on forest productivity has been predicted to decrease over time as pools of available N in soil become depleted, but empirical support for such progressive N limitation has been lacking. Increased N acquisition from soil depleted in inorganic nitrogen requires stimulation of the microbial processing of organic N, possibly through increasing C supply to soil by plant roots or mycorrhizal hyphae. Increases in (mycorr)rhizosphere C fluxes could stimulate microbes to produce extra-cellular enzymes that release N from SOM, feeding back from soil microsites to ecosystem-scale processes. We investigated the influence of elevated CO2 on root exudation and soil enzyme activity at the Duke Forest FACE site, USA, where loblolly pine (Pinus taeda L.) stands have been exposed to elevated CO2 for 14 years and N fertilization for five years. In each plot, root boxes containing acetate windows were installed in 2008. Two years after installation, we collected soils adjacent to root tips (the rhizosphere), hyphal tips (the hyphosphere) and bulk soil. We measured in situ root exudation rates from intact pine roots. Study objectives were to analyze (i) the influence of atmospheric CO2 on root exudation and extra-cellular enzyme activities, (ii) the influence of soil N availability in regulating these activities, and (iii) the relationship between the activities of enzymes involved in N cycling in soils and gross N transformations at soil microsites. Elevated atmospheric CO2 significantly increased the activity of β-1-4-N-acetylglucosaminidase (NAG) in the rhizosphere by almost 2.5 times (39 to 95 nmol h-1 g-1), and 1.6fold in the hyphosphere relative to ambient plots. NAG is an enzyme involved in the degradation of chitin from the cell walls of soil organisms, releasing absorbable forms of nitrogen. The activity of peroxidase, which degrades aromatic C compounds of SOM, increased significantly in the

  20. Diagnosis and quantification of glycerol assimilating denitrifying bacteria in an integrated fixed-film activated sludge reactor via 13C DNA stable-isotope probing.

    PubMed

    Lu, Huijie; Chandran, Kartik

    2010-12-01

    Glycerol, a byproduct of biodiesel and oleo-chemical manufacturing operations, represents an attractive alternate to methanol as a carbon and electron donor for enhanced denitrification. However, unlike methanol, little is known about the diversity and activity of glycerol assimilating bacteria in activated sludge. In this study, the microbial ecology of glycerol assimilating denitrifying bacteria in a sequencing batch integrated fixed film activated sludge (SB-IFAS) reactor was investigated using (13)C-DNA stable isotope probing (SIP). During steady state SB-IFAS reactor operation, near complete nitrate removal (92.7 ± 5.8%) was achieved. Based on (13)C DNA clone libraries obtained after 360 days of SB-IFAS reactor operation, bacteria related to Comamonas spp. and Diaphorobacter spp. dominated in the suspended phase communities. (13)C assimilating members in the biofilm community were phylogenetically more diverse and were related to Comamonas spp., Bradyrhizobium spp., and Tessaracoccus spp. Possibly owing to greater substrate availability in the suspended phase, the glycerol-assimilating denitrifying populations (quantified by real-time PCR) were more abundant therein than in the biofilm phase. The biomass in the suspended phase also had a higher specific denitrification rate than the biofilm phase (p = 4.33e-4), and contributed to 69.7 ± 4.5% of the overall N-removal on a mass basis. The kinetics of glycerol based denitrification by suspended phase biomass were approximately 3 times higher than with methanol. Previously identified methanol assimilating denitrifying bacteria were not associated with glycerol assimilation, thereby suggesting limited cross-utilization of these two substrates for denitrification in the system tested.

  1. Isolation of maize soil and rhizosphere bacteria with antagonistic activity against Aspergillus flavus and Fusarium verticillioides.

    PubMed

    Palumbo, Jeffrey D; O'Keeffe, Teresa L; Abbas, Hamed K

    2007-07-01

    Bacterial isolates from Mississippi maize field soil and maize rhizosphere samples were evaluated for their potential as biological control agents against Aspergillus flavus and Fusarium verticillioides. Isolated strains were screened for antagonistic activities in liquid coculture against A. flavus and on agar media against A. flavus and F. verticillioides. We identified 221 strains that inhibited growth of both fungi. These bacteria were further differentiated by their production of extracellular enzymes that hydrolyzed chitin and yeast cell walls and by production of antifungal metabolites. Based on molecular and nutritional identification of the bacterial strains, the most prevalent genera isolated from rhizosphere samples were Burkholderia and Pseudomonas, and the most prevalent genera isolated from nonrhizosphere soil were Pseudomonas and Bacillus. Less prevalent genera included Stenotrophomonas, Agrobacterium, Variovorax, Wautersia, and several genera of coryneform and enteric bacteria. In quantitative coculture assays, strains of P. chlororaphis and P. fluorescens consistently inhibited growth of A. flavus and F. verticillioides in different media. These results demonstrate the potential for developing individual biocontrol agents for simultaneous control of the mycotoxigenic A. flavus and F. verticillioides. PMID:17685333

  2. Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season.

    PubMed

    Siczek, Anna; Lipiec, Jerzy

    2016-01-01

    Inoculation of legume seeds with Rhizobium affects soil microbial community and processes, especially in the rhizosphere. This study aimed at assessing the effect of Rhizobium inoculation on microbial activity in the faba bean rhizosphere during the growing season in a field experiment on a Haplic Luvisol derived from loess. Faba bean (Vicia faba L.) seeds were non-inoculated (NI) or inoculated (I) with Rhizobium leguminosarum bv. viciae and sown. The rhizosphere soil was analyzed for the enzymatic activities of dehydrogenases, urease, protease and acid phosphomonoesterase, and functional diversity (catabolic potential) using the Average Well Color Development, Shannon-Weaver, and Richness indices following the community level physiological profiling from Biolog EcoPlate™. The analyses were done on three occasions corresponding to the growth stages of: 5-6 leaf, flowering, and pod formation. The enzymatic activities were higher in I than NI (p < 0.05) throughout the growing season. However, none of the functional diversity indices differed significantly under both treatments, regardless of the growth stage. This work showed that the functional diversity of the microbial communities was a less sensitive tool than enzyme activities in assessment of rhizobial inoculation effects on rhizosphere microbial activity. PMID:27213363

  3. Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season

    PubMed Central

    Siczek, Anna; Lipiec, Jerzy

    2016-01-01

    Inoculation of legume seeds with Rhizobium affects soil microbial community and processes, especially in the rhizosphere. This study aimed at assessing the effect of Rhizobium inoculation on microbial activity in the faba bean rhizosphere during the growing season in a field experiment on a Haplic Luvisol derived from loess. Faba bean (Vicia faba L.) seeds were non-inoculated (NI) or inoculated (I) with Rhizobium leguminosarum bv. viciae and sown. The rhizosphere soil was analyzed for the enzymatic activities of dehydrogenases, urease, protease and acid phosphomonoesterase, and functional diversity (catabolic potential) using the Average Well Color Development, Shannon-Weaver, and Richness indices following the community level physiological profiling from Biolog EcoPlate™. The analyses were done on three occasions corresponding to the growth stages of: 5–6 leaf, flowering, and pod formation. The enzymatic activities were higher in I than NI (p < 0.05) throughout the growing season. However, none of the functional diversity indices differed significantly under both treatments, regardless of the growth stage. This work showed that the functional diversity of the microbial communities was a less sensitive tool than enzyme activities in assessment of rhizobial inoculation effects on rhizosphere microbial activity. PMID:27213363

  4. Numerically dominant denitrifying bacteria from world soils.

    PubMed

    Gamble, T N; Betlach, M R; Tiedje, J M

    1977-04-01

    Nineteen soils, three freshwater lake sediments, and oxidized poultry manure were examined to determine the dominant denitrifier populations. The samples, most shown or expected to support active denitrification, were from eight countries and included rice paddy, temperate agricultural, rain forest, organic, and waste-treated soils. Over 1,500 organisms that could grow anaerobically on nitrate agar were isolated. After purification, 146 denitrifiers were obtained, as verified by production of N(2) from NO(3) (-). These isolates were characterized by 52 properties appropriate for the Pseudomonas-Alcaligenes group. Numerical taxonomic procedures were used to group the isolates and compare them with nine known denitrifier species. The major group isolated was representative of Pseudonomas fluorescens biotype II. The second most prevalent group was representative of Alcaligenes. Other Pseudomonas species as well as members of the genus Flavobacterium, the latter previously not known to denitrify, also were identified. One-third of the isolates could not utilize glucose or other carbohydrates as sole carbon sources. Significantly, none of the numerically dominant denitrifiers we isolated resembled the most studied species: Pseudomonas denitrificans, Pseudomonas perfectomarinus, and Paracoccus denitrificans. Denitrification appears to be a property of a very diverse group of gram-negative, motile bacteria, as shown by the large number (22.6%) of ungrouped organisms. The diversity of denitrifiers from a given sample was usually high, with at least two groups present. Denitrifiers, nitrite accumulators, and organisms capable of anaerobic growth were present in the ratio of 0.20+/-0.23:0.81+/-0.23:1. There were few correlations between their numbers and the sample characteristics measured. However, the temperatures at which isolates could grow were significantly related to the temperatures of the environments from which they were isolated. Regression analysis revealed few

  5. Soil zymography - A novel technique for mapping enzyme activity in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Spohn, Marie

    2014-05-01

    The effect plant roots on microbial activity in soil at the millimeter scale is poorly understood. One reason for this is that spatially explicit methods for the study of microbial activity in soil are limited. Here we present a quantitative in situ technique for mapping the distribution of exoenzymes in soil along with some results about the effects of roots on exoenzyme activity in soil. In the first study we showed that both acid and alkaline phosphatase activity were up to 5.4-times larger in the rhizosphere of Lupinus albus than in the bulk soil. While acid phosphatase activity (produced by roots and microorganisms) was closely associated with roots, alkaline phosphatase activity (produced only by microorganisms) was more widely distributed, leading to a 2.5-times larger area of activity of alkaline than of acid phosphatase. These results indicate a spatial differentiation of different ecophysiological groups of organic phosphorus mineralizing organisms in the rhizosphere which might alleviate a potential competition for phosphorus between them. In a second study cellulase, chitinase and phosphatase activities were analyzed in the presence of living Lupinus polyphyllus roots and dead/dying roots (in the same soils 10, 20 and 30 days after cutting the L. polyphyllus shoots). The activity of all three enzymes was 9.0 to 13.9-times higher at the living roots compared to the bulk soil. Microhotspots of cellulase, chitinase and phosphatase activity in the soil were found up to 60 mm away from the living roots. 10 days after shoot cutting, the areas of high activities of cellulase and phosphatase activity were extend up to 55 mm away from the next root, while the extension of the area of chitinase activity did not change significantly. At the root, cellulase and chitinase activity increased first at the root tips after shoot cutting and showed maximal activity 20 days after shoot cutting. The number and activity of microhotspots of chitinase activity was maximal 10

  6. Denitrification Activity of a Remarkably Diverse Fen Denitrifier Community in Finnish Lapland Is N-Oxide Limited

    PubMed Central

    Palmer, Katharina; Horn, Marcus A.

    2015-01-01

    Peatlands cover more than 30% of the Finnish land area and impact N2O fluxes. Denitrifiers release N2O as an intermediate or end product. In situ N2O emissions of a near pH neutral pristine fen soil in Finnish Lapland were marginal during gas chamber measurements. However, nitrate and ammonium fertilization significantly stimulated in situ N2O emissions. Stimulation with nitrate was stronger than with ammonium. N2O was produced and subsequently consumed in gas chambers. In unsupplemented anoxic microcosms, fen soil produced N2O only when acetylene was added to block nitrous oxide reductase, suggesting complete denitrification. Nitrate and nitrite stimulated denitrification in fen soil, and maximal reaction velocities (vmax) of nitrate or nitrite dependent denitrification where 18 and 52 nmol N2O h-1 gDW-1, respectively. N2O was below 30% of total produced N gases in fen soil when concentrations of nitrate and nitrite were <500 μM. vmax for N2O consumption was up to 36 nmol N2O h-1 gDW-1. Denitrifier diversity was assessed by analyses of narG, nirK/nirS, and nosZ (encoding nitrate-, nitrite-, and nitrous oxide reductases, respectively) by barcoded amplicon pyrosequencing. Analyses of ~14,000 quality filtered sequences indicated up to 25 species-level operational taxonomic units (OTUs), and up to 359 OTUs at 97% sequence similarity, suggesting diverse denitrifiers. Phylogenetic analyses revealed clusters distantly related to publicly available sequences, suggesting hitherto unknown denitrifiers. Representatives of species-level OTUs were affiliated with sequences of unknown soil bacteria and Actinobacterial, Alpha-, Beta-, Gamma-, and Delta-Proteobacterial sequences. Comparison of the 4 gene markers at 97% similarity indicated a higher diversity of narG than for the other gene markers based on Shannon indices and observed number of OTUs. The collective data indicate (i) a high denitrification and N2O consumption potential, and (ii) a highly diverse, nitrate limited

  7. Site-specific variability in BTEX biodegradation under denitrifying conditions

    SciTech Connect

    Kao, C.M.; Borden, R.C.

    1997-03-01

    Laboratory microcosm experiments were conducted to evaluate the feasibility of benzene, toluene, ethylbenzene, m-xylene, and o-xylene (BTEX) biodegradation under denitrifying conditions. Nine different sources of inocula, including contaminated and uncontaminated soil cores from four different sites and activated sludge, were used to establish microcosms. BTEX was not degraded under denitrifying conditions in microcosms inoculated with aquifer material from Rocky Point and Traverse City. However, rapid depletion of glucose under denitrifying conditions was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing aquifer material from Fort Bragg and Sleeping Bear Dunes and sewage sludge. Benzene was recalcitrant in all microcosms tested. The degradation of o-xylene ceased after toluene, ethylbenzene, and m-xylene were depleted in the Fort Bragg and sludge microcosms, but o-xylene continued to degrade in microcosms with contaminated Sleeping Bear Dunes soil. The most probable number (MPN) of denitrifiers in these nine different inocula were measured using a microtiter technique. There was no correlation between the MPN of denitrifiers and the TEX degradation rate under denitrifying conditions. Experimental results indicate that the degradation sequence and TEX degradation rate under denitrifying conditions may differ among sites. Results also indicate that denitrification alone may not be a suitable bioremediation technology for gasoline-contaminated aquifers because of the inability of denitrifiers to degrade benzene.

  8. Hotspots in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Kuzyakov, Y.

    2009-04-01

    Rhizosphere is an interface in soil with very intensive interactions between living (roots and microorganisms), solid (minerals and organics), liquid (water with dissolved organic and mineral substances) and gaseous phases. Biogeochemical environment in the rhizosphere is completely different from that of the root free soil. These differences are mainly induced by the release of easily available organic substances by roots into the soil and subsequent changes of microbial composition, activity, turnover rates of organics and weathering rates etc. An overview of microbial hotspots in rhizosphere is presented. 14C budget studies showed that the amount of easily available organics released by roots in such hotspots is very large and corresponds to 15-25% of net assimilated plant C. As shown by autoradiography and phosphor imaging, these high amounts of available C are allocated mainly on root tips and so, produce small hotspots with properties completely different from the root free soil. The lifetime of the individual hotspots in the rhizosphere is short - not longer than 10 days. Thereafter, the released exudates are completely decomposed and partly utilized by rhizosphere microorganisms. The spatial extension of the rhizosphere based on diffusion of 14C labeled exudates released from roots is maximal 10-15 mm from the root surface. However, based on diffusion profiles of the main nutrients to the roots, the extension of the rhizosphere is much shorter and does not extend 2-3 mm. As shown by microbial growth kinetics after substrate addition, the rhizosphere microorganisms have 25% higher specific growth rates compared to that of the root-free soil. Wright-Hobbie approach reveals that maximal mineralization potential for organic substances increase in the rhizosphere for 2.5 times. All these changes induced by growing roots, lead to accelerated turnover of soil organic matter for 10% to more than 100%. Also the weathering of minerals is accelerated for 2-20 times in

  9. Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment

    PubMed Central

    Clark, Ian M.; Buchkina, Natalya; Jhurreea, Deveraj; Goulding, Keith W. T.; Hirsch, Penny R.

    2012-01-01

    Bacterial denitrification results in the loss of fertilizer nitrogen and greenhouse gas emissions as nitrous oxides, but ecological factors in soil influencing denitrifier communities are not well understood, impeding the potential for mitigation by land management. Communities vary in the relative abundance of the alternative dissimilatory nitrite reductase genes nirK and nirS, and the nitrous oxide reductase gene nosZ; however, the significance for nitrous oxide emissions is unclear. We assessed the influence of different long-term fertilization and cultivation treatments in a 160-year-old field experiment, comparing the potential for denitrification by soil samples with the size and diversity of their denitrifier communities. Denitrification potential was much higher in soil from an area left to develop from arable into woodland than from a farmyard manure-fertilized arable treatment, which in turn was significantly higher than inorganic nitrogen-fertilized and unfertilized arable plots. This correlated with abundance of nirK but not nirS, the least abundant of the genes tested in all soils, showing an inverse relationship with nirK. Most genetic variation was seen in nirK, where sequences resolved into separate groups according to soil treatment. We conclude that bacteria containing nirK are most probably responsible for the increased denitrification potential associated with nitrogen and organic carbon in this soil. PMID:22451109

  10. The Rhizosphere

    ERIC Educational Resources Information Center

    Feiro, Arthur D.

    1978-01-01

    The rhizosphere is the area directly surrounding the roots of a plant and an area of tremendous microbial growth. This article described techniques for studying this soil biome. Illustrations are included. (MA)

  11. Vegetation, soil and hydrology management influence denitrification activity and the composition of nirK-type denitrifier communities in a newly afforested riparian buffer.

    PubMed

    Boz, Bruno; Mizanur Rahman, Md; Bottegal, Mariangela; Basaglia, Marina; Squartini, Andrea; Gumiero, Bruna; Casella, Sergio

    2013-09-25

    Soil microbial community composition and activity could be affected by suitable manipulation of the environment they live in. If correctly applied such an approach could become a very effective way to remediate excess of chemicals. The concentration of nitrogen, especially nitrate deriving from agricultural managements, is generally found to increase in water flow. Therefore, by forcing the water flow through a buffer strip specifically designed and possibly afforested with suitable plant species, may result effective in reducing high nitrogen contents. The management of a riparian buffer may definitely affect the soil microbial activities, including denitrification, as well as the composition of the community. The present study reports on the changes occurred in terms of denitrifying microbial community composition, as compared to that of a neighbouring agricultural area, as a consequence of hydraulic management coupled to the suspension of farming practices and to the development of the woody and herbaceous vegetation. With this aim, denitrification was repeatedly measured and the data obtained were related to those deriving from a specific analysis of bacterial groups involved in denitrification. nirK, encoding for nitrite reductase, an enzyme essential for the conversion of nitrite to nitric oxide and considered the key step in the denitrification process, was chosen as the target gene. The main results obtained indicated that denitrification activity changes in riparian buffer as compared to agricultural soil and it is strongly influenced by carbon availability and soil depth. Although no significant differences on the community composition between superficial (0-15 cm) and medium (40-55 cm) layers were observed, the nirK-type denitrifier community was shown to significantly differ between riparian and agricultural soils in both surface and medium layers.

  12. Impact of Transgenic Wheat with wheat yellow mosaic virus Resistance on Microbial Community Diversity and Enzyme Activity in Rhizosphere Soil

    PubMed Central

    Xu, Jianhong; Du, Juan; Ji, Fang; Dong, Fei; Li, Xinhai; Shi, Jianrong

    2014-01-01

    The transgenic wheat line N12-1 containing the WYMV-Nib8 gene was obtained previously through particle bombardment, and it can effectively control the wheat yellow mosaic virus (WYMV) disease transmitted by Polymyxa graminis at turngreen stage. Due to insertion of an exogenous gene, the transcriptome of wheat may be altered and affect root exudates. Thus, it is important to investigate the potential environmental risk of transgenic wheat before commercial release because of potential undesirable ecological side effects. Our 2-year study at two different experimental locations was performed to analyze the impact of transgenic wheat N12-1 on bacterial and fungal community diversity in rhizosphere soil using polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE) at four growth stages (seeding stage, turngreen stage, grain-filling stage, and maturing stage). We also explored the activities of urease, sucrase and dehydrogenase in rhizosphere soil. The results showed that there was little difference in bacterial and fungal community diversity in rhizosphere soil between N12-1 and its recipient Y158 by comparing Shannon's, Simpson's diversity index and evenness (except at one or two growth stages). Regarding enzyme activity, only one significant difference was found during the maturing stage at Xinxiang in 2011 for dehydrogenase. Significant growth stage variation was observed during 2 years at two experimental locations for both soil microbial community diversity and enzyme activity. Analysis of bands from the gel for fungal community diversity showed that the majority of fungi were uncultured. The results of this study suggested that virus-resistant transgenic wheat had no adverse impact on microbial community diversity and enzyme activity in rhizosphere soil during 2 continuous years at two different experimental locations. This study provides a theoretical basis for environmental impact monitoring of transgenic wheat when the introduced gene is

  13. Impact of transgenic wheat with wheat yellow mosaic virus resistance on microbial community diversity and enzyme activity in rhizosphere soil.

    PubMed

    Wu, Jirong; Yu, Mingzheng; Xu, Jianhong; Du, Juan; Ji, Fang; Dong, Fei; Li, Xinhai; Shi, Jianrong

    2014-01-01

    The transgenic wheat line N12-1 containing the WYMV-Nib8 gene was obtained previously through particle bombardment, and it can effectively control the wheat yellow mosaic virus (WYMV) disease transmitted by Polymyxa graminis at turngreen stage. Due to insertion of an exogenous gene, the transcriptome of wheat may be altered and affect root exudates. Thus, it is important to investigate the potential environmental risk of transgenic wheat before commercial release because of potential undesirable ecological side effects. Our 2-year study at two different experimental locations was performed to analyze the impact of transgenic wheat N12-1 on bacterial and fungal community diversity in rhizosphere soil using polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE) at four growth stages (seeding stage, turngreen stage, grain-filling stage, and maturing stage). We also explored the activities of urease, sucrase and dehydrogenase in rhizosphere soil. The results showed that there was little difference in bacterial and fungal community diversity in rhizosphere soil between N12-1 and its recipient Y158 by comparing Shannon's, Simpson's diversity index and evenness (except at one or two growth stages). Regarding enzyme activity, only one significant difference was found during the maturing stage at Xinxiang in 2011 for dehydrogenase. Significant growth stage variation was observed during 2 years at two experimental locations for both soil microbial community diversity and enzyme activity. Analysis of bands from the gel for fungal community diversity showed that the majority of fungi were uncultured. The results of this study suggested that virus-resistant transgenic wheat had no adverse impact on microbial community diversity and enzyme activity in rhizosphere soil during 2 continuous years at two different experimental locations. This study provides a theoretical basis for environmental impact monitoring of transgenic wheat when the introduced gene is

  14. Melanogenic actinomycetes from rhizosphere soil-antagonistic activity against Xanthomonas oryzae and plant-growth-promoting traits.

    PubMed

    Muangham, Supattra; Pathom-Aree, Wasu; Duangmal, Kannika

    2015-02-01

    A total of 210 melanogenic actinomycetes were isolated from 75 rhizospheric soils using ISP6 and ISP7 agar supplemented with antifungal and antibacterial agents. Their morphological characteristics and the presence of ll-diaminopimelic acid in whole-cell hydrolyzates revealed that all isolates belonged to the genus Streptomyces. Their ability to inhibit the growth of 2 pathogenic rice bacteria, Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, was observed using the agar overlay method. The results indicated that 61.9% of the isolates could inhibit at least one of the tested rice pathogens. Among these, isolate TY68-3 showed the highest antibacterial activity and siderophore production. The 16S rRNA gene sequence analysis of 46 representative isolates revealed that isolates with high similarity to Streptomyces bungoensis were frequently found. The present study indicated the potential of melanogenic actinomycetes for use as biocontrol agents against X. oryzae as well as their diversity in rhizospheric soils.

  15. Aerobic Denitrifying Bacteria That Produce Low Levels of Nitrous Oxide

    PubMed Central

    Takaya, Naoki; Catalan-Sakairi, Maria Antonina B.; Sakaguchi, Yasushi; Kato, Isao; Zhou, Zhemin; Shoun, Hirofumi

    2003-01-01

    Most denitrifiers produce nitrous oxide (N2O) instead of dinitrogen (N2) under aerobic conditions. We isolated and characterized novel aerobic denitrifiers that produce low levels of N2O under aerobic conditions. We monitored the denitrification activities of two of the isolates, strains TR2 and K50, in batch and continuous cultures. Both strains reduced nitrate (NO3−) to N2 at rates of 0.9 and 0.03 μmol min−1 unit of optical density at 540 nm−1 at dissolved oxygen (O2) (DO) concentrations of 39 and 38 μmol liter−1, respectively. At the same DO level, the typical denitrifier Pseudomonas stutzeri and the previously described aerobic denitrifier Paracoccus denitrificans did not produce N2 but evolved more than 10-fold more N2O than strains TR2 and K50 evolved. The isolates denitrified NO3− with concomitant consumption of O2. These results indicated that strains TR2 and K50 are aerobic denitrifiers. These two isolates were taxonomically placed in the β subclass of the class Proteobacteria and were identified as P. stutzeri TR2 and Pseudomonas sp. strain K50. These strains should be useful for future investigations of the mechanisms of denitrifying bacteria that regulate N2O emission, the single-stage process for nitrogen removal, and microbial N2O emission into the ecosystem. PMID:12788710

  16. Spatial distribution of enzyme activities along the root and in the rhizosphere of different plants

    NASA Astrophysics Data System (ADS)

    Razavi, Bahar S.; Zarebanadkouki, Mohsen; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2015-04-01

    spatial distribution of enzyme activities in the rhizosphere hotspots. References Spohn, M., Kuzyakov, Y., 2013. Phosphorus mineralization can be driven by microbial need for carbon. Soil Biology & Biochemistry 61: 69-75

  17. Rhizosphere priming: a nutrient perspective.

    PubMed

    Dijkstra, Feike A; Carrillo, Yolima; Pendall, Elise; Morgan, Jack A

    2013-01-01

    Rhizosphere priming is the change in decomposition of soil organic matter (SOM) caused by root activity. Rhizosphere priming plays a crucial role in soil carbon (C) dynamics and their response to global climate change. Rhizosphere priming may be affected by soil nutrient availability, but rhizosphere priming itself can also affect nutrient supply to plants. These interactive effects may be of particular relevance in understanding the sustained increase in plant growth and nutrient supply in response to a rise in atmospheric CO2 concentration. We examined how these interactions were affected by elevated CO2 in two similar semiarid grassland field studies. We found that an increase in rhizosphere priming enhanced the release of nitrogen (N) through decomposition of a larger fraction of SOM in one study, but not in the other. We postulate that rhizosphere priming may enhance N supply to plants in systems that are N limited, but that rhizosphere priming may not occur in systems that are phosphorus (P) limited. Under P limitation, rhizodeposition may be used for mobilization of P, rather than for decomposition of SOM. Therefore, with increasing atmospheric CO2 concentrations, rhizosphere priming may play a larger role in affecting C sequestration in N poor than in P poor soils. PMID:23908649

  18. Rhizosphere priming: a nutrient perspective

    PubMed Central

    Dijkstra, Feike A.; Carrillo, Yolima; Pendall, Elise; Morgan, Jack A.

    2013-01-01

    Rhizosphere priming is the change in decomposition of soil organic matter (SOM) caused by root activity. Rhizosphere priming plays a crucial role in soil carbon (C) dynamics and their response to global climate change. Rhizosphere priming may be affected by soil nutrient availability, but rhizosphere priming itself can also affect nutrient supply to plants. These interactive effects may be of particular relevance in understanding the sustained increase in plant growth and nutrient supply in response to a rise in atmospheric CO2 concentration. We examined how these interactions were affected by elevated CO2 in two similar semiarid grassland field studies. We found that an increase in rhizosphere priming enhanced the release of nitrogen (N) through decomposition of a larger fraction of SOM in one study, but not in the other. We postulate that rhizosphere priming may enhance N supply to plants in systems that are N limited, but that rhizosphere priming may not occur in systems that are phosphorus (P) limited. Under P limitation, rhizodeposition may be used for mobilization of P, rather than for decomposition of SOM. Therefore, with increasing atmospheric CO2 concentrations, rhizosphere priming may play a larger role in affecting C sequestration in N poor than in P poor soils. PMID:23908649

  19. Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem.

    PubMed

    Das, Suvendu; Chou, Mon-Lin; Jean, Jiin-Shuh; Liu, Chia-Chuan; Yang, Huai-Jen

    2016-01-15

    Although rice cultivated under water-saturated conditions as opposed to submerged conditions has received considerable attention with regard to reducing As levels in rice grain, the rhizosphere microbiome potentially influencing As-biotransformation and bioavailability in a rice ecosystem has rarely been studied. In this study, the impacts of flooded, non-flooded and alternate wetting and drying (AWD) practices on rhizosphere bacterial composition and activities that could potentially impact As speciation and accumulation in rhizosphere soil and pore water, As fractions in rhizosphere soil and As speciation and distribution in plant parts were assessed. The results revealed that in addition to pore water As concentration, non-specifically sorbed As fraction, specifically sorbed As fraction and amorphous iron oxide bound As fraction in soil were bio-available to rice plants. In the flooded treatment, As(III) in the pore water was the predominant As species, accounting for 87.3-93.6% of the total As, whereas in the non-flooded and AWD treatments, As(V) was the dominant As species, accounting for 89.6-96.2% and 73.0-83.0%, respectively. The genera Ohtaekwangia, Geobacter, Anaeromyxobacter, Desulfuromonas, Desulfocapsa, Desulfobulbus, and Lacibacter were found in relatively high abundance in the flooded soil, whereas the genera Acinetobacter, Ignavibacterium, Thiobacillus, and Lysobacter were detected in relatively high abundance in the non-flooded soil. Admittedly, the decrease in As level in rice cultivated under the non-flooded and AWD conditions was mostly linked to a relatively high soil redox potential, low As(III) concentration in the soil pore water, a decrease in the relative abundance of As-, Fe- and sulfur-reducing bacteria and an increase in the relative abundance of As-, Fe- and sulfur-oxidizing bacteria in the rhizosphere soil of the rice. This study demonstrated that with substantial reduction in grain As levels and higher water productivity, AWD

  20. Survival of native Pseudomonas in soil and wheat rhizosphere and antagonist activity against plant pathogenic fungi.

    PubMed

    Fischer, Sonia E; Jofré, Edgardo C; Cordero, Paula V; Gutiérrez Mañero, Francisco J; Mori, Gladys B

    2010-03-01

    Survival of Pseudomonas sp. SF4c and Pseudomonas sp. SF10b (two plant-growth-promoting bacteria isolated from wheat rhizosphere) was investigated in microcosms. Spontaneous rifampicin-resistant mutants derived from these strains (showing both growth rate and viability comparable to the wild-strains) were used to monitor the strains in bulk soil and wheat rhizosphere. Studies were carried out for 60 days in pots containing non-sterile fertilized or non-fertilized soil. The number of viable cells of both mutant strains declined during the first days but then became established in the wheat rhizosphere at an appropriate cell density in both kinds of soil. Survival of the strains was better in the rhizosphere than in the bulk soil. Finally, the antagonism of Pseudomonas spp. against phytopatogenic fungi was evaluated in vitro. Both strains inhibited the mycelial growth (or the resistance structures) of some of the phytopathogenic fungi tested, though variation in this antagonism was observed in different media. This inhibition could be due to the production of extracellular enzymes, hydrogen cyanide or siderophores, signifying that these microorganisms might be applied in agriculture to minimize the utilization of chemical pesticides and fertilizers. PMID:20020326

  1. Quantitative molecular biology and gas flux measurements demonstrate soil treatment and depth affects on the distribution and activity of denitrifiers

    NASA Astrophysics Data System (ADS)

    Barrett, M. M.; Jahangir, M.; Cardenas, L.; Khalil, M.; Richards, K. R.; O'Flaherty, V.

    2010-12-01

    The growing industrialisation of agriculture has led to a dramatic increase in organic and inorganic nitrogen (N) fertiliser inputs to agro-ecosystems. This increase has had negative effects on the quality of water ecosystems and greenhouse gas emissions.The study objective was to quantify denitrification and denitrifying microorganisms, using real-time PCR assays of the nitrite reductase(nir) and nitrous oxide reductase(nos) functional gene copy concentrations (GCC g[soil]-1) in Irish agricultural surface and subsoils. Soil cores from 3 soil horizons (A:0-10 cm; B:45-55 cm; C:120-130cm) were amended with 3 alternate N- and C-source amendments (NO3-; NO3-+glucose-C; NO3-+Dissolved Organic Carbon (DOC). Real-time production of N2O and N2 was recorded by gas chromatography in a specialized He/O2 environment. N2O and Total Denitrification (TDN) (N2O+N2) production was generally greater in surface soil (2.052 mg/kg/d TDN) than in subsoils (0.120 mg/kg/d TDN). The abundance of denitrifying nirS, nirK (nir) and nos genes was higher in the surface soil, decreasing with soil depth, except in incubations amended with NO3- and DOC, where the carbon source directly positively affected gene copy numbers and fluxes of N2O and N2 production. C addition increased soil denitrification rates, and resulted in higher N2O/(N2O+N2) ratios in surface soil (0.39) than subsoils (0.005), indicating that the subsoil had higher potential for complete reduction of N2O to N2. In the subsoils, complete reduction of NO3- due to glucose-C and DOC addition was observed. Interestingly, at all 3 soil depths, lower nirK abundance (2.78 105 GCC) was recorded, compared to nirS (1.45 107 GCC), but the overall abundance of nir (S+K) i.e. (1.54 107GCC), corresponded with N2O emission fluxes (3.34 mg/kg/d) Statistical analysis indicates negative correlation between nirK GCC and N2O production, but a strong positive correlation was observed between nirS GCC and N2O. We therefore hypothesize that the

  2. Atypical Polyphosphate Accumulation by the Denitrifying Bacterium Paracoccus denitrificans

    PubMed Central

    Barak, Yoram; van Rijn, Jaap

    2000-01-01

    Polyphosphate accumulation by Paracoccus denitrificans was examined under aerobic, anoxic, and anaerobic conditions. Polyphosphate synthesis by this denitrifier took place with either oxygen or nitrate as the electron acceptor and in the presence of an external carbon source. Cells were capable of poly-β-hydroxybutyrate (PHB) synthesis, but no polyphosphate was produced when PHB-rich cells were incubated under anoxic conditions in the absence of an external carbon source. By comparison of these findings to those with polyphosphate-accumulating organisms thought to be responsible for phosphate removal in activated sludge systems, it is concluded that P. denitrificans is capable of combined phosphate and nitrate removal without the need for alternating anaerobic/aerobic or anaerobic/anoxic switches. Studies on additional denitrifying isolates from a denitrifying fluidized bed reactor suggested that polyphosphate accumulation is widespread among denitrifiers. PMID:10698794

  3. Role of chemotaxis in the ecology of denitrifiers

    NASA Technical Reports Server (NTRS)

    Kennedy, M. J.; Lawless, J. G.

    1985-01-01

    It has been recognized that the process of denitrification represents a major sequence in the nitrogen cycle. It involves the anaerobic reduction of nitrate or nitrite to nitrous oxide or elemental nitrogen. This process is responsible for significant losses of nitrogen from agricultural soils. Up to now, little attention has been paid to the ecology of the organisms responsible for denitrification. It is pointed out that chemotaxis would probably offer a strong competitive mechanism for denitrifiers, since chemotaxis would allow denitrifiers to actively reach nitrate by directed motility, rather than by random movement or diffusion of nitrate. The present investigation was initiated to examine the chemotactic responses of several denitrifiers to nitrate and nitrite. Attention is given to bacterial strains, culture media and cell preparation, chemotaxis assays, and competition experiments. It was found that several denitrifiers, including P. aeruginosa, P. fluorescens, and P. Stutzeri, were strongly attracted to NO3(-) and NO2(-).

  4. [Effects of combined application of biogas slurry and chemical fertilizer on winter wheat rhizosphere soil microorganisms and enzyme activities].

    PubMed

    Feng, Wei; Guan, Tao; Wang, Xiao-yu; Zhu, Yun-ji; Guo, Tian-cai

    2011-04-01

    This paper studied the effects of combined application of biogas slurry and chemical fertilizer under same N application rate on the quantities of bacteria, actinomycetes and fungi as well as the activities of urease, protease and catalase in winter wheat rhizosphere soil. With the growth of winter wheat, the quantities of test microorganisms and the activities of urease and catalase showed a trend of increasing after an initial decrease, while the protease activity showed an S-type change. Combined application of biogas slurry and chemical fertilizer increased the quantities of test microorganisms significantly, and improved the activities of soil urease and protease. Applying 50% biogas slurry N as basal plus 50% chemical N as topdressing and applying 25% biogas slurry N as basal plus 75% chemical N as topdressing had the best effect, while applying single conventional urea or biogas slurry had the worst effect. At all growth stages, the activity of soil catalase was the highest in treatments 25% biogas slurry N as basal plus 75% chemical N as topdressing and single biogas slurry, but had greater differences in other treatments among the growth stages. The results suggested that proper biogas slurry application combined with chemical fertilization could increase the microbial quantity and enzyme activities in winter wheat rhizosphere soil.

  5. Tissue-specific changes of glutamine synthetase activity in oats after rhizosphere infestation by Pseudomonas syringae pv. tabaci. Final report

    SciTech Connect

    Knight, T.J.; Temple, S.; Sengupta-Gopalan, C.

    1996-05-15

    Oats (Avena sativa L. lodi) tolerant of rhizosphere infestation by Pseudomonas syringae pv. tabaci when challenged by the pathogen experience tissue-specific alterations of ammonia assimilatory capabilities. Altered ammonia assimilatory potentials between root and leaf tissue result from selective inactivation of glutamine synthetase (GS) by the toxin Tabtoxinine-B-lactam (TBL). Root GS is sensitive and leaf GSs are resistant to TBL inactivation. With prolonged challenge by the pathogen root GS activity decreases but leaf GS specific activity increase. Higher leaf GS activity is due to decreased rates of degradation rather than increased GS synthesis. Higher leaf GS activity and elevated levels of GS polypeptide appear to result from a limited interaction between GS and TBL leading to the accumulation of a less active but more stable GS holoenzyme. Tolerant challenged oats besides surviving rhizosphere infestation, experience enhanced growth. A strong correlation exists between leaf GS activity and whole plant fresh weight, suggesting that tissue-specific changes in ammonia assimilatory capability provides the plant a more efficient mechanism for uptake and utilization of nitrogen.

  6. [Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

    PubMed

    Li, Min; Wu, Feng-zhi

    2014-12-01

    Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance. PMID:25876408

  7. [Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

    PubMed

    Li, Min; Wu, Feng-zhi

    2014-12-01

    Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance.

  8. Characterization and Fungal Inhibition Activity of Siderophore from Wheat Rhizosphere Associated Acinetobacter calcoaceticus Strain HIRFA32.

    PubMed

    Maindad, D V; Kasture, V M; Chaudhari, H; Dhavale, D D; Chopade, B A; Sachdev, D P

    2014-09-01

    Acinetobacter calcoaceticus HIRFA32 from wheat rhizosphere produced catecholate type of siderophore with optimum siderophore (ca. 92 % siderophore units) in succinic acid medium without FeSO4 at 28 °C and 24 h of incubation. HPLC purified siderophore appeared as pale yellow crystals with molecular weight [M(+1)] m/z 347.18 estimated by LCMS. The structure elucidated by (1)H NMR, (13)C NMR, HMQC, HMBC, NOESY and decoupling studies, revealed that siderophore composed of 2,3-dihydroxybenzoic acid with hydroxyhistamine and threonine as amino acid subunits. In vitro study demonstrated siderophore mediated mycelium growth inhibition (ca. 46.87 ± 0.5 %) of Fusarium oxysporum. This study accounts to first report on biosynthesis of acinetobactin-like siderophore by the rhizospheric strain of A. calcoaceticus and its significance in inhibition of F. oxysporum.

  9. [Effect of presowing treatment of spring wheat seeds with wheat germ agglutinin on the chlorophyll content, lectin activity in leaves and nitrogen-fixing capacity of rhizospheric microorganisms].

    PubMed

    Kyrychenko, O V

    2008-01-01

    The response of spring wheat and rhizospheric nitrogen-fixing micro-organisms to the presowing treatment of seeds by wheat germ agglutinin was investigated in conditions of green house experiments. It was shown, that exogenous lectin induced the metabolic changes in plants and caused an increase in chlorophyll content and activity of endogenous lectins in the leaves, as well as enhanced accumulation of plants biomass and nitrogen-fixing capacity of the rhizospheric micro-organisms. These results evidence for the considerable role of exogenous lectin as a regulator of growth and development of plants and activity of the nitrogen-fixing microorganisms. PMID:18710035

  10. Natural attenuation of perchlorate in denitrified groundwater.

    PubMed

    Robertson, William D; Roy, James W; Brown, Susan J; Van Stempvoort, Dale R; Bickerton, Greg

    2014-01-01

    Monitoring of a well-defined septic system groundwater plume and groundwater discharging to two urban streams located in southern Ontario, Canada, provided evidence of natural attenuation of background low level (ng/L) perchlorate (ClO4⁻) under denitrifying conditions in the field. The septic system site at Long Point contains ClO4⁻ from a mix of waste water, atmospheric deposition, and periodic use of fireworks, while the nitrate plume indicates active denitrification. Plume nitrate (NO3⁻ -N) concentrations of up to 103 mg/L declined with depth and downgradient of the tile bed due to denitrification and anammox activity, and the plume was almost completely denitrified beyond 35 m from the tile bed. The ClO4⁻ natural attenuation occurs at the site only when NO3⁻ -N concentrations are <0.3 mg/L, after which ClO4⁻ concentrations decline abruptly from 187 ± 202 to 11 ± 15 ng/L. A similar pattern between NO3⁻ -N and ClO4⁻ was found in groundwater discharging to the two urban streams. These findings suggest that natural attenuation (i.e., biodegradation) of ClO4⁻ may be commonplace in denitrified aquifers with appropriate electron donors present, and thus, should be considered as a remediation option for ClO4⁻ contaminated groundwater. PMID:23448242

  11. Natural attenuation of perchlorate in denitrified groundwater.

    PubMed

    Robertson, William D; Roy, James W; Brown, Susan J; Van Stempvoort, Dale R; Bickerton, Greg

    2014-01-01

    Monitoring of a well-defined septic system groundwater plume and groundwater discharging to two urban streams located in southern Ontario, Canada, provided evidence of natural attenuation of background low level (ng/L) perchlorate (ClO4⁻) under denitrifying conditions in the field. The septic system site at Long Point contains ClO4⁻ from a mix of waste water, atmospheric deposition, and periodic use of fireworks, while the nitrate plume indicates active denitrification. Plume nitrate (NO3⁻ -N) concentrations of up to 103 mg/L declined with depth and downgradient of the tile bed due to denitrification and anammox activity, and the plume was almost completely denitrified beyond 35 m from the tile bed. The ClO4⁻ natural attenuation occurs at the site only when NO3⁻ -N concentrations are <0.3 mg/L, after which ClO4⁻ concentrations decline abruptly from 187 ± 202 to 11 ± 15 ng/L. A similar pattern between NO3⁻ -N and ClO4⁻ was found in groundwater discharging to the two urban streams. These findings suggest that natural attenuation (i.e., biodegradation) of ClO4⁻ may be commonplace in denitrified aquifers with appropriate electron donors present, and thus, should be considered as a remediation option for ClO4⁻ contaminated groundwater.

  12. Toxicity of TiO₂ nanoparticle to denitrifying strain CFY1 and the impact on microbial community structures in activated sludge.

    PubMed

    Li, Dapeng; Li, Bin; Wang, Qiaoruo; Hou, Ning; Li, Chunyan; Cheng, Xiaosong

    2016-02-01

    The antibacterial activity of titanium dioxide nanoparticles (TiO2 NPs) is well described, but little is known of their impact on specific microbial functions such as denitrification, nor on microbial community structure. In this study, a denitrifier (named as Pseudomonas stutzeri CFY1), which was isolated from the activated sludge and could remove up to 111.68 mg/L of NO3(-)-N under aerobic conditions, was utilized to evaluate the influences of TiO2 NPs on its nitrogen removal ability and associated gene expression under aerobic conditions. The variations of the bacterial diversity of activated sludge were also observed. The results showed that antibacterial activity increased with increasing concentrations of TiO2 NPs. Increased production of reactive oxygen species was responsible for TiO2 NPs toxicity. An up-regulation of denitrification genes was observed with increasing concentrations of TiO2 NPs under aerobic conditions. Accordingly, denitrification by P. stutzeri was accelerated when the concentration of TiO2 NPs was increased to 50 mg/L. However, the denitrification of CFY1 was inhibited at low concentrations of TiO2 NPs (5-25 mg/L), indicating that assimilatory and dissimilatory denitrification were synchronized in P. stutzeri CFY1; the latter process plays a major role in denitrification. Further study of the community using 454 pyrosequencing showed that after 7 days of exposure to 50 mg/L TiO2 NPs, the microbial composition of the activated sludge was significantly different and had a lower diversity compared to the controls. PMID:26479452

  13. Effect of the nitrogen fertilizer type on the enzyme activity in the rhizosphere of calcic chernozem and soybean production

    NASA Astrophysics Data System (ADS)

    Emnova, E. E.; Daraban, O. V.; Bizgan, Ya. V.; Toma, S. I.; Vozian, V. I.; Iacobuta, M. D.

    2015-05-01

    Three varieties (Aura, Magie, and Indra) of soybean ( Glycine max [L.] Merr.) were grown in a small-plot experiment on a calcic chernozem with the application of two types of nitrogen fertilizers: ammonium nitrate (Nan) or carbamide (Nc). These fertilizers at the rate of 20 kg N/ha were applied before sowing together with potassium phosphate (60 kg P2O5/ha). The microbial nitrification capacity and the activity of enzymes related to the nitrogen cycle (urease and nitrate reductase) were measured in the rhizosphere (0-20 cm) at the stage of soybean flowering. It was determined that the biological (enzyme) activity of the calcic chernozem in the soybean rhizosphere was more intense on the plots with the Nan fertilizer than on the plots with the Nc fertilizer. The urease activity depended on the type of nitrogen fertilizer (Nan or Nc) under the conditions of soil water deficiency. In the soil under the Aura variety, the urease activity was significantly lower in the treatments with Nc application, and this was accompanied by a decrease in the crop yield. The nitrification capacity of the calcic chernozem was generally low; in the case of the Nc fertilizer, it was significantly lower than in the case of the Nan fertilizer. The nitrate reductase activity of the soil was also lower in the case of the Nc fertilizer. Each of the three soybean varieties had its own response to changes in the nitrogen nutrition aimed at improving the soybean tolerance to fluctuations in the soil water content during the growing season.

  14. Antimicrobial activities of rhizobacterial strains of Pseudomonas and Bacillus strains isolated from rhizosphere soil of carnation (Dianthus caryophyllus cv. Sunrise).

    PubMed

    Sharma, Sapna; Kaur, Mohinder

    2010-06-01

    Under the present study, an attempt was made to characterize rhizobacteria i.e. Pseudomonas and Bacillus species isolated from rhizosphere of carnation to evaluate their growth promoting effect on carnation so as to select and develop more efficient indigenous plant growth promoting and disease suppressing bioagents of specific soil type and specific plant type. Maximum strains of Pseudomonas and Bacillus sp. showed significant antimicrobial activities against most of the microorganisms tested. On the basis of in vitro antagonistic activities, the best strains were selected and used in field trial to study the influence of these strains on the growth of carnation. Results have shown marked effect on growth parameters and disease incidence has also been reduced significantly.

  15. New strigolactone analogs as plant hormones with low activities in the rhizosphere.

    PubMed

    Boyer, François-Didier; de Saint Germain, Alexandre; Pouvreau, Jean-Bernard; Clavé, Guillaume; Pillot, Jean-Paul; Roux, Amélie; Rasmussen, Amanda; Depuydt, Stephen; Lauressergues, Dominique; Frei Dit Frey, Nicolas; Heugebaert, Thomas S A; Stevens, Christian V; Geelen, Danny; Goormachtig, Sofie; Rameau, Catherine

    2014-04-01

    Strigolactones (SLs) are known not only as plant hormones, but also as rhizosphere signals for establishing symbiotic and parasitic interactions. The design of new specific SL analogs is a challenging goal in understanding the basic plant biology and is also useful to control plant architectures without favoring the development of parasitic plants. Two different molecules (23 (3'-methyl-GR24), 31 (thia-3'-methyl-debranone-like molecule)) already described, and a new one (AR36), for which the synthesis is presented, are biologically compared with the well-known GR24 and the recently identified CISA-1. These different structures emphasize the wide range of parts attached to the D-ring for the bioactivity as a plant hormone. These new compounds possess a common dimethylbutenolide motif but their structure varies in the ABC part of the molecules: 23 has the same ABC part as GR24, while 31 and AR36 carry, respectively, an aromatic ring and an acyclic carbon chain. Detailed information is given for the bioactivity of such derivatives in strigolactone synthesis or in perception mutant plants (pea rms1 and rms4, Arabidopsis max2 and, max4) for different hormonal functions along with their action in the rhizosphere on arbuscular mycorrhizal hyphal growth and parasitic weed germination.

  16. The Rhizosphere Zone: A Hot Spot of Microbial Activity and Methylmercury Production in Saltmarsh Sediments of San Francisco Bay, California

    NASA Astrophysics Data System (ADS)

    Windham-Myers, L.; Marvin-Dipasquale, M.; Voytek, M.; Kirshtein, J.; Krabbenhoft, D. P.; Agee, J. L.; Cox, M.; Kakouros, E.; Collins, J. N.; Yee, D.

    2008-12-01

    Tidal marshes of varying hydrology and salinity have been shown to have high rates of microbial methylmercury (MeHg) production, especially the periodically flooded, higher elevations which are densely vegetated with shallowly rooted plants. The specific influence of emergent wetland plants and their active rhizosphere (root zone) on mercury (Hg) biogeochemistry, however, is poorly understood. Seasonal and spatial patterns of Hg biogeochemistry were examined in 2005 and 2006 at three marshes along a salinity gradient of the Petaluma River, in Northern San Francisco Bay, California. In addition, to directly examine the influence of rhizosphere activity on MeHg production, a suite of devegetation experiments was conducted in 2006 within each marsh using paired vegetated and devegetated plots in two marsh subhabitats: poorly- drained interior sites and well-drained "edge" sites near slough channels. Surface sediment (0-2cm) was sampled in both April and August from these plots, as well as from 1st and 3rd order slough channels that were naturally free of vegetation. Vegetated marsh sites produced 3- to19-fold more MeHg than did slough sites, and MeHg production rates were greater in marsh interior sites compared to more oxic marsh "edge" sites. Microbial biomass (ng DNA gdrysed) was greater in vegetated marsh settings, compared to slough channels, and increased significantly between April and August at all marsh sites. Despite this seasonal increase in microbial biomass, MeHg concentrations and production rates decreased from April to August in vegetated surface sediments. Microbial indicators of methylation also decreased from April to August, including rates of microbial sulfate reduction and the abundance of iron- and sulfate- reducing bacterial DNA. Results from the devegetated plots suggest that root exudation of fermentative labile carbon to surface soils is responsible for the higher microbial biomass, and the higher relative abundance of iron- and sulfate

  17. Plant roots can actively regulate hydraulic redistribution by modifying the hydraulic properties of the rhizosphere using exudates

    NASA Astrophysics Data System (ADS)

    Ghezzehei, Teamrat; Bogie, Nathaniel; Albalasmeh, Ammar

    2015-04-01

    The phenomenon of hydraulic lift by roots of plants has been observed in many arid and semi-arid regions. The process involves water transfer from moist deep soil zone to shallow and dry layers, typically at night when transpiration is shut off. The widely held explanation is that hydraulic lift receives the strong water potential gradient created during the day when the plants are actively transpiring. However, it is not fully understood whether hydraulic lift is actively controlled by plants or it is a spontaneous response to the occurrence of pressure gradient. Here, we will present modeling study that demonstrates that plant roots can exert significant control on hydraulic redistribution via exudation and formation of rhizospheath. The model is based on results of potted experiments conducted by Nambiar in 1976 (Plant and Soil, 44:267-271), which have shown that plants are able to acquire essential micronutrients from very dry soil so long as water is available to the root system in sufficient quantity elsewhere. He also observed that the roots in the water-depleted zones exhibited evidence of substantial root exudation, which suggests that exudates are needed in order to provide moisture for mobilization and diffusion of nutrients in the dry regions. In addition, our own recent model-based research demonstrated that exudates play important role in facilitating water flow in otherwise dry rhizosphere region. Our models show that exudates facilitate the release of hydraulically lifted water to the rhizosphere by ensuring hydraulic continuity between the root walls and the surrounding dry soil. In addition, the high water retention capacity of root exudates permits the hydraulic conductivity to remain elevated even at low potential conditions. The results of this modeling study suggest that hydraulic lift is an actively controlled adaptation mechanism that allows plants to remain active during long dry spells by acquiring nutrients from the dry near surface soils

  18. Phosphorus removal and N₂O production in anaerobic/anoxic denitrifying phosphorus removal process: long-term impact of influent phosphorus concentration.

    PubMed

    Wang, Zhen; Meng, Yuan; Fan, Ting; Du, Yuneng; Tang, Jie; Fan, Shisuo

    2015-03-01

    This study was conducted to investigate the long-term impact of influent phosphorus concentration on denitrifying phosphorus removal and N2O production during denitrifying phosphorous removal process. The results showed that, denitrifying phosphate accumulating organisms (DPAOs) could become dominant populations quickly in anaerobic/anoxic SBR by providing optimum cultivating conditions, and the reactor performed well for denitrifying phosphorus removal. The influent phosphorus concentration significantly affected anaerobic poly-β-hydroxyalkanoates (PHA) synthesis, denitrifying phosphorus removal, and N2O production during the denitrifying phosphorus removal process. As the influent phosphorus concentration was more than 20 mg L(-1), the activity of DPAOs began to be inhibited due to the transformation of the available carbon source type. Meanwhile, N2O production was inhibited with the mitigation of anoxic NO2(-)-N accumulation. Adoption of a modified feeding could enhance denitrifying phosphorus removal and inhibit N2O production during denitrifying phosphorous removal processes.

  19. The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots.

    PubMed

    York, Larry M; Carminati, Andrea; Mooney, Sacha J; Ritz, Karl; Bennett, Malcolm J

    2016-06-01

    Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance. PMID:26980751

  20. Effect of phosphoric fertilizer and starter rates of nitrogen fertilizers on the phosphatase activity in the rhizosphere soil and nonlignified soybean roots under drought conditions

    NASA Astrophysics Data System (ADS)

    Emnova, E. E.; Daraban, O. V.; Bizgan, I. V.; Toma, S. I.

    2014-02-01

    In a small-plot field experiment, two soybean ( Glycine max L.) cultivars were grown on a calcareous chernozem under the drought conditions of 2012 with the preplanting application of simple superphosphate (Ps) at 60 kg/ha, urea (Nu) at 10 and 20 kg/ha, and ammonium nitrate (Nan) at 20 kg/ha. The phosphatase activity was measured in the rhizosphere soil (0- to 20-cm layer) and the fine nonlignified roots of soybean plants at the blossoming and pod-formation stages (the soil water content was 19 and 33% of the total water capacity, respectively). The maximum content of available phosphorus in the rhizosphere of both soybean cultivars (4.3-4.8 mg/100 g dry soil) was found at the simultaneous application of Ps and Nu20. Higher activities of the predominant phosphatases (alkaline phosphatase in the rhizosphere and acid phosphatase in the roots) were observed in the root-inhabited zone of the soil under the Indra cultivar compared to the Aura cultivar, which correlated with the lower content of available phosphorus in the rhizosphere soil (especially at the simultaneous application of Ps and Nu20) and the higher productivity of this cultivar in this treatment.

  1. A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury.

    PubMed

    Mathew, Dony Chacko; Ho, Ying-Ning; Gicana, Ronnie Gicaraya; Mathew, Gincy Marina; Chien, Mei-Chieh; Huang, Chieh-Chen

    2015-01-01

    Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg x kg(-1) mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg x kg(-1), 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury. PMID:25816328

  2. A Rhizosphere-Associated Symbiont, Photobacterium spp. Strain MELD1, and Its Targeted Synergistic Activity for Phytoprotection against Mercury

    PubMed Central

    Mathew, Dony Chacko; Ho, Ying-Ning; Gicana, Ronnie Gicaraya; Mathew, Gincy Marina; Chien, Mei-Chieh; Huang, Chieh-Chen

    2015-01-01

    Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg . kg-1 mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg . kg-1, 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury. PMID:25816328

  3. Respiration and respiratory enzyme activity in aerobic and anaerobic cultures of the marine denitrifying bacterium, Pseudomonas perfectomarinus

    NASA Astrophysics Data System (ADS)

    Packard, T. T.; Garfield, P. C.; Martinez, R.

    1983-03-01

    Oxygen consumption, nitrate reduction, respiratory electron transport activity, and nitrate reductase activity were measured in aerobic and anaerobic cultures of the marine bacterium, Pseudomonas perfectomarinus. The respiratory electron transport activity was closely correlated with oxygen consumption ( r = 0.98) in aerobic cultures and nearly as well correlated with nitrate reductase activity ( r = 0.91) and nitrate reduction ( r = 0.85) in anaerobic cultures. It was also well correlated with biomass in both aerobic ( r = 0.99) and anaerobic ( r = 0.94) cultures supporting the use of tetrazolium reduction as an index of living biomass. Time courses of nitrate and nitrate in the anaerobic cultures demonstrated that at nitrate concentrations above 1 mM, denitrification proceeds stepwise. Time courses of pH in anaerobic cultures revealed a rise from 7 to 8.5 during nitrite reduction indicating net proton utilization. This proton utilization is predicted by the stoichiometry of denitrification. Although the experiments were not under 'simulated in situ' conditions, the results are relevant to studies of denitrification, to bacterial ATP production, and to the respiratory activity of marine plankton in the ocean.

  4. Stepwise calibration of the activated sludge model no. 1 at a partially denitrifying large wastewater treatment plant.

    PubMed

    Fall, C; Espinosa-Rodriguez, M A; Flores-Alamo, N; van Loosdrecht, M C M; Hooijmans, C M

    2011-11-01

    Activated sludge modeling technology is maturing; however, currently, there exists a great need to increase its use in daily engineering practice worldwide. A good way for building the capacities of the practitioners is to promote good modeling practices and standardize the protocols. In this study, a systematic procedure was proposed to calibrate the Activated Sludge Model No. 1 (ASM1) at a large wastewater treatment plant, by which the model adequately predicted the quality of the effluent and the sludge quantities. A hydraulics model was set up and validated through a tracer test. The Vesilind settling constants were measured and combined with the default value of the flocculent zone settling parameter, to calibrate the clarifiers. A virtual anoxic tank was installed in the return activated sludge to mimic the denitrification occurring in the settlers. In ASM1, the calibrated parameters were only two influent chemical oxygen demand fractions and one kinetic constant (oxygen half-saturation coefficient).

  5. Screening and identification of aerobic denitrifiers

    NASA Astrophysics Data System (ADS)

    Shao, K.; Deng, H. M.; Chen, Y. T.; Zhou, H. J.; Yan, G. X.

    2016-08-01

    With the standards of the effluent quality more stringent, it becomes a quite serious problem for municipalities and industries to remove nitrogen from wastewater. Bioremediation is a potential method for the removal of nitrogen and other pollutants because of its high efficiency and low cost. Seven predominant aerobic denitrifiers were screened and characterized from the activated sludge in the CAST unit. Some of these strains removed 87% nitrate nitrogen at least. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as the genera of Ralstonia, Achromobacter, Aeromonas and Enterobacter.

  6. [Quorum sensing systems of regulation, synthesis of phenazine antibiotics, and antifungal (corrected) activity in rhizospheric bacterium Pseudomonas chlororaphis 449].

    PubMed

    Veselova, M a; Klein, Sh; Bass, I A; Lipasova, V A; Metlitskaia, A Z; Ovadis, M I; Chernin, L S; Khmel', I A

    2008-12-01

    Strain Pseudomonas chlororaphis 449, an antagonist of a broad spectrum of phytopathogenic microorganisms isolated from the maize rhizosphere, was shown to produce three phenazine antibiotics: phenazine-1-carboxylic acid (PCA), 2-hydroxylphenazine-1-carboxylic acid (2-OH-PCA), and 2-hydroxylphenazine (2-OH-PHZ). Two Quorum Sensing (QS) systems of regulation were identified: PhzIR and CsaI/R. Genes phzI and csaI were cloned and sequenced. Cells of strain 449 synthesize at least three types of AHL: N-butanoyl-L-homoserine lactone (C4-AHL), N-hexanoyl-L-homoserine lactone (C6-AHL), and N-(3-oxo-hexanoyl)-L-homoserine lactone (30C6-AHL). Transposon mutagenesis was used to generate mutants of strain 449 deficient in synthesis of phenazines, which carried inactivated phzA and phzB genes of the phenazine operon and gene phzO. Mutations phzA- and phzB-caused a drastic reduction in the antagonistic activity of bacteria toward phytopathogenic fungi. Both mutants lost the ability to protect cucumber and leguminous plants against phytopathogenic fungi Rhizoctonia solani and Sclerotinia sclerotiorum. These results suggest a significant role of phenazines in the antagonistic activity of P. chlororaphis 449. PMID:19178080

  7. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

    PubMed Central

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. PMID:26388851

  8. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.

    PubMed

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. PMID:26388851

  9. Effect of fungicides on plant growth promoting activities of phosphate solubilizing Pseudomonasputida isolated from mustard (Brassica compestris) rhizosphere.

    PubMed

    Ahemad, Munees; Khan, Mohammad Saghir

    2012-03-01

    This study was navigated to examine the effects of fungicide-stress on the activities of plant-growth-promoting rhizobacterium Pseudomonasputida with inherent phosphate solubilizing activity. The fungicide-tolerant and phosphate solubilizing P.putida strain PS9 was isolated from the mustard rhizosphere and tentatively identified following standard morphological, physiological and biochemical tests. To further consolidate the identity of the strain PS9, the 16S rDNA sequence analysis was performed. Following the BLAST program, the strain PS9 was identified as P.putida. In the presence of the varying concentrations (0-3200 μg mL(-1); at a two fold dilution interval) of four fungicides of different chemical families (tebuconazole, hexaconazole, metalaxyl and kitazin) amended in minimal salt agar medium, the P.putida strain PS9 showed a variable tolerance levels (1400-3200 μg mL(-1)) against the tested fungicides. The strain PS9 produced plant-growth-promoting (PGP) substances in significant amount in the absence of fungicides. In general, fungicides applied at the recommended, two and three times of the recommended rates, decreased the PGP attributes of P.putida the strain PS9 and affected the PGP activities in concentration-dependent manner. Fungicides at the recommended dose had minor reducing effect while the doses higher than the recommended dose significantly reduced the PGP activities (phosphate solubilization, salicylic acid, 2,3-dihydroxy benzoic acid, and indole-3-acetic acid production except exo-polysaccharides, hydrogen cyanate and ammonia production). Of the four fungicides, tebuconazole generally, showed maximum toxicity to the PGP activities of the strain PS9. This study inferred that fungicides must be examined in vitro for their possible adverse effects on soil micro flora before their application in agricultural fields. Moreover, the results also suggested the prerequisite of application of fungicide-tolerant PGPR strains as bioinoculants so that

  10. Development of micro push-pull tests to investigate rhizosphere processes

    NASA Astrophysics Data System (ADS)

    Knecht, K.; Nowack, B.; Schroth, M. H.; Schulin, R.

    2009-04-01

    The rhizosphere differs from the bulk soil due to the influence of the roots and the associated microbial and fungal activity. Most mechanistic rhizosphere research is undertaken in microcosms, often in the absence of soil. This has resulted in a fragmented understanding of many rhizospheric processes. The use of micro-techniques for the collection of soil solution enables non-destructive in situ observation of soil solution chemistry and aspects of soil solution biology. In conjunction with rhizoboxes that allow observing the development of root systems through a transparent front plate, micro-suction cups have been used successfully to collect soil solution adjacent to roots. This permits the determination of solute concentrations in the rhizosphere at high spatial and temporal resolution. Our goal now is to combine micro-suction cups with the technique of push-pull tests to create a miniaturized system that will be applicable to study reactions and exudation rates in the rhizosphere under conditions as undisturbed as possible. Push-pull tests have been used extensively on a larger scale for the investigation of chemical, physical and biological pollutant transport and degradation processes in aquifers. In a push-pull test, a solution containing reactive and non-reactive tracers is injected into an aquifer. After a defined time the test-solution/groundwater mixture is then extracted from the same location. As a first step we developed and tested a micro push-pull test procedure in sand-filled boxes under water-saturated conditions. We slowly injected about 250 μl solution and extracted 800 μl solution in increments of about 70 μl. As conservative tracers we used Acid Red 1 and bromide. The data were successfully modeled taking account of advection, dispersion and molecular diffusion. To study microbial degradation of exudates (e.g. citrate), push-pull tests were carried out in sand-filled boxes inoculated with denitrifying bacteria in the absence and presence

  11. Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms.

    PubMed

    Peralta, Ariane L; Matthews, Jeffrey W; Kent, Angela D

    2014-08-01

    Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.

  12. Soil microflora and enzyme activities in rhizosphere of Transgenic Bt cotton hybrid under different intercropping systems and plant protection schedules

    NASA Astrophysics Data System (ADS)

    Biradar, D. P.; Alagawadi, A. R.; Basavanneppa, M. A.; Udikeri, S. S.

    2012-04-01

    Field experiments were conducted over three rainy seasons of 2005-06 to 2007-08 on a Vertisol at Dharwad, Karnataka, India to study the effect of intercropping and plant protection schedules on productivity, soil microflora and enzyme activities in the rhizosphere of transgenic Bt cotton hybrid. The experiment consisted of four intercropping systems namely, Bt cotton + okra, Bt cotton + chilli, Bt cotton + onion + chilli and Bt cotton + redgram with four plant protection schedules (zero protection, protection for Bt cotton, protection for intercrop and protection for both crops). Observations on microbial populations and enzyme activities were recorded at 45, 90, 135 and 185 (at harvest) days after sowing (DAS). Averaged over years, Bt cotton + okra intercropping had significantly higher total productivity than Bt cotton + chilli and Bt cotton + redgram intercropping system and was similar to Bt cotton + chilli + onion intercropping system. With respect to plant protection schedules for bollworms, protection for both cotton and intercrops recorded significantly higher yield than the rest of the treatments. Population of total bacteria, fungi, actinomycetes, P-solubilizers, free-living N2 fixers as well as urease, phosphatase and dehydrogenase enzyme activities increased up to 135 days of crop growth followed by a decline. Among the intercropping systems, Bt cotton + chilli recorded significantly higher population of microorganisms and enzyme activities than other cropping systems. While Bt cotton with okra as intercrop recorded the least population of total bacteria and free-living N2 fixers as well as urease activity. Intercropping with redgram resulted in the least population of actinomycetes, fungi and P-solubilizers, whereas Bt cotton with chilli and onion recorded least activities of dehydrogenase and phosphatase. Among the plant protection schedules, zero protection recorded maximum population of microorganisms and enzyme activities. This was followed by the

  13. Methyl t-Butyl Ether Mineralization in Surface-Water Sediment Microcosms under Denitrifying Conditions

    USGS Publications Warehouse

    Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

    2001-01-01

    Mineralization of [U-14C] methyl t-butyl ether (MTBE) to 14CO2 without accumulation of t-butyl alcohol (TBA) was observed in surface-water sediment microcosms under denitrifying conditions. Methanogenic activity and limited transformation of MTBE to TBA were observed in the absence of denitrification. Results indicate that bed sediment microorganisms can effectively degrade MTBE to nontoxic products under denitrifying conditions.

  14. Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth.

    PubMed

    Jog, Rahul; Pandya, Maharshi; Nareshkumar, G; Rajkumar, Shalini

    2014-04-01

    The application of plant-growth-promoting rhizobacteria (PGPR) at field scale has been hindered by an inadequate understanding of the mechanisms that enhance plant growth, rhizosphere incompetence and the inability of bacterial strains to thrive in different soil types and environmental conditions. Actinobacteria with their sporulation, nutrient cycling, root colonization, bio-control and other plant-growth-promoting activities could be potential field bio-inoculants. We report the isolation of five rhizospheric and two root endophytic actinobacteria from Triticum aestivum (wheat) plants. The cultures exhibited plant-growth-promoting activities, namely phosphate solubilization (1916 mg l(-1)), phytase (0.68 U ml(-1)), chitinase (6.2 U ml(-1)), indole-3-acetic acid (136.5 mg l(-1)) and siderophore (47.4 mg l(-1)) production, as well as utilizing all the rhizospheric sugars under test. Malate (50-55 mmol l(-1)) was estimated in the culture supernatant of the highest phosphate solublizer, Streptomyces mhcr0816. The mechanism of malate overproduction was studied by gene expression and assays of key glyoxalate cycle enzymes - isocitrate dehydrogenase (IDH), isocitrate lyase (ICL) and malate synthase (MS). The significant increase in gene expression (ICL fourfold, MS sixfold) and enzyme activity (ICL fourfold, MS tenfold) of ICL and MS during stationary phase resulted in malate production as indicated by lowered pH (2.9) and HPLC analysis (retention time 13.1 min). Similarly, the secondary metabolites for chitinase-independent biocontrol activity of Streptomyces mhcr0817, as identified by GC-MS and (1)H-NMR spectra, were isoforms of pyrrole derivatives. The inoculation of actinobacterial isolate mhce0811 in T. aestivum (wheat) significantly improved plant growth, biomass (33%) and mineral (Fe, Mn, P) content in non-axenic conditions. Thus the actinobacterial isolates reported here were efficient PGPR possessing significant antifungal activity and may have potential field

  15. Cultivation of Denitrifying Bacteria: Optimization of Isolation Conditions and Diversity Study†

    PubMed Central

    Heylen, Kim; Vanparys, Bram; Wittebolle, Lieven; Verstraete, Willy; Boon, Nico; De Vos, Paul

    2006-01-01

    An evolutionary algorithm was applied to study the complex interactions between medium parameters and their effects on the isolation of denitrifying bacteria, both in number and in diversity. Growth media with a pH of 7 and a nitrogen concentration of 3 mM, supplemented with 1 ml of vitamin solution but not with sodium chloride or riboflavin, were the most successful for the isolation of denitrifiers from activated sludge. The use of ethanol or succinate as a carbon source and a molar C/N ratio of 2.5, 20, or 25 were also favorable. After testing of 60 different medium parameter combinations and comparison with each other as well as with the standard medium Trypticase soy agar supplemented with nitrate, three growth media were highly suitable for the cultivation of denitrifying bacteria. All evaluated isolation conditions were used to study the cultivable denitrifier diversity of activated sludge from a municipal wastewater treatment plant. One hundred ninety-nine denitrifiers were isolated, the majority of which belonged to the Betaproteobacteria (50.4%) and the Alphaproteobacteria (36.8%). Representatives of Gammaproteobacteria (5.6%), Epsilonproteobacteria (2%), and Firmicutes (4%) and one isolate of the Bacteroidetes were also found. This study revealed a much more diverse denitrifying community than that previously described in cultivation-dependent research on activated sludge. PMID:16597968

  16. Effects of Betaine Aldehyde Dehydrogenase-Transgenic Soybean on Phosphatase Activities and Rhizospheric Bacterial Community of the Saline-Alkali Soil

    PubMed Central

    Wang, Da-qing; Yu, Song

    2016-01-01

    The development of transgenic soybean has produced numerous economic benefits; however the potential impact of root exudates upon soil ecological systems and rhizospheric soil microbial diversity has also received intensive attention. In the present study, the influence of saline-alkali tolerant transgenic soybean of betaine aldehyde dehydrogenase on bacterial community structure and soil phosphatase during growth stages was investigated. The results showed that, compared with nontransgenic soybean as a control, the rhizospheric soil pH of transgenic soybean significantly decreased at the seedling stage. Compared to HN35, organic P content was 13.5% and 25.4% greater at the pod-filling stage and maturity, respectively. The acid phosphatase activity of SRTS was significantly better than HN35 by 12.74% at seedling, 14.03% at flowering, and 59.29% at podding, while alkaline phosphatase achieved maximum activity in the flowering stage and was markedly lower than HN35 by 13.25% at pod-filling. The 454 pyrosequencing technique was employed to investigate bacterial diversity, with a total of 25,499 operational taxonomic units (OTUs) obtained from the 10 samples. Notably, the effect of SRTS on microbial richness and diversity of rhizospheric soil was marked at the stage of podding and pod-filling. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla among all samples. Compared with HN35, the relative abundance of Proteobacteria was lower by 2.01%, 2.06%, and 5.28% at the stage of seedling, at pod-bearing, and at maturity. In genus level, the relative abundance of Gp6, Sphingomonas sp., and GP4 was significantly inhibited by SRTS at the stage of pod-bearing and pod-filling. PMID:27689079

  17. Effects of Betaine Aldehyde Dehydrogenase-Transgenic Soybean on Phosphatase Activities and Rhizospheric Bacterial Community of the Saline-Alkali Soil

    PubMed Central

    Wang, Da-qing; Yu, Song

    2016-01-01

    The development of transgenic soybean has produced numerous economic benefits; however the potential impact of root exudates upon soil ecological systems and rhizospheric soil microbial diversity has also received intensive attention. In the present study, the influence of saline-alkali tolerant transgenic soybean of betaine aldehyde dehydrogenase on bacterial community structure and soil phosphatase during growth stages was investigated. The results showed that, compared with nontransgenic soybean as a control, the rhizospheric soil pH of transgenic soybean significantly decreased at the seedling stage. Compared to HN35, organic P content was 13.5% and 25.4% greater at the pod-filling stage and maturity, respectively. The acid phosphatase activity of SRTS was significantly better than HN35 by 12.74% at seedling, 14.03% at flowering, and 59.29% at podding, while alkaline phosphatase achieved maximum activity in the flowering stage and was markedly lower than HN35 by 13.25% at pod-filling. The 454 pyrosequencing technique was employed to investigate bacterial diversity, with a total of 25,499 operational taxonomic units (OTUs) obtained from the 10 samples. Notably, the effect of SRTS on microbial richness and diversity of rhizospheric soil was marked at the stage of podding and pod-filling. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla among all samples. Compared with HN35, the relative abundance of Proteobacteria was lower by 2.01%, 2.06%, and 5.28% at the stage of seedling, at pod-bearing, and at maturity. In genus level, the relative abundance of Gp6, Sphingomonas sp., and GP4 was significantly inhibited by SRTS at the stage of pod-bearing and pod-filling.

  18. Stimulation of nitrogen removal in the rhizosphere of aquatic duckweed by root exudate components.

    PubMed

    Lu, Yufang; Zhou, Yingru; Nakai, Satoshi; Hosomi, Masaaki; Zhang, Hailin; Kronzucker, Herbert J; Shi, Weiming

    2014-03-01

    Plants can stimulate bacterial nitrogen (N) removal by secretion of root exudates that may serve as carbon sources as well as non-nutrient signals for denitrification. However, there is a lack of knowledge about the specific non-nutrient compounds involved in this stimulation. Here, we use a continuous root exudate-trapping system in two common aquatic duckweed species, Spirodela polyrrhiza (HZ1) and Lemna minor (WX3), under natural and aseptic conditions. An activity-guided bioassay using denitrifying bacterium Pseudomonas fluorescens showed that crude root exudates of the two species strongly enhanced the nitrogen-removal efficiency (NRE) of P. fluorescens (P < 0.05) under both conditions. Water-insoluble fractions (F) obtained under natural conditions stimulated NRE to a significant extent, promoting rates by about 30%. Among acidic, neutral and basic fractions, a pronounced stimulatory effect was also observed for the neutral fractions from HZ1 and WX3 under both conditions, whereas the acidic fractions from WX3 displayed an inhibitory effect. Analysis of the active fractions using gas chromatography/mass spectrometry (GC/MS) revealed that duckweed released fatty acid methyl esters and fatty acid amides, specifically: methyl hexadecanoate, methyl (Z)-7-hexadecenoate, methyl dodecanoate, methyl-12-hydroxystearate, oleamide, and erucamide. Methyl (Z)-7-hexadecenoate and erucamide emerged as the effective N-removal stimulants (maximum stimulation of 25.9 and 33.4%, respectively), while none of the other tested compounds showed stimulatory effects. These findings provide the first evidence for a function of fatty acid methyl esters and fatty acid amides in stimulating N removal of denitrifying bacteria, affording insight into the "crosstalk" between aquatic plants and bacteria in the rhizosphere.

  19. nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

    PubMed

    Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

    2016-10-01

    For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China. PMID:27311565

  20. Dynamics of the rhizosphere effect in soils

    NASA Astrophysics Data System (ADS)

    Yevdokimov, I. V.

    2013-06-01

    In a greenhouse experiment with continuous labeling of oat plants in a 13CO2 atmosphere, the ratios between different carbon and nitrogen pools in the rhizosphere and nonrhizosphere soil, i.e., the values of the rhizosphere factor R f , were determined. The mean values of the rhizosphere factor varied from 0.9 (the water-soluble nitrogen pool) to 4.6 (the pool of 13C-labeled dissolved organic carbon). We split the carbon and nitrogen pools into three groups depending on the mean R f value. Group I with high R f values (>2) included the most labile labeled organic carbon pools and the active component of the soil microbial biomass. Group II with the rhizosphere factor values 1 < R f < 2 included the more conservative pools of the total dissolved organic carbon and the microbial biomass in the soil. The only representative of group III ( R f < 1) was the water-soluble nitrogen pool. The dynamics of the rhizosphere factor had a maximum during the period of the rapid root growth rate (the tillering, booting, and earing stages) for most members of group I; a maximum during the period of the intensive root turnover (the milk ripeness and wax stages) was detected for the pools-representatives of group II. The dynamics of the rhizosphere factor for the soluble nitrogen had no prominent trends.

  1. Nitrogen removal from wastewater by anaerobic methane-driven denitrification in a lab-scale reactor: heterotrophic denitrifiers associated with denitrifying methanotrophs.

    PubMed

    He, Zhanfei; Wang, Jiaqi; Zhang, Xu; Cai, Chaoyang; Geng, Sha; Zheng, Ping; Xu, Xinhua; Hu, Baolan

    2015-12-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) is a newly discovered bioprocess that reduces nitrite to dinitrogen with methane as electron donor, which has promising potential to remove nitrogen from wastewater. In this work, a lab-scale sequencing batch reactor (SBR) was operated for 609 days with methane as the sole external electron donor. In the SBR, nitrite in synthetic wastewater was removed continuously; the final volumetric nitrogen removal rate was 12.22±0.02 mg N L(-1) day(-1) and the percentage of nitrogen removal was 98.5 ± 0.2 %. Microbial community analysis indicated that denitrifying methanotrophs dominated (60-70 %) the population of the final sludge. Notably, activity testing and microbial analysis both suggested that heterotrophic denitrifiers existed in the reactor throughout the operation period. After 609 days, the activity testing indicated the nitrogen removal percentage of heterotrophic denitrification was 17 ± 2 % and that of n-damo was 83 ± 2 %. A possible mutualism may be developed between the dominated denitrifying methanotrophs and the associated heterotrophs through cross-feed. Heterotrophs may live on the microbial products excreted by denitrifying methanotrophs and provide growth factors that are required by denitrifying methanotrophs.

  2. Nitrogen removal from wastewater by anaerobic methane-driven denitrification in a lab-scale reactor: heterotrophic denitrifiers associated with denitrifying methanotrophs.

    PubMed

    He, Zhanfei; Wang, Jiaqi; Zhang, Xu; Cai, Chaoyang; Geng, Sha; Zheng, Ping; Xu, Xinhua; Hu, Baolan

    2015-12-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) is a newly discovered bioprocess that reduces nitrite to dinitrogen with methane as electron donor, which has promising potential to remove nitrogen from wastewater. In this work, a lab-scale sequencing batch reactor (SBR) was operated for 609 days with methane as the sole external electron donor. In the SBR, nitrite in synthetic wastewater was removed continuously; the final volumetric nitrogen removal rate was 12.22±0.02 mg N L(-1) day(-1) and the percentage of nitrogen removal was 98.5 ± 0.2 %. Microbial community analysis indicated that denitrifying methanotrophs dominated (60-70 %) the population of the final sludge. Notably, activity testing and microbial analysis both suggested that heterotrophic denitrifiers existed in the reactor throughout the operation period. After 609 days, the activity testing indicated the nitrogen removal percentage of heterotrophic denitrification was 17 ± 2 % and that of n-damo was 83 ± 2 %. A possible mutualism may be developed between the dominated denitrifying methanotrophs and the associated heterotrophs through cross-feed. Heterotrophs may live on the microbial products excreted by denitrifying methanotrophs and provide growth factors that are required by denitrifying methanotrophs. PMID:26342737

  3. Antifungal Activity of Selected Indigenous Pseudomonas and Bacillus from the Soybean Rhizosphere

    PubMed Central

    León, M.; Yaryura, P. M.; Montecchia, M. S.; Hernández, A. I.; Correa, O. S.; Pucheu, N. L.; Kerber, N. L.; García, A. F.

    2009-01-01

    The purpose of this study was to isolate and select indigenous soil Pseudomonas and Bacillus bacteria capable of developing multiple mechanisms of action related to the biocontrol of phytopathogenic fungi affecting soybean crops. The screening procedure consisted of antagonism tests against a panel of phytopathogenic fungi, taxonomic identification, detection by PCR of several genes related to antifungal activity, in vitro detection of the antifungal products, and root colonization assays. Two isolates, identified and designated as Pseudomonas fluorescens BNM296 and Bacillus amyloliquefaciens BNM340, were selected for further studies. These isolates protected plants against the damping-off caused by Pythium ultimum and were able to increase the seedling emergence rate after inoculation of soybean seeds with each bacterium. Also, the shoot nitrogen content was higher in plants when seeds were inoculated with BNM296. The polyphasic approach of this work allowed us to select two indigenous bacterial strains that promoted the early development of soybean plants. PMID:20016811

  4. OPTIMIZING BTEX BIODEGRADATION UNDER DENITRIFYING CONDITIONS

    EPA Science Inventory

    Laboratory tests were conducted to determine optimum conditions for benzene, toluene, ethylbenzene, and xylene (collectively known as BTEX) biodegradation by aquifer microorganisms under denitrifying conditions. Microcosms, constructed with aquifer samples from Traverse City, Mic...

  5. Effects of low molecular-weight organic acids and dehydrogenase activity in rhizosphere sediments of mangrove plants on phytoremediation of polycyclic aromatic hydrocarbons.

    PubMed

    Wang, Yuanyuan; Fang, Ling; Lin, Li; Luan, Tiangang; Tam, Nora F Y

    2014-03-01

    This work evaluated the roles of the low-molecular-weight organic acids (LMWOAs) from root exudates and the dehydrogenase activity in the rhizosphere sediments of three mangrove plant species on the removal of mixed PAHs. The results showed that the concentrations of LMWOAs and dehydrogenase activity changed species-specifically with the levels of PAH contamination. In all plant species, the concentration of citric acid was the highest, followed by succinic acid. For these acids, succinic acid was positively related to the removal of all the PAHs except Chr. Positive correlations were also found between the removal percentages of 4-and 5-ring PAHs and all LMWOAs, except citric acid. LMWOAs enhanced dehydrogenase activity, which positively related to PAH removal percentages. These findings suggested that LMWOAs and dehydrogenase activity promoted the removal of PAHs. Among three mangrove plants, Bruguiera gymnorrhiza, the plant with the highest root biomass, dehydrogenase activity and concentrations of LMWOAs, was most efficient in removing PAHs. PMID:24287262

  6. Effects of low molecular-weight organic acids and dehydrogenase activity in rhizosphere sediments of mangrove plants on phytoremediation of polycyclic aromatic hydrocarbons.

    PubMed

    Wang, Yuanyuan; Fang, Ling; Lin, Li; Luan, Tiangang; Tam, Nora F Y

    2014-03-01

    This work evaluated the roles of the low-molecular-weight organic acids (LMWOAs) from root exudates and the dehydrogenase activity in the rhizosphere sediments of three mangrove plant species on the removal of mixed PAHs. The results showed that the concentrations of LMWOAs and dehydrogenase activity changed species-specifically with the levels of PAH contamination. In all plant species, the concentration of citric acid was the highest, followed by succinic acid. For these acids, succinic acid was positively related to the removal of all the PAHs except Chr. Positive correlations were also found between the removal percentages of 4-and 5-ring PAHs and all LMWOAs, except citric acid. LMWOAs enhanced dehydrogenase activity, which positively related to PAH removal percentages. These findings suggested that LMWOAs and dehydrogenase activity promoted the removal of PAHs. Among three mangrove plants, Bruguiera gymnorrhiza, the plant with the highest root biomass, dehydrogenase activity and concentrations of LMWOAs, was most efficient in removing PAHs.

  7. Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season

    PubMed Central

    Zhou, Dinggang; Xu, Liping; Gao, Shiwu; Guo, Jinlong; Luo, Jun; You, Qian; Que, Youxiong

    2016-01-01

    Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes. PMID:27014291

  8. Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

    SciTech Connect

    DeAngelis, K.M.; Lindow, S.E.; Firestone, M.K.

    2008-10-01

    Plant photosynthate fuels carbon-limited microbial growth and activity, resulting in increased rhizosphere nitrogen (N)-mineralization. Most soil organic N is macromolecular (chitin, protein, nucleotides); enzymatic depolymerization is likely rate-limiting for plant N accumulation. Analyzing Avena (wild oat) planted in microcosms containing sieved field soil, we observed increased rhizosphere chitinase and protease specific activities, bacterial cell densities, and dissolved organic nitrogen (DON) compared to bulk soil. Low-molecular weight DON (<3000 Da) was undetectable in bulk soil but comprised 15% of rhizosphere DON. Extracellular enzyme production in many bacteria requires quorum sensing (QS), cell-density dependent group behavior. Because proteobacteria are considered major rhizosphere colonizers, we assayed the proteobacterial QS signals acyl-homoserine lactones (AHLs), which were significantly increased in the rhizosphere. To investigate the linkage between soil signaling and N cycling, we characterized 533 bacterial isolates from Avena rhizosphere: 24% had chitinase or protease activity and AHL production; disruption of QS in 7 of 8 eight isolates disrupted enzyme activity. Many {alpha}-Proteobacteria were newly found with QS-controlled extracellular enzyme activity. Enhanced specific activities of N-cycling enzymes accompanied by bacterial density-dependent behaviors in rhizosphere soil gives rise to the hypothesis that QS could be a control point in the complex process of rhizosphere N-mineralization.

  9. Impact of Land Use Management and Soil Properties on Denitrifier Communities of Namibian Savannas.

    PubMed

    Braker, Gesche; Matthies, Diethart; Hannig, Michael; Brandt, Franziska Barbara; Brenzinger, Kristof; Gröngröft, Alexander

    2015-11-01

    We studied potential denitrification activity and the underlying denitrifier communities in soils from a semiarid savanna ecosystem of the Kavango region in NE Namibia to help in predicting future changes in N(2)O emissions due to continuing changes of land use in this region. Soil type and land use (pristine, fallow, and cultivated soils) influenced physicochemical characteristics of the soils that are relevant to denitrification activity and N(2)O fluxes from soils and affected potential denitrification activity. Potential denitrification activity was assessed by using the denitrifier enzyme activity (DEA) assay as a proxy for denitrification activity in the soil. Soil type and land use influenced C and N contents of the soils. Pristine soils that had never been cultivated had a particularly high C content. Cultivation reduced soil C content and the abundance of denitrifiers and changed the composition of the denitrifier communities. DEA was strongly and positively correlated with soil C content and was higher in pristine than in fallow or recently cultivated soils. Soil type and the composition of both the nirK- and nirS-type denitrifier communities also influenced DEA. In contrast, other soil characteristics like N content, C:N ratio, and pH did not predict DEA. These findings suggest that due to greater availability of soil organic matter, and hence a more effective N cycling, the natural semiarid grasslands emit more N(2)O than managed lands in Namibia.

  10. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

    PubMed Central

    Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J. R.; Sinninghe Damsté, Jaap S.; Villanueva, Laura

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments. PMID:27812355

  11. Isolation and characterization of genetic variability in bacteria with β-hemolytic and antifungal activity isolated from the rhizosphere of Medicago truncatula plants.

    PubMed

    Hernández-Salmerón, J E; Prieto-Barajas, C M; Valencia-Cantero, E; Moreno-Hagelsieb, G; Santoyo, G

    2014-07-04

    In the present study, we analyzed the frequency of hemolytic and antifungal activities in bacterial isolates from the rhizosphere of Medicago truncatula plants. Of the 2000 bacterial colonies, 96 showed β-hemolytic activities (frequency, 4.8 x 10(-2)). Hemolytic isolates were analyzed for their genetic diversity by using random amplification of polymorphic DNA, yielding 88 haplotypes. The similarity coefficient of Nei and Li showed a polymorphic diversity ranging from 0.3 to 1. Additionally, 8 of the hemolytic isolates showed antifungal activity toward plant pathogens, Diaporthe phaseolorum, Colletotrichum acutatum, Rhizoctonia solani, and Fusarium oxysporum. The 16S ribosomal sequencing analysis showed that antagonistic bacterial isolates corresponded to Bacillus subtilis (UM15, UM33, UM42, UM49, UM52, and UM91), Bacillus pumilus (UM24), and Bacillus licheniformis (UM88). The present results revealed a higher genetic diversity among hemolytic isolates compared to that of isolates with antifungal action.

  12. Denitrifier Community in the Oxygen Minimum Zone of a Subtropical Deep Reservoir

    PubMed Central

    Yu, Zheng; Yang, Jun; Liu, Lemian

    2014-01-01

    Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the narG gene recorded the highest abundance among the denitrifying genes (2.76×109 copies L−1 for DNA and 4.19×108 copies L−1 for RNA), and the lowest value was nosZ gene (7.56×105 copies L−1 for DNA and undetected for RNA). The RNA: DNA ratios indicated that narG gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the narG gene was dominated by Albidiferax, while nirS gene was dominated by Dechloromonas. The main OTU of nirK gene was Rhodopseudomonas palustris, but for norB and nosZ genes, they were Bacillus and Bradyrhizobium, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets. PMID:24664112

  13. Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir.

    PubMed

    Yu, Zheng; Yang, Jun; Liu, Lemian

    2014-01-01

    Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the narG gene recorded the highest abundance among the denitrifying genes (2.76×109 copies L-1 for DNA and 4.19×108 copies L-1 for RNA), and the lowest value was nosZ gene (7.56×105 copies L-1 for DNA and undetected for RNA). The RNA: DNA ratios indicated that narG gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the narG gene was dominated by Albidiferax, while nirS gene was dominated by Dechloromonas. The main OTU of nirK gene was Rhodopseudomonas palustris, but for norB and nosZ genes, they were Bacillus and Bradyrhizobium, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets.

  14. Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

    PubMed Central

    Lopes, Lucas D.; Pereira e Silva, Michele de Cássia; Andreote, Fernando D.

    2016-01-01

    The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization. PMID:27610108

  15. Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization.

    PubMed

    Lopes, Lucas D; Pereira E Silva, Michele de Cássia; Andreote, Fernando D

    2016-01-01

    The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization. PMID:27610108

  16. Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

    PubMed Central

    Lopes, Lucas D.; Pereira e Silva, Michele de Cássia; Andreote, Fernando D.

    2016-01-01

    The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.

  17. Geochemical control of microbial Fe(III) reduction potential in wetlands: Comparison of the rhizosphere to non-rhizosphere soil

    USGS Publications Warehouse

    Weiss, J.V.; Emerson, D.; Megonigal, J.P.

    2004-01-01

    We compared the reactivity and microbial reduction potential of Fe(III) minerals in the rhizosphere and non-rhizosphere soil to test the hypothesis that rapid Fe(III) reduction rates in wetland soils are explained by rhizosphere processes. The rhizosphere was defined as the area immediately adjacent to a root encrusted with Fe(III)-oxides or Fe plaque, and non-rhizosphere soil was 0.5 cm from the root surface. The rhizosphere had a significantly higher percentage of poorly crystalline Fe (66??7%) than non-rhizosphere soil (23??7%); conversely, non-rhizosphere soil had a significantly higher proportion of crystalline Fe (50??7%) than the rhizosphere (18??7%, P<0.05 in all cases). The percentage of poorly crystalline Fe(III) was significantly correlated with the percentage of FeRB (r=0.76), reflecting the fact that poorly crystalline Fe(III) minerals are labile with respect to microbial reduction. Abiotic reductive dissolution consumed about 75% of the rhizosphere Fe(III)-oxide pool in 4 h compared to 23% of the soil Fe(III)-oxide pool. Similarly, microbial reduction consumed 75-80% of the rhizosphere pool in 10 days compared to 30-40% of the non-rhizosphere soil pool. Differences between the two pools persisted when samples were amended with an electron-shuttling compound (AQDS), an Fe(III)-reducing bacterium (Geobacter metallireducens), and organic carbon. Thus, Fe(III)-oxide mineralogy contributed strongly to differences in the Fe(III) reduction potential of the two pools. Higher amounts of poorly crystalline Fe(III) and possibly humic substances, and a higher Fe(III) reduction potential in the rhizosphere compared to the non-rhizosphere soil, suggested the rhizosphere is a site of unusually active microbial Fe cycling. The results were consistent with previous speculation that rapid Fe cycling in wetlands is due to the activity of wetland plant roots. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

  18. Micro push-pull tests under unsaturated conditions: A new technique to investigate rhizosphere processes

    NASA Astrophysics Data System (ADS)

    Knecht, Kajsa; Nowack, Bernd; Schroth, Martin Herbert; Schulin, Rainer

    2010-05-01

    The rhizosphere differs in many aspects from the bulk soil. The growth of roots or uptake of water by plants alters directly the physical properties of the rhizosphere. Root activities such as absorption, respiration or exudation can change many chemical properties in the rhizosphere. The aim of this study is to develop a new micro technique that allows studying rhizosphere processes at microscopic scale in-situ. Our goal is to combine the technique of micro-suction cups with that of push-pull tests, creating a miniaturized system that is applicable to study not only concentrations but also reactions and exudation rates in the rhizosphere under conditions as undisturbed as possible. Push-pull tests have been used extensively on a larger scale for the investigation of chemical, physical and biological pollutant transport and transformation processes in aquifers. In a push-pull test, a solution containing reactive and non-reactive tracers is injected into a porous medium. After a defined time the test-solution/soilwater mixture is then extracted back from the same location. At first, we developed and validated a micro push-pull test procedure that works under saturated conditions in sand-filled boxes. It was possible to inject about 250 µl solution and extract 850 µl solution at a low and constant injection/extraction rate. The data were analyzed and successfully modeled considering advection, dispersion and molecular diffusion. Tracer concentrations of the extracted solution could be very well predicted without using any adjustable parameters. Molecular diffusion was found to play a significant role in determining the shape of the extraction curve. In a subsequent experiment using this technique, it was possible to quantify the degradation rate of citrate injected into a water-saturated, sand-filled box inoculated with denitrifying bacteria. The new technique thus proved to be an adequate tool to observe local biodegradation processes in situ. Now, we are

  19. Nitrification and denitrifying phosphorus removal in an upright continuous flow reactor.

    PubMed

    Reza, Maryam; Alvarez Cuenca, Manuel

    2016-01-01

    Simultaneous nitrification and denitrifying phosphorus removal was achieved in a single-sludge continuous flow bioreactor. The upright bioreactor was aligned with a biomass fermenter (BF) and operated continuously for over 350 days. This study revealed that unknown bacteria of the Saprospiraceae class may have been responsible for the successful nutrient removal in this bioreactor. The successive anoxic-aerobic stages of the bioreactor with upright alignment along with a 60 L BF created a unique ecosystem for the growth of nitrifier, denitrifiers, phosphorus accumulating organisms and denitrifying phosphorus accumulating organisms. Furthermore, total nitrogen to chemical oxygen demand (COD) ratio and total phosphorus to COD ratio of 0.6 and 0.034, respectively, confirmed the comparative advantages of this advanced nutrient removal process relative to both sequencing batch reactors and activated sludge processes. The process yielded 95% nitrogen removal and over 90% phosphorus removal efficiencies. PMID:27148710

  20. Nitrification and denitrifying phosphorus removal in an upright continuous flow reactor.

    PubMed

    Reza, Maryam; Alvarez Cuenca, Manuel

    2016-01-01

    Simultaneous nitrification and denitrifying phosphorus removal was achieved in a single-sludge continuous flow bioreactor. The upright bioreactor was aligned with a biomass fermenter (BF) and operated continuously for over 350 days. This study revealed that unknown bacteria of the Saprospiraceae class may have been responsible for the successful nutrient removal in this bioreactor. The successive anoxic-aerobic stages of the bioreactor with upright alignment along with a 60 L BF created a unique ecosystem for the growth of nitrifier, denitrifiers, phosphorus accumulating organisms and denitrifying phosphorus accumulating organisms. Furthermore, total nitrogen to chemical oxygen demand (COD) ratio and total phosphorus to COD ratio of 0.6 and 0.034, respectively, confirmed the comparative advantages of this advanced nutrient removal process relative to both sequencing batch reactors and activated sludge processes. The process yielded 95% nitrogen removal and over 90% phosphorus removal efficiencies.

  1. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    EPA Science Inventory

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213).

    Seagrasses ...

  2. Tillage Management and Seasonal Effects on Denitrifier Community Abundance, Gene Expression and Structure over Winter.

    PubMed

    Tatti, Enrico; Goyer, Claudia; Burton, David L; Wertz, Sophie; Zebarth, Bernie J; Chantigny, Martin; Filion, Martin

    2015-10-01

    Tillage effects on denitrifier communities and nitrous oxide (N2O) emissions were mainly studied during the growing season. There is limited information for the non-growing season, especially in northern countries where winter has prolonged periods with sub-zero temperatures. The abundance and structure of the denitrifier community, denitrification gene expression and N2O emissions in fields under long-term tillage regimes [no-tillage (NT) vs conventional tillage (CT)] were assessed during two consecutive winters. NT exerted a positive effect on nirK and nosZ denitrifier abundance in both winters compared to CT. Moreover, the two contrasting managements had an opposite influence on nirK and nirS RNA/DNA ratios. Tillage management resulted in different denitrifier community structures during both winters. Seasonal changes were observed in the abundance and the structure of denitrifiers. Interestingly, the RNA/DNA ratios were greater in the coldest months for nirK, nirS and nosZ. N2O emissions were not influenced by management but changed over time with two orders of magnitude increase in the coldest month of both winters. In winter of 2009-2010, emissions were mainly as N2O, whereas in 2010-2011, when soil temperatures were milder due to persistent snow cover, most emissions were as dinitrogen. Results indicated that tillage management during the growing season induced differences in denitrifier community structure that persisted during winter. However, management did not affect the active cold-adapted community structure.

  3. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil.

    PubMed

    Yin, Chang; Fan, Fenliang; Song, Alin; Cui, Peiyuan; Li, Tingqiang; Liang, Yongchao

    2015-07-01

    Preferable inorganic fertilization over the last decades has led to fertility degradation of black soil in Northeast China. However, how fertilization regimes impact denitrification and its related bacterial community in this soil type is still unclear. Here, taking advantage of a suit of molecular ecological tools in combination of assaying the potential denitrification (DP), we explored the variation of activity, community structure, and abundance of nirS and nirK denitrifiers under four different fertilization regimes, namely no fertilization control (N0M0), organic pig manure (N0M1), inorganic fertilization (N1M0), and combination of inorganic fertilizer and pig manure (N1M1). The results indicated that organic fertilization increased DP, but inorganic fertilization had no impacts. The increase of DP was mirrored by the shift of nirS denitrifiers' community structure but not by that of nirK denitrifiers'. Furthermore, the change of DP coincided with the variation of abundances of both denitrifiers. Shifts of community structure and abundance of nirS and nirK denitrifiers were correlated with the change of soil pH, total nitrogen (TN), organic matter (OM), C:P, total phosphorus (TP), and available phosphorus (Olsen P). Our results suggest that the change of DP under these four fertilization regimes was closely related to the shift of denitrifying bacteria communities resulting from the variation of properties in the black soil tested.

  4. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil.

    PubMed

    Yin, Chang; Fan, Fenliang; Song, Alin; Cui, Peiyuan; Li, Tingqiang; Liang, Yongchao

    2015-07-01

    Preferable inorganic fertilization over the last decades has led to fertility degradation of black soil in Northeast China. However, how fertilization regimes impact denitrification and its related bacterial community in this soil type is still unclear. Here, taking advantage of a suit of molecular ecological tools in combination of assaying the potential denitrification (DP), we explored the variation of activity, community structure, and abundance of nirS and nirK denitrifiers under four different fertilization regimes, namely no fertilization control (N0M0), organic pig manure (N0M1), inorganic fertilization (N1M0), and combination of inorganic fertilizer and pig manure (N1M1). The results indicated that organic fertilization increased DP, but inorganic fertilization had no impacts. The increase of DP was mirrored by the shift of nirS denitrifiers' community structure but not by that of nirK denitrifiers'. Furthermore, the change of DP coincided with the variation of abundances of both denitrifiers. Shifts of community structure and abundance of nirS and nirK denitrifiers were correlated with the change of soil pH, total nitrogen (TN), organic matter (OM), C:P, total phosphorus (TP), and available phosphorus (Olsen P). Our results suggest that the change of DP under these four fertilization regimes was closely related to the shift of denitrifying bacteria communities resulting from the variation of properties in the black soil tested. PMID:25715781

  5. Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

    PubMed Central

    Thomas, François; Cébron, Aurélie

    2016-01-01

    Over the last decades, understanding of the effects of plants on soil microbiomes has greatly advanced. However, knowledge on the assembly of rhizospheric communities in aged-contaminated industrial soils is still limited, especially with regard to transcriptionally active microbiomes and their link to the quality or quantity of carbon sources. We compared the short-term (2–10 days) dynamics of bacterial communities and potential PAH-degrading bacteria in bare or ryegrass-planted aged-contaminated soil spiked with phenanthrene, put in relation with dissolved organic carbon (DOC) sources and polycyclic aromatic hydrocarbon (PAH) pollution. Both resident and active bacterial communities (analyzed from DNA and RNA, respectively) showed higher species richness and smaller dispersion between replicates in planted soils. Root development strongly favored the activity of Pseudomonadales within the first 2 days, and of members of Actinobacteria, Caulobacterales, Rhizobiales, and Xanthomonadales within 6–10 days. Plants slowed down the dissipation of phenanthrene, while root exudation provided a cocktail of labile substrates that might preferentially fuel microbial growth. Although the abundance of PAH-degrading genes increased in planted soil, their transcription level stayed similar to bare soil. In addition, network analysis revealed that plants induced an early shift in the identity of potential phenanthrene degraders, which might influence PAH dissipation on the long-term. PMID:26903971

  6. Anaerobic ferrous oxidation by heterotrophic denitrifying enriched culture.

    PubMed

    Wang, Ru; Zheng, Ping; Xing, Ya-Juan; Zhang, Meng; Ghulam, Abbas; Zhao, Zhi-Qing; Li, Wei; Wang, Lan

    2014-05-01

    Heterotrophic denitrifying enriched culture (DEC) from a lab-scale high-rate denitrifying reactor was discovered to perform nitrate-dependent anaerobic ferrous oxidation (NAFO). The DEC was systematically investigated to reveal their denitrification activity, their NAFO activity, and the predominant microbial population. The DEC was capable of heterotrophic denitrification with methanol as the electron donor, and autotrophic denitrification with ferrous salt as the electron donor named NAFO. The conversion ratios of ferrous-Fe and nitrate-N were 87.41 and 98.74 %, and the consumption Fe/N ratio was 2.3:1 (mol/mol). The maximum reaction velocity and half saturation constant of Fe were 412.54 mg/(l h) and 8,276.44 mg/l, and the counterparts of N were 20.87 mg/(l h) and 322.58 mg/l, respectively. The predominant bacteria were Hyphomicrobium, Thauera, and Flavobacterium, and the predominant archaea were Methanomethylovorans, Methanohalophilus, and Methanolobus. The discovery of NAFO by heterotrophic DEC is significant for the development of wastewater treatment and the biogeochemical iron cycle and nitrogen cycle. PMID:24619339

  7. Arbuscular mycorrhiza mediates glomalin-related soil protein production and soil enzyme activities in the rhizosphere of trifoliate orange grown under different P levels.

    PubMed

    Wu, Qiang-Sheng; Li, Yan; Zou, Ying-Ning; He, Xin-Hua

    2015-02-01

    Glomalin-related soil protein (GRSP) is beneficial to soil and plants and is affected by various factors. To address whether mycorrhizal-induced GRSP and relevant soil enzymes depend on external P levels, a pot study evaluated effects of the arbuscular mycorrhizal fungus (AMF) Funneliformis mosseae on GRSP production and soil enzyme activities. Three GRSP categories, as easily-extractable GRSP (EE-GRSP), difficultly-extractable GRSP (DE-GRSP), and total (EE-GRSP + DE-GRSP) GRSP (T-GRSP), were analyzed, together with five enzyme activities (β-glucosidase, catalase, peroxidase, phosphatase, polyphenol oxidase) in the rhizosphere of trifoliate orange (Poncirus trifoliata) grown under 0, 3, and 30 mM KH2PO4 in a sand substrate. After 4 months, root AM colonization and substrate hyphal length decreased with increasing P levels. Shoot, root, and total biomass production was significantly increased by AM colonization, regardless of P levels, but more profound under 0 mM P than under 30 mM KH2PO4. In general, production of these three GRSP categories under 0 or 30 mM KH2PO4 was similar in non-mycorrhizosphere but decreased in mycorrhizosphere. Mycorrhization significantly increased the production of EE-GRSP, DE-GRSP and T-GRSP, soil organic carbon (SOC), and activity of substrate β-glucosidase, catalase, peroxidase, and phosphatase, but decreased polyphenol oxidase activity, irrespective of P levels. Production of EE-GRSP, DE-GRSP, and T-GRSP significantly positively correlated with SOC and β-glucosidase, catalase, and peroxidase activity, negatively with polyphenol oxidase activity, but not with hyphal length or phosphatase activity. These results indicate that AM-mediated production of GRSP and relevant soil enzyme activities may not depend on external P concentrations.

  8. Changes of microbial activities and soil aggregation in rhizosphere soil of lettuce plants by drought and the possible influence of inoculation with AM fungi and/or PGPR

    NASA Astrophysics Data System (ADS)

    Kohler, J.; Caravaca, F.; Roldán, A.

    2009-04-01

    The effect of different arbuscular mycorrhizal (AM) fungi, Glomus intraradices (Schenk & Smith) or Glomus mosseae (Nicol & Gerd.) Gerd. & Trappe, and plant growth-promoting rhizobacteria (PGPR) (Pseudomonas mendocina Palleroni), alone or in combination, on structural stability and microbial activity in the rhizosphere soil of Lactuca sativa L. was assessed under well-watered conditions and two levels of drought. Desiccation caused an increase in aggregate stability and water-soluble and total carbohydrates but there were no significant differences among treated soils and the control soil. The glomalin-related soil protein (GRSP) levels in both the <2 mm and 0.2-4 mm soil fractions increased with medium water stress, whereas under severe water stress they did not differ with respect to those of well-watered soils. The values of GRSP in soils inoculated with PGPR and AM fungi were higher than in the control or fertilised soil under well-watered and severe-drought conditions, while under medium-drought conditions all soils showed similar GRSP values. Soils inoculated with AM fungi and PGPR generally presented higher dehydrogenase and phosphatase activities than the control soil, independent of the water regime.

  9. Dynamic Metabolic Modeling of Denitrifying Bacterial Growth: The Cybernetic Approach

    SciTech Connect

    Song, Hyun-Seob; Liu, Chongxuan

    2015-06-29

    Denitrification is a multistage reduction process converting nitrate ultimately to nitrogen gas, carried out mostly by facultative bacteria. Modeling of the denitrification process is challenging due to the complex metabolic regulation that modulates sequential formation and consumption of a series of nitrogen oxide intermediates, which serve as the final electron acceptors for denitrifying bacteria. In this work, we examined the effectiveness and accuracy of the cybernetic modeling framework in simulating the growth dynamics of denitrifying bacteria in comparison with kinetic models. In four different case studies using the literature data, we successfully simulated diauxic and triauxic growth patterns observed in anoxic and aerobic conditions, only by tuning two or three parameters. In order to understand the regulatory structure of the cybernetic model, we systematically analyzed the effect of cybernetic control variables on simulation accuracy. The results showed that the consideration of both enzyme synthesis and activity control through u- and v-variables is necessary and relevant and that uvariables are of greater importance in comparison to v-variables. In contrast, simple kinetic models were unable to accurately capture dynamic metabolic shifts across alternative electron acceptors, unless an inhibition term was additionally incorporated. Therefore, the denitrification process represents a reasonable example highlighting the criticality of considering dynamic regulation for successful metabolic modeling.

  10. Sulfide oxidation under chemolithoautotrophic denitrifying conditions.

    PubMed

    Cardoso, Ricardo Beristain; Sierra-Alvarez, Reyes; Rowlette, Pieter; Flores, Elias Razo; Gómez, Jorge; Field, Jim A

    2006-12-20

    Chemolithoautotrophic denitrifying microorganisms oxidize reduced inorganic sulfur compounds coupled to the reduction of nitrate as an electron acceptor. These denitrifiers can be applied to the removal of nitrogen and/or sulfur contamination from wastewater, groundwater, and gaseous streams. This study investigated the physiology and kinetics of chemolithotrophic denitrification by an enrichment culture utilizing hydrogen sulfide, elemental sulfur, or thiosulfate as electron donor. Complete oxidation of sulfide to sulfate was observed when nitrate was supplemented at concentrations equal or exceeding the stoichiometric requirement. In contrast, sulfide was only partially oxidized to elemental sulfur when nitrate concentrations were limiting. Sulfide was found to inhibit chemolithotrophic sulfoxidation, decreasing rates by approximately 21-fold when the sulfide concentration increased from 2.5 to 10.0 mM, respectively. Addition of low levels of acetate (0.5 mM) enhanced denitrification and sulfate formation, suggesting that acetate was utilized as a carbon source by chemolithotrophic denitrifiers. The results of this study indicate the potential of chemolithotrophic denitrification for the removal of hydrogen sulfide. The sulfide/nitrate ratio can be used to control the fate of sulfide oxidation to either elemental sulfur or sulfate.

  11. Plant growth promoting bacteria from Crocus sativus rhizosphere.

    PubMed

    Ambardar, Sheetal; Vakhlu, Jyoti

    2013-12-01

    Present study deals with the isolation of rhizobacteria and selection of plant growth promoting bacteria from Crocus sativus (Saffron) rhizosphere during its flowering period (October-November). Bacterial load was compared between rhizosphere and bulk soil by counting CFU/gm of roots and soil respectively, and was found to be ~40 times more in rhizosphere. In total 100 bacterial isolates were selected randomly from rhizosphere and bulk soil (50 each) and screened for in-vitro and in vivo plant growth promoting properties. The randomly isolated bacteria were identified by microscopy, biochemical tests and sequence homology of V1-V3 region of 16S rRNA gene. Polyphasic identification categorized Saffron rhizobacteria and bulk soil bacteria into sixteen different bacterial species with Bacillus aryabhattai (WRF5-rhizosphere; WBF3, WBF4A and WBF4B-bulk soil) common to both rhizosphere as well as bulk soil. Pseudomonas sp. in rhizosphere and Bacillus and Brevibacterium sp. in the bulk soil were the predominant genera respectively. The isolated rhizobacteria were screened for plant growth promotion activity like phosphate solubilization, siderophore and indole acetic acid production. 50 % produced siderophore and 33 % were able to solubilize phosphate whereas all the rhizobacterial isolates produced indole acetic acid. The six potential PGPR showing in vitro activities were used in pot trial to check their efficacy in vivo. These bacteria consortia demonstrated in vivo PGP activity and can be used as PGPR in Saffron as biofertilizers.This is the first report on the isolation of rhizobacteria from the Saffron rhizosphere, screening for plant growth promoting bacteria and their effect on the growth of Saffron plant.

  12. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages.

    PubMed

    Shi, Shengjing; Nuccio, Erin E; Shi, Zhou J; He, Zhili; Zhou, Jizhong; Firestone, Mary K

    2016-08-01

    While interactions between roots and microorganisms have been intensively studied, we know little about interactions among root-associated microbes. We used random matrix theory-based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat (Avena fatua) over two seasons in greenhouse microcosms. Rhizosphere networks were substantially more complex than those in surrounding soils, indicating the rhizosphere has a greater potential for interactions and niche-sharing. Network complexity increased as plants grew, even as diversity decreased, highlighting that community organisation is not captured by univariate diversity. Covariations were predominantly positive (> 80%), suggesting that extensive mutualistic interactions may occur among rhizosphere bacteria; we identified quorum-based signalling as one potential strategy. Putative keystone taxa often had low relative abundances, suggesting low-abundance taxa may significantly contribute to rhizosphere function. Network complexity, a previously undescribed property of the rhizosphere microbiome, appears to be a defining characteristic of this habitat. PMID:27264635

  13. [Concentrations of different carbon and nitrogen fractions in rhizosphere and non-rhizosphere soils of typical plant species in mountainous area of southern Ningxia, Northwest China].

    PubMed

    Zhu, Qiu-lian; Xing, Xiao-yi; Cheng, Man; Xue, Zhi-jing; An, Shao-shan

    2013-04-01

    Taking the rhizosphere and non-rhizosphere soils of five typical plants Agropyron cristatum, Artemisia frigida, Pseudoraphis bungeana, Thymus mongolicus, and Artemisia sacrorum in a mountainous area of southern Ningxia as test objects, this paper studied their C and N forms contents. The C and N forms contents in the rhizosphere and non-rhizosphere soils differed with plant species. In the rhizosphere soil of A. sacrorum, the C content was the highest, with the total soil organic C (TOC), light fraction organic C (LFOC), and heavy fraction organic C contents being 22.94, 1.95, and 20. 88 g kg-1, respectively. In the rhizosphere soil of P. bungeana, the N content was the highest, with the total N (TN), mineralizable N (MN), and available N contents being 2.05 g kg-1 , 23.73 mg kg-1, and 11.99 mg kg-1 , respectively. In the rhizosphere soil of A. frigida, the LFOC/TOC and MN/TN ratios were the highest, which benefited the C and N transformed into more active forms. Light fraction organic C and mineralizable N could be used as the sensitive indicators of plant habitat change. For the five plant species, the contents of different C and N forms in the rhizosphere soil were generally higher than those in the non-rhizosphere soil. PMID:23898655

  14. [Performance Recoverability of Denitrifying Granular Sludge Under the Stressing Effect of Nanoscale Zero-valent Iron].

    PubMed

    Wang, Fan-fan; Qian, Fei-yue; Shen, Yao-liang; Wang, Jian-fang; Zhang, Yue-ru; Liu, Guo-xun

    2016-04-15

    To explore the potential stressing effect of nanoscale zero-valent iron (nZVI) on denitrifying granular sludge (DGS), the evolution of DGS denitrifying performance under different C/N ratios was investigated in this study, by carrying out batch tests of eight successive periods with the nZVI shock-loading. The results showed that the specific denitrification rate of µ value decreased when the nZVI dosage was higher than 5 mg · L⁻¹. Meanwhile, a positive correlation between the inhibition ratio (IR) of µ value and substrate C/N ratios or nZVI dosage was observed. When the nZVI dosage reached 100 mg · L⁻¹, both extracellular protein and polysaccharides concentrations decreased obviously. It would be beneficial to promote the recovery of DGS denitrifying activity and reduce the COD demanding to remove unit mass of nitrate, by increasing external carbon source with C/N ratios of higher than 4. On the basis of Freundlich and Langmuir adsorption isotherms, when higher C/N ratio was provided, stronger bioadsorption of nZVI would be achieved. During the recovery period, a significant improvement of DCS denitrifying performance under the high C/N ratio was expected, due to the continuous washout of total iron in sludge phase (Qe), while the µ value would reach or approach the one of the control group when Qe was lower than 0.4 mg · g⁻¹. PMID:27548972

  15. [Rhizosphere enhanced remediation of petroleum contaminated soil].

    PubMed

    Lu, Mang; Zhang, Zhong-zhi; Sun, Shan-shan; Qiao, Wei; Liu, Xiao

    2009-12-01

    The effects of growing tall fescue on the biodegradation of hydrocarbons was studied in laboratory scale pots. Degradation of hydrocarbons as well as microbial counts, soil fluorescein diacetate activity, catalase activity and dehydrogenase activity were determined. The results showed that, in the rhizosphere soil system, total petroleum hydrocarbons disappeared faster than that in unvegetated pots soil. After 10 weeks, 11.8% and 27.4% of spiked petroleum hydrocarbons disappeared from the bulk and rhizosphere soils respectively. Abiotic loss of petroleum hydrocarbons by evaporation was of minor significance in the test. The microbial plate counts and soil enzyme activities were significantly higher in the rhizosphere than in the bulk soil. Petroleum compounds had significant effect on fluorescein diacetate hydrolyzing activity. Vegetation resulted in significantly greater first-order decay constants compared to the unvegetated control. Oxygenated polycyclic aromatic hydrocarbons that were present in the soil were generally degraded more slowly than the parent compounds, suggesting that they were formed during the treatment or that they are more persistent. Four oxidation products of polycyclic aromatic hydrocarbons, 1-acenaphthenone, 9-fluorenone, anthraquinone, and benzfluorenone were found at significantly higher concentrations at the end of the study.

  16. Microbial activity and water-soluble trace element species in the rhizosphere of spring wheat (Triticum aestivum cv. USU-Perigee).

    PubMed

    Turmel, Marie-Claude; Courchesne, François; Cloutier-Hurteau, Benoît

    2011-04-01

    The influence of microbial activity on the concentration and speciation of trace elements (TEs) was assessed in a study on the bioavailability of TEs for edible plants. A growth chamber experiment with spring wheat (Triticum aestivum cv. USU-Perigee) was conducted and the bulk (Bk) and the rhizosphere (Rz) soil components were collected at maturity. A characterization of the microbial activity and population was made by measuring the microbial biomass, enzymes (acid phosphatase, arylsulfatase, dehydrogenase and urease) and 16S rDNA DGGE profiles. In soil water extracts, major solutes (H(+), Ca, Mg, Na, NH(4), K, Cl, NO(3), SO(4), total N, DON and DOC) and trace elements (Al, As, Cd, Ce, Cr, Cu, Fe, Pb, Tl, and Zn) including monomeric Al species, free Cu(2+) and labile Zn were determined. The partition of the variation indicated that 12.1% of the distribution of TEs in the Bk soil was significantly and exclusively explained by chemical properties while this value was less than 0.1% for the Rz soil. To the contrary, microbial properties contributed significantly to 12.3% of the distribution of TEs in the Rz soil whereas it explained less than 0.1% for the Bk soil. Detailed redundancy analyses identified several potential mechanisms (e.g. weathering of primary mineral, solubilisation of sesquioxides, bacterial effect on the redox status) explaining the fate of TEs in the Bk and Rz soils. This study revealed that microbial activity is strongly associated to the speciation of trace elements in the Rz of edible plants and points to some microbial processes influencing TE speciation.

  17. Rhizosphere microflora of plants used for the phytoremediation of bitumen-contaminated soil.

    PubMed

    Muratova, Anna; Hübner, Thorsten; Narula, Neeru; Wand, Helmut; Turkovskaya, Olga; Kuschk, Peter; Jahn, Richard; Merbach, Wolfgang

    2003-01-01

    The microbial communities and their degradative potential in rhizospheres of alfalfa (Medicago sativa) and reed (Phragmites australis) and in unplanted soil in response to bitumen contamination of soil were studied in pot experiments. According to the results of fluorescence microscopy, over a period of 27 months, bitumen contamination of soil reduced the total number of microorganisms more significantly (by 75%) in unplanted than in rhizosphere soil (by 42% and 7% for reed and alfalfa, respectively) and had various effects on some important physiological groups of microorganisms such as actinomycetes as well as nitrogen-fixing, nitrifying, denitrifying, ammonifying, phosphate-solubilizing, sulphur-oxidizing, cellulolytic and hydrocarbon-degrading microorganisms. The changes in the physiological structure of the microbial community under bitumen contamination were found to hinge on not merely the presence of plants but also their type. It was noted that the rhizosphere microflora of alfalfa was less inhibited by hydrocarbon pollution and had a higher degradative potential than the rhizosphere microflora of reed. PMID:12906388

  18. Low molecular carbon compounds present in the rhizosphere control denitrification kinetics

    NASA Astrophysics Data System (ADS)

    Herold, M.; Morley, N.; Baggs, E.

    2013-12-01

    Nitrogen and carbon cycles play key roles in plant-microbe interactions in soils. Carbon is supplied by plants to microbes in the form of root exudates which includes both high and low molecular compounds. Nitrogen in turn is taken up by plants and rhizosphere microbes metabolise nitrogen compounds in several biochemical pathways. The conversion of nitrogen compounds to volatile products in the process of denitrification leads to increasing amounts of nitrous oxide (N2O) in the atmosphere. Nitrous oxide is a potent greenhouse gas and increasing emissions of N2O through intense agriculture have lead to intensified research to find possible mitigation strategies to reduce N2O production from soil. In our study we show the effect of low molecular carbon compounds, typically found in root exudates, on the dynamics of denitrification as well as the dose response effect of the single compounds. The hypothesis was tested that different compound groups change the kinetics of the different reduction steps in the biochemical pathway of denitrification, which results in lower N2O production. Experiments were performed in soil-microcosms using 15N labelling approaches to monitor denitrification products . Microcosms were maintained as slurries in order to create oxygen limiting conditions, which favours denitrification. Carbon dioxide and N2O were monitored throughout the experiments and on three destructive sampling days NO3, NO2, NO and 15N-N2 were measured. Results showed that the denitrification process was differently affected by amino acids and organic acids with higher denitrification activity observed in the presence of organic acids. The dynamics of the single reduction steps were time dependent which indicates that substrate availability plays an important role in soil microbial activity. We concluded that the activity of denitrifiers are significantly influenced by different carbon compounds, and that further studies on the effects of the composition of root

  19. Soil Type Dependent Rhizosphere Competence and Biocontrol of Two Bacterial Inoculant Strains and Their Effects on the Rhizosphere Microbial Community of Field-Grown Lettuce

    PubMed Central

    Schreiter, Susanne; Sandmann, Martin; Smalla, Kornelia; Grosch, Rita

    2014-01-01

    Rhizosphere competence of bacterial inoculants is assumed to be important for successful biocontrol. Knowledge of factors influencing rhizosphere competence under field conditions is largely lacking. The present study is aimed to unravel the effects of soil types on the rhizosphere competence and biocontrol activity of the two inoculant strains Pseudomonas jessenii RU47 and Serratia plymuthica 3Re4-18 in field-grown lettuce in soils inoculated with Rhizoctonia solani AG1-IB or not. Two independent experiments were carried out in 2011 on an experimental plot system with three soil types sharing the same cropping history and weather conditions for more than 10 years. Rifampicin resistant mutants of the inoculants were used to evaluate their colonization in the rhizosphere of lettuce. The rhizosphere bacterial community structure was analyzed by denaturing gradient gel electrophoresis of 16S rRNA gene fragments amplified from total community DNA to get insights into the effects of the inoculants and R. solani on the indigenous rhizosphere bacterial communities. Both inoculants showed a good colonization ability of the rhizosphere of lettuce with more than 106 colony forming units per g root dry mass two weeks after planting. An effect of the soil type on rhizosphere competence was observed for 3Re4-18 but not for RU47. In both experiments a comparable rhizosphere competence was observed and in the presence of the inoculants disease symptoms were either significantly reduced, or at least a non-significant trend was shown. Disease severity was highest in diluvial sand followed by alluvial loam and loess loam suggesting that the soil types differed in their conduciveness for bottom rot disease. Compared to effect of the soil type of the rhizosphere bacterial communities, the effects of the pathogen and the inoculants were less pronounced. The soil types had a surprisingly low influence on rhizosphere competence and biocontrol activity while they significantly affected

  20. Soil type dependent rhizosphere competence and biocontrol of two bacterial inoculant strains and their effects on the rhizosphere microbial community of field-grown lettuce.

    PubMed

    Schreiter, Susanne; Sandmann, Martin; Smalla, Kornelia; Grosch, Rita

    2014-01-01

    Rhizosphere competence of bacterial inoculants is assumed to be important for successful biocontrol. Knowledge of factors influencing rhizosphere competence under field conditions is largely lacking. The present study is aimed to unravel the effects of soil types on the rhizosphere competence and biocontrol activity of the two inoculant strains Pseudomonas jessenii RU47 and Serratia plymuthica 3Re4-18 in field-grown lettuce in soils inoculated with Rhizoctonia solani AG1-IB or not. Two independent experiments were carried out in 2011 on an experimental plot system with three soil types sharing the same cropping history and weather conditions for more than 10 years. Rifampicin resistant mutants of the inoculants were used to evaluate their colonization in the rhizosphere of lettuce. The rhizosphere bacterial community structure was analyzed by denaturing gradient gel electrophoresis of 16S rRNA gene fragments amplified from total community DNA to get insights into the effects of the inoculants and R. solani on the indigenous rhizosphere bacterial communities. Both inoculants showed a good colonization ability of the rhizosphere of lettuce with more than 10(6) colony forming units per g root dry mass two weeks after planting. An effect of the soil type on rhizosphere competence was observed for 3Re4-18 but not for RU47. In both experiments a comparable rhizosphere competence was observed and in the presence of the inoculants disease symptoms were either significantly reduced, or at least a non-significant trend was shown. Disease severity was highest in diluvial sand followed by alluvial loam and loess loam suggesting that the soil types differed in their conduciveness for bottom rot disease. Compared to effect of the soil type of the rhizosphere bacterial communities, the effects of the pathogen and the inoculants were less pronounced. The soil types had a surprisingly low influence on rhizosphere competence and biocontrol activity while they significantly affected

  1. Evaluation of the environmental specificity of Fluorescence In Situ Hybridization (FISH) using Fluorescence-Activated Cell Sorting (FACS) of probe (PSE1284)-positive cells extracted from rhizosphere soil.

    PubMed

    Gougoulias, Christos; Shaw, Liz J

    2012-12-01

    We explicitly tested for the first time the 'environmental specificity' of traditional 16S rRNA-targeted Fluorescence In Situ Hybridization (FISH) through comparison of the bacterial diversity actually targeted in the environment with the diversity that should be exactly targeted (i.e. without mismatches) according to in silico analysis. To do this, we exploited advances in modern Flow Cytometry that enabled improved detection and therefore sorting of sub-micron-sized particles and used probe PSE1284 (designed to target Pseudomonads) applied to Lolium perenne rhizosphere soil as our test system. The 6-carboxyfluorescein (6-FAM)-PSE1284-hybridized population, defined as displaying enhanced green fluorescence in Flow Cytometry, represented 3.51±1.28% of the total detected population when corrected using a nonsense (NON-EUB338) probe control. Analysis of 16S rRNA gene libraries constructed from Fluorescence Activated Cell Sorted-recovered fluorescent populations (n=3), revealed that 98.5% (Pseudomonas spp. comprised 68.7% and Burkholderia spp. 29.8%) of the total sorted population was specifically targeted as evidenced by the homology of the 16S rRNA sequences to the probe sequence. In silico evaluation of probe PSE1284 with the use of RDP-10 probeMatch justified the existence of Burkholderia spp. among the sorted cells. The lack of novelty in Pseudomonas spp. sequences uncovered was notable, probably reflecting the well-studied nature of this functionally important genus. To judge the diversity recorded within the FACS-sorted population, rarefaction and DGGE analysis were used to evaluate, respectively, the proportion of Pseudomonas diversity uncovered by the sequencing effort and the representativeness of the Nycodenz(®) method for the extraction of bacterial cells from soil.

  2. Effect of different plant species on nutrient removal and rhizospheric microorganisms distribution in horizontal-flow constructed wetlands.

    PubMed

    Meng, Panpan; Hu, Wenrong; Pei, Haiyan; Hou, Qingjie; Ji, Yan

    2014-01-01

    Three macrophyte species, Phragmites australis, Arundo donax L., and Typha latifolia L. have been separately grown in a horizontal-flow (HF) constructed wetland (CW) fed with domestic wastewater to investigate effects of plant species on nutrient removal and rhizospheric microorganisms. All the three mesocosms have been in operation for eight months under the loading rates of 1.14 g Nm(-2) d(-1) and 0.014gP m(-2) d(-1). Appropriately 34-43% phosphorus (P) was removed in HF CWs, and no distinct difference was found among the plants. In the growing season, A. donax L. removed 31.19 gm(-2) of nitrogen (N), followed by P. australis (29.96 g m(-2)), both of which were significantly higher than T. latifolia L. (7.21 g m(-2). Depending on the species, plants absorbed 1.73-7.15% of the overall N, and 0.06-0.56% of the P input. At least 10 common dominant microorganisms were found in the rhizosphere of all the three plants, and 6 of the 10 kinds of bacteria had close relationship with denitrifying bacteria, implying that denitrifiers were dominant microorganism distributed in rhizosphere of wetland plants.

  3. Effects of earthworms and substrate on diversity and abundance of denitrifying genes (nirS and nirK) and denitrifying rate during rural domestic wastewater treatment.

    PubMed

    Wang, Longmian; Zhang, Yimin; Luo, Xingzhang; Zhang, Jibiao; Zheng, Zheng

    2016-07-01

    This study investigated the performance of an ecological filter (EF) and vermifiltration (VF) system, the effects of substrate and earthworms on the diversity and abundance of denitrifying genes coding for nitrite (nirS and nirK) reductases and on denitrifying rate, and the factors influencing denitrification. The majority of organic matter, ammonia nitrogen and total nitrogen from sewage was removed by the soil layer in both reactors, and their total removal efficiencies increased in VF compared with those in EF. Additionally, substrate in the reactors significantly influenced the Shannon diversity index and abundance of nirS and nirK, as well as the denitrifying rate. However, the earthworms only significantly influenced nirS diversity. Furthermore, evaluation of the factors controlling denitrification implied that increasing NH3-N availability, diversity and abundance of nirS and nirK or decreasing available NO3-N might be responsible for the enhanced denitrification activity obtained using VF for rural domestic wastewater treatment. PMID:27099942

  4. Effects of earthworms and substrate on diversity and abundance of denitrifying genes (nirS and nirK) and denitrifying rate during rural domestic wastewater treatment.

    PubMed

    Wang, Longmian; Zhang, Yimin; Luo, Xingzhang; Zhang, Jibiao; Zheng, Zheng

    2016-07-01

    This study investigated the performance of an ecological filter (EF) and vermifiltration (VF) system, the effects of substrate and earthworms on the diversity and abundance of denitrifying genes coding for nitrite (nirS and nirK) reductases and on denitrifying rate, and the factors influencing denitrification. The majority of organic matter, ammonia nitrogen and total nitrogen from sewage was removed by the soil layer in both reactors, and their total removal efficiencies increased in VF compared with those in EF. Additionally, substrate in the reactors significantly influenced the Shannon diversity index and abundance of nirS and nirK, as well as the denitrifying rate. However, the earthworms only significantly influenced nirS diversity. Furthermore, evaluation of the factors controlling denitrification implied that increasing NH3-N availability, diversity and abundance of nirS and nirK or decreasing available NO3-N might be responsible for the enhanced denitrification activity obtained using VF for rural domestic wastewater treatment.

  5. The influence of nitrogen fertilization on the magnitude of rhizosphere effects

    NASA Astrophysics Data System (ADS)

    Zhu, B.; Panke-Buisse, K.; Kao-Kniffin, J.

    2012-12-01

    The labile carbon released from roots to the rhizosphere enhances soil microbial activity and nutrient availability, but factors that regulate such "rhizosphere effects" are poorly understood. Nitrogen fertilization may suppress rhizosphere effects by reducing plant carbon allocation belowground. Here we investigated the impact of nitrogen fertilization (+100 mg NH4NO3-N kg soil-1) on the magnitude of rhizosphere effects of two grass species (Bermuda grass Cynodon dactylon and smooth crabgrass Digitaria ischaemum) grown in a nutrient-poor soil for 80-100 days inside a growth chamber. Rhizosphere effects were estimated by the percentage difference between the planted soil (rhizosphere soil) and the unplanted soil (bulk soil) for several assays. We found that the rhizosphere soil of both plants had higher pH (+ 0.5~0.7 units), similar microbial biomass carbon, but lower microbial biomass nitrogen (- 27~37%) compared to the bulk soil. The rate of net N mineralization and the activity of three soil enzymes that degrade chitin (NAG), protein (LAP) and lignin (peroxidase) and produce mineral nitrogen were generally enhanced by the rhizosphere effects (up to 80%). Although nitrogen fertilization significantly increased plant biomass, it generally affected microbial biomass, activity and net N mineralization rate to a similar extent between rhizosphere soil and bulk soil, and thus did not significantly impact the magnitude of rhizosphere effects. Moreover, the community structure of soil bacteria (indicated by T-RFLP) showed remarkable divergence between the planted and unplanted soils, but not between the control and fertilized soils. Collectively, these results suggest that grass roots affects soil microbial activity and community structure, but short-term nitrogen fertilization may not significantly influence these rhizosphere effects.

  6. Nitrogen loss by anaerobic oxidation of ammonium in rice rhizosphere

    PubMed Central

    Nie, San'an; Li, Hu; Yang, Xiaoru; Zhang, Zhaoji; Weng, Bosen; Huang, Fuyi; Zhu, Gui-Bing; Zhu, Yong-Guan

    2015-01-01

    Anaerobic oxidation of ammonium (anammox) is recognized as an important process for nitrogen (N) cycling, yet its role in agricultural ecosystems, which are intensively fertilized, remains unclear. In this study, we investigated the presence, activity, functional gene abundance and role of anammox bacteria in rhizosphere and non-rhizosphere paddy soils using catalyzed reporter deposition–fluorescence in situ hybridization, isotope-tracing technique, quantitative PCR assay and 16S rRNA gene clone libraries. Results showed that rhizosphere anammox contributed to 31–41% N2 production with activities of 0.33–0.64 nmol N2 g−1 soil h−1, whereas the non-rhizosphere anammox bacteria contributed to only 2–3% N2 production with lower activities of 0.08–0.26 nmol N2 g−1 soil h−1. Higher anammox bacterial cells were observed (0.75–1.4 × 107 copies g−1 soil) in the rhizosphere, which were twofold higher compared with the non-rhizosphere soil (3.7–5.9 × 106 copies g−1 soil). Phylogenetic analysis of the anammox bacterial 16S rRNA genes indicated that two genera of ‘Candidatus Kuenenia' and ‘Candidatus Brocadia' and the family of Planctomycetaceae were identified. We suggest the rhizosphere provides a favorable niche for anammox bacteria, which are important to N cycling, but were previously largely overlooked. PMID:25689022

  7. Warming-induced changes in denitrifier community structure modulate the ability of phototrophic river biofilms to denitrify.

    PubMed

    Boulêtreau, Stéphanie; Lyautey, Emilie; Dubois, Sophie; Compin, Arthur; Delattre, Cécile; Touron-Bodilis, Aurélie; Mastrorillo, Sylvain; Garabetian, Frédéric

    2014-01-01

    Microbial denitrification is the main nitrogen removing process in freshwater ecosystems. The aim of this study was to show whether and how water warming (+2.5 °C) drives bacterial diversity and structuring and how bacterial diversity affects denitrification enzymatic activity in phototrophic river biofilms (PRB). We used water warming associated to the immediate thermal release of a nuclear power plant cooling circuit to produce natural PRB assemblages on glass slides while testing 2 temperatures (mean temperature of 17 °C versus 19.5 °C). PRB were sampled at 2 sampling times during PRB accretion (6 and 21days) in both temperatures. Bacterial community composition was assessed using ARISA. Denitrifier community abundance and denitrification gene mRNA levels were estimated by q-PCR and qRT-PCR, respectively, of 5 genes encoding catalytic subunits of the denitrification key enzymes. Denitrification enzyme activity (DEA) was measured by the acetylene-block assay at 20 °C. A mean water warming of 2.5 °C was sufficient to produce contrasted total bacterial and denitrifier communities and, therefore, to affect DEA. Indirect temperature effect on DEA may have varied between sampling time, increasing by up to 10 the denitrification rate of 6-day-old PRB and decreasing by up to 5 the denitrification rate of 21-day-old PRB. The present results suggest that indirect effects of warming through changes in bacterial community composition, coupled to the strong direct effect of temperature on DEA already demonstrated in PRB, could modulate dissolved nitrogen removal by denitrification in rivers and streams.

  8. Rhizosphere Competence of Pythium oligandrum.

    PubMed

    Al-Rawahi, A K; Hancock, J G

    1997-09-01

    ABSTRACT The associations of Pythium oligandrum with the root cortex, rhizoplane, and rhizosphere were measured with 11 crop species. This work was expedited by the use of a semiselective technique for isolation of P. oligandrum from soil and plant material. Cortical colonization of roots by P. oligandrum was not detected, and the rhizoplanes of the roots of most crops were free of the fungus. However, P. oligandrum was detected in large quantities with every crop tested when roots with adhering soil (rhizosphere soil) were assayed. Different crop species and cultivars of cantaloupe, cauliflower, and tomato varied in rhizosphere densities of P. oligandrum, but rhizosphere population densities of the fungus were consistently higher than in nonrhizosphere soils with plants grown in P. oligandrum-infested sterilized potting mix or an unsterilized mineral soil. After transplanting tomatoes into potting mix infested with P. oligandrum, increases in CFU occurred over time in the rhizosphere but not in the nonrhizosphere soil. In trials on delivery methods of inoculum of P. oligandrum, the rhizosphere populations of tomato plants grown in potting mix were about sixfold higher compared to seed-coat treatments when ground, alginate pelleted oospores were applied to seedlings growing in plug containers prior to transplanting or to pots containing potting mix before direct seeding. PMID:18945067

  9. Changes in rhizosphere bacterial gene expression following glyphosate treatment.

    PubMed

    Newman, Molli M; Lorenz, Nicola; Hoilett, Nigel; Lee, Nathan R; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-05-15

    In commercial agriculture, populations and interactions of rhizosphere microflora are potentially affected by the use of specific agrichemicals, possibly by affecting gene expression in these organisms. To investigate this, we examined changes in bacterial gene expression within the rhizosphere of glyphosate-tolerant corn (Zea mays) and soybean (Glycine max) in response to long-term glyphosate (PowerMAX™, Monsanto Company, MO, USA) treatment. A long-term glyphosate application study was carried out using rhizoboxes under greenhouse conditions with soil previously having no history of glyphosate exposure. Rhizosphere soil was collected from the rhizoboxes after four growing periods. Soil microbial community composition was analyzed using microbial phospholipid fatty acid (PLFA) analysis. Total RNA was extracted from rhizosphere soil, and samples were analyzed using RNA-Seq analysis. A total of 20-28 million bacterial sequences were obtained for each sample. Transcript abundance was compared between control and glyphosate-treated samples using edgeR. Overall rhizosphere bacterial metatranscriptomes were dominated by transcripts related to RNA and carbohydrate metabolism. We identified 67 differentially expressed bacterial transcripts from the rhizosphere. Transcripts downregulated following glyphosate treatment involved carbohydrate and amino acid metabolism, and upregulated transcripts involved protein metabolism and respiration. Additionally, bacterial transcripts involving nutrients, including iron, nitrogen, phosphorus, and potassium, were also affected by long-term glyphosate application. Overall, most bacterial and all fungal PLFA biomarkers decreased after glyphosate treatment compared to the control. These results demonstrate that long-term glyphosate use can affect rhizosphere bacterial activities and potentially shift bacterial community composition favoring more glyphosate-tolerant bacteria. PMID:26901800

  10. Changes in rhizosphere bacterial gene expression following glyphosate treatment.

    PubMed

    Newman, Molli M; Lorenz, Nicola; Hoilett, Nigel; Lee, Nathan R; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-05-15

    In commercial agriculture, populations and interactions of rhizosphere microflora are potentially affected by the use of specific agrichemicals, possibly by affecting gene expression in these organisms. To investigate this, we examined changes in bacterial gene expression within the rhizosphere of glyphosate-tolerant corn (Zea mays) and soybean (Glycine max) in response to long-term glyphosate (PowerMAX™, Monsanto Company, MO, USA) treatment. A long-term glyphosate application study was carried out using rhizoboxes under greenhouse conditions with soil previously having no history of glyphosate exposure. Rhizosphere soil was collected from the rhizoboxes after four growing periods. Soil microbial community composition was analyzed using microbial phospholipid fatty acid (PLFA) analysis. Total RNA was extracted from rhizosphere soil, and samples were analyzed using RNA-Seq analysis. A total of 20-28 million bacterial sequences were obtained for each sample. Transcript abundance was compared between control and glyphosate-treated samples using edgeR. Overall rhizosphere bacterial metatranscriptomes were dominated by transcripts related to RNA and carbohydrate metabolism. We identified 67 differentially expressed bacterial transcripts from the rhizosphere. Transcripts downregulated following glyphosate treatment involved carbohydrate and amino acid metabolism, and upregulated transcripts involved protein metabolism and respiration. Additionally, bacterial transcripts involving nutrients, including iron, nitrogen, phosphorus, and potassium, were also affected by long-term glyphosate application. Overall, most bacterial and all fungal PLFA biomarkers decreased after glyphosate treatment compared to the control. These results demonstrate that long-term glyphosate use can affect rhizosphere bacterial activities and potentially shift bacterial community composition favoring more glyphosate-tolerant bacteria.

  11. Adaptation of Denitrifying Populations to Low Soil pH †

    PubMed Central

    Parkin, Timothy B.; Sexstone, Alan J.; Tiedje, James M.

    1985-01-01

    Natural denitrification rates and activities of denitrifying enzymes were measured in an agricultural soil which had a 20-year past history of low pH (pH ca. 4) due to fertilization with acid-generating ammonium salts. The soil adjacent to this site had been limed and had a pH of ca. 6.0. Natural denitrification rates of these areas were of similar magnitude: 158 ng of N g−1 of soil day−1 for the acid soil and 390 ng of N g−1 of soil day−1 at the neutral site. Estimates of in situ denitrifying enzyme activity were higher in the neutral soil, but substantial enzyme activity was also detected in the acid soil. Rates of nitrous oxide reduction were very low, even when NO3− and NO2− were undetectable, and were ca. 400 times lower than the rates of N2O production from NO3−. Denitrification rates measured in slurries of the acid and neutral soil showed distinctly different pH optima (pH 3.9 and pH 6.3) which were near the pH values of the two soils. This suggests that an acid-tolerant denitrifying population had been selected during the 20-year period of low pH. PMID:16346780

  12. Development of Denitrifying and Nitrifying Bacteria and Their Co-occurrence in Newly Created Biofilms in Urban Streams

    NASA Astrophysics Data System (ADS)

    Vaessen, T. N.; Martí Roca, E.; Pinay, G.; Merbt, S. N.

    2015-12-01

    Biofilms play a pivotal role on nutrient cycling in streams, which ultimately dictates the export of nutrients to downstream ecosystems. The extent to which biofilms influence the concentration of dissolved nutrients, oxygen and pH in the water column may be determined by the composition of the microbial assemblages and their activity. Evidence of biological interactions among bacteria and algae are well documented. However, the development, succession and co-occurence of nitrifying and denitrifying bacteria remain poorly understood. These bacteria play a relevant role on the biogeochemical process associated to N cycling, and their relative abundance can dictate the fate of dissolved inorganic nitrogen in streams. In particular, previous studies indicated that nitrifiers are enhanced in streams receiving inputs from wastewater treatment plant (WWTP) effluents due to both increases in ammonium concentration and inputs of nitrifiers. However, less is known about the development of denitrifiers in receiving streams, although environmental conditions seem to favor it. We conducted an in situ colonization experiment in a stream receiving effluent from a WWTP to examine how this input influences the development and co-occurrence of nitrifying and denitrifying bacteria. We placed artificial substrata at different locations relative to the effluent and sampled them over time to characterize the developed biofilm in terms of bulk measurements (organic matter content and algae) as well as in terms of abundance of nitrifiers and denitrifiers (using qPCR). The results of this study contribute to a better understanding of the temporal dynamics of denitrifiers and nitrifiers in relation to the developed organic matter, dissolved oxygen and pH and the biomass accrual in stream biofilms under the influence of nutrients inputs from WWTP effluent. Ultimately, the results provide insights on the potential role of nitrifiers and denitrifiers on N cycling in WWTP effluent receiving

  13. Relative rates of nitric oxide and nitrous oxide production by nitrifiers, denitrifiers, and nitrate respirers

    NASA Technical Reports Server (NTRS)

    Anderson, I. C.; Levine, J. S.

    1986-01-01

    An account is given of the atmospheric chemical and photochemical effects of biogenic nitric and nitrous oxide emissions. The magnitude of the biogenic emission of NO is noted to remain uncertain. Possible soil sources of NO and N2O encompass nitrification by autotropic and heterotropic nitrifiers, denitrification by nitrifiers and denitrifiers, nitrate respiration by fermenters, and chemodenitrification. Oxygen availability is the primary determinant of these organisms' relative rates of activity. The characteristics of this major influence are presently investigated in light of the effect of oxygen partial pressure on NO and N2O production by a wide variety of common soil-nitrifying, denitrifying, and nitrate-respiring bacteria under laboratory conditions. The results obtained indicate that aerobic soils are primary sources only when there is sufficient moisture to furnish anaerobic microsites for denitrification.

  14. Visualization of the Dynamic Rhizosphere Environment: Microbial and Biogeochemical Perspectives

    NASA Astrophysics Data System (ADS)

    Cardon, Z. G.; Forbes, E. S.; Thomas, F.; Herron, P. M.; Gage, D. J.; Thomas, S.; Larsen, M.; Arango Pinedo, C.; Sievert, S. M.; Giblin, A. E.

    2014-12-01

    The rhizosphere is a hotbed of nutrient cycling fueled by carbon from plants and controlled by microbes. Plants also strongly affect the rhizosphere by driving water flow into and out of roots, and by oxygenating saturated soil and sediment. Location and dynamics of plant-spurred microbial growth and activities are impossible to discern with destructive soil assays mixing microbe-scale soil microenvironments in a single"snap-shot" sample. Yet data are needed to inform (and validate) models describing microbial activity and biogeochemistry in the ebb and flow of the dynamic rhizosphere. Dynamics and localization of rapid microbial growth in the rhizosphere can be assessed over time using living soil microbiosensors. We used the bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constituitive promoter nptII and luxCDABE(genes coding for light production). High light production by KT2440/pZKH2 correlated with rapid microbial growth supported by high carbon availability. Biosensors were used in clear-sided microcosms filled with non-sterile soil in which corn, black poplar or tomato were growing. KT2440/pZKH2 revealed that root tips are not necessarily the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots. Roots can also be sources of oxygen (O2) to the rhizosphere in saturated soil. We quantified spatial distributions of O2 using planar optodes placed against the face of sediment blocks cut from vegetated salt marsh at Plum Island Ecosystems LTER. Integrated over time, Spartina alterniflora roots were O2 sources to the rhizosphere. However, "sun-up" (light on) did not uniformly enhance rhizosphere O2 concentrations (as stomata opened and O2 production commenced). In some regions, the balance of O2 supply (from roots) and O2 demand (root and microbial) tipped toward demand at sun-up (repeatedly, over days). We speculate that in

  15. Molecular Characterization of Diazotrophic and Denitrifying Bacteria Associated with Mangrove Roots▿

    PubMed Central

    Flores-Mireles, Ana L.; Winans, Stephen C.; Holguin, Gina

    2007-01-01

    An analysis of the molecular diversity of N2 fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N2 fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments. PMID:17827324

  16. Microbial and metabolic characterization of a denitrifying phosphorus-uptake/side stream phosphorus removal system for treating domestic sewage.

    PubMed

    Jin, Zhan; Ji, Fang-Ying; Xu, Xuan; Xu, Xiao-Yi; Chen, Qing-Kong; Li, Qi

    2014-11-01

    In this study, an advanced wastewater treatment process, the denitrifying phosphorus/side stream phosphorus removal system (DPR-Phostrip), was developed for the purpose of enhancing denitrifying phosphorus removal. The enrichment of denitrifying phosphorus-accumulating organisms (DPAOs) and the microbial community structure of DPR-Phostrip were evaluated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and the metabolic activity of seed sludge and activated sludge collected after 55 days of operation were evaluated by Biolog™ analysis. This experimental study of DPR-Phostrip operation showed that nutrients were removed effectively, and denitrifying phosphorus removal was observed during the pre-anoxic period. PCR-DGGE analysis indicated that DPR-Phostrip supported DPAO growth while inhibiting PAOs and GAOs. The major dominant species in DPR-Phostrip were Bacteroidetes bacterium, Saprospiraceae bacterium, and Chloroflexi bacterium. Moreover, the functional diversity indices calculated on the basis of Biolog analysis indicated that DPR-Phostrip had almost no effect on microbial community diversity but was associated with a shift in the dominant species, which confirms the results of the PCR-DGGE analysis. The results for average well color development, calculated via Biolog analysis, showed that DPR-Phostrip had a little impact on the metabolic activity of sludge. Further principal component analysis suggested that the ability to utilize low-molecular-weight organic compounds was reduced in DPR-Phostrip.

  17. Microbial and metabolic characterization of a denitrifying phosphorus-uptake/side stream phosphorus removal system for treating domestic sewage.

    PubMed

    Jin, Zhan; Ji, Fang-Ying; Xu, Xuan; Xu, Xiao-Yi; Chen, Qing-Kong; Li, Qi

    2014-11-01

    In this study, an advanced wastewater treatment process, the denitrifying phosphorus/side stream phosphorus removal system (DPR-Phostrip), was developed for the purpose of enhancing denitrifying phosphorus removal. The enrichment of denitrifying phosphorus-accumulating organisms (DPAOs) and the microbial community structure of DPR-Phostrip were evaluated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and the metabolic activity of seed sludge and activated sludge collected after 55 days of operation were evaluated by Biolog™ analysis. This experimental study of DPR-Phostrip operation showed that nutrients were removed effectively, and denitrifying phosphorus removal was observed during the pre-anoxic period. PCR-DGGE analysis indicated that DPR-Phostrip supported DPAO growth while inhibiting PAOs and GAOs. The major dominant species in DPR-Phostrip were Bacteroidetes bacterium, Saprospiraceae bacterium, and Chloroflexi bacterium. Moreover, the functional diversity indices calculated on the basis of Biolog analysis indicated that DPR-Phostrip had almost no effect on microbial community diversity but was associated with a shift in the dominant species, which confirms the results of the PCR-DGGE analysis. The results for average well color development, calculated via Biolog analysis, showed that DPR-Phostrip had a little impact on the metabolic activity of sludge. Further principal component analysis suggested that the ability to utilize low-molecular-weight organic compounds was reduced in DPR-Phostrip. PMID:25073616

  18. 13C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline.

    PubMed

    Hannula, S E; Boschker, H T S; de Boer, W; van Veen, J A

    2012-05-01

    • The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). • The microbes receiving (13)C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). • Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. • We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant.

  19. Biodegradation of three- and four-ring polycyclic aromatic hydrocarbons under aerobic and denitrifying conditions

    SciTech Connect

    McNally, D.L.; Mihelcic, J.R.; Lueking, D.R.

    1998-09-01

    PAHs are thought to be particularly persistent in environments where anaerobic conditions exist. This study presents evidence for the biodegradation of three- and four-ringed PAHs (anthracene, phenanthrene, and pyrene) under strict anaerobic, denitrifying conditions. Three pseudomonad strains, isolated from contrasting environments, were used in this study. All three strains were known PAH degraders and denitrifiers. Degradation proceeded to nondetectable levels in 12--80 h for anthracene, 12--44 h for phenanthrene, and 24--72 h for pyrene. The rates of anaerobic degradation were typically slower than under aerobic conditions in almost all cases, except for strain SAG-R which had similar removal rates for all three and four-ring PAHs. Denitrification activity was verified by monitoring nitrate utilization and nitrous oxide production. Although none of the pseudomonads were adapted to the denitrifying conditions, only the pseudomonad isolated from a noncontaminated site consistently exhibited an adaptation period which approximated 12 h. This study supports growing evidence that the degradation of aromatic hydrocarbons coupled to denitrification may be an important factor affecting the fate of these compounds in natural and engineered systems.

  20. Interaction between rhizosphere microorganisms and plant roots: 13C fluxes in the rhizosphere after pulse labeling

    NASA Astrophysics Data System (ADS)

    Yevdokimov, I. V.; Ruser, R.; Buegger, F.; Marx, M.; Munch, J. C.

    2007-07-01

    The input dynamics of labeled C into pools of soil organic matter and CO2 fluxes from soil were studied in a pot experiment with the pulse labeling of oats and corn under a 13CO2 atmosphere, and the contribution of the root and microbial respiration to the emission of CO2 from the soil was determined from the fluxes of labeled C in the microbial biomass and the evolved carbon dioxide. A considerable amount of 13C (up to 96% of the total amount of the label found in the rhizosphere soil) was incorporated into the biomass of the rhizosphere microorganisms. The diurnal fluctuations of the labeled C pools in the microbial biomass, dissolved organic carbon, and CO2 released in the rhizosphere of oats and corn were related to the day/night changes, i.e., to the on and off periods of the photosynthetic activity of the plants. The average contribution of the corn root respiration (70% of the total CO2 emission from the soil surface) was higher than that of the oats roots (44%), which was related to the lower incorporation of rhizodeposit carbon into the microbial biomass in the soil under the corn plants than in the soil under the oats plants.

  1. Rates of Root and Organism Growth, Soil Conditions, and Temporal and Spatial Development of the Rhizosphere

    PubMed Central

    WATT, MICHELLE; SILK, WENDY K.; PASSIOURA, JOHN B.

    2006-01-01

    • Background Roots growing in soil encounter physical, chemical and biological environments that influence their rhizospheres and affect plant growth. Exudates from roots can stimulate or inhibit soil organisms that may release nutrients, infect the root, or modify plant growth via signals. These rhizosphere processes are poorly understood in field conditions. • Scope and Aims We characterize roots and their rhizospheres and rates of growth in units of distance and time so that interactions with soil organisms can be better understood in field conditions. We review: (1) distances between components of the soil, including dead roots remnant from previous plants, and the distances between new roots, their rhizospheres and soil components; (2) characteristic times (distance2/diffusivity) for solutes to travel distances between roots and responsive soil organisms; (3) rates of movement and growth of soil organisms; (4) rates of extension of roots, and how these relate to the rates of anatomical and biochemical ageing of root tissues and the development of the rhizosphere within the soil profile; and (5) numbers of micro-organisms in the rhizosphere and the dependence on the site of attachment to the growing tip. We consider temporal and spatial variation within the rhizosphere to understand the distribution of bacteria and fungi on roots in hard, unploughed soil, and the activities of organisms in the overlapping rhizospheres of living and dead roots clustered in gaps in most field soils. • Conclusions Rhizosphere distances, characteristic times for solute diffusion, and rates of root and organism growth must be considered to understand rhizosphere development. Many values used in our analysis were estimates. The paucity of reliable data underlines the rudimentary state of our knowledge of root–organism interactions in the field. PMID:16551700

  2. Using T-RFLP data on denitrifier community composition to inform understanding of denitrification in stream sediments (Invited)

    NASA Astrophysics Data System (ADS)

    Wang, S.; Somers, K.; Sudduth, E.; Hassett, B.; Bernhardt, E. S.; Urban, D. L.

    2010-12-01

    We used terminal restriction fragment length polymorphism (T-RFLP), a molecular fingerprinting method, to characterize denitrifier communities in sediments taken from 48 study streams in North Carolina, USA. In addition to characterizing denitrifier communities, we also used denitrification enzyme activity (DEA) assays to measure potential denitrification rates. Due to differences in watershed land-use, study streams covered a gradient of nitrogen and carbon concentrations, as well as a gradient of contaminant loading from stormwater and sanitary sewers. Nitrogen and carbon (i.e., substrate) concentrations are commonly used to make predictions about denitrification rates in streams. Such models do not take into account denitrifier community composition, which may be an important, independent control of denitrification rates, particularly under stressful conditions (e.g., high contaminant loading) that prevent communities from capitalizing on high substrate availability. Our results indicate that substrate availability by itself was a weak predictor of denitrification rates; the same was also true for denitrifier community composition. However, when both factors were incorporated in a multiple regression model, the percent variation explained increased substantially. These findings suggest that T-RFLP, a relatively cost-effective method, can be used to improve our understanding of controls on denitrification rates in streams with varying watershed land-uses.

  3. Effects of ethanol on benzene degradation under denitrifying conditions.

    PubMed

    Wu, Yaoguo; Li, Yunfeng; Hui, Lin; Tan, Ying; Jin, Song

    2009-02-01

    As a popular fuel oxygenate, ethanol frequently co-occurs with petroleum hydrocarbons, including benzene, in groundwater that is contaminated by gasoline. Anaerobic pathways have been identified in benzene biodegradation. Limited reports focus on denitrifying degradation of benzene; however, the role of ethanol in this pathway is unknown. This study investigated the effects of ethanol on benzene degradation under denitrifying condition by using groundwater and sediment samples collected from locations with known history of benzene contamination. Results indicate that benzene can be biodegraded under denitrifying conditions. When concentrations of nitrate were in the range of 480-920 mg/L, there is a critical value in ethanol concentration:Ethanol at concentration less than the critical value enhanced the denitrifying degradation of benzene over a period of time; in contrast, ethanol at concentration higher than the critical value, which was degraded before benzene, demonstrated an inhibitory effect. And the critical value varied with nitrate concentration. It appears that the role of ethanol may be closely associated with its own and nitrate concentrations. Two mathematical equations were established based on the data and may be used to determine if ethanol presents an enhancing or inhibitory effect on denitrification of benzene. The roles of ethanol in COD/NO(3) (-)-N and the subsequent denitrification of benzene were also studied. An optimal COD/NO(3) (-)-N ratio of 1.32 was obtained for this testing system, in which the highest rate of benzene degradation can be achieved under denitrifying conditions.

  4. Relevance of extracellular DNA in rhizosphere

    NASA Astrophysics Data System (ADS)

    Pietramellara, Giacomo; Ascher, Judith; Baraniya, Divyashri; Arfaioli, Paola; Ceccherini, Maria Teresa; Hawes, Martha

    2013-04-01

    One of the most promising areas for future development is the manipulation of the rhizosphere to produce sustainable and efficient agriculture production systems. Using Omics approaches, to define the distinctive features of eDNA systems and structures, will facilitate progress in rhizo-enforcement and biocontrol studies. The relevance of these studies results clear when we consider the plethora of ecological functions in which eDNA is involved. This fraction can be actively extruded by living cells or discharged during cellular lysis and may exert a key role in the stability and variability of the soil bacterial genome, resulting also a source of nitrogen and phosphorus for plants due to the root's capacity to directly uptake short DNA fragments. The adhesive properties of the DNA molecule confer to eDNA the capacity to inhibit or kill pathogenic bacteria by cation limitation induction, and to facilitate formation of biofilm and extracellular traps (ETs), that may protect microorganisms inhabiting biofilm and plant roots against pathogens and allelopathic substances. The ETs are actively extruded by root border cells when they are dispersed in the rhizosphere, conferring to plants the capacity to extend an endogenous pathogen defence system outside the organism. Moreover, eDNA could be involved in rhizoremediation in heavy metal polluted soil acting as a bioflotation reagent.

  5. Accelerated biodegradation of pyrene and benzo[a]pyrene in the Phragmites australis rhizosphere by bacteria-root exudate interactions.

    PubMed

    Toyama, Tadashi; Furukawa, Tetsuya; Maeda, Noritaka; Inoue, Daisuke; Sei, Kazunari; Mori, Kazuhiro; Kikuchi, Shintaro; Ike, Michihiko

    2011-02-01

    We investigated the biodegradation of pyrene and benzo[a]pyrene in Phragmites australis rhizosphere sediment. We collected P. australis plants, rhizosphere sediments, and unvegetated sediments from natural aquatic sites and conducted degradation experiments using sediments spiked with pyrene or benzo[a]pyrene. Accelerated removal of pyrene and benzo[a]pyrene was observed in P. australis rhizosphere sediments with plants, whereas both compounds persisted in unvegetated sediments without plants and in autoclaved rhizosphere sediments with sterilized plants, suggesting that the accelerated removal resulted largely from biodegradation by rhizosphere bacteria. Initial densities of pyrene-utilizing bacteria were substantially higher in the rhizosphere than in unvegetated sediments, but benzo[a]pyrene-utilizing bacteria were not detected in rhizosphere sediments. Mycobacterium gilvum strains isolated from rhizosphere sediments utilized pyrene aerobically as a sole carbon source and were able to degrade benzo[a]pyrene when induced with pyrene. Phragmites australis root exudates containing phenolic compounds supported growth as a carbon source for the one Mycobacterium strain tested, and induced benzo[a]pyrene-degrading activity of the strain. The stimulatory effect on benzo[a]pyrene biodegradation and the amounts of phenolic compounds in root exudates increased when P. australis was exposed to pyrene. Our results show that Mycobacterium-root exudate interactions can accelerate biodegradation of pyrene and benzo[a]pyrene in P. australis rhizosphere sediments.

  6. Acidophilic denitrifiers dominate the N2O production in a 100-year-old tea orchard soil.

    PubMed

    Huang, Ying; Long, Xi-En; Chapman, Stephen J; Yao, Huaiying

    2015-03-01

    Aerobic denitrification is the main process for high N2O production in acid tea field soil. However, the biological mechanisms for the high emission are not fully understood. In this study, we examined N2O emission and denitrifier communities in 100-year-old tea soils with four pH levels (3.71, 5.11, 6.19, and 7.41) and four nitrate concentration (0, 50, 200, and 1000 mg kg(-1) of NO3 (-)-N) addition. Results showed the highest N2O emission (10.1 mg kg(-1) over 21 days) from the soil at pH 3.71 with 1000 mg kg(-1) NO3 (-) addition. The N2O reduction and denitrification enzyme activity in the acid soils (pH <7.0) were significantly higher than that of soils at pH 7.41. Moreover, TRF 78 of nirS and TRF 187 of nosZ dominated in soils of pH 3.71, suggesting an important role of acidophilic denitrifiers in N2O production and reduction. CCA analysis also showed a negative correlation between the dominant denitrifier ecotypes (nirS TRF 78, nosZ TRF 187) and soil pH. The representative sequences were identical to those of cultivated denitrifiers from acidic soils via phylogenetic tree analysis. Our results showed that the acidophilic denitrifier adaptation to the acid environment results in high N2O emission in this highly acidic tea soil.

  7. Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance.

    PubMed

    Thion, Cécile E; Poirel, Jessica D; Cornulier, Thomas; De Vries, Franciska T; Bardgett, Richard D; Prosser, James I

    2016-07-01

    The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers (AO) is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology.

  8. Arsenic uptake by rice is influenced by microbe-mediated arsenic redox changes in the rhizosphere.

    PubMed

    Jia, Yan; Huang, Hai; Chen, Zheng; Zhu, Yong-Guan

    2014-01-21

    Arsenic (As) uptake by rice is largely determined by As speciation, which is strongly influenced by microbial activities. However, little is known about interactions between root and rhizosphere microbes, particularly on arsenic oxidation and reduction. In this study, two rice cultivars with different radial oxygen loss (ROL) ability were used to investigate the impact of microbially mediated As redox changes in the rhizosphere on As uptake. Results showed that the cultivar with higher ROL (Yangdao) had lower As uptake than that with lower ROL (Nongken). The enhancement of the rhizospheric effect on the abundance of the arsenite (As(III)) oxidase gene (aroA-like) was greater than on the arsenate (As(V)) reductase gene (arsC), and As(V) respiratory reductase gene (arrA), resulting in As oxidation and sequestration in the rhizosphere, particularly for cultivar Yangdao. The community of As(III)-oxidizing bacteria in the rhizosphere was dominated by α-Proteobacteria and β-Proteobacteria and was influenced by rhizospheric effects, rice straw application, growth stage, and cultivar. Application of rice straw into the soil increased As release and accumulation into rice plants. These results highlighted that uptake of As by rice is influenced by microbial processes, especially As oxidation in the rhizosphere, and these processes are influenced by root ROL and organic matter application. PMID:24383760

  9. Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance.

    PubMed

    Thion, Cécile E; Poirel, Jessica D; Cornulier, Thomas; De Vries, Franciska T; Bardgett, Richard D; Prosser, James I

    2016-07-01

    The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers (AO) is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology. PMID:27130939

  10. Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities.

    PubMed

    Hanke, Anna; Berg, Jasmine; Hargesheimer, Theresa; Tegetmeyer, Halina E; Sharp, Christine E; Strous, Marc

    2015-01-01

    In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°C. Whereas denitrification rates at 25°C were more or less stable over time, at 10°C denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences (WGS) and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10°C selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase) and nitrous oxide reduction. At 25°C, denitrifying populations affiliated with Rhodobacteraceae were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding). Overall, our results suggest that a mixture of competition-for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population -, and cross feeding-between fermentative and denitrifying populations-controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment. PMID:26779132

  11. Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities

    PubMed Central

    Hanke, Anna; Berg, Jasmine; Hargesheimer, Theresa; Tegetmeyer, Halina E.; Sharp, Christine E.; Strous, Marc

    2016-01-01

    In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°C. Whereas denitrification rates at 25°C were more or less stable over time, at 10°C denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences (WGS) and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10°C selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase) and nitrous oxide reduction. At 25°C, denitrifying populations affiliated with Rhodobacteraceae were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding). Overall, our results suggest that a mixture of competition—for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population –, and cross feeding—between fermentative and denitrifying populations—controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment. PMID:26779132

  12. Impact of plant domestication on rhizosphere microbiome assembly and functions.

    PubMed

    Pérez-Jaramillo, Juan E; Mendes, Rodrigo; Raaijmakers, Jos M

    2016-04-01

    The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.

  13. Distinctive denitrifying capabilities lead to differences in N2O production by denitrifying polyphosphate accumulating organisms and denitrifying glycogen accumulating organisms.

    PubMed

    Ribera-Guardia, Anna; Marques, Ricardo; Arangio, Corrado; Carvalheira, Monica; Oehmen, Adrian; Pijuan, Maite

    2016-11-01

    This study aims at investigating the denitrification kinetics in two separate enriched cultures of denitrifying polyphosphate accumulating organisms (dPAO) and denitrifying glycogen accumulating organisms (dGAO) and compare their N2O accumulation potential under different conditions. Two sequencing batch reactors were inoculated to develop dPAO and dGAO enriched microbial communities separately. Seven batch tests with different combinations of electron acceptors (nitrate, nitrite and/or nitrous oxide) were carried out with the enriched biomass from both reactors. Results indicate that in almost all batch tests, N2O accumulated for both cultures, however dPAOs showed a higher denitrification capacity compared to dGAOs due to their higher nitrogen oxides reduction rates. Additionally, the effect of the simultaneous presence of several electron acceptors in the reduction rates of the different nitrogen oxides was also assessed in dPAOs and dGAOs. PMID:27479801

  14. [Roles of rhizosphere in remediation of contaminated soils and its mechanisms].

    PubMed

    Wei, Shuhe; Zhou, Qixing; Zhang, Kaisong; Liang, Jidong

    2003-01-01

    Rhizosphere is a special 'ecological remediation unit' to treat contaminated soils, which contains a great quantity of microorganisms such as fungi and rhizobacteria living with plant roots. Thus, physiological and ecological roles of plant roots to remedy contaminated soils, to accumulate and to solidify heavy metals, to absorb and degrade organic pollutants in rhizosphere were illustrated, and the function of mycorrhizospheric fungi to absorb, barrier and chelate heavy metals, to degrade organic pollutants through their metabolism activities, the action of rhizobacteria to absorb and solidify heavy metals, to degrade organic pollutants in rhizosphere through their active living activities, and the combined remediation of fungi and bacteria to pollutants in rhizosphere and their relevant mechanisms were explained. It was suggested that the remediation role of rhizosphere was the main part of phytoremediation, and one of the main basic theories to remedy contaminated soils by the activity of green plants and other organisms. The use of hyperaccumulative plants in remedying soils contaminated by some heavy metals would be prospective. It would be one of the important approach to contaminated soils remediation by organic pollutants through the mechanism of screening some special plants whose roots had strong secreting ability to absorb and accumulate dissolvent organic pollutants on the basis of inoculating specific or non-specific fungi and bacteria from the rhizosphere. This will be a developing trend of research on the remediation of contaminated soils by organic pollutants.

  15. Role of the denitrifying Haloarchaea in the treatment of nitrite-brines.

    PubMed

    Nájera-Fernández, Cindy; Zafrilla, Basilio; Bonete, María José; Martínez-Espinosa, Rosa María

    2012-09-01

    Haloferax mediterranei is a denitrifying halophilic archaeon able to reduce nitrate and nitrite under oxic and anoxic conditions. In the presence of oxygen, nitrate and nitrite are used as nitrogen sources for growth. Under oxygen scarcity, this haloarchaeon uses both ions as electron acceptors via a denitrification pathway. In the present work, the maximal nitrite concentration tolerated by this organism was determined by studying the growth of H. mediterranei in minimal medium containing 30, 40 and 50 mM nitrite as sole nitrogen source and under initial oxic conditions at 42 degrees C. The results showed the ability of H. mediterranei to withstand nitrite concentrations up to 50 mM. At the beginning of the incubation, nitrate was detected in the medium, probably due to the spontaneous oxidation of nitrite under the initial oxic conditions. The complete removal of nitrite and nitrate was accomplished in most of the tested conditions, except in culture medium containing 50 mM nitrite, suggesting that this concentration compromised the denitrification capacity of the cells. Nitrite and nitrate reductases activities were analyzed at different growth stages of H. mediterranei. In all cases, the activities of the respiratory enzymes were higher than their assimilative counterparts; this was especially the case for NirK. The denitrifying and possibly detoxifying role of this enzyme might explain the high nitrite tolerance of H. mediterranei. This archaeon was also able to remove 60% of the nitrate and 75% of the nitrite initially present in brine samples collected from a wastewater treatment facility. These results suggest that H. mediterranei, and probably other halophilic denitrifying Archaea, are suitable candidates for the bioremediation of brines with high nitrite and nitrate concentrations.

  16. Hydraulic flow characteristics of agricultural residues for denitrifying bioreactor media

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Denitrifying bioreactors are a promising technology to mitigate agricultural subsurface drainage nitrate-nitrogen losses, a critical water quality goal for the Upper Mississippi River Basin. This study was conducted to evaluate the hydraulic properties of agricultural residues that are potential bio...

  17. Denitrifying bioreactors for nitrate removal from tile drained cropland

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Denitrification bioreactors are a promising technology for mitigation of nitrate-nitrogen (NO3-N) losses in subsurface drainage water. Bioreactors are constructed with carbon substrates, typically wood chips, to provide a substrate for denitrifying microorganisms. Researchers in Iowa found that for ...

  18. Physiological factors affecting carbon tetrachloride dehalogenation by the denitrifying bacterium Pseudomonas sp. strain KC.

    PubMed Central

    Lewis, T A; Crawford, R L

    1993-01-01

    Pseudomonas sp. strain KC was grown on a medium with a low content of transition metals in order to examine the conditions for carbon tetrachloride (CT) transformation. Several carbon sources, including acetate, glucose, glycerol, and glutamate, were able to support CT transformation. The chelators 2,2'-dipyridyl and 1,10-phenanthroline stimulated CT transformation in a rich medium that otherwise did not support this activity. Low (< 10 microM) additions of dissolved iron(II), iron(III), and cobalt(II), as well as an insoluble iron(III) compound, ferric oxyhydroxide, inhibited CT transformation. The addition of 50 microM iron to actively growing cultures resulted in delayed inhibition of CT transformation. CT transformation was seen in aerobic cultures of KC, but with reduced efficiency compared with denitrifying cultures. Inhibition of CT transformation by iron was also seen in aerobically grown cultures. Optimal conditions were used in searching for effective CT transformation activity among denitrifying enrichments grown from samples of aquifer material. No activity comparable to that of Pseudomonas sp. strain KC was found among 16 samples tested. PMID:8517754

  19. Are Isotopologue Signatures of N2O from Bacterial Denitrifiers Indicative of NOR Type?

    NASA Astrophysics Data System (ADS)

    Well, R.; Braker, G.; Giesemann, A.; Flessa, H.

    2010-12-01

    Nitrous oxide (N2O) fluxes from soils result from its production by nitrification and denitrification and reduction during denitrification. The structure of the denitrifying microbial community contributes to the control of net N2O fluxes. Although molecular techniques are promising for identifying the active community of N2O producers, there are few data until now because methods to explore gene expression of N2O production are laborious and disregard regulation of activity at the enzyme level. The isotopologue signatures of N2O including δ18O, average δ15N (δ15Nbulk) and 15N site preference (SP = difference in δ15N between the central and peripheral N positions of the asymmetric N2O molecule) have been used to estimate the contribution of partial processes to net N2O fluxes to the atmosphere. However, the use of this approach to study N2O dynamics in soils requires knowledge of isotopic signatures of N2O precursors and isotopologue fractionation factors (ɛ) of all processes of N2O production and consumption. In contrast to δ18O and δ15Nbulk, SP is independent of precursor signatures and hence is a promising parameter here. It is assumed that SP of produced N2O is almost exclusively controlled by the enzymatic isotope effects of NO reductases (NOR). These enzymes are known to be structurally different between certain classes of N2O producers with each class causing different isotope effects (Schmidt et al., 2004). The NH2OH-to-N2O step of nitrifiers and the NO3-to-N2O step of fungal denitrifiers are associated with large site-specific 15N effects with SP of 33 to 37 ‰ (Sutka et al., 2006, 2008) while the few tested species of gram-negative bacterial denitrifiers (cNOR group) exhibited low SP of -5 to 0‰ (Sutka et al., 2006; Toyoda et al., 2005). The aim of our study was to determine site-specific fractionation factors of the NO3-to-N2O step (ɛSP) for several species of denitrifiers representing each of the known NOR-types of bacteria, i.e. cNOR, q

  20. Trace Gas Emission from in-Situ Denitrifying Bioreactors

    NASA Astrophysics Data System (ADS)

    Pluer, W.; Walter, M. T.; Geohring, L.

    2014-12-01

    Despite decades of concerted effort to mitigate nonpoint source nitrate (NO3-) pollution from agricultural lands, these efforts have not been sufficient to arrest eutrophication. A primary process for removing excess NO3- from water is denitrification, where denitrifying bacteria use NO3- for respiration in the absence of oxygen. Denitrification results in reduced forms of nitrogen, often dinitrogen gas (N2) but also nitrous oxide (N2O), an aggressive greenhouse gas. A promising solution to NO3- pollution is to intercept agricultural discharges with denitrifying bioreactors (DNBRs). DNBRs provide conditions ideal for denitrifiers: an anaerobic environment, sufficient organic matter, and excess NO3-. These conditions are also ideal for methanogens, which produce methane (CH4), another harmful trace gas. While initial results from bioreactor studies show that they can cost-effectively remove NO3-, trace gas emissions are an unintended consequence. This study's goal was to determine how bioreactor design promotes denitrification while limiting trace gas production. Reactor inflow and outflow water samples were tested for nutrients, including NO3-, and dissolved inflow and outflow gas samples were tested for N2O and CH4. NO3- reduction and trace gas production were evaluated at various residence times, pHs, and inflow NO3- concentrations in field and lab-scale reactors. Low NO3- reduction indicated conditions that stressed denitrifying bacteria while high reductions indicated designs that optimized pollutant treatment for water quality. Several factors influenced high N2O, suggesting non-ideal conditions for the final step of complete denitrification. High CH4 emissions pointed to reactor media choice for discouraging methanogens, which may remove competition with denitrifiers. It is critical to understand all of potential impacts that DNBRs may have, which means identifying processes and design specifications that may affect them.

  1. Microbial growth and carbon use efficiency in the rhizosphere and root-free soil.

    PubMed

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

    2014-01-01

    Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)-the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed. PMID:24722409

  2. Mineralization Capacity of Bacteria and Fungi from the Rhizosphere-Rhizoplane of a Semiarid Grassland

    PubMed Central

    Nakas, J. P.; Klein, D. A.

    1980-01-01

    A radiotracer glucose mineralization assay was used with streptomycin and actidione to monitor the relative seasonal contributions of bacteria and fungi to mineralization processes in soils derived from the rhizosphere-rhizoplane zone of plants from a shortgrass prairie ecosystem. Bacteria played a major role in glucose mineralization in both the rhizosphere and rhizoplane. These results indicate that the bacteria may play a greater role in glucose mineralization processes in the rhizosphere and rhizoplane zones of a semiarid grassland than would be assumed, based on available biomass estimates. This technique appears to be valuable for determining bacterial versus fungal contributions to glucose mineralization in the rhizosphere and rhizoplane and may be useful for measuring the decomposition of other more complex substances in this zone of intense microbial activity. PMID:16345485

  3. High-rate denitrification using polyethylene glycol gel carriers entrapping heterotrophic denitrifying bacteria.

    PubMed

    Isaka, Kazuichi; Kimura, Yuya; Osaka, Toshifumi; Tsuneda, Satoshi

    2012-10-15

    This study evaluated the nitrogen removal performance of polyethylene glycol (PEG) gel carriers containing entrapped heterotrophic denitrifying bacteria. A laboratory-scale denitrification reactor was operated for treatment of synthetic nitrate wastewater. The nitrogen removal activity gradually increased in continuous feed experiments, reaching 4.4 kg N m(-3) d(-1) on day 16 (30 °C). A maximum nitrogen removal rate of 5.1 kg N m(-3) d(-1) was observed. A high nitrogen removal efficiency of 92% on average was observed at a high loading rate. In batch experiments, the denitrifying gel carriers were characterized by temperature. Nitrate and total nitrogen removal activities both increased with increasing temperature, reaching a maximum at 37 and 43 °C, respectively. Apparent activation energies for nitrate and nitrite reduction were 52.1 and 71.9 kJ mol(-1), respectively. Clone library analysis performed on the basis of the 16S rRNA gene revealed that Hyphomicrobium was mainly involved in denitrification in the methanol-fed denitrification reactors. PMID:22828382

  4. Diazotrophic diversity in the rhizosphere of two exotic weed plants, Prosopis juliflora and Parthenium hysterophorus.

    PubMed

    Cibichakravarthy, B; Preetha, R; Sundaram, S P; Kumar, K; Balachandar, D

    2012-02-01

    This study is aimed at assessing culturable diazotrophic bacterial diversity in the rhizosphere of Prosopis juliflora and Parthenium hysterophorus, which grow profusely in nutritionally-poor soils and environmentally-stress conditions so as to identify some novel strains for bioinoculant technology. Diazotrophic isolates from Prosopis and Parthenium rhizosphere were characterized for nitrogenase activity by Acetylene Reduction Assay (ARA) and 16S rRNA gene sequencing. Further, the culture-independent quantitative PCR (qPCR) was performed to compare the abundance of diazotrophs in rhizosphere with bulk soils. The proportion of diazotrophs in total heterotrophs was higher in rhizosphere than bulk soils and 32 putative diazotrophs from rhizosphere of two plants were identified by nifH gene amplification. The ARA activity of the isolates ranged from 40 to 95 nmol ethylene h(-1) mg protein(-1). The 16S rRNA gene analysis identified the isolates to be members of alpha, beta and gamma Proteobacteria and firmicutes. The qPCR assay also confirmed that abundance of nif gene in rhizosphere of these two plants was 10-fold higher than bulk soil.

  5. Metaproteomic analysis of ratoon sugarcane rhizospheric soil

    PubMed Central

    2013-01-01

    Background The current study was undertaken to elucidate the mechanism of yield decline in ratoon sugarcane using soil metaproteomics combined with community level physiological profiles (CLPP) analysis. Results The available stalk number, stalk diameter, single stalk weight and theoretical yield of ratoon cane (RS) were found to be significantly lower than those of plant cane (NS). The activities of several carbon, nitrogen and phosphorus processing enzymes, including invertase, peroxidase, urease and phosphomonoesterase were found to be significantly lower in RS soil than in NS soil. BIOLOG analysis indicated a significant decline in average well-color development (AWCD), Shannon’s diversity and evenness indices in RS soil as compared to NS soil. To profile the rhizospheric metaproteome, 109 soil protein spots with high resolution and repeatability were successfully identified. These proteins were found to be involved in carbohydrate/energy, amino acid, protein, nucleotide, auxin and secondary metabolisms, membrane transport, signal transduction and resistance, etc. Comparative metaproteomics analysis revealed that 38 proteins were differentially expressed in the RS soil as compared to the control soil or NS soil. Among these, most of the plant proteins related to carbohydrate and amino acid metabolism and stress response were up-regulated in RS soil. Furthermore, several microbial proteins related to membrane transport and signal transduction were up-regulated in RS soil. These proteins were speculated to function in root colonization by microbes. Conclusions Our experiments revealed that sugarcane ratooning practice induced significant changes in the soil enzyme activities, the catabolic diversity of microbial community, and the expression level of soil proteins. They influenced the biochemical processes in the rhizosphere ecosystem and mediated the interactions between plants and soil microbes. PMID:23773576

  6. Fate of aniline and sulfanilic acid in UASB bioreactors under denitrifying conditions.

    PubMed

    Pereira, Raquel; Pereira, Luciana; van der Zee, Frank P; Madalena Alves, M

    2011-01-01

    Two upflow anaerobic sludge blanket (UASB) reactors were operated to investigate the fate of aromatic amines under denitrifying conditions. The feed consisted of synthetic wastewater containing aniline and/or sulfanilic acid and a mixture of volatile fatty acids (VFA) as the primary electron donors. Reactor 1 (R1) contained a stoichiometric concentration of nitrate and Reactor 2 (R2) a stoichiometric nitrate and nitrite mixture as terminal electron acceptors. The R1 results demonstrated that aniline could be degraded under denitrifying conditions while sulfanilic acid remains. The presence of nitrite in the influent of R2, caused a chemical reaction that led to immediate disappearance of both aromatic amines and the formation of an intense yellow coloured solution. HPLC analysis of the influent solution, revealed the emergence of three product peaks: the major one at retention time (R(t)) 14.3 min and two minor at R(t) 17.2 and 21.5 min. In the effluent, the intensity of the peaks at R(t) 14.3 and 17.2 min was very low and of that at R(t) 21.5 min increased (∼3-fold). Based on the mass spectrometry analysis, we propose the structures of some possible products, mainly azo compounds. Denitrification activity tests suggest that biomass needed to adapt to the new coloured compounds, but after a 3 days lag phase, activity is recovered and the final (N(2) + N(2)O) is even higher than that of the control.

  7. Understanding Aquatic Rhizosphere Processes Through Metabolomics and Metagenomics Approach

    NASA Astrophysics Data System (ADS)

    Lee, Yong Jian; Mynampati, Kalyan; Drautz, Daniela; Arumugam, Krithika; Williams, Rohan; Schuster, Stephan; Kjelleberg, Staffan; Swarup, Sanjay

    2013-04-01

    20mg/L of naphthalene and reached a new steady state within 72 hours. An active microbial biofilm was formed during this process, which was imaged by light microscopy and confocal laser scanning microscopy and showed active changes in the biofilm. We have begun to unravel the complexity of rhizobacterial communities associated with aquatic plants. Using fluorescence in-situ hybridization (FISH) and Illumina Miseq Next Generation Sequencing of metagenomic DNA, we investigated the root-associated microbial community of P. amaryllifolius grown in two different water sources. The community structure of rhizobacteria from plants grown in freshwater lake or rainwater stored in tanks are highly similar. The top three phyla in both setups belonged to Proteobacteria, Bacteriocedes and Actinobacteria, as validated by FISH analyses. This suggests that the rhizosphere have an innate ability to attract and recruit rhizobacterial communities, possibly through the metabolic compounds secreted through root exudation. The selection pressure through plant host is higher compared to environmental pressures that are different between the two water sources. In comparison with the terrestrial rhizosphere, the aquatic rhizosphere microbiome seems more specialised and has a high influence by the host. We are using these findings to further understand the role of microbes in the performance of freshwater aquatic plants.

  8. Rhizosphere priming effects in two contrasting soils

    NASA Astrophysics Data System (ADS)

    Lloyd, Davidson; Kirk, Guy; Ritz, Karl

    2015-04-01

    Inputs of fresh plant-derived carbon may stimulate the turnover of existing soil organic matter by so-called priming effects. Priming may occur directly, as a result of nutrient 'mining' by existing microbial communities, or indirectly via population adjustments. However the mechanisms are poorly understood. We planted C4 Kikuyu grass (Pennisetum clandestinum) in pots with two contrasting C3 soils (clayey, fertile TB and sandy, acid SH), and followed the soil CO2 efflux and its δ13C. The extent of C deposition in the rhizosphere was altered by intermittently clipping the grass in half the pots; there were also unplanted controls. At intervals, pots were destructively sampled for root and shoot biomass. Total soil CO2 efflux was measured using a gas-tight PVC chamber fitted over bare soil, and connected to an infra-red gas analyser; the δ13C of efflux was measured in air sub-samples withdrawn by syringe. The extent of priming was inferred from the δ13C of efflux and the δ13C of the plant and soil end-members. In unclipped treatments, in both soils, increased total soil respiration and rhizosphere priming effects (RPE) were apparent compared to the unplanted controls. The TB soil had greater RPE overall. The total respiration in clipped TB soil was significantly greater than in the unplanted controls, but in the clipped SH soil it was not significantly different from the controls. Clipping affected plant C partitioning with greater allocation to shoot regrowth from about 4 weeks after planting. Total plant biomass decreased in the order TB unclipped > SH unclipped >TB clipped > SH clipped. The results are consistent with priming driven by microbial activation stimulated by rhizodeposits and by nitrogen demand from the growing plants under N limited conditions. Our data suggest that photosynthesis drives RPE and soil differences may alter the rate and intensity of RPE but not the direction.

  9. Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential.

    PubMed

    Haldar, Shyamalina; Sengupta, Sanghamitra

    2015-01-01

    Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration.

  10. Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential

    PubMed Central

    Haldar, Shyamalina; Sengupta, Sanghamitra

    2015-01-01

    Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration. PMID:25926899

  11. Plant--rhizosphere-microflora association during phytoremediation of PAH-contaminated soil.

    PubMed

    Muratova, A; Hūbner, Th; Tischer, S; Turkovskaya, O; Möder, M; Kuschk, P

    2003-01-01

    The capability of plants to promote the microbial degradation of pollutants in rhizosphere soil is a principal mechanism of phytoremediation of PAH-contaminated soil. The formation of a specific rhizosphere microbocenosis with a high degradative potential toward contaminants is largely determined by plant species. The comparative PAH-degradation in unplanted soil and in soil planted with reed (Phragmites australis) and alfalfa (Medicago sativa) was studied in pot experiments during 2 years. Both alfalfa and reed successfully remediated contaminated soil by degrading 74.5 and 68.7% of PAHs, respectively. The study of the rhizosphere, rhizoplane, and unplanted-soil microflora in experimental pots showed that alfalfa stimulated the rhizosphere microflora of PAH-contaminated soil more effectively than did reed. Alfalfa clearly enhanced both the total number of microorganisms (1.3 times, according to fluorescence microscopy data) and the rate of the PAH-degrading population (almost seven times, according to plate counting). The degradative potential of its rhizosphere microflora toward PAHs was higher than the degradative activity of the reed rhizosphere. This study provides relevant information for the successful application of alfalfa to phytoremediate PAH-contaminated soil.

  12. Autotrophic, hydrogen-oxidizing, denitrifying bacteria in groundwater, potential agents for bioremediation of nitrate contamination

    USGS Publications Warehouse

    Smith, R.L.; Ceazan, M.L.; Brooks, M.H.

    1994-01-01

    Addition of hydrogen or formate significantly enhanced the rate of consumption of nitrate in slurried core samples obtained from an active zone of denitrification in a nitrate-contaminated sand and gravel aquifer (Cape Cod, Mass.). Hydrogen uptake by the core material was immediate and rapid, with an apparent K(m) of 0.45 to 0.60 ??M and a V(max) of 18.7 nmol cm-3 h-1 at 30??C. Nine strains of hydrogen-oxidizing denitrifying bacteria were subsequently isolated from the aquifer. Eight of the strains grew autotrophically on hydrogen with either oxygen or nitrate as the electron acceptor. One strain grew mixotrophically. All of the isolates were capable of heterotrophic growth, but none were similar to Paracoccus denitrificans, a well-characterized hydrogen-oxidizing denitrifier. The kinetics for hydrogen uptake during denitrification were determined for each isolate with substrate depletion progress curves; the K(m)s ranged from 0.30 to 3.32 ??M, with V(max)s of 1.85 to 13.29 fmol cell-1 h-1. Because these organisms appear to be common constituents of the in situ population of the aquifer, produce innocuous end products, and could be manipulated to sequentially consume oxygen and then nitrate when both were present, these results suggest that these organisms may have significant potential for in situ bioremediation of nitrate contamination in groundwater.

  13. Autotrophic, hydrogen-oxidizing, denitrifying bacteria in groundwater, potential agents for bioremediation of nitrate contamination.

    PubMed

    Smith, R L; Ceazan, M L; Brooks, M H

    1994-06-01

    Addition of hydrogen or formate significantly enhanced the rate of consumption of nitrate in slurried core samples obtained from an active zone of denitrification in a nitrate-contaminated sand and gravel aquifer (Cape Cod, Mass.). Hydrogen uptake by the core material was immediate and rapid, with an apparent K(m) of 0.45 to 0.60 muM and a V(max) of 18.7 nmol cm h at 30 degrees C. Nine strains of hydrogen-oxidizing denitrifying bacteria were subsequently isolated from the aquifer. Eight of the strains grew autotrophically on hydrogen with either oxygen or nitrate as the electron acceptor. One strain grew mixotrophically. All of the isolates were capable of heterotrophic growth, but none were similar to Paracoccus denitrificans, a well-characterized hydrogen-oxidizing denitrifier. The kinetics for hydrogen uptake during denitrification were determined for each isolate with substrate depletion progress curves; the K(m)s ranged from 0.30 to 3.32 muM, with V(max)s of 1.85 to 13.29 fmol cell h. Because these organisms appear to be common constituents of the in situ population of the aquifer, produce innocuous end products, and could be manipulated to sequentially consume oxygen and then nitrate when both were present, these results suggest that these organisms may have significant potential for in situ bioremediation of nitrate contamination in groundwater.

  14. Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor

    PubMed Central

    Bin, Zhang; Bin, Xue; Zhigang, Qiu; Zhiqiang, Chen; Junwen, Li; Taishi, Gong; Wenci, Zou; Jingfeng, Wang

    2015-01-01

    Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3−-N could be removed or reduced, some amount of NO2−-N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy. PMID:26257096

  15. Molecular characterization of denitrifying bacteria isolated from the anoxic reactor of a modified DEPHANOX plant performing enhanced biological phosphorus removal.

    PubMed

    Zafiriadis, Ilias; Ntougias, Spyridon; Mirelis, Paraskevi; Kapagiannidis, Anastasios G; Aivasidis, Alexander

    2012-06-01

    Enhanced Biological Phosphorus Removal (EBPR) under anoxic conditions was achieved using a Biological Nutrient Removal (BNR) system based on a modification of the DEPHANOX configuration. Double-probe Fluorescence in Situ Hybridization (FISH) revealed that Polyphosphate Accumulating Organisms (PAOs) comprised 12.3 +/- 3.2% of the total bacterial population in the modified DEPHANOX plant. The growing bacterial population on blood agar and Casitone Glycerol Yeast Autolysate agar (CGYA) medium was 16.7 +/- 0.9 x 10(5) and 3.0 +/- 0.6 x 10(5) colony forming units (cfu) mL(-1) activated sludge, respectively. A total of 121 bacterial isolates were characterized according to their denitrification ability, with 26 bacterial strains being capable of reducing nitrate to gas. All denitrifying isolates were placed within the alpha-, beta-, and gamma-subdivisions of Proteobacteria and the family Flavobacteriaceae. Furthermore, a novel denitrifying bacterium within the genus Pseudomonas was identified. This is the first report on the isolation and molecular characterization of denitrifying bacteria from EBPR sludge using a DEPHANOX-type plant.

  16. Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor

    NASA Astrophysics Data System (ADS)

    Bin, Zhang; Bin, Xue; Zhigang, Qiu; Zhiqiang, Chen; Junwen, Li; Taishi, Gong; Wenci, Zou; Jingfeng, Wang

    2015-08-01

    Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3--N could be removed or reduced, some amount of NO2--N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy.

  17. PLANT RHIZOSPHERE EFFECTS ON METAL MOBILIZATION AND TRANSPORT

    SciTech Connect

    Fan, Teresa W.-M; Higashi, Richard M.; Crowley, David E.

    2000-12-31

    The myriad of human activities including strategic and energy development at various DOE installations have resulted in the contamination of soils and waterways that can seriously threaten human and ecosystem health. Development of efficacious and economical remediation technologies is needed to ameliorate these immensely costly problems. Bioremediation (both plant and microbe-based) has promising potential to meet this demand but still requires advances in fundamental knowledge. For bioremediation of heavy metals, the three-way interaction of plant root, microbial community, and soil organic matter (SOM) in the rhizosphere is critically important for long-term sustainability but often underconsidered. Particularly urgent is the need to understand processes that lead to metal ion stabilization in soils, which is crucial to all of the goals of bioremediation: removal, stabilization, and transformation. We have developed the tools for probing the chemistry of plant rhizosphere and generated information regarding the role of root exudation and metabolism for metal mobilization and sequestration.

  18. Interactions of methanogens and denitrifiers in degradation of phenols

    SciTech Connect

    Fang, H.H.P.; Zhou, G.M.

    1999-01-01

    Experiments were conducted at 37 C in an upflow anaerobic sludge blanket reactor treating wastewater containing phenol, m-cresol, and nitrate at various concentrations. Results show that anaerobic sludge was able to conduct denitrification without much acclimation. Denitrifiers outcompeted methanogens for substrates for carbon and electron supplies. They were able to use phenol and m-cresol as substrate without a carbohydrate cosubstrate. Denitrifying 1 g of NO{sub 3}{sup {minus}}-N ratios greater than 3.34. At the ratio of 5.23, over 98% of phenol but only 60% of m-cresol were degraded jointly by denitrifiers and methanogens with 1 day of hydraulic retention. At ratios less than 3.34, methanogenesis ceased to take place and denitrification became incomplete because of insufficient supply of substrate. Batch tests further confirmed that degradation of m-cresol was enhanced not only by the presence of nitrate, but also by the presence of either sucrose or phenol as cosubstrate.

  19. Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens and plant growth promoting abilities.

    PubMed

    Adam, Eveline; Müller, Henry; Erlacher, Armin; Berg, Gabriele

    2016-01-01

    The Serratia plymuthica strains 3Rp8 and 3Re4-18 are motile, Gram-negative, non-sporulating bacteria. Strain 3Rp8 was isolated from the rhizosphere of Brassica napus L. and strain 3Re4-18 from the endorhiza of Solanum tuberosum L. Studies have shown in vitro activity against the soil-borne fungi Verticillium dahliae Kleb., Rhizoctonia solani Kühn, and Sclerotinia sclerotiorum. Here, we announce and describe the complete genome sequence of S. plymuthica 3Rp8 consisting of a single circular chromosome of 5.5 Mb that encodes 4954 protein-coding and 108 RNA-only encoding genes and of S. plymuthica 3Re4-18 consisting of a single circular chromosome of 5.4 Mb that encodes 4845 protein-coding and 109 RNA-only encoding genes. The whole genome sequences and annotations are available in NCBI under the locus numbers CP012096 and CP012097, respectively. The genome analyses revealed genes putatively responsible for the promising plant growth promoting and biocontrol properties including predicting factors such as secretion systems, iron scavenging siderophores, chitinases, secreted proteases, glucanases and non-ribosomal peptide synthetases, as well as unique genomic islands. PMID:27602183

  20. Purple Phototrophic Bacterium Enhances Stevioside Yield by Stevia rebaudiana Bertoni via Foliar Spray and Rhizosphere Irrigation

    PubMed Central

    Wu, Jing; Wang, Yiming; Lin, Xiangui

    2013-01-01

    This study was conducted to compare the effects of foliar spray and rhizosphere irrigation with purple phototrophic bacteria (PPB) on growth and stevioside (ST) yield of Stevia. rebaudiana. The S. rebaudiana plants were treated by foliar spray, rhizosphere irrigation, and spray plus irrigation with PPB for 10 days, respectively. All treatments enhanced growth of S. rebaudiana, and the foliar method was more efficient than irrigation. Spraying combined with irrigation increased the ST yield plant -1 by 69.2% as compared to the control. The soil dehydrogenase activity, S. rebaudiana shoot biomass, chlorophyll content in new leaves, and soluble sugar in old leaves were affected significantly by S+I treatment, too. The PPB probably works in the rhizosphere by activating the metabolic activity of soil bacteria, and on leaves by excreting phytohormones or enhancing the activity of phyllosphere microorganisms. PMID:23825677

  1. Atrazine degradation in a containerized rhizosphere system.

    PubMed

    Costa, R M; Camper, N D; Riley, M B

    2000-11-01

    The effect of atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) on rhizosphere microorganisms and its fate in a containerized rhizosphere system was studied. The rhizosphere system consisted of corn grown in pot containing a defined potting mix of sand and bark with atrazine. Sterilized potting mix and a container without plants served as controls. Atrazine was extracted and analyzed via HPLC. Fluorescent pseudomonad populations increased 100-fold in the rhizposphere during a 60-day incubation period as compared to the nonvegetated control. Atrazine degradation was higher in the rhizosphere system (half-life of 7 days) compared to the nonvegetated control (half-life of greater than 45 days). The major degradation product detected in the rhizosphere system was deisopropylatrazine; other products detected included deethylatrazine, deethylhydroxyatrazine, deisopropylatrazine and hydroxyatrazine. Hydroxyatrazine was detected in the nonvegetated and sterile controls. The containerized rhizosphere system provides an experimental system to study the fate of pesticidal chemicals as well as the effects on microbial populations. PMID:11069012

  2. Plant-Microbial Interactions Define Potential Mechanisms of Organic Matter Priming in the Rhizosphere

    NASA Astrophysics Data System (ADS)

    Zhalnina, K.; Cho, H. J.; Hao, Z.; Mansoori, N.; Karaoz, U.; Jenkins, S.; White, R. A., III; Lipton, M. S.; Deng, K.; Zhou, J.; Pett-Ridge, J.; Northen, T.; Firestone, M. K.; Brodie, E.

    2015-12-01

    In the rhizosphere, metabolic processes of plants and microorganisms are closely coupled, and together with soil minerals, their interactions regulate the turnover of soil organic C (SOC). Plants provide readily assimilable metabolites for microorganisms through exudation, and it has been hypothesized that increasing concentrations of exudate C may either stimulate or suppress rates of SOC mineralization (rhizosphere priming). Both positive and negative rhizosphere priming has been widely observed, however the underlying mechanisms remain poorly understood. To begin to identify the molecular mechanisms underlying rhizosphere priming, we isolated a broad range of soil bacteria from a Mediterranean grassland dominated by annual grass. Thirty-nine heterotrophic bacteria were selected for genome sequencing and both rRNA gene analysis and metagenome coverage suggest that these isolates represent naturally abundant strain variants. We analyzed their genomes for potential metabolic traits related to life in the rhizosphere and the decomposition of polymeric SOC. While the two dominant groups, Alphaproteobacteria and Actinobacteria, were enriched in polymer degrading enzymes, Alphaproteobacterial isolates contained greater gene copies of transporters related to amino acid, organic acid and auxin uptake or export, suggesting an enhanced metabolic potential for life in the root zone. To verify this metabolic potential, we determined the enzymatic activities of these isolates and revealed preferences of strains to degrade certain polymers (xylan, cellulose or lignin). Fourier Transform Infrared spectroscopy is being used to determine which polymeric components of plant roots are targeted by specific strains and how exudates may impact their degradation. To verify the potential of isolates to assimilate root exudates and export key metabolites we are using LC-MS/MS based exometabolomic profiling. The traits hypothesized and verified here (transporters, enzymes, exudate uptake

  3. Halobacterium denitrificans sp. nov. - An extremely halophilic denitrifying bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  4. Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  5. Rhizosphere impacts on peat decomposition and nutrient cycling across a natural water table gradient

    NASA Astrophysics Data System (ADS)

    Gill, A. L.; Finzi, A.

    2014-12-01

    High latitude forest and peatland soils represent a major terrestrial carbon store sensitive to climate change. Warming temperatures and increased growing-season evapotranspiration are projected to reduce water table (WT) height in continental peatlands. WT reduction increases peat aerobicity and facilitates vascular plant and root growth. Root-associated microbial communities are exposed to a different physical and chemical environment than microbial communities in non-root associated "bulk" peat, and therefore have distinct composition and function within the soil system. As the size of the peatland rhizosphere impacts resources available to the microbial communities, transitions from a root-free high water table peatland to a root-dominated low WT peatland may alter seasonal patterns of microbial community dynamics, enzyme production, and carbon storage within the system. We used a natural water table gradient in Caribou Bog near Orono, ME to explore the influence of species composition, root biomass, and rhizosphere size on seasonal patterns in microbial community structure, enzyme production, and carbon mineralization. We quantified root biomass across the water table gradient and measured microbial biomass carbon and nitrogen, C mineralization, N mineralization, and exoenzyme activity in root-associated and bulk peat samples throughout the 2013 growing season. Microbial biomass was consistently higher in rhizosphere-associated soils and peaked in the spring. Microbial biomass CN and enzyme activity was higher in rhizosphere-associated soil, likely due to increased mycorrhizal abundance. Exoenzyme activity peaked in the fall, with a larger relative increase in enzyme activity in rhizosphere peat, while carbon mineralization rates did not demonstrate a strong seasonal pattern. The results suggest that rhizosphere-associated peat sustains higher and more variable rates of enzyme activity throughout the growing season, which results in higher rates of carbon

  6. Distribution of 152Eu and 154Eu in the 'alluvial soil-rhizosphere-plant roots' system.

    PubMed

    Kropatcheva, Marya; Chuguevsky, Alexei; Melgunov, Mikhail

    2012-04-01

    Accumulation of (152)Eu and (15)(4)Eu isotopes in bulk soil and rhizosphere soil in the near-field zone of influence of the Krasnoyarsk Mining and Chemical Combine was studied. An uneven distribution of specific activity of Eu isotopes was observed, with the gross specific activities of the isotopes in the bulk soil exceeding those of the rhizosphere. In the most contaminated locations the fine and the coarse granulometric fractions are enriched with the isotopes. A laboratory experiment indicated potential removal of soluble Eu isotopes by river flood waters may amount to 3% of the total Eu in both bulk and rhizosphere soils. The root system of plants growing in the contaminated territory accumulates (152)Eu and (154)Eu, although the isotopes were not discovered in aboveground parts of plants. Root-hairs were found to be the most contaminated.

  7. Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

    NASA Astrophysics Data System (ADS)

    Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

    2012-12-01

    Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant

  8. Rhizosphere: a leverage for tolerance to water deficits of soil microflora ?

    NASA Astrophysics Data System (ADS)

    Bérard, Annette; Ruy, Stéphane; Coronel, Anaïs; Toussaint, Bruce; Czarnes, Sonia; Legendre, Laurent; Doussan, Claude

    2015-04-01

    Microbial soil communities play a fundamental role in soil organic matter mineralization, which is a key process for plant nutrition, growth and production in agro-ecosystems. A number of these microbial processes take place in the rhizosphere: the soil zone influenced by plant roots activity, which is a "hotspot " of biological and physico-chemical activity, transfers and biomass production. The knowledge of rhizosphere processes is however still scanty, especially regarding the interactions between physico-chemical processes occurring there and soil microorganisms. The rhizosphere is a place where soil aggregates are more stable, and where bulk density, porosity, water and nutrients transfer are modified with respect to the bulk soil (e.g. because of production of mucilage, of which exo-polysaccharides (EPS) produced by roots and microorganisms. During a maize field experiment, rhizospheric soil (i.e. soil strongly adhering to maize roots) and bulk soil were sampled twice in spring and summer. These soil samples were characterized for physicochemical parameters (water retention curves and analysis of exopolysaccarides) and microflora (microbial biomass, catabolic capacities of the microbial communities assessed with the MicroRespTM technique, stability of soil microbial respiration faced to a heat-drought disturbance). We observed differences between rhizospheric and bulk soils for all parameters studied: Rhizospheric soils showed higher microbial biomasses, higher quantities of exopolysaccarides and a higher water retention capacity compared to bulk soil measurements. Moreover, microbial soil respiration showed a higher stability confronted to heat-drought stress in the rhizospheric soils compared to bulk soils. Results were more pronounced during summer compared to spring. Globally these data obtained from field suggest that in a changing climate conditions, the specific physico-biological conditions in the rhizosphere partially linked to exopolysaccarides

  9. Anaerobic metabolism of phthalate and other aromatic compounds by a denitrifying bacterium. [Pseudomonas sp

    SciTech Connect

    Nozawa, T.; Maruyama, Y. )

    1988-12-01

    The anaerobic metabolism of phthalate and other aromatic compounds by the denitrifying bacterium Pseudomonas sp. strain P136 was studied. Benzoate, cyclohex-1-ene-carboxylate, 2-hydroxycyclohexanecarboxylate, and pimelate were detected as predominant metabolic intermediates during the metabolism of three isomers of phthalate, m-hydroxybenzoate, p-hydroxybenzoate, and cyclohex-3-ene-carboxylate. Inducible acyl-coeznyme A synthetase activities for phthalates, benzoate, cyclohex-1-ene-carboxylate, and cyclohex-3-ene-carboxylate were detected in the cells grown on aromatic compounds. Simultaneous adaptation to these aromatic compounds also occurred. A similar phenomenon was observed in the aerobic metabolism of aromatic compounds by this strain. A new pathway for the anaerobic metabolism of phthalate and a series of other aromatic compounds by this strain was proposed. Some properties of the regulation of this pathway were also discussed.

  10. Isolation and functional analysis of denitrifiers in an aquifer with high potential for denitrification.

    PubMed

    Bellini, M Inés; Gutiérrez, Lucía; Tarlera, Silvana; Scavino, Ana Fernández

    2013-10-01

    Aquifers are among the main freshwater sources. The Raigón aquifer is susceptible to contamination, mainly by nitrate and pesticides, such as atrazine, due to increasing agricultural activities in the area. The capacity of indigenous bacteria to attenuate nitrate contamination in different wells of this aquifer was assessed by measuring denitrification rates with either acetate plus succinate or nitrate amendments. Denitrification activity in nitrate-amended assays was significantly higher than in unamended assays, particularly in groundwater from wells where nitrate concentration was 33.5 mg L(-1) or lower. Furthermore, groundwater denitrifiers capable of using acetate or succinate as electron donors were isolated, identified by 16S rRNA gene sequencing and evaluated for functional denitrification genes (nirS, nirK and nosZ). Phylogenetic affiliation of 54 isolates showed that all members belonged to nine different genera within the Proteobacteria (Bosea, Ochrobactrum, Azospira, Zoogloea, Acidovorax, Achromobacter, Vogesella, Stenotrophomonas and Pseudomonas). In addition, isolate AR28 that clustered separately from validly described species could potentially belong to a new genus. The majority of the isolates were related to species belonging to previously reported denitrifying genera. However, the phylogeny of the nirS and nosZ genes revealed new sequences of these functional genes. To our knowledge, this is the first isolation and sequencing of the nirS gene from the genus Vogesella, as well as the nosZ gene from the genera Acidovorax and Zoogloea. The results indicated that indigenous bacteria in the Raigón aquifer had the capacity to overcome high nitrate contamination and exhibited functional gene diversity.

  11. Continuous nitrous oxide abatement in a novel denitrifying off-gas bioscrubber.

    PubMed

    Frutos, Osvaldo D; Arvelo, Ilan A; Pérez, Rebeca; Quijano, Guillermo; Muñoz, Raúl

    2015-04-01

    The potential of a bioscrubber composed of a packed bed absorption column coupled to a stirred tank denitrification bioreactor (STR) was assessed for 95 days for the continuous abatement of a diluted air emission of N2O at different liquid recycling velocities. N2O removal efficiencies of up to 40 ± 1 % were achieved at the highest recirculation velocity (8 m h(-1)) at an empty bed residence time of 3 min using a synthetic air emission containing N2O at 104 ± 12 ppmv. N2O was absorbed in the packed bed column and further reduced in the STR at efficiencies >80 % using methanol as electron donor. The long-term operation of the bioscrubber suggested that the specialized N2O degrading community established was not able to use N2O as nitrogen source. Additional nitrification assays showed that the activated sludge used as inoculum was not capable of aerobically oxidizing N2O to nitrate or nitrite, regardless of the inorganic carbon concentration tested. Denitrification assays confirmed the ability of non-acclimated activated sludge to readily denitrify N2O at a specific rate of 3.9 mg N2O g VSS h(-1) using methanol as electron donor. This study constitutes, to the best of our knowledge, the first systematic assessment of the continuous abatement of N2O in air emission. A characterization of the structure of the microbial population in the absorption column by DGGE-sequencing revealed a high microbial diversity and the presence of heterotrophic denitrifying methylotrophs. PMID:25547842

  12. Effects of preconditioning the rhizosphere of different plant species on biotic methane oxidation kinetics.

    PubMed

    Ndanga, Éliane M; Lopera, Carolina B; Bradley, Robert L; Cabral, Alexandre R

    2016-09-01

    The rhizosphere is known as the most active biogeochemical layer of the soil. Therefore, it could be a beneficial environment for biotic methane oxidation. The aim of this study was to document - by means of batch incubation tests - the kinetics of CH4 oxidation in rhizosphere soils that were previously exposed to methane. Soils from three pre-exposure to CH4 zones were sampled: the never-before pre-exposed (NEX), the moderately pre-exposed (MEX) and the very pre-exposed (VEX). For each pre-exposure zone, the rhizosphere of several plant species was collected, pre-incubated, placed in glass vials and submitted to CH4 concentrations varying from 0.5% to 10%. The time to the beginning of CH4 consumption and the CH4 oxidation rate were recorded. The results showed that the fastest CH4 consumption occurred for the very pre-exposed rhizosphere. Specifically, a statistically significant difference in CH4 oxidation half-life was found between the rhizosphere of the VEX vegetated with a mixture of different plants and the NEX vegetated with ryegrass. This difference was attributed to the combined effect of the preconditioning level and plant species as well as to the organic matter content. Regardless of the preconditioning level, the oxidation rate values obtained in this study were comparable to those reported in the reviewed literature for mature compost.

  13. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Yuan, Quan; Conrad, Ralf

    2015-03-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  14. Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

    PubMed Central

    Hernández, Marcela; Yuan, Quan; Conrad, Ralf

    2015-01-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the “Spartobacteria” and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  15. Influence of ozone and simulated acidic rain on microorganisms in the rhizosphere of Sorghum.

    PubMed

    Shafer, S R

    1988-01-01

    Seedlings of a sorghum x sudangrass hybrid in pots of non-sterile soil-sand mix were exposed to ozone (O(3)) at 0, 0.15, or 0.30 microl litre(-1) (7 h day(-1), 3 days week(-1)) and simulated rain (SR) adjusted with H(2)SO(4) + HNO(3) to pH 5.5, 4.0, or 2.5 (2 cm in 1.5 h per event; 2 events week(-1)) over 3 weeks in a greenhouse. Ozone suppressed shoot and root growth, but increased acid content (i.e. pH < 5.5) of SR stimulated shoot growth and had inconsistent effects on root growth. Ozone x SR chemistry interactions significantly affected plant growth. Data for 'total' bacterial populations in the rhizosphere (number of colony-forming units per gram of rhizosphere soil) exhibited a curvilinear relationship with O(3) (maximum at 0.15 microl liter(-1)). Increased acid content of SR stimulated numbers of 'total' bacteria but suppressed populations of amylolytic bacteria. Ozone and acid content of SR tended to stimulate numbers of fungal propagules in the rhizosphere, but this effect was not significant. Numbers of rhizosphere bacteria capable of phosphatase activity increased linearly with O(3), but only when SR chemistry was characterised by pH 4.0. Data for other populations of rhizosphere microorganisms did not exhibit significant relationships to O3 x SR chemistry interactions.

  16. Isolation and characterization of phenol-degrading denitrifying bacteria.

    PubMed

    van Schie, P M; Young, L Y

    1998-07-01

    Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, N.Y., a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus. The results of this study add three new members to the genus Azoarcus, which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.

  17. Isolation and characterization of phenol-degrading denitrifying bacteria

    SciTech Connect

    Schie, P.M. van; Young, L.Y.

    1998-07-01

    Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, NY, a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus. The results of this study add three new members to the genus Azoarcus, which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.

  18. Characterization of selected groups of microorganisms occurring in soil rhizosphere and phyllosphere of oats.

    PubMed

    Rekosz-Burlaga, Hanna; Garbolińska, Magdalena

    2006-01-01

    Studies were carried out on the microflora of phyllosphere and soil rhizosphere of hulled (Chwat variety) and naked (Akt variety) oats. The material taken for study embraced samples of leaves and soil rhizosphere taken from cultivations differing in extent of nitrogen fertilization. The studies involved determination of total number of aerobic heterotrophic bacteria belonging to the genus Pseudomonas and microscopic hyphal fungi. Qualitative determinations focused on bacteria belonging to the genera Azotobacter and Azospirillum were also made. Our results point to differences in number of microscopic hyphal fungi in the phyllosphere of both varieties of oats, depending on nitrogen fertilization dose. However, there were no significant differences in the number of bacteria of the different genera determined in the phyllosphere and rhizosphere. Strains of oligonitrophilic and diazotrophic bacteria were isolated from samples of the phyllosphere of oats and their N2-fixing activity was determined by the acetylene reduction method using gas chromatography.

  19. Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants

    PubMed Central

    Bourceret, Amélia; Leyval, Corinne; de Fouquet, Chantal; Cébron, Aurélie

    2015-01-01

    Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH) biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi), and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging) revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron. PMID:26599438

  20. Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments

    PubMed Central

    Fan, Haoxin; Bolhuis, Henk; Stal, Lucas J.

    2015-01-01

    The fixation of dinitrogen (N2) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L−1 d−1 and from undetectable to 8.2 nmol N g−1 d−1 in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 μmol m−2 d−1 and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen

  1. Rate of denitrification and the accumulation of intermediates in a denitrifying bioreactor

    NASA Astrophysics Data System (ADS)

    Parsignault, D. R.; Gursky, H.; Kellogg, E. M.; Matilsky, T.; Murray, S.; Schreier, E.; Tananbaum, H.; Giacconi, R.; Brinkman, A. C.

    2012-12-01

    Denitrifying bioreactors (DNBRs) are an emerging mechanism to mitigate the impact of excess reactive nitrogen by harnessing the activity of ubiquitous denitrifying soil microbes. DNBRs fundamentally consist of an organic carbon energy source sufficiently saturated to develop anaerobic conditions and support heterotrophic reduction of nitrate to dinitrogen. Although recent research has well established achievable nitrate removal in DNBRs upwards of 90%, few studies experimentally determine the fate of nitrogen in these systems. This study differentiates between denitrification to inert nitrogen gas, which permanently removes reactive nitrogen from an enriched ecosystem, and transformation of nitrate to another bioavailable form (such as N2O or NOX, powerful greenhouse gases). Previous research has failed to make this distinction and as both are perceived as a reduction in nitrate concentration at the outlet, the utility of DNBRs in reducing downstream reactive nitrogen has not been sufficiently established. In order to quantify the rate of nitrate removal and the products produced, dissolved gas samples are collected from the DNBR with passive diffusion gas samplers while the influent and effluent nitrate concentration and chemical oxygen demand are monitored in real time with spectrometer probes. Nitrate removal is compared with the denitrification rate and the ratio of dinitrogen to nitrous oxide is reported. Denitrification is quantified from the proportion of nitrogen gas products produced from the nitrate pool, indicated by the negative congruence of the regression of 15N enrichment in the nitrate pool and temporal depletion in the gaseous products. The proportion of nitrous oxide to dinitrogen is examined with respect to saturation and redox potential. This research informs the interpretation of previous studies as well as advises the focus of long-term system level monitoring that will provide further information on the design and application of DNBRs to

  2. In vivo emission of dinitrogen by earthworms via denitrifying bacteria in the gut.

    PubMed

    Horn, Marcus A; Mertel, Ralph; Gehre, Matthias; Kästner, Matthias; Drake, Harold L

    2006-02-01

    Earthworms emit the greenhouse gas nitrous oxide (N2O), and ingested denitrifiers in the gut appear to be the main source of this N2O. The primary goal of this study was to determine if earthworms also emit dinitrogen (N2), the end product of complete denitrification. When [15N]nitrate was injected into the gut, the earthworms Aporrectodea caliginosa and Lumbricus terrestris emitted labeled N2 (and also labeled N2O) under in vivo conditions; emission of N2 by these two earthworms was relatively linear and approximated 1.2 and 6.6 nmol N2 per h per g (fresh weight), respectively. Isolated gut contents also produced [15N]nitrate-derived N2 and N2O under anoxic conditions. N2 is formed by N2O reductase, and acetylene, an inhibitor of this enzyme, inhibited the emission of [15N]nitrate-derived N2 by living earthworms. Standard gas chromatographic analysis demonstrated that the amount of N2O emitted was relatively linear during initial incubation periods and increased in response to acetylene. The calculated rates for the native emissions of N2 (i.e., without added nitrate) by A. caliginosa and L. terrestris were 1.1 and 1.5 nmol N2 per h per g (fresh weight), respectively; these emission rates approximated that of N2O. These collective observations indicate that (i) earthworms emit N2 concomitant with the emission of N2O via the in situ activity of denitrifying bacteria in the gut and (ii) N2O is quantitatively an important denitrification-derived end product under in situ conditions.

  3. Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments.

    PubMed

    Fan, Haoxin; Bolhuis, Henk; Stal, Lucas J

    2015-01-01

    The fixation of dinitrogen (N2) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L(-1) d(-1) and from undetectable to 8.2 nmol N g(-1) d(-1) in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 μmol m(-2) d(-1) and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen

  4. Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.

    PubMed

    Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M Dolors; Colprim, Jesús; Bañeras, Lluís

    2013-01-01

    The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A · m(-3) NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A · m(-3) NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.

  5. Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea.

    PubMed

    Yang, Shan; Sun, Wei; Zhang, Fengli; Li, Zhiyong

    2013-10-01

    To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis. PMID:23564007

  6. Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

    PubMed Central

    Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M. Dolors; Colprim, Jesús; Bañeras, Lluís

    2013-01-01

    The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m−3 NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m−3 NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation. PMID:23717427

  7. In vivo emission of dinitrogen by earthworms via denitrifying bacteria in the gut.

    PubMed

    Horn, Marcus A; Mertel, Ralph; Gehre, Matthias; Kästner, Matthias; Drake, Harold L

    2006-02-01

    Earthworms emit the greenhouse gas nitrous oxide (N2O), and ingested denitrifiers in the gut appear to be the main source of this N2O. The primary goal of this study was to determine if earthworms also emit dinitrogen (N2), the end product of complete denitrification. When [15N]nitrate was injected into the gut, the earthworms Aporrectodea caliginosa and Lumbricus terrestris emitted labeled N2 (and also labeled N2O) under in vivo conditions; emission of N2 by these two earthworms was relatively linear and approximated 1.2 and 6.6 nmol N2 per h per g (fresh weight), respectively. Isolated gut contents also produced [15N]nitrate-derived N2 and N2O under anoxic conditions. N2 is formed by N2O reductase, and acetylene, an inhibitor of this enzyme, inhibited the emission of [15N]nitrate-derived N2 by living earthworms. Standard gas chromatographic analysis demonstrated that the amount of N2O emitted was relatively linear during initial incubation periods and increased in response to acetylene. The calculated rates for the native emissions of N2 (i.e., without added nitrate) by A. caliginosa and L. terrestris were 1.1 and 1.5 nmol N2 per h per g (fresh weight), respectively; these emission rates approximated that of N2O. These collective observations indicate that (i) earthworms emit N2 concomitant with the emission of N2O via the in situ activity of denitrifying bacteria in the gut and (ii) N2O is quantitatively an important denitrification-derived end product under in situ conditions. PMID:16461643

  8. Different response of nitrifiers and denitrifiers to re-wetting shape the NO release from soils in laboratory incubation experiments

    NASA Astrophysics Data System (ADS)

    Behrendt, Thomas; Wu, Dianming; Song, Guozheng; Pommerenke, Bianca; Braker, Gesche

    2014-05-01

    Laboratory incubation studies incubating soils at a wide range of soil moistures, soil temperatures and mixing ratios of NO in the headspace and inorganic nutrient contents (NH4+,NO3-, NO2-) showed that release rates of NO follow an exponential function with increasing soil temperature and an optimum function for soil moisture. This approach assumes that environmental factors play the dominant role in shaping an ecosystem and thereby microbial communities and control the NO release from soil. We determined the NO release rate for a dryland farming soil under flooding irrigation in Xinjiang, China, a mid-latitude agricultural soil (Mainz, Germany), and a rice paddy (Ambai, India) upon wetting and subsequent drying out of soils. Only the release rate for the mid-latitude agricultural soil followed an optimum function for soil moisture. Release rates for the dryland farming soil and rice paddy, however, followed a two maxima function with distinct maxima at higher and lower soil moisture. Acknowledgement of two distinct maxima is critical for more accurately assessing regional biogenic NO emissions of soils under field conditions. To analyse the response of nitrifiers and denitrifiers involved in NO turnover in more detail we linked molecular analysis of functional gene expression (nirK and nirS, bacterial and archaeal amoA) and microbial community composition to NO release rates. We could show that the maximal transcriptional activity of denitrifiers and ammonia oxidizers differs with soil moisture and that higher transcriptional activity of nirS-type denitrifiers at higher soil moisture and of archaeal ammonia oxidizers at lower soil moisture may explain the two maxima for NO release.

  9. Effects of elevated CO2 concentrations on denitrifying and nitrifying popualtions at terrestrial CO2 leakeage analogous sites

    NASA Astrophysics Data System (ADS)

    Christine, Dictor Marie; Catherine, Joulian; Valerie, Laperche; Stephanie, Coulon; Dominique, Breeze

    2010-05-01

    CO2 capture and geological storage (CCS) is recognized to be an important option for carbon abatement in Europe. One of the risks of CCS is the leakage from storage site. A laboratory was conducted on soil samples sampled near-surface from a CO2 leakage analogous site (Latera, Italy) in order to evaluate the impact of an elevated soil CO2 concentration on terrestrial bacterial ecosystems form near surface terrestrial environments and to determine a potential bacterial indicator of CO2 leakage from storage site. Surveys were conducted along a 50m long transect across the vent centre, providing a spectrum of CO2 flux rates, soil gas concentrations and compositions (Beaubien et al., 2007). A bacterial diversity studies, performed by CE-SSCP technique, on a soil profile with increasing CO2 soil concentrations (from 0.3% to 100%) showed that a change on bacterial diversity was noted when CO2 concentration was above 50 % of CO2. From this result, 3 soil samples were taken at 70 cm depth in 3 distinct zones (background soil CO2 content, soil CO2 content of 20% and soil CO2 content of 50%). Then theses soil samples were incubated under closed jars flushed with different air atmospheres (20, 50 and 90 % of CO2) during 18 months. At initial, 3, 6, 12 and 18 months, some soil samples were collected in order to estimate the denitrifying, nitrifying activities as a function of CO2 concentration content and times. Theses enzymatic activities were chosen because one occurs under anaerobic conditions (denitrification) and the other occurs under aerobic conditions (nitrification). Both of them were involved in the nitrogen cycle and are major actors of soil function and groundwater quality preservation. Metabolic diversity using BIOLOG Ecoplates was determined on every soil samples. Physico-chemical parameters (e.g. pH, bulk chemistry, mineralogy) were analyzed to have some information about the evolution of the soil during the incubation with increasing soil CO2 concentrations

  10. Allelochemicals from the Rhizosphere Soil of Cultivated Astragalus hoantchy.

    PubMed

    Guo, Kai; He, Xiaofeng; Yan, Zhiqiang; Li, Xiuzhuang; Ren, Xia; Pan, Le; Qin, Bo

    2016-05-01

    Astragalus hoantchy, a widely cultivated medicinal plant species in traditional Chinese and Mongolian medicine, has been often hampered by replant failure during cultivation, like many other herbs of the genus Astragalus. Root aqueous extracts of Astragalus herbs were reported to exhibit allelopathic activity against other plants and autotoxic activity on their own seedlings, but the allelochemicals released by Astragalus plants have not been specified so far. Ten compounds were isolated from the rhizosphere soil extract of cultivated A. hoantchy and elucidated by spectroscopic analysis. Compounds 1-6 observably showed allelopathic activity against Lactuca sativa seedlings and autotoxic activity against A. hoantchy seedlings. The isolated compounds were further confirmed and quantified by high-performance liquid chromatography (HPLC) in the rhizosphere soil, with a total concentration of 9.78 μg/g (dry weight). These results specify and verify the allelochemicals released by cultivated A. hoantchy into the soil environment, which may provide new insights into the allelopathic mechanisms of this medicinal plant and probably assist in clarifying the replant problems of Astragalus plants. PMID:27074954

  11. Greenhouse Gas Emission from In-situ Denitrifying Bioreactors

    NASA Astrophysics Data System (ADS)

    Pluer, W.; Walter, M. T.; Geohring, L.

    2013-12-01

    Despite decades of concerted effort to mitigate nonpoint source nitrate (NO3-) pollution from agricultural lands, these efforts have not been sufficient to arrest eutrophication, which continues to be a serious and chronic problem. Two primary processes for removing excess NO3- from water are biological assimilation and denitrification. Denitrifying bacteria use NO3- as the electron acceptor for respiration in the absence of oxygen. Denitrification results in reduced forms of nitrogen, often dinitrogen gas (N2) but also nitrous oxide (N2O), an aggressive greenhouse gas (GHG). A promising solution to NO3- pollution is to intercept agricultural discharges with denitrifying bioreactors (DNBRs), though research has been limited to NO3- level reduction and omitted process mechanisms. DNBRs work by providing an anaerobic environment with plenty of organic matter (commonly woodchips) for denitrifying bacteria to flourish. While, initial results from bioreactor studies show that they can cost-effectively remove NO3-, GHG emission could be an unintended consequence. The study's goal is to determine how bioreactor design promotes microbial denitrification while limiting N2O production. It specifically focuses on expanding the body of knowledge concerning DNBRs in the areas of design implications and internal processes by measuring intermediate compounds and not solely NO3-. Nutrient samples are collected at inflow and outflow structures and tested for NO3- and nitrite (NO2-). Dissolved and headspace gas samples are collected and tested for N2O. Additional gas samples will be analyzed for naturally-occurring isotopic N2 to support proposed pathways. Designs will be analyzed both through the N2O/N2 production ratio and NO2- production caused by various residence times and inflow NO3- concentrations. High GHG ratios and NO2- production suggest non-ideal conditions or flow patterns for complete denitrification. NO3- reduction is used for comparison with previous studies. Few

  12. Metabolic potential and community structure of endophytic and rhizosphere bacteria associated with the roots of the halophyte Aster tripolium L.

    PubMed

    Szymańska, Sonia; Płociniczak, Tomasz; Piotrowska-Seget, Zofia; Złoch, Michał; Ruppel, Silke; Hrynkiewicz, Katarzyna

    2016-01-01

    The submitted work assumes that the abundance and diversity of endophytic and rhizosphere microorganisms co-existing with the halophytic plant Aster tripolium L. growing in a salty meadow in the vicinity of a soda factory (central Poland) represent unique populations of cultivable bacterial strains. Endophytic and rhizosphere bacteria were (i) isolated and identified based on 16S rDNA sequences; (ii) screened for nifH and acdS genes; and (iii) analyzed based on selected metabolic properties. Moreover, total microbial biomass and community structures of the roots (endophytes), rhizosphere and soil were evaluated using a cultivation-independent technique (PLFA) to characterize plant-microbial interactions under natural salt conditions. The identification of the isolated strains showed domination by Gram-positive bacteria (mostly Bacillus spp.) both in the rhizosphere (90.9%) and roots (72.7%) of A. tripolium. Rhizosphere bacterial strains exhibited broader metabolic capacities, while endophytes exhibited higher specificities for metabolic activity. The PLFA analysis showed that the total bacterial biomass decreased in the following order (rhizosphere

  13. Metabolic potential and community structure of endophytic and rhizosphere bacteria associated with the roots of the halophyte Aster tripolium L.

    PubMed

    Szymańska, Sonia; Płociniczak, Tomasz; Piotrowska-Seget, Zofia; Złoch, Michał; Ruppel, Silke; Hrynkiewicz, Katarzyna

    2016-01-01

    The submitted work assumes that the abundance and diversity of endophytic and rhizosphere microorganisms co-existing with the halophytic plant Aster tripolium L. growing in a salty meadow in the vicinity of a soda factory (central Poland) represent unique populations of cultivable bacterial strains. Endophytic and rhizosphere bacteria were (i) isolated and identified based on 16S rDNA sequences; (ii) screened for nifH and acdS genes; and (iii) analyzed based on selected metabolic properties. Moreover, total microbial biomass and community structures of the roots (endophytes), rhizosphere and soil were evaluated using a cultivation-independent technique (PLFA) to characterize plant-microbial interactions under natural salt conditions. The identification of the isolated strains showed domination by Gram-positive bacteria (mostly Bacillus spp.) both in the rhizosphere (90.9%) and roots (72.7%) of A. tripolium. Rhizosphere bacterial strains exhibited broader metabolic capacities, while endophytes exhibited higher specificities for metabolic activity. The PLFA analysis showed that the total bacterial biomass decreased in the following order (rhizosphere

  14. Pyrosequencing assessment of rhizosphere fungal communities from a soybean field.

    PubMed

    Sugiyama, Akifumi; Ueda, Yoshikatsu; Takase, Hisabumi; Yazaki, Kazufumi

    2014-10-01

    Soil fungal communities play essential roles in soil ecosystems, affecting plant growth and health. Rhizosphere bacterial communities have been shown to undergo dynamic changes during plant growth. This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth. Members of the Ascomycota and Basiodiomycota dominated in all soils. There were no statistically significant changes at the phylum level among growth stages or between bulk and rhizosphere soils. In contrast, the relative abundance of small numbers of operational taxonomic units, 4 during growth and 28 between bulk and rhizosphere soils, differed significantly. Clustering analysis revealed that rhizosphere fungal communities were different from bulk fungal communities during growth stages of soybeans. Taken together, these results suggest that in contrast to rhizosphere bacterial communities, most constituents of rhizosphere fungal communities remained stable during soybean growth. PMID:25264806

  15. Buffet hypothesis for microbial nutrition at the rhizosphere.

    PubMed

    López-Guerrero, Martha G; Ormeño-Orrillo, Ernesto; Rosenblueth, Mónica; Martinez-Romero, Julio; Martïnez-Romero, Esperanza

    2013-01-01

    An emphasis is made on the diversity of nutrients that rhizosphere bacteria may encounter derived from roots, soil, decaying organic matter, seeds, or the microbial community. This nutrient diversity may be considered analogous to a buffet and is contrasting to the hypothesis of oligotrophy at the rhizosphere. Different rhizosphere bacteria may have preferences for some substrates and this would allow a complex community to be established at the rhizosphere. To profit from diverse nutrients, root-associated bacteria should have large degrading capabilities and many transporters (seemingly inducible) that may be encoded in a significant proportion of the large genomes that root-associated bacteria have. Rhizosphere microbes may have a tendency to evolve toward generalists. We propose that many genes with unknown function may encode enzymes that participate in degrading diverse rhizosphere substrates. Knowledge of bacterial genes required for nutrition at the rhizosphere will help to make better use of bacteria as plant-growth promoters in agriculture.

  16. Degradation of n-Hexadecane and Its Metabolites by Pseudomonas aeruginosa under Microaerobic and Anaerobic Denitrifying Conditions

    PubMed Central

    Chayabutra, Chawala; Ju, Lu-Kwang

    2000-01-01

    A strategy for sequential hydrocarbon bioremediation is proposed. The initial O2-requiring transformation is effected by aerobic resting cells, thus avoiding a high oxygen demand. The oxygenated metabolites can then be degraded even under anaerobic conditions when supplemented with a highly water-soluble alternative electron acceptor, such as nitrate. To develop the new strategy, some phenomena were studied by examining Pseudomonas aeruginosa fermentation. The effects of dissolved oxygen (DO) concentration on n-hexadecane biodegradation were investigated first. Under microaerobic conditions, the denitrification rate decreased as the DO concentration decreased, implying that the O2-requiring reactions were rate limiting. The effects of different nitrate and nitrite concentrations were examined next. When cultivated aerobically in tryptic soy broth supplemented with 0 to 0.35 g of NO2−-N per liter, cells grew in all systems, but the lag phase was longer in the presence of higher nitrite concentrations. However, under anaerobic denitrifying conditions, even 0.1 g of NO2−-N per liter totally inhibited cell growth. Growth was also inhibited by high nitrate concentrations (>1 g of NO3−-N per liter). Cells were found to be more sensitive to nitrate or nitrite inhibition under denitrifying conditions than under aerobic conditions. Sequential hexadecane biodegradation by P. aeruginosa was then investigated. The initial fermentation was aerobic for cell growth and hydrocarbon oxidation to oxygenated metabolites, as confirmed by increasing dissolved total organic carbon (TOC) concentrations. The culture was then supplemented with nitrate and purged with nitrogen (N2). Nitrate was consumed rapidly initially. The live cell concentration, however, also decreased. The aqueous-phase TOC level decreased by about 40% during the initial active period but remained high after this period. Additional experiments confirmed that only about one-half of the derived TOC was readily

  17. Screening of endoglucanase-producing bacteria in the saline rhizosphere of Rhizophora mangle.

    PubMed

    Sá, André Luís Braghini; Dias, Armando Cavalcante Franco; Quecine, Maria Carolina; Cotta, Simone Raposo; Fasanella, Cristiane Cipola; Andreote, Fernando Dini; de Melo, Itamar Soares

    2014-01-01

    In screening the culturable endoglucanase-producing bacteria in the rhizosphere of Rhizophora mangle, we found a prevalence of genera Bacillus and Paenibacillus. These bacteria revealed different activities in endoglucolysis and biofilm formation when exposed to specific NaCl concentrations, indicating modulated growth under natural variations in mangrove salinity.

  18. [Screening, identification, and antagonism assessment, of dominant bacteria in Ageratina adenophora Sprengel rhizosphere soil].

    PubMed

    Niu, Hong-Bang; Liu, Wan-Xue; Wan, Fang-Hao; Liu, Bo

    2007-12-01

    By using isolation and culture method, 25 strains of dominant bacteria in Ageratina adenophora rhizosphere soil were isolated and identified, of which, 8 strains were assessed for their antagonistic activity. The results showed that Bacillus and Pseudomonas were highly abundant in A. adenophora rhizosphere soil, of which, B. subtilis and B. megaterium were most abundant and occupied 55.6% of the total identified bacteria. These dominant bacteria had different level antagonistic activity to Fusarium oxysporum and Ralstonia solanacearum, and B. subtilis BS-5 and B. thuringiensis BT-1 had the strongest antagonistic effect on F. oxysporum, with the antagonistic activity of their metabolic products being 85.5% and 83.8%, respectively. The metabolic products of the dominant antagonistic bacteria had even more stronger antagonistic effect on pathogens than the dominant antagonistic bacteria themselves. The existence of abundant bacterial groups with strong antagonistic activity in A. adenophora rhizosphere soil could help A. adenophora to resist harmful soil-borne diseases and escape its natural enemies. Through the feedback actions of the beneficial rhizosphere microbes, A. adenophora probably earned its competition superiority directly or indirectly, being favorable to its rapid expansion.

  19. Teaching Plant-Soil Relationships with Color Images of Rhizosphere pH.

    ERIC Educational Resources Information Center

    Heckman, J. R.; Strick, J. E.

    1996-01-01

    Presents a laboratory exercise that uses a simple imaging technique to illustrate the profound effects that living roots exert on the pH of the surrounding soil environment. Achieves visually stimulating results that can be used to reinforce lectures on rhizosphere pH, nutrient availability, plant tolerance of soil acidity, microbial activity, and…

  20. Screening of endoglucanase-producing bacteria in the saline rhizosphere of Rhizophora mangle.

    PubMed

    Sá, André Luís Braghini; Dias, Armando Cavalcante Franco; Quecine, Maria Carolina; Cotta, Simone Raposo; Fasanella, Cristiane Cipola; Andreote, Fernando Dini; de Melo, Itamar Soares

    2014-01-01

    In screening the culturable endoglucanase-producing bacteria in the rhizosphere of Rhizophora mangle, we found a prevalence of genera Bacillus and Paenibacillus. These bacteria revealed different activities in endoglucolysis and biofilm formation when exposed to specific NaCl concentrations, indicating modulated growth under natural variations in mangrove salinity. PMID:24948930

  1. Screening of endoglucanase-producing bacteria in the saline rhizosphere of Rhizophora mangle

    PubMed Central

    Sá, André Luís Braghini; Dias, Armando Cavalcante Franco; Quecine, Maria Carolina; Cotta, Simone Raposo; Fasanella, Cristiane Cipola; Andreote, Fernando Dini; de Melo, Itamar Soares

    2014-01-01

    In screening the culturable endoglucanase-producing bacteria in the rhizosphere of Rhizophora mangle, we found a prevalence of genera Bacillus and Paenibacillus. These bacteria revealed different activities in endoglucolysis and biofilm formation when exposed to specific NaCl concentrations, indicating modulated growth under natural variations in mangrove salinity. PMID:24948930

  2. [Effects of tobacco garlic crop rotation and intercropping on tobacco yield and rhizosphere soil phosphorus fractions].

    PubMed

    Tang, Biao; Zhang, Xi-zhou; Yang, Xian-bin

    2015-07-01

    A field plot experiment was conducted to investigate the tobacco yield and different forms of soil phosphorus under tobacco garlic crop rotation and intercropping patterns. The results showed that compared with tobacco monoculture, the tobacco yield and proportion of middle/high class of tobacco leaves to total leaves were significantly increased in tobacco garlic crop rotation and intercropping, and the rhizosphere soil available phosphorus contents were 1.3 and 1.7 times as high as that of tobacco monoculture at mature stage of lower leaf. For the inorganic phosphorus in rhizosphere and non-rhizosphere soil in different treatments, the contents of O-P and Fe-P were the highest, followed by Ca2-P and Al-P, and Ca8-P and Ca10-P were the lowest. Compared with tobacco monoculture and tobacco garlic crop intercropping, the Ca2-P concentration in rhizosphere soil under tobacco garlic crop rotation at mature stage of upper leaf, the Ca8-P concentration at mature stage of lower leaf, and the Ca10-P concentration at mature stage of middle leaf were lowest. The Al-P concentrations under tobacco garlic crop rotation and intercropping were 1.6 and 1.9 times, and 1.2 and 1.9 times as much as that under tobacco monoculture in rhizosphere soil at mature stages of lower leaf and middle leaf, respectively. The O-P concentrations in rhizosphere soil under tobacco garlic crop rotation and intercropping were significantly lower than that under tobacco monoculture. Compared with tobacco garlic crop intercropping, the tobacco garlic crop rotation could better improve tobacco yield and the proportion of high and middle class leaf by activating O-P, Ca10-P and resistant organic phosphorus in soil. PMID:26710622

  3. [Effects of tobacco garlic crop rotation and intercropping on tobacco yield and rhizosphere soil phosphorus fractions].

    PubMed

    Tang, Biao; Zhang, Xi-zhou; Yang, Xian-bin

    2015-07-01

    A field plot experiment was conducted to investigate the tobacco yield and different forms of soil phosphorus under tobacco garlic crop rotation and intercropping patterns. The results showed that compared with tobacco monoculture, the tobacco yield and proportion of middle/high class of tobacco leaves to total leaves were significantly increased in tobacco garlic crop rotation and intercropping, and the rhizosphere soil available phosphorus contents were 1.3 and 1.7 times as high as that of tobacco monoculture at mature stage of lower leaf. For the inorganic phosphorus in rhizosphere and non-rhizosphere soil in different treatments, the contents of O-P and Fe-P were the highest, followed by Ca2-P and Al-P, and Ca8-P and Ca10-P were the lowest. Compared with tobacco monoculture and tobacco garlic crop intercropping, the Ca2-P concentration in rhizosphere soil under tobacco garlic crop rotation at mature stage of upper leaf, the Ca8-P concentration at mature stage of lower leaf, and the Ca10-P concentration at mature stage of middle leaf were lowest. The Al-P concentrations under tobacco garlic crop rotation and intercropping were 1.6 and 1.9 times, and 1.2 and 1.9 times as much as that under tobacco monoculture in rhizosphere soil at mature stages of lower leaf and middle leaf, respectively. The O-P concentrations in rhizosphere soil under tobacco garlic crop rotation and intercropping were significantly lower than that under tobacco monoculture. Compared with tobacco garlic crop intercropping, the tobacco garlic crop rotation could better improve tobacco yield and the proportion of high and middle class leaf by activating O-P, Ca10-P and resistant organic phosphorus in soil.

  4. The influence of phosphorus availability and Laccaria bicolor symbiosis on phosphate acquisition, antioxidant enzyme activity, and rhizospheric carbon flux in Populus tremuloides.

    PubMed

    Desai, Shalaka; Naik, Dhiraj; Cumming, Jonathan R

    2014-07-01

    Many forest tree species are dependent on their symbiotic interaction with ectomycorrhizal (ECM) fungi for phosphorus (P) uptake from forest soils where P availability is often limited. The ECM fungal association benefits the host plant under P limitation through enhanced soil exploration and increased P acquisition by mycorrhizas. To study the P starvation response (PSR) and its modification by ECM fungi in Populus tremuloides, a comparison was made between nonmycorrhizal (NM) and mycorrhizal with Laccaria bicolor (Myc) seedlings grown under different concentrations of phosphate (Pi) in sand culture. Although differences in growth between NM and Myc plants were small, Myc plants were more effective at acquiring P from low Pi treatments, with significantly lower k m values for root and leaf P accumulation. Pi limitation significantly increased the activity of catalase, ascorbate peroxidase, and guaiacol-dependent peroxidase in leaves and roots to greater extents in NM than Myc P. tremuloides. Phosphoenolpyruvate carboxylase activity also increased in NM plants under P limitation, but was unchanged in Myc plants. Formate, citrate, malonate, lactate, malate, and oxalate and total organic carbon exudation by roots was stimulated by P limitation to a greater extent in NM than Myc plants. Colonization by L. bicolor reduced the solution Pi concentration thresholds where PSR physiological changes occurred, indicating that enhanced Pi acquisition by P. tremuloides colonized by L. bicolor altered host P homeostasis and plant stress responses to P limitation. Understanding these plant-symbiont interactions facilitates the selection of more P-efficient forest trees and strategies for tree plantation production on marginal soils.

  5. Performance of Denitrifying Microbial Fuel Cell with Biocathode over Nitrite

    PubMed Central

    Zhao, Huimin; Zhao, Jianqiang; Li, Fenghai; Li, Xiaoling

    2016-01-01

    Microbial fuel cell (MFC) with nitrite as an electron acceptor in cathode provided a new technology for nitrogen removal and electricity production simultaneously. The influences of influent nitrite concentration and external resistance on the performance of denitrifying MFC were investigated. The optimal effectiveness were obtained with the maximum total nitrogen (TN) removal rate of 54.80 ± 0.01 g m−3 d−1. It would be rather desirable for the TN removal than electricity generation at lower external resistance. Denaturing gradient gel electrophoresis suggested that Proteobacteria was the predominant phylum, accounting for 35.72%. Thiobacillus and Afipia might benefit to nitrite removal. The presence of nitrifying Devosia indicated that nitrite was oxidized to nitrate via a biochemical mechanism in the cathode. Ignavibacterium and Anaerolineaceae was found in the cathode as a heterotrophic bacterium with sodium acetate as substrate, which illustrated that sodium acetate in anode was likely permeated through proton exchange membrane to the cathode. PMID:27047462

  6. Denitrifying sulfide removal process on high-tetracycline wastewater.

    PubMed

    Liu, Chunshuang; Xu, Jian; Lee, Duu-Jong; Yu, Daoyong; Liu, Lihong

    2016-04-01

    Antibiotics wastewater from tetracycline (TC) production unit can have high levels of chemical oxygen demand, ammonium and sulfate and up to a few hundreds of milligrams per liter of TC. Denitrifying sulfide removal (DSR) process is set up for simultaneously removal of sulfur, carbon and nitrogen from waters. The DSR process was for the first time studied for treating TC wastewaters. The TC stress has no adverse effects on removal rates of nitrate and acetate; however, it moderately deteriorated sulfide removal rates and S(0) accumulation rates when the concentration is higher than 100mgL(-1) TC. The Thauera sp., and Pseudomonas sp. present the heterotrophs and Sulfurovum sp. presented the autotroph for the present DSR reactions. The high tolerance of TC stress by the tested consortium was explained by the excess production of extracellular polymeric substances at high TC concentration, which can bind with TC for minimizing its inhibition effects. PMID:26810146

  7. Effect of prefermentation on denitrifying phosphorus removal in slaughterhouse wastewater.

    PubMed

    Merzouki, M; Bernet, N; Delgenès, J P; Benlemlih, M

    2005-08-01

    An anaerobic-anoxic sequencing batch reactor (A2 SBR) coupled with a fixed-bed nitrification reactor for simultaneous carbon, nitrogen and phosphorus removal was evaluated using slaughterhouse wastewater. Whereas the treatment could not be successfully carried out on the raw wastewater, the process showed very good nutrient removal performances after prefermentation. The removals of COD, N-NH4 and P-PO4 achieved were 99%, 85% and 99%, respectively. The increase in volatile fatty acid (VFA) and phosphate concentrations in the effluent after prefermentation may explain the high levels of biological carbon, nitrogen and phosphorus removal observed. A simple prefermentation is, therefore, necessary but sufficient to ensure good performances of the denitrifying enhanced biological phosphorus removal (EBPR) process.

  8. Different responses of rhizosphere and non-rhizosphere soil microbial communities to consecutive Piper nigrum L. monoculture

    PubMed Central

    Li, Zhigang; Zu, Chao; Wang, Can; Yang, Jianfeng; Yu, Huan; Wu, Huasong

    2016-01-01

    Soil microorganisms have important influences on plant growth and health. In this study, four black pepper fields consecutively monocultured for 12, 18, 28 and 38 years were selected for investigating the effect of planting age on rhizosphere and non-rhizosphere soil microbial communities and soil physicochemical properties. The results revealed that the relative abundance of the dominant bacterial phyla in rhizosphere soil increased considerably with long-term consecutive monoculture but decreased in non-rhizosphere soil with a significant decline in Firmicutes. For fungi, an increasing trend over time was observed in both rhizosphere and non-rhizosphere soils, with the abundance of the pathogenic fungi Fusarium increasing significantly accompanied by a decrease in the bacteria Pseudomonas and Bacillus that is beneficial for black pepper. Consecutive monoculture, especially for 38 years, considerably decreased soil microbial diversity. Additionally, the rhizosphere soil pH and organic matter and available K contents decreased with increasing planting duration, though available N and P increased. All soil nutrient contents and microbial diversity indices were higher in rhizosphere soil compared to non-rhizosphere soil. The results suggest that long-term consecutive monoculture leads to variations in soil microbial community composition and physicochemical properties in both rhizosphere and non-rhizosphere soils, thus inhibiting the black pepper growth. PMID:27775000

  9. Imprint of denitrifying bacteria on the global terrestrial biosphere.

    PubMed

    Houlton, Benjamin Z; Bai, Edith

    2009-12-22

    Loss of nitrogen (N) from land limits the uptake and storage of atmospheric CO(2) by the biosphere, influencing Earth's climate system and myriads of the global ecological functions and services on which humans rely. Nitrogen can be lost in both dissolved and gaseous phases; however, the partitioning of these vectors remains controversial. Particularly uncertain is whether the bacterial conversion of plant available N to gaseous forms (denitrification) plays a major role in structuring global N supplies in the nonagrarian centers of Earth. Here, we use the isotope composition of N ((15)N/(14)N) to constrain the transfer of this nutrient from the land to the water and atmosphere. We report that the integrated (15)N/(14)N of the natural terrestrial biosphere is elevated with respect to that of atmospheric N inputs. This cannot be explained by preferential loss of (14)N to waterways; rather, it reflects a history of low (15)N/(14)N gaseous N emissions to the atmosphere owing to denitrifying bacteria in the soil. Parameterizing a simple model with global N isotope data, we estimate that soil denitrification (including N(2)) accounts for approximately 1/3 of the total N lost from the unmanaged terrestrial biosphere. Applying this fraction to estimates of N inputs, N(2)O and NO(x) fluxes, we calculate that approximately 28 Tg of N are lost annually via N(2) efflux from the natural soil. These results place isotopic constraints on the widely held belief that denitrifying bacteria account for a significant fraction of the missing N in the global N cycle.

  10. Plant treatment, pollutant load, and soil type effects in rhizosphere ecology of trace element polluted soils.

    PubMed

    Belén Hinojosa, M; Carreira, José A; García-Ruíz, Roberto; Rodríguez-Maroto, José M; Daniell, Tim J; Griffiths, Bryan S

    2010-07-01

    Re-vegetation of trace element contaminated soils can alter the pH and chelating capacity in the rhizosphere, increasing the mobility of pollutants, which, in turn, may impact on rhizosphere ecology. In this study a short-term pot experiment was carried out in order to investigate the multi-factorial effects of: buffering capacity (sandy-loam and loam soils); pollutant load (0%, 1.3%, and 4% of pyrite sludge), and the presence/absence of plant (Lolium perenne L. and Medicago sativa L.) on the mobility of trace elements, soil biochemical functionality (hydrolase activities), and biological diversity (bacterial and nematode communities). The experiment was carried out with representative soils from the Guadiamar basin (SW Spain), an area where the Aznalcóllar mining spill affected over 4000ha. Results indicated that the development of rhizospheres in polluted soils (coarse-textured) increases the mobilization of trace elements. In general the presence of roots has stimulatory effects on soil quality indicators such as hydrolase activities and both bacterial and nematode communities. However, the presence of high amount of metals interferes with these beneficial effects. This study provided evidence about the complexity of the impact of growing plants on trace element polluted soils. Trace element mobilization, hydrolase activities and bacterial and nematode communities in the rhizosphere are dependent on plant species, soil type, and pollution dose.

  11. The rhizosphere and hyphosphere differ in their impacts on carbon and nitrogen cycling in forests exposed to elevated CO₂.

    PubMed

    Meier, Ina C; Pritchard, Seth G; Brzostek, Edward R; McCormack, M Luke; Phillips, Richard P

    2015-02-01

    While multiple experiments have demonstrated that trees exposed to elevated CO₂ can stimulate microbes to release nutrients from soil organic matter, the importance of root- versus mycorrhizal-induced changes in soil processes are presently unknown. We analyzed the contribution of roots and mycorrhizal activities to carbon (C) and nitrogen (N) turnover in a loblolly pine (Pinus taeda) forest exposed to elevated CO₂ by measuring extracellular enzyme activities at soil microsites accessed via root windows. Specifically, we quantified enzyme activity from soil adjacent to root tips (rhizosphere), soil adjacent to hyphal tips (hyphosphere), and bulk soil. During the peak growing season, CO₂ enrichment induced a greater increase of N-releasing enzymes in the rhizosphere (215% increase) than in the hyphosphere (36% increase), but a greater increase of recalcitrant C-degrading enzymes in the hyphosphere (118%) than in the rhizosphere (19%). Nitrogen fertilization influenced the magnitude of CO₂ effects on enzyme activities in the rhizosphere only. At the ecosystem scale, the rhizosphere accounted for c. 50% and 40% of the total activity of N- and C-releasing enzymes, respectively. Collectively, our results suggest that root exudates may contribute more to accelerated N cycling under elevated CO₂ at this site, while mycorrhizal fungi may contribute more to soil C degradation.

  12. BIODEGRADATION OF AROMATIC COMPOUNDS UNDER MIXED OXYGEN/DENITRIFYING CONDITIONS: A REVIEW

    EPA Science Inventory

    Bioremediation of aromatic hydrocarbons in groundwater and sediments is often limited by dissolved oxygen. Many aromatic hydrocarbons degrade very slowly or not at all under anaerobic conditions. Nitrate is a good alternative electron acceptor to oxygen, and denitrifying bacteria...

  13. Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor.

    PubMed

    Gómez-Silván, C; Vílchez-Vargas, R; Arévalo, J; Gómez, M A; González-López, J; Pieper, D H; Rodelas, B

    2014-10-01

    The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal.

  14. Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor.

    PubMed

    Gómez-Silván, C; Vílchez-Vargas, R; Arévalo, J; Gómez, M A; González-López, J; Pieper, D H; Rodelas, B

    2014-10-01

    The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal. PMID:25043345

  15. Urban stormwater runoff drives denitrifying community composition through changes in sediment texture and carbon content.

    PubMed

    Perryman, Shane E; Rees, Gavin N; Walsh, Christopher J; Grace, Michael R

    2011-05-01

    The export of nitrogen from urban catchments is a global problem, and denitrifying bacteria in stream ecosystems are critical for reducing in-stream N. However, the environmental factors that control the composition of denitrifying communities in streams are not well understood. We determined whether denitrifying community composition in sediments of nine streams on the eastern fringe of Melbourne, Australia was correlated with two measures of catchment urban impact: effective imperviousness (EI, the proportion of a catchment covered by impervious surfaces with direct connection to streams) or septic tank density (which affects stream water chemistry, particularly stream N concentrations). Denitrifying community structure was examined by comparing terminal restriction fragment length polymorphisms of nosZ genes in the sediments, as the nosZ gene codes for nitrous oxide reductase, the last step in the denitrification pathway. We also determined the chemical and physical characteristics of the streams that were best correlated with denitrifying community composition. EI was strongly correlated with community composition and sediment physical and chemical properties, while septic tank density was not. Sites with high EI were sandier, with less fine sediment and lower organic carbon content, higher sediment cations (calcium, sodium and magnesium) and water filterable reactive phosphorus concentrations. These were also the best small-scale environmental variables that explained denitrifying community composition. Among our study streams, which differed in the degree of urban stormwater impact, sediment grain size and carbon content are the most likely drivers of change in community composition. Denitrifying community composition is another in a long list of ecological indicators that suggest the profound degradation of streams is caused by urban stormwater runoff. While the relationships between denitrifying community composition and denitrification rates are yet to be

  16. [Desorption characteristics of phosphorus in tea tree rhizosphere soil].

    PubMed

    Yang, Wei; Zhou, Wei-Jun; Bao, Chun-Hong; Miao, Xiao-Lin; Hu, Wen-Min

    2013-07-01

    In order to explore the phosphorus (P) release process and its supply mechanism in tea tree rhizosphere soil, an exogenous P adsorption and culture experiment was conducted to study the P desorption process and characters in the tea tree rhizosphere soils having been cultivated for different years and derived from different parent materials. The least squares method was used to fit the isotherms of P desorption kinetics. There was an obvious difference in the P desorption process between the rhizosphere soils and non-rhizosphere soils. The P desorption ability of the rhizosphere soils was significantly higher than that of the non-rhizosphere soils. As compared with non-rhizosphere soils, rhizosphere soils had higher available P content, P desorption rate, and beta value (desorbed P of per unit adsorbed P), with the average increment being 5.49 mg x kg(-1), 1.7%, and 24.4%, respectively. The P desorption ability of the rhizosphere soils derived from different parent materials was in the order of granite > quaternary red clay > slate. The average available P content and P desorption ability of the rhizosphere soils increased with increasing cultivation years. PMID:24175512

  17. [Desorption characteristics of phosphorus in tea tree rhizosphere soil].

    PubMed

    Yang, Wei; Zhou, Wei-Jun; Bao, Chun-Hong; Miao, Xiao-Lin; Hu, Wen-Min

    2013-07-01

    In order to explore the phosphorus (P) release process and its supply mechanism in tea tree rhizosphere soil, an exogenous P adsorption and culture experiment was conducted to study the P desorption process and characters in the tea tree rhizosphere soils having been cultivated for different years and derived from different parent materials. The least squares method was used to fit the isotherms of P desorption kinetics. There was an obvious difference in the P desorption process between the rhizosphere soils and non-rhizosphere soils. The P desorption ability of the rhizosphere soils was significantly higher than that of the non-rhizosphere soils. As compared with non-rhizosphere soils, rhizosphere soils had higher available P content, P desorption rate, and beta value (desorbed P of per unit adsorbed P), with the average increment being 5.49 mg x kg(-1), 1.7%, and 24.4%, respectively. The P desorption ability of the rhizosphere soils derived from different parent materials was in the order of granite > quaternary red clay > slate. The average available P content and P desorption ability of the rhizosphere soils increased with increasing cultivation years.

  18. Isolation and Characterization of Diverse Halobenzoate-Degrading Denitrifying Bacteria from Soils and Sediments

    PubMed Central

    Song, Bongkeun; Palleroni, Norberto J.; Häggblom, Max M.

    2000-01-01

    Denitrifying bacteria capable of degrading halobenzoates were isolated from various geographical and ecological sites. The strains were isolated after initial enrichment on one of the monofluoro-, monochloro-, or monobromo-benzoate isomers with nitrate as an electron acceptor, yielding a total of 33 strains isolated from the different halobenzoate-utilizing enrichment cultures. Each isolate could grow on the selected halobenzoate with nitrate as the terminal electron acceptor. The isolates obtained on 2-fluorobenzoate could use 2-fluorobenzoate under both aerobic and denitrifying conditions, but did not degrade other halobenzoates. In contrast, the 4-fluorobenzoate isolates degraded 4-fluorobenzoate under denitrifying conditions only, but utilized 2-fluorobenzoate under both aerobic and denitrifying conditions. The strains isolated on either 3-chlorobenzoate or 3-bromobenzoate could use 3-chlorobenzoate, 3-bromobenzoate, and 2- and 4-fluorobenzoates under denitrifying conditions. The isolates were identified and classified on the basis of 16S rRNA gene sequence analysis and their cellular fatty acid profiles. They were placed in nine genera belonging to either the α-, β-, or γ-branch of the Proteobacteria, namely, Acidovorax, Azoarcus, Bradyrhizobium, Ochrobactrum, Paracoccus, Pseudomonas, Mesorhizobium, Ensifer, and Thauera. These results indicate that the ability to utilize different halobenzoates under denitrifying conditions is ubiquitously distributed in the Proteobacteria and that these bacteria are widely distributed in soils and sediments. PMID:10919805

  19. nirS-containing denitrifier communities in the water column and sediment of the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Falk, S.; Hannig, M.; Gliesche, C.; Wardenga, R.; Köster, M.; Jürgens, K.; Braker, G.

    2007-05-01

    The aim of this study was to compare structural differences in the nirS-type denitrifying microbial communities along the environmental gradients observed in the water column and coastal sediments of the Baltic Sea. To link community structure and environmental gradients, denitrifier communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) based on nirS as a functional marker gene for denitrification. nirS-type denitrifier community composition was further evaluated by phylogenetic analysis of nirS sequences from clone libraries. T-RFLP analysis indicated some overlap but also major differences between communities from the water column and the sediment. Shifts in community composition along the biogeochemical gradients were observed only in the water column while denitrifier communities were rather uniform within the upper 30 mm of the sediment. Specific terminal restriction fragments (T-RFs) indicative of the sulfidic zone suggest the presence of nitrate-reducing and sulfide-oxidizing microorganisms that were previously shown to be important at the suboxic-sulfidic interface in the water column of the Baltic Sea. Phylogenetic analysis of nirS genes from the Baltic Sea and of sequences from marine habitats all over the world indicated distinct denitrifier communities that grouped mostly according to their habitats. We suggest that these subgroups of denitrifiers had developed after selection through several factors, i.e. their habitats (water column or sediment), impact by prevalent environmental conditions and isolation by large geographic distances between habitats.

  20. Coexistence of nitrifying, anammox and denitrifying bacteria in a sequencing batch reactor

    PubMed Central

    Langone, Michela; Yan, Jia; Haaijer, Suzanne C. M.; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Andreottola, Gianni

    2014-01-01

    Elevated nitrogen removal efficiencies from ammonium-rich wastewaters have been demonstrated by several applications, that combine nitritation and anammox processes. Denitrification will occur simultaneously when organic carbon is also present. In this study, the activity of aerobic ammonia oxidizing, anammox and denitrifying bacteria in a full scale sequencing batch reactor, treating digester supernatants, was studied by means of batch-assays. AOB and anammox activities were maximum at pH of 8.0 and 7.8–8.0, respectively. Short term effect of nitrite on anammox activity was studied, showing nitrite up to 42 mg/L did not result in inhibition. Both denitrification via nitrate and nitrite were measured. To reduce nitrite-oxidizing activity, high NH3-N (1.9–10 mg NH3-N/L) and low nitrite (3–8 mg TNN/L) are required conditions during the whole SBR cycle. Molecular analysis showed the nitritation-anammox sludge harbored a high microbial diversity, where each microorganism has a specific role. Using ammonia monooxygenase α–subunit (amoA) gene as a marker, our analyses suggested different macro- and micro-environments in the reactor strongly affect the AOB community, allowing the development of different AOB species, such as N. europaea/eutropha and N. oligotropha groups, which improve the stability of nitritation process. A specific PCR primer set, used to target the 16S rRNA gene of anammox bacteria, confirmed the presence of the “Ca. Brocadia fulgida” type, able to grow in presence of organic matter and to tolerate high nitrite concentrations. The diversity of denitrifiers was assessed by using dissimilatory nitrite reductase (nirS) gene-based analyses, who showed denitifiers were related to different betaproteobacterial genera, such as Thauera, Pseudomonas, Dechloromonas and Aromatoleum, able to assist in forming microbial aggregates. Concerning possible secondary processes, no n-damo bacteria were found while NOB from the genus Nitrobacter was detected

  1. Influence of rhizosphere microbial ecophysiological parameters from different plant species on butachlor degradation in a riparian soil.

    PubMed

    Yang, Changming; Wang, Mengmeng; Li, Jianhua

    2012-01-01

    Biogeochemical processes in riparian zones regulate contaminant movement to receiving waters and often mitigate the impact of upland sources of contaminants on water quality. However, little research has been reported on the microbial process and degradation potential of herbicide in a riparian soil. Field sampling and incubation experiments were conducted to investigate differences in microbial parameters and butachlor degradation in the riparian soil from four plant communities in Chongming Island, China. The results suggested that the rhizosphere soil had significantly higher total organic C and water-soluble organic C relative to the nonrhizosphere soil. Differences in rhizosphere microbial community size and physiological parameters among vegetation types were significant. The rhizosphere soil from the mixed community of Phragmites australis and Acorus calamus had the highest microbial biomass and biochemical activity, followed by A. calamus, P. australis and Zizania aquatica. Microbial ATP, dehydrogenase activity (DHA), and basal soil respiration (BSR) in the rhizosphere of the mixed community of P. australis and A. calamus were 58, 72, and 62% higher, respectively, than in the pure P. australis community. Compared with the rhizosphere soil of the pure plant communities, the mixed community of P. australis and A. calamus displayed a significantly greater degradation rate of butachlor in the rhizosphere soil. Residual butachlor concentrations in rhizosphere soil of the mixed community of P. australis and A. calamus and were 48, 63, and 68% lower than three pure plant communities, respectively. Butachlor degradation rates were positively correlated to microbial ATP, DHA, and BSR, indicating that these microbial parameters may be useful in assessing butachlor degradation potential in the riparian soil.

  2. Bacterial stimulation of copper phytoaccumulation by bioaugmentation with rhizosphere bacteria.

    PubMed

    Andreazza, Robson; Okeke, Benedict C; Lambais, Márcio Rodrigues; Bortolon, Leandro; de Melo, George Wellington Bastos; Camargo, Flávio Anastácio de Oliveira

    2010-11-01

    Copper contaminated areas pose environmental health risk to living organisms. Remediation processes are thus required for both crop production and industrial activities. This study employed bioaugmentation with copper resistant bacteria to improve phytoremediation of vineyard soils and copper mining waste contaminated with high copper concentrations. Oatmeal plant (Avena sativa L.) was used for copper phytoextraction. Three copper resistant bacterial isolates from oatmeal rhizosphere (Pseudomonas putida A1; Stenotrophomonas maltophilia A2 and Acinetobacter calcoaceticus A6) were used for the stimulation of copper phytoextraction. Two long-term copper contaminated vineyard soils (Mollisol and Inceptisol) and copper mining waste from Southern Brazil were evaluated. Oatmeal plants substantially extracted copper from vineyard soils and copper mining waste. As much as 1549 mg of Cu kg⁻¹ dry mass was extracted from plants grown in Inceptisol soil. The vineyard Mollisol copper uptake (55 mg Cu kg⁻¹ of dry mass) in the shoots was significantly improved upon inoculation of oatmeal plants with isolate A2 (128 mg of Cu kg⁻¹ of shoot dry mass). Overall oatmeal plant biomass displayed higher potential of copper phytoextraction with inoculation of rhizosphere bacteria in vineyard soil to the extent that 404 and 327 g ha⁻¹ of copper removal were respectively observed in vineyard Mollisol bioaugmented with isolate A2 (S. maltophilia) and isolate A6 (A. calcoaceticus). Results suggest potential application of bacterial stimulation of phytoaccumulation of copper for biological removal of copper from contaminated areas.

  3. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

    SciTech Connect

    Green, Stefan; Prakash, Om; Jasrotia, Puja; Overholt, Will; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M.; Watson, David B; Schadt, Christopher Warren; Brooks, Scott C; Kostka, Joel

    2011-01-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of ribosomal RNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure, and denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as concentration of nitrogen species, oxygen and sampling season did not appear to strongly influence the distribution of Rhodanobacter. Results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  4. Removal of nitrogen and phosphorus from the secondary effluent in tertiary denitrifying biofilters combined with micro-coagulation.

    PubMed

    Wei, Nan; Shi, Yunhong; Wu, Guangxue; Hu, Hongying; Guo, Yumei; Wu, Yihui; Wen, Hui

    2016-01-01

    Effective control of nitrogen and phosphorus in secondary effluent can reduce or avoid the eutrophication of receiving water bodies. Two denitrifying biofilters (DNBFs) packed with different sizes of quartz sands combined with micro-coagulation were operated for simultaneous removal of nitrogen and phosphorus from the secondary effluent. The quartz sand size in one DNBF was 2-4 mm (DNBFS), and in the other was 4-6 mm (DNBFL). In both DNBFs, methanol was used as the electron donor and different organic carbon to nitrogen (C/N) ratios were applied. Under C/N ratios of 1.5, 1.25, and 0.75 g/g, the nitrate nitrogen (NO3(-)-N) removal percentages were 73%, 77%, and 50% in DNBFS, and 43%, 25%, and 21% in DNBFL; the effluent total phosphorus concentrations were 0.15, 0.14, and 0.18 mg/L in DNBFS, and 0.29, 0.35, and 0.24 mg/L in DNBFL. The performance of both biofilters was quite stable within a backwashing cycle. The NO3(-)-N reduction rates were 1.31, 1.10, and 0.48 mg/(L·min) in DNBFS, and 0.97, 0.27, and 0.10 mg/(L·min) in DNBFL. For biomass detached from both biofilters, their denitrifying activities were similar. Biofilm biomass in DNBFS was higher than that in DNBFL, inducing a high denitrification efficiency in DNBFS.

  5. Screening and characterizing a denitrifying phosphorus-accumulating bacterium isolated from a circular plug-flow reactor.

    PubMed

    Xie, En; Ding, Aizhong; Zheng, Lei; Dou, Junfeng; Anderson, Bruce; Huang, Xiaolong; Jing, Ruoting

    2016-11-01

    Denitrifying phosphorus-accumulating organisms (DNPAO) are viewed as one of the most effective means to solve the removal contradiction of nitrogen and phosphorus in wastewater treatment. In this study, we isolated a DNPAO (C-17, accession number: KU745702) from activated sludge in a patented circular plug-flow reactor, physiologically to Pseudomonas sp. based on 16S rRNA sequence and phenotypic characteristics. The results of denitrifying phosphorus-accumulating experiment showed that Pseudomonas C-17 has high removal efficiencies for [Formula: see text] and NO3-N, 75% and 87%, respectively. The ratio of phosphorus release was 25.0 mg [Formula: see text] (with anabolism) and 26.8 mg [Formula: see text] (without anabolism), respectively. Our results indicated that Pseudomonas C-17 had strong capacity of phosphorus release, and its uptake is often imprecisely evaluated by ignoring the part of metabolic consumption. Pseudomonas C-17 is capable of utilizing oxygen, nitrate and nitrite as electron acceptors under experimental conditions.

  6. Removal of nitrogen and phosphorus from the secondary effluent in tertiary denitrifying biofilters combined with micro-coagulation.

    PubMed

    Wei, Nan; Shi, Yunhong; Wu, Guangxue; Hu, Hongying; Guo, Yumei; Wu, Yihui; Wen, Hui

    2016-01-01

    Effective control of nitrogen and phosphorus in secondary effluent can reduce or avoid the eutrophication of receiving water bodies. Two denitrifying biofilters (DNBFs) packed with different sizes of quartz sands combined with micro-coagulation were operated for simultaneous removal of nitrogen and phosphorus from the secondary effluent. The quartz sand size in one DNBF was 2-4 mm (DNBFS), and in the other was 4-6 mm (DNBFL). In both DNBFs, methanol was used as the electron donor and different organic carbon to nitrogen (C/N) ratios were applied. Under C/N ratios of 1.5, 1.25, and 0.75 g/g, the nitrate nitrogen (NO3(-)-N) removal percentages were 73%, 77%, and 50% in DNBFS, and 43%, 25%, and 21% in DNBFL; the effluent total phosphorus concentrations were 0.15, 0.14, and 0.18 mg/L in DNBFS, and 0.29, 0.35, and 0.24 mg/L in DNBFL. The performance of both biofilters was quite stable within a backwashing cycle. The NO3(-)-N reduction rates were 1.31, 1.10, and 0.48 mg/(L·min) in DNBFS, and 0.97, 0.27, and 0.10 mg/(L·min) in DNBFL. For biomass detached from both biofilters, their denitrifying activities were similar. Biofilm biomass in DNBFS was higher than that in DNBFL, inducing a high denitrification efficiency in DNBFS. PMID:27232413

  7. Dynamics of rhizosphere properties and antioxidative responses in wheat (Triticum aestivum L.) under cadmium stress.

    PubMed

    Li, Yonghua; Wang, Li; Yang, Linsheng; Li, Hairong

    2014-04-01

    In this study, we performed a rhizobox experiment to examine the dynamic changes in the rhizosphere properties and antioxidant enzyme responses of Triticum aestivum L. under three levels of cadmium stress. A set of micro-techniques (i.e., Rhizobox and Rhizon SMS) were applied for the dynamically non-destructive collection of the rhizosphere soil solution to enable the observation at a high temporal resolution. The dynamics of soluble cadmium and dissolved organic carbon (DOC) in the rhizosphere soil solutions of the Triticum aestivum L. were characterised by the sequence week 0 after sowing (WAS0)<3 weeks after sowing (WAS3)<10 weeks after sowing (WAS10), whereas the soil solution pH was found to follow an opposite distribution pattern. Systematically, both superoxide dismutase (SOD) and catalase (CAT) activities in the leaves of the Triticum aestivum L. increased concomitantly with increasing cadmium levels (p>0.05) and growth duration (p<0.05), whilst ascorbate peroxidase (APX) activity was induced to an elevated level at moderate cadmium stress with a decrease at high cadmium stress (p>0.05). These results suggested the enhancement of DOC production and the greater antioxidant enzyme activities were two important protective mechanisms of Triticum aestivum L. under cadmium stress, whereas rhizosphere acidification might be an important mechanism for the mobilisation of soil cadmium. The results also revealed that plant-soil interactions strongly influence the soil solution chemistry in the rhizosphere of Triticum aestivum L., that, in turn, can stimulate chemical and biochemical responses in the plants. In most cases, these responses to cadmium stress were sensitive and might allow us to develop strategies for reducing the risks of the cadmium contamination to crop production.

  8. Effects of warming and drought on potential N2O emissions and denitrifying bacteria abundance in grasslands with different land-use.

    PubMed

    Keil, Daniel; Niklaus, Pascal A; von Riedmatten, Lars R; Boeddinghaus, Runa S; Dormann, Carsten F; Scherer-Lorenzen, Michael; Kandeler, Ellen; Marhan, Sven

    2015-07-01

    Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity.

  9. Effects of warming and drought on potential N2O emissions and denitrifying bacteria abundance in grasslands with different land-use.

    PubMed

    Keil, Daniel; Niklaus, Pascal A; von Riedmatten, Lars R; Boeddinghaus, Runa S; Dormann, Carsten F; Scherer-Lorenzen, Michael; Kandeler, Ellen; Marhan, Sven

    2015-07-01

    Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity. PMID:26092950

  10. Rhizosphere biophysics and root water uptake

    NASA Astrophysics Data System (ADS)

    Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

    2016-04-01

    The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its

  11. Effects of organochlorines on microbial diversity and community structure in Phragmites australis rhizosphere.

    PubMed

    San Miguel, Angélique; Roy, Julien; Gury, Jérôme; Monier, Armelle; Coissac, Eric; Ravanel, Patrick; Geremia, Roberto A; Raveton, Muriel

    2014-05-01

    This study investigated the impacts of an organochlorine (OC, γ-hexachlorocyclohexane and chlorobenzenes) mixture on microbial communities associated to Phragmites australis rhizosphere. Seventy-eight distinct colony morphotypes were isolated, cultivated and analysed by 16S rDNA sequence analysis. Toxicity tests confirmed sensitivity (e.g. Hevizibacter, Acidovorax) or tolerance (e.g. Bacillus, Aeromonas, Pseudomonas, Sphingomonas) of isolates. Rhizosphere analysis by pyrosequencing showed the microbial adaptation induced by OC exposure. Among the most abundant molecular operational taxonomic units, 80 % appeared to be tolerant (55 % opportunist, 25 % unaffected) and 20 % sensitive. P. australis rhizosphere exposed to OCs was dominated by phylotypes related to α-, β- and γ-Proteobacteria. Specific genera were identified which were previously described as chlorinated organic pollutant degraders: Sphingomonas sp., Pseudomonas sp., Devosia sp. and Sphingobium sp. P. australis could be suitable plants to maintain their rhizosphere active microbial population which can tolerate OCs and potentially improve the OC remediation process in part by biodegradation.

  12. Metabolic status of bacteria and fungi in the rhizosphere of ponderosa pine seedlings

    SciTech Connect

    Norton, J.M.; Firestone, M.K. )

    1991-04-01

    The authors determined the quantity and metabolic status of bacteria and fungi in rhizosphere and nonrhizosphere soil from microcosms containing ponderosa pine seedlings. Rhizosphere soil was sampled adjacent to coarse, fine, or young roots. The biovolume and metabolic status of bacterial and fungal cells was determined microscopically and converted to total and active biomass values. Cells were considered active if they possessed the ability to reduce the artificial electron acceptor 2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyltetrazolium chloride (INT) to visible intracellular deposits of INT formazan. A colorimetric assay of INT formazan production was also used to assess dehydrogenase activity. INT-active microorganisms made up 44 to 55% of the microbial biomass in the soils studied. The proportion of fungal biomass that exhibited INT-reducing activity (40 to 50%) was higher than previous estimates of the active proportion of soil fungi determined by using fluorescein diacetate. Comparison between soils from different root zones revealed that the highest total and INT-active fungal biomass was adjacent to fine mycorrhizal roots, whereas the highest total and active bacterial biomass was adjacent to the young growing root tips. These observations suggest that fungi are enhanced adjacent to the fine roots compared with the nonrhizosphere soil, whereas bacteria are more responsive than fungi to labile carbon inputs in the young root zone. Colorimetric dehydrogenase assays detected gross differences between bulk and rhizosphere soil activity but were unable to detect more subtle differences due to root types.

  13. Rapid degradation of butachlor in wheat rhizosphere soil.

    PubMed

    Yu, Y L; Chen, Y X; Luo, Y M; Pan, X D; He, Y F; Wong, M H

    2003-02-01

    The degradative characteristics of butachlor in non-rhizosphere, wheat rhizosphere, and inoculated rhizosphere soils were measured. The rate constants for the degradation of butachlor in non-rhizosphere, rhizosphere, and inoculated rhizosphere soils were measured to be 0.0385, 0.0902, 0.1091 at 1 mg/kg, 0.0348, 0.0629, 0.2355 at 10 mg/kg, and 0.0299, 0.0386, 0.0642 at 100 mg/kg, respectively. The corresponding half-lives for butachlor in the soils were calculated to be 18.0, 7.7, 6.3 days at 1 mg/kg, 19.9, 11.0, 2.9 days at 10 mg/kg, and 23.2, 18.0, 10.8 days at 100 mg/kg, respectively. The experimental results show that the degradation of butachlor can be enhanced greatly in wheat rhizosphere, and especially in the rhizosphere inoculated with the bacterial community designated HD which is capable of degrading butachlor. It could be concluded that rhizosphere soil inoculated with microorganisms-degrading target herbicides is a useful pathway to achieve rapid degradation of the herbicides in soil.

  14. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-01-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  15. Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

    PubMed Central

    Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

    2014-01-01

    Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887

  16. Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates.

    PubMed

    Mao, Yuejian; Li, Xiangzhen; Smyth, Eoghan M; Yannarell, Anthony C; Mackie, Roderick I

    2014-06-01

    Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.

  17. Metabolic behavior and enzymatic aspects of denitrifying EBPR sludge in a continuous-flow anaerobic-anoxic system.

    PubMed

    Zafiriadis, Ilias; Ntougias, Spyridon; Kapagiannidis, Anastasios G; Aivasidis, Alexander

    2013-10-01

    The metabolic aspects of enhanced biological phosphorus removal (EBPR) were investigated for the first time in a continuous-flow anaerobic-anoxic plant fed with acetate, propionate, or substrates which are involved in the tricarboxylic acid and/or glyoxylate cycle, i.e., fumarate, malate, or oxaloacetate, as the sole carbon source. Although the polyphosphate-accumulating organisms (PAOs) population remained stable with any carbon source examined, no typical EBPR metabolism was observed during fumarate, malate, or oxaloacetate utilization. Specific enzymatic activities related to EBPR were determined in activated sludge homogenates and directly correlated with the nutrient metabolic rates. The experimental results indicated the direct involvement of alkaline phosphatase, pyrophosphatase, and exopolyphosphatase in the denitrifying EBPR process. Metabolic aspects of glyoxylate cycle enzymes are discussed with regard to the biomass anaerobic and anoxic activity. Process performance was highly influenced by the kind of substrate utilized, indicating that specific metabolic pathways should be followed to favor efficient EBPR.

  18. Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination

    SciTech Connect

    Green, Stefan; Prakash, Om; Gihring, Thomas; Akob, Denise M.; Jasrotia, Puja; Jardine, Philip M; Watson, David B; Brown, Steven D; Palumbo, Anthony Vito; Kostka, Joel

    2010-01-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available with which to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy s Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria) and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were confirmed as complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. Ribosomal RNA gene analyses reveal that bacteria from the genus Rhodanobacter comprise a diverse population of circumneutral to moderately acidophilic denitrifiers at the ORIFRC site, with a high relative abundance in areas of the acidic source zone. Rhodanobacter species do not contain a periplasmic nitrite reductase and have not been previously detected in functional gene surveys of denitrifying bacteria at the OR-IFRC site. Sequences of nitrite and nitrous oxide reductase genes were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation, genomic and metagenomic data are essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifying microorganisms. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

  19. Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.

    PubMed

    Green, Stefan J; Prakash, Om; Gihring, Thomas M; Akob, Denise M; Jasrotia, Puja; Jardine, Philip M; Watson, David B; Brown, Steven D; Palumbo, Anthony V; Kostka, Joel E

    2010-05-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria), and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface. PMID:20305024

  20. Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.

    PubMed

    Green, Stefan J; Prakash, Om; Gihring, Thomas M; Akob, Denise M; Jasrotia, Puja; Jardine, Philip M; Watson, David B; Brown, Steven D; Palumbo, Anthony V; Kostka, Joel E

    2010-05-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria), and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

  1. Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste Contamination▿ †

    PubMed Central

    Green, Stefan J.; Prakash, Om; Gihring, Thomas M.; Akob, Denise M.; Jasrotia, Puja; Jardine, Philip M.; Watson, David B.; Brown, Steven D.; Palumbo, Anthony V.; Kostka, Joel E.

    2010-01-01

    In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria), and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface. PMID:20305024

  2. Characteristics of a Novel Aerobic Denitrifying Bacterium, Enterobacter cloacae Strain HNR.

    PubMed

    Guo, Long-Jie; Zhao, Bin; An, Qiang; Tian, Meng

    2016-03-01

    A novel aerobic denitrifier strain HNR, isolated from activated sludge, was identified as Enterobacter cloacae by16S rRNA sequencing analysis. Glucose was considered as the most favorable C-source for strain HNR. The logistic equation well described the bacterial growth, yielding a maximum growth rate (μmax) of 0.283 h(-1) with an initial NO3 (-)-N concentration of 110 mg/L. Almost all NO3 (-)-N was removed aerobically within 30 h with an average removal rate of 4.58 mg N L(-1) h(-1). Nitrogen balance analysis revealed that proximately 70.8 % of NO3 (-)-N was removed as gas products and only 20.7 % was transformed into biomass. GC-MS result indicates that N2 was the end product of aerobic denitrification. The enzyme activities of nitrate reductase and nitrite reductase, which are related to the process of aerobic denitrification, were 0.0688 and 0.0054 U/mg protein, respectively. Thus, the aerobic denitrification of reducing NO3 (-) to N2 by strain HNR was demonstrated. The optimal conditions for nitrate removal were C/N ratio 13, pH value 8, shaking speed 127 rpm and temperature 30 °C. These findings show that E. cloacae strain HNR has a potential application on wastewater treatment to achieve nitrate removal under aerobic conditions.

  3. Anaerobic degradation of toluene by a denitrifying bacterium.

    PubMed Central

    Evans, P J; Mang, D T; Kim, K S; Young, L Y

    1991-01-01

    A denitrifying bacterium, designated strain T1, that grew with toluene as the sole source of carbon under anaerobic conditions was isolated. The type of agar used in solid media and the toxicity of toluene were determinative factors in the successful isolation of strain T1. Greater than 50% of the toluene carbon was oxidized to CO2, and 29% was assimilated into biomass. The oxidation of toluene to CO2 was stoichiometrically coupled to nitrate reduction and denitrification. Strain T1 was tolerant of and grew on 3 mM toluene after a lag phase. The rate of toluene degradation was 1.8 mumol min-1 liter-1 (56 nmol min-1 mg of protein-1) in a cell suspension. Strain T1 was distinct from other bacteria that oxidize toluene anaerobically, but it may utilize a similar biochemical pathway of oxidation. In addition, o-xylene was transformed to a metabolite in the presence of toluene but did not serve as the sole source of carbon for growth of strain T1. This transformation was dependent on the degradation of toluene. Images PMID:2059037

  4. Removal of pharmaceutical and personal care products (PPCPs) under nitrifying and denitrifying conditions.

    PubMed

    Suarez, Sonia; Lema, Juan M; Omil, Francisco

    2010-05-01

    The contribution of volatilization, sorption and transformation to the removal of 16 Pharmaceutical and Personal Care Products (PPCPs) in two lab-scale conventional activated sludge reactors, working under nitrifying (aerobic) and denitrifying (anoxic) conditions for more than 1.5 years, have been assessed. Pseudo-first order biological degradation rate constants (k(biol)) were calculated for the selected compounds in both reactors. Faster degradation kinetics were measured in the nitrifying reactor compared to the denitrifying system for the majority of PPCPs. Compounds could be classified according to their k(biol) into very highly (k(biol)>5Lg(SS)(-1)d(-1)), highly (175%) and anoxic (>65%) conditions, whereas naproxen (NPX), ethinylestradiol (EE2), roxithromycin (ROX) and erythromycin (ERY) were only significantly transformed in the aerobic reactor (>80%). The anti-depressant citalopram (CTL) was moderately biotransformed under both, aerobic and anoxic conditions (>60% and >40%, respectively). Some compounds, as carbamazepine (CBZ), diazepam (DZP), sulfamethoxazole (SMX) and trimethoprim (TMP), manifested high resistance to biological transformation. Solids Retention Time (SRT(aerobic) >50d and <50d; SRT(anoxic) >20d and <20d) had a slightly positive effect on the removal of FLX, NPX, CTL, EE2 and natural estrogens (increase in removal efficiencies <10%). Removal of diclofenac (DCF) in the aerobic reactor was positively affected by the development of nitrifying biomass and increased from 0% up to 74%. Similarly, efficient anoxic transformation of ibuprofen (75%) was observed after an adaptation period of 340d. Temperature (16-26 degrees C) only had a slight effect on the removal of

  5. Expression of nifH genes by diazotrophic bacteria in the rhizosphere of short form Spartina alterniflora.

    PubMed

    Brown, Michelle M; Friez, Michael J; Lovell, Charles R

    2003-04-01

    Abstract A diverse assemblage of diazotrophic bacteria exists in the rhizosphere of the smooth cordgrass, Spartina alterniflora, but the taxa actively involved in nitrogen fixation have not been determined. In order to identify the diazotrophs that were actively expressing nifH, the gene encoding the nitrogenase iron protein, mRNA was extracted from Spartina rhizosphere samples and nifH-specific seminested reverse transcriptase-PCR performed. Expressed nifH sequences were recovered from organisms affiliated with the (gamma-+beta-) Proteobacteria and the anaerobes. Most of the expressed nifH sequences were highly similar (>/=95% similarity) to sequences previously recovered from Spartina rhizosphere DNA using conventional nifH-specific PCR. These sequences were also similar, although not identical to the nifH sequences of Pseudomonas stutzeri, Vibrio diazotrophicus, Desulfovibrio africanus, and Desulfovibrio gigas.

  6. Mycological composition in the rhizosphere of winter wheat in different crop production systems

    NASA Astrophysics Data System (ADS)

    Frac, Magdalena; Lipiec, Jerzy; Usowicz, Boguslaw

    2010-05-01

    Fungi play an important role in the soil ecosystem as decomposers of plant residues, releasing nutrients that sustain and stimulate processes of plant growth. Some fungi possess antagonistic properties towards plant pathogens. The structure of plant and soil communities is influenced by the interactions among its component species and also by anthropogenic pressure. In the study of soil fungi, particular attention is given to the rhizosphere. Knowledge of the structure and diversity of the fungal community in the rhizosphere lead to the better understanding of pathogen-antagonist interactions. The aim of this study was to evaluate the mycological composition of the winter wheat rhizosphere in two different crop production systems. The study was based on a field experiment established in 1994 year at the Experimental Station in South-East Poland. The experiment was conducted on grey-brown podzolic soil. In this experiment winter wheat were grown in two crop production systems: ecological and conventional - monoculture. The research of fungi composition was conducted in 15th year of experiment. Rhizosphere was collected two times during growing season, in different development stage: shooting phase and full ripeness phase. Martin medium and the dilutions 10-3 and 10-4 were used to calculate the total number cfu (colony forming units) of fungi occurring in the rhizosphere of winter wheat. The fungi were identified using Czapeka-Doxa medium for Penicillium, potato dextrose agar for all fungi and agar Nirenberga (SNA) for Fusarium. High number of antagonistic fungi (Penicillium sp., Trichoderma sp.) was recorded in the rhizosphere of wheat in ecological system. The presence of these fungi can testify to considerable biological activity, which contributes to the improvement of the phytosanitary condition of the soil. However, the decrease of the antagonistic microorganism number in the crop wheat in monoculture can be responsible for appearance higher number of the

  7. Rhizospheric fungi of Panax notoginseng: diversity and antagonism to host phytopathogens

    PubMed Central

    Miao, Cui-Ping; Mi, Qi-Li; Qiao, Xin-Guo; Zheng, You-Kun; Chen, You-Wei; Xu, Li-Hua; Guan, Hui-Lin; Zhao, Li-Xing

    2015-01-01

    Background Rhizospheric fungi play an essential role in the plant–soil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China. Methods Culture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng. Results A total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequences was high, accounting for 12.9% and 5.5%, respectively. In total, 113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus. Conclusion Our results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens. PMID:27158233

  8. Effects of Selected Rhizosphere Microorganisms and Carbon on Soybean Cyst Nematode Population Density and Reproduction in Different Tillage Regimes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean cyst nematode (SCN) population density can be influenced by tillage practices. Data were collected over two growing seasons on total and active bacteria, total and active fungi, and protozoans (amobae, flagellates, ciliates) in the soybean rhizosphere to determine whether the levels of these...

  9. Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

    PubMed

    Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

    2015-10-01

    Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

  10. Selection of denitrifying phosphorous accumulating organisms in IFAS systems: comparison of nitrite with nitrate as an electron acceptor.

    PubMed

    Jabari, Pouria; Munz, Giulio; Oleszkiewicz, Jan A

    2014-08-01

    Nitrite and nitrate were compared as electron acceptors to select for denitrifying phosphorous accumulating organisms (DPAO) in two integrated fixed film activated sludge (IFAS 1 and IFAS 2) systems operated as sequencing batch reactors. The bench-scale experiment lasted one year and synthetic wastewater was used as feed. During anoxic conditions 20mgNO3(-)-NL(-1) were dosed into IFAS-1 and 20mgNO2(-)-NL(-1) were dosed into IFAS-2. Long term phosphorous and ammonia removal via nitritation were achieved in both systems and both attached and suspended biomass contributed to phosphorous and ammonia removal. DPAO showed no specific adaptation to the electron acceptor as evidenced by short term switch of feeding with nitrate or nitrite. Anoxic phosphorus uptake rate was significantly higher with nitrite than with nitrate. Results showed that DPAO activity with nitrite could be integrated into attached and suspended biomass of IFAS systems in long term operation.

  11. Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

    PubMed Central

    Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J.; Fusi, Marco; Bariselli, Paola; Reddy, Muppala; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

    2016-01-01

    Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes. PMID:27597846

  12. Cropping practices modulate the impact of glyphosate on arbuscular mycorrhizal fungi and rhizosphere bacteria in agroecosystems of the semiarid prairie.

    PubMed

    Sheng, Min; Hamel, Chantal; Fernandez, Myriam R

    2012-08-01

    A growing body of evidence obtained from studies performed under controlled conditions suggests that glyphosate use can modify microbial community assemblages. However, few studies have examined the influence of glyphosate in agroecosystems. We examined 4 wheat-based production systems typical of the Canadian prairie over 2 years to answer the following question: Does preseeding of glyphosate impact soil rhizosphere microorganisms? If so, do cropping practices influence this impact? Glyphosate caused a shift in the species dominating the arbuscular mycorrhizal fungal community in the rhizosphere, possibly through the modification of host plant physiology. Glyphosate stimulated rhizobacterial growth while having no influence on saprotrophic fungi, suggesting a greater abundance of glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in bacteria than in fungi. Glyphosate stimulated rhizosphere bacteria in pea but not in urea-fertilized durum wheat, which is consistent with inhibition of EPSPS tolerance to residual glyphosate through high ammonium levels. Mitigation of the effects of glyphosate on rhizosphere bacteria through tillage suggests a reduction in residual glyphosate activity through increased adsorption to soil binding sites upon soil mixing. The influence of glyphosate on Gram-negative bacteria was mitigated under drought conditions in 2007. Our experiment suggests that interactions between soil fertility, tillage, and cropping practices shape the influence of glyphosate use on rhizosphere microorganisms.

  13. Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

    PubMed Central

    Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J.; Fusi, Marco; Bariselli, Paola; Reddy, Muppala; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

    2016-01-01

    Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

  14. Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth.

    PubMed

    Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J; Fusi, Marco; Bariselli, Paola; Reddy, Muppala; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

    2016-01-01

    Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes. PMID:27597846

  15. Manipulation of Rhizosphere Bacterial Communities to Induce Suppressive Soils

    PubMed Central

    Mazzola, Mark

    2007-01-01

    Naturally occurring disease-suppressive soils have been documented in a variety of cropping systems, and in many instances the biological attributes contributing to suppressiveness have been identified. While these studies have often yielded an understanding of operative mechanisms leading to the suppressive state, significant difficulty has been realized in the transfer of this knowledge into achieving effective field-level disease control. Early efforts focused on the inundative application of individual or mixtures of microbial strains recovered from these systems and known to function in specific soil suppressiveness. However, the introduction of biological agents into non-native soil ecosystems typically yielded inconsistent levels of disease control. Of late, greater emphasis has been placed on manipulation of the cropping system to manage resident beneficial rhizosphere microorganisms as a means to suppress soilborne plant pathogens. One such strategy is the cropping of specific plant species or genotypes or the application of soil amendments with the goal of selectively enhancing disease-suppressive rhizobacteria communities. This approach has been utilized in a system attempting to employ biological elements resident to orchard ecosystems as a means to control the biologically complex phenomenon termed apple replant disease. Cropping of wheat in apple orchard soils prior to re-planting the site to apple provided control of the fungal pathogen Rhizoctonia solani AG-5. Disease control was elicited in a wheat cultivar-specific manner and functioned through transformation of the fluorescent pseudomonad population colonizing the rhizosphere of apple. Wheat cultivars that induced disease suppression enhanced populations of specific fluorescent pseudomonad genotypes with antagonistic activity toward R. solani AG-5, but cultivars that did not elicit a disease-suppressive soil did not modify the antagonistic capacity of this bacterial community. Alternatively

  16. Growth rates of rhizosphere microorganisms depend on competitive abilities of plants for nitrogen

    NASA Astrophysics Data System (ADS)

    Blagodatskaya, Evgenia; Littschwager, Johanna; Lauerer, Marianna; Kuzyakov, Yakov

    2010-05-01

    Rhizosphere - one of the most important ‘hot spots' in soil - is characterized not only by accelerated turnover of microbial biomass and nutrients but also by strong intra- and inter-specific competition. Intra-specific competition occurs between individual plants of the same species, while inter-specific competition can occur both at population level (plant species-specific, microbial species-specific interactions) and at community level (plant - microbial interactions). Such plant - microbial interactions are mainly governed by competition for available N sources, since N is one of the main growth limiting nutrients in natural ecosystems. Functional structure and activity of microbial community in rhizosphere is not uniform and is dependent on quantity and quality of root exudates which are plant specific. It is still unclear how microbial growth and turnover in the rhizosphere are dependent on the features and competitive abilities of plants for N. Depending on C and N availability, acceleration and even retardation of microbial activity and carbon mineralization can be expected in the rhizosphere of plants with high competitive abilities for N. We hypothesized slower microbial growth rates in the rhizosphere of plants with smaller roots, as they usually produce less exudates compared to plants with small shoot-to-root ratio. As the first hypothesis is based solely on C availability, we also expected the greater effect of N availability on microbial growth in rhizosphere of plants with smaller root mass. These hypothesis were tested for two plant species of strawberry: Fragaria vesca L. (native species), and Duchesnea indica (Andrews) Focke (an invasive plant in central Europe) growing in intraspecific and interspecific competition. Microbial biomass and the kinetic parameters of microbial growth in the rhizosphere were estimated by dynamics of CO2 emission from the soil amended with glucose and nutrients. Specific growth rate (µ) of soil microorganisms was

  17. Characterization of the microbial community in the rhizosphere of Phragmites australis (cav.) trin ex. steudel growing in the Sun Island Wetland.

    PubMed

    Ma, Fang; Wu, Jieting; Wang, Li; Yang, Jixian; Li, Shiyang; Li, Zhe; Zhag, Xue

    2014-03-01

    Rhizospheric microorganisms are important for environmental conservancy. The constancy and variability of the microorganisms in the rhizosphere of Phragmites australis in relation to the spatiotemporal variations in wetland ecosystems were studied. During the peak and trough of the vegetative period of the Phragmites australis growing across the hydrologic gradients of the Sun Island Wetland, Biolog and denaturing gradient gel electrophoresis (DGGE) were used to investigate the rhizospheric microbial characteristics. Both methods demonstrated that the microbial activity, richness, and diversity decreased from summer to autumn. However, these properties did not show significant correlation with hydrologic gradient, except that the genetic richness and diversity of the fungi decreased with it. Cluster analysis also demonstrated that the rhizospheric microbial community seemed to be largely affected by a vegetative period. In addition, this research was extended to a broader range of determining the universal microorganisms, which showed notable adaptability.

  18. Use of Stable-Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescence In Situ Hybridization-Microautoradiography To Study a Methanol-Fed Denitrifying Microbial Community

    PubMed Central

    Ginige, Maneesha P.; Hugenholtz, Philip; Daims, Holger; Wagner, Michael; Keller, Jürg; Blackall, Linda L.

    2004-01-01

    A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO3−-N mg of mixed-liquor volatile suspended solids (MLVSS)−1 h−1 to a steady-state value of 0.06 mg of NO3−-N mg of MLVSS−1 h−1 over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [13C]methanol to biomark the DNA of the denitrifiers. The extracted [13C]DNA and [12C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [13C]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [12C]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with

  19. Influence of humic substances on plant-microbes interactions in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Puglisi, Edoardo; Pascazio, Silvia; Spaccini, Riccardo; Crecchio, Carmine; Trevisan, Marco; Piccolo, Alessandro

    2013-04-01

    Humic substances are known to play a wide range of effects on the physiology of plant and microbes. This is of particular relevance in the rhizosphere of terrestrial environments, where the reciprocal interactions between plants roots, soil constituents and microorganisms strongly influence the plants acquisition of nutrients. Chemical advances are constantly improving our knowledge on humic substances: their supra-molecular architecture, as well as the moltitude of their chemical constituents, many of which are biologically active. An approach for linking the structure of humic substances with their biological activity in the rhizosphere is the use of rhizoboxes, which allow applying a treatment (e.g., an amendment with humic substances) in an upper soil-plant compartment and take measurements in a lower isolated rhizosphere compartment that can be sampled at desired distances from the rhizoplane. This approach can be adopted to assess the effects of several humic substances, as well as composted materials, on maize plants rhizodeposition of carbon, and in turn on the structure and activity of rhizosphere microbial communities. In order to gain a complete understanding of processes occurring in the complex soil-plant-microorganisms tripartite system, rhizobox experiments can be coupled with bacterial biosensors for the detection and quantification of bioavailable nutrients, chemical analyses of main rhizodeposits constituents, advanced chemical characterizations of humic substances, DNA-fingerprinting of microbial communities, and multivariate statistical approaches to manage the dataset produced and to infer general conclusions. By such an approach it was found that humic substances are significantly affecting the amount of carbon deposited by plant roots. This induction effect is more evident for substances with more hydrophobic and complex structure, thus supporting the scientific hypothesis of the "microbial loop model", which assumes that plants feed

  20. Microbial Community Structure in the Rhizosphere of Rice Plants.

    PubMed

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G

    2015-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  1. Microbial Community Structure in the Rhizosphere of Rice Plants

    PubMed Central

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  2. Arsenic in the rhizosphere soil solution of ferns.

    PubMed

    Wei, Chaoyang; Zheng, Huan; Yu, Jiangping

    2012-12-01

    The aim of this study was to explore the evidence of arsenic hyperaccumulation in plant rhizosphere solutions. Six common fern plants were selected and grown in three types of substrate: arsenic (As) -tailings, As-spiked soil, and soil-As-tailing composites. A rhizobox was designed with an in-situ collection of soil solutions to analyze changes in the As concentration and valence as well as the pH, dissolved organic carbon (DOC) and total nitrogen (TN). Arsenite composed less than 20% of the total As, and As depletion was consistent with N depletion in the rhizosphere solutions of the various treatments. The As concentrations in the rhizosphere and non-rhizosphere solutions in the presence of plants were lower than in the respective controls without plants, except for in the As-spiked soils. The DOC concentrations were invariably higher in the rhizosphere versus non-rhizosphere solutions from the various plants; however, no significant increase in the DOC content was observed in Pteris vittata, in which only a slight decrease in pH appeared in the rhizosphere compared to non-rhizosphere solutions. The results showed that As reduction by plant roots was limited, acidification-induced solubilization was not the mechanism for As hyperaccumulation.

  3. Differential Isotopic Fractionation during Cr(VI) Reduction by an Aquifer-Derived Bacterium under Aerobic versus Denitrifying Conditions

    SciTech Connect

    Han, R.; Qin, L.; Brown, S. T.; Christensen, J. N.; Beller, H. R.

    2012-01-27

    We studied Cr isotopic fractionation during Cr(VI) reduction by Pseudomonas stutzeri strain RCH2. Finally, despite the fact that strain RCH2 reduces Cr(VI) cometabolically under both aerobic and denitrifying conditions and at similar specific rates, fractionation was markedly different under these two conditions (ε was ~2‰ aerobically and ~0.4‰ under denitrifying conditions).

  4. The role of paraffin oil on the interaction between denitrifying anaerobic methane oxidation and Anammox processes.

    PubMed

    Fu, Liang; Ding, Zhao-Wei; Ding, Jing; Zhang, Fang; Zeng, Raymond J

    2015-10-01

    Methane is sparingly soluble in water, resulting in a slow reaction rate in the denitrifying anaerobic methane oxidation (DAMO) process. The slow rate limits the feasibility of research to examine the interaction between the DAMO and the anaerobic ammonium oxidation (Anammox) process. In this study, optimized 5 % (v/v) paraffin oil was added as a second liquid phase to improve methane solubility in a reactor containing DAMO and Anammox microbes. After just addition, methane solubility was found to increase by 25 % and DAMO activity was enhanced. After a 100-day cultivation, the paraffin reactor showed almost two times higher consumption rates of NO3 (-) (0.2268 mmol/day) and NH4 (+) (0.1403 mmol/day), compared to the control reactor without paraffin oil. The microbes tended to distribute in the oil-water interface. The quantitative (q) PCR result showed the abundance of gene copies of DAMO archaea, DAMO bacteria, and Anammox bacteria in the paraffin reactor were higher than those in the control reactor after 1 month. Fluorescence in situ hybridization revealed that the percentages of the three microbes were 55.5 and 77.6 % in the control and paraffin reactors after 100 days, respectively. A simple model of mass balance was developed to describe the interactions between DAMO and Anammox microbes and validate the activity results. A mechanism was proposed to describe the possible way that paraffin oil enhanced DAMO activity. It is quite clear that paraffin oil enhances not only DAMO activity but also Anammox activity via the interaction between them; both NO3 (-) and NH4 (+) consumption rates were about two times those of the control.

  5. Natural rice rhizospheric microbes suppress rice blast infections

    PubMed Central

    2014-01-01

    Background The natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease. Results Naturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70–15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice. Conclusions Out of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with

  6. [Influences of long-term application of organic and inorganic fertilizers on the composition and abundance of nirS-type denitrifiers in black soil].

    PubMed

    Yin, Chang; Fan, Fen-Liang; Li, Zhao-Jun; Song, A-Lin; Zhu, Ping; Peng, Chang; Liang, Yong-Chao

    2012-11-01

    The objectives of this study were to explore the effects of long-term organic and inorganic fertilizations on the composition and abundance of nirS-type denitrifiers in black soil. Soil samples were collected from 4 treatments (i. e. no fertilizer treatment, CK; organic manure treatment, OM; chemical fertilizer treatment (NPK) and combination of organic and chemical fertilizers treatment (MNPK)) in Gongzhuling Long-term Fertilization Experiment Station. Composition and abundance of nirS-type denitrifiers were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR (Q-PCR), respectively. Denitrification enzyme activity (DEA) and soil properties were also measured. Application of organic fertilizers (OM and MNPK) significantly increased the DEAs of black soil, with the DEAs in OM and MNPK being 5.92 and 6.03 times higher than that in CK treatment, respectively, whereas there was no significant difference between NPK and CK. OM and MNPK treatments increased the abundances of nirS-type denitrifiers by 2.73 and 3.83 times relative to that of CK treatment, respectively. The abundance of nirS-type denitrifiers in NPK treatment was not significantly different from that of CK. The T-RFLP analysis of nirS genes showed significant differences in community composition between organic and inorganic treatments, with the emergence of a 79 bp T-RF, a significant decrease in relative abundance of the 84 bp T-RF and a loss of the 99 bp T-RF in all organic treatments. Phylogenetic analysis indicated that the airS-type denitrifiers in the black soil were mainly composed of alpha, beta and gamma-Proteobacteria. The 79 bp-type denitrifiers inhabiting exclusively in organic treatments (OM and MNPK) were affiliated to Pseudomonadaceae in gamma-Proteobacteria and Burkholderiales in beta-Proteobacteria. The 84 bp-types were related to Burkholderiales and Rhodocyclales. Correlation analysis indicated that pH, concentrations of total nitrogen

  7. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils.

    PubMed

    Barrett, M; Khalil, M I; Jahangir, M M R; Lee, C; Cardenas, L M; Collins, G; Richards, K G; O'Flaherty, V

    2016-04-01

    The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P < 0.03). Denitrifier gene copy concentrations per gram of soil (GCC) varied in response to carbon type amendment (P < 0.01). Denitrifier GCCs were high (ca. 10(7)) and the bac:nirK, bac:nirS, bac:nir (T) , and bac:nosZ ratios were low (ca. 10(-1)/10) in horizon A in all three respective treatments. Glucose-C amendment favored partial denitrification, resulting in higher nir abundance and higher N2O fluxes compared to the control. DOC amendment, by contrast, resulted in relatively higher nosZ abundance and N2 emissions, thus favoring complete denitrification. We also noted soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.

  8. Abundance and composition of denitrifiers in response to Spartina alterniflora invasion in estuarine sediment.

    PubMed

    Zhang, Qiufang; Peng, Jingjing; Chen, Qian; Yang, Xiaoru; Hong, Youwei; Su, Jianqiang

    2013-12-01

    Nitrite reduction is regulated by nitrite reductase encoded by nirK and nirS genes. This study aimed to investigate the abundance and composition of nirK- and nirS-containing denitrifiers in response to Spartina alterniflora invasion at the Jiulong River estuary, China. The sediment samples (depth: 0-5.0 and 5.1-20 cm) were collected from 3 vegetation zones, 1 dominated by the exotic plant S. alterniflora, 1 dominated by the native plant Kandelia candel, and 1 dominated by the native plant Cyperus malaccensis, and from an unvegetated flat zone. nirK- and nirS-containing denitrifier population sizes were lower in the invaded and nonvegetated zones than in those dominated by native K. candel and C. malaccensis, which were impacted by depth - vegetation species interaction. The ratios of nirS to nirK abundance ranged from 42.10 to 677.27, with the lowest ratio found for the upper layer in the invaded zone. The nirK-containing denitrifier compositions showed a 35% similarity between invaded zone and others. Most of the sequences of nirK genes recovered from the S. alterniflora zone were specific and distinct from those of nirK genes recovered from other vegetation types; nirS genes in the invaded zone were highly divergent. These results reveal that S. alterniflora invasion has a significant effect on the abundance and composition of both nirK- and nirS-containing denitrifiers, and nirS-containing denitrifiers were less responsive to invasion than nirK-containing denitrifiers. PMID:24313455

  9. Feasibility of enhanced biodegradation of petroleum compounds in groundwater under denitrifying conditions.

    PubMed

    Jin, Song; Fallgren, Paul; Luo, Haiping

    2010-03-01

    Groundwater was collected from a petroleum hydrocarbon contaminated site and characterized for microbial and physiochemical properties to assess the feasibility of enhanced natural attenuation. Results demonstrate the depletion of nitrate and dominance of denitrifying bacteria in the groundwater. Microcosm studies of amending nitrate and nutrients were attempted to enhanced biodegradation of petroleum compounds under denitrifying condition. Results show that 75% of petroleum compounds was degraded within 152-day in microcosms amended with nitrate, compared to 25% removal in the non-amended controls. Data indicate that nitrate amendment to groundwater may offer a viable remedy for enhanced natural attenuation of petroleum compounds.

  10. Rhizosphere chemical dialogues: plant-microbe interactions

    SciTech Connect

    Badri, D.V.; van der Lelie, D.; Weir, T. L.; Vivanco, J. M.

    2009-12-01

    Every organism on earth relies on associations with its neighbors to sustain life. For example, plants form associations with neighboring plants, microflora, and microfauna, while humans maintain symbiotic associations with intestinal microbial flora, which is indispensable for nutrient assimilation and development of the innate immune system. Most of these associations are facilitated by chemical cues exchanged between the host and the symbionts. In the rhizosphere, which includes plant roots and the surrounding area of soil influenced by the roots, plants exude chemicals to effectively communicate with their neighboring soil organisms. Here we review the current literature pertaining to the chemical communication that exists between plants and microorganisms and the biological processes they sustain.

  11. [Microbial flora in Cerasus sachalinensis rhizosphere].

    PubMed

    Yu, Cui; Lü, De-Guo; Qin, Si-Jun; Du, Guo-Dong; Liu, Guo-Cheng

    2007-10-01

    By using selected culture media, the microbes in Cerasus sachalinensis rhizosphere were isolated, identified and classified, with their community structure and dynamic changes at different growth stages of C. sachalinensis studied. The bacteria isolated were belonged to 15 genera, among which, Bacillus, Pseudomonas and Flavobacterium were the dominant ones. Flavus and Albosporus were the two dominant genera in seven groups of Actinomyces, and Mucor, Aspergillus and Penicillium were the main genera of fungi. The microbial flora varied with C. sachalinensis growth stage, being the richest at defoliation stage and the least at budding stage. PMID:18163310

  12. Induced Systemic Resistance and the Rhizosphere Microbiome

    PubMed Central

    Bakker, Peter A.H.M.; Doornbos, Rogier F.; Zamioudis, Christos; Berendsen, Roeland L.; Pieterse, Corné M.J.

    2013-01-01

    Microbial communities that are associated with plant roots are highly diverse and harbor tens of thousands of species. This so-called microbiome controls plant health through several mechanisms including the suppression of infectious diseases, which is especially prominent in disease suppressive soils. The mechanisms implicated in disease suppression include competition for nutrients, antibiosis, and induced systemic resistance (ISR). For many biological control agents ISR has been recognized as the mechanism that at least partly explains disease suppression. Implications of ISR on recruitment and functioning of the rhizosphere microbiome are discussed. PMID:25288940

  13. Comparative study of microflora in Rhizospheric soils of Argania spinosa and Acacia raddiana of the arid zone from Oued El Ma (Tindouf)

    NASA Astrophysics Data System (ADS)

    Tissouras, Fatiha; Habib, Semira; Missoum, Malika; Louacini, Braim Kamel

    2016-04-01

    Desert soils occupy a large area in Algeria (80Moreover, exploitation of the Saharan soil microorganisms has several interests and especially in maintaining the ecological equilibrium of ecosystems. Unfortunately, few of microbiological studies have been conducted so far about the Saharan soil Algerian, with the exception of some work done on the desert soils in the region of Beni Ounif. This work falls within the framework of Project CNEPRU F02320100009. The study focuses on an evaluation of the main germs rhizosphere soils from Argania spinosa and Acacia raddiana of the region of Oued El-ma (wilaya of Tindouf), located in southwest Algeria, followed by physicochemical analysis of some parameters (soil texture, pH, moisture content, organic matter). The results reveal that both rhizosphere soils have a sandy silt texture of alkali pH, with very low water content slightly different. Organic material of the rate varies from 0.2 to 1The type of vegetation influences positively the quantity and the dynamics of microbial population. Indeed, the two soils have an interesting microbial diversity, with densities of azotobacters, fungi, aerobic bacteria and actinomycetes are very high, followed germs ammonifiants, nitrifying and denitrifying. In the presence of Argania spinosa the microbial growth is most important (6.53 × 107 germs /g soil), compared with Acacia raddiana (3.13 × 107 germs /g). This shows the stimulating effect of the vegetation on the increase in the rate of these microorganisms in the soil. Well as the strong Fitness of adaptation the microbial biomass to drought. Keywords: Argania spinoza; Acacia raddiana; rhizospheric soil; microbiology evaluation.

  14. Accelerated biodegradation of nitrophenols in the rhizosphere of Spirodela polyrrhiza.

    PubMed

    Kristanti, Risky Ayu; Kanbe, Masahiro; Toyama, Tadashi; Tanaka, Yasuhiro; Tang, Yueqin; Wu, Xiaolei; Mori, Kazuhiro

    2012-01-01

    We investigated the biodegradation of 2-nitrophenol (2-NP), 4-nitrophenol (4-NP), and 2,4-dinitrophenol (2,4-DNP) in the rhizosphere of Spirodela polyrrhiza plants by conducting degradation experiments with three river water samples supplemented with each nitrophenol (NP). We then isolated NP-degrading bacteria both from the S. polyrrhiza roots and from the river water. In the river water samples, removal of the three NP was accelerated in the presence of S. polyrrhiza plants. The three NPs persisted in an autoclaved solution with sterile plants suggests that NP removal was accelerated largely by bacterial NP biodegradation rather than by adsorption and uptake by the plants. We isolated 8 strains of NP-degrading bacteria: 6 strains from the S. polyrrhiza roots and 2 strains from river water without the plants. The 2-NP- and 2,4-DNP-degrading bacteria were isolated only from the S. polyrrhiza roots. The 4-NP-degrading bacteria different from those isolated from the river water samples were also found on S. polyrrhiza roots. The 2-NP- and 4-NP-degrading strains isolated from the roots utilized the corresponding NP (0.5 mmol/L) as the sole carbon and energy source. The 2,4-DNP-degrading strains isolated from the roots showed substantial 2,4-DNP-degrading activity, but the presence of other carbon and energy sources was required for their growth. The isolated NP-degrading bacteria from the roots must have contributed to the accelerated degradation of the three NPs in the rhizosphere of S. polyrrhiza. Our results suggested that rhizoremediation with S. polyrrhiza may be effective for NP-contaminated surface water.

  15. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    SciTech Connect

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; Zhou, Jizhong; Firestone, Mary

    2015-08-04

    It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal

  16. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    DOE PAGES

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; et al

    2015-08-04

    It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

  17. Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing.

    PubMed

    Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin; Zhou, Zhi; Wu, Chen; Nagarajan, Sanjay

    2015-01-01

    Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere.

  18. Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing

    PubMed Central

    Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin; Zhou, Zhi; Wu, Chen; Nagarajan, Sanjay

    2015-01-01

    Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere. PMID:26539189

  19. Colonization of lettuce rhizosphere and roots by tagged Streptomyces.

    PubMed

    Bonaldi, Maria; Chen, Xiaoyulong; Kunova, Andrea; Pizzatti, Cristina; Saracchi, Marco; Cortesi, Paolo

    2015-01-01

    Beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. We studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified Streptomyces spp. Five Streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, Sclerotinia sclerotiorum, were transformed with pIJ8641 plasmid harboring an enhanced green fluorescent protein marker and resistance to apramycin. The fitness of transformants was compared to the wild-type strains and all of them grew and sporulated at similar rates and retained the production of enzymes and selected secondary metabolites as well as in vitro inhibition of S. sclerotiorum. The tagged ZEA17I strain was selected to study the dynamics of lettuce roots and rhizosphere colonization in non-sterile growth substrate. The transformed strain was able to colonize soil, developing roots, and rhizosphere. When the strain was inoculated directly on the growth substrate, significantly more t-ZEA17I was re-isolated both from the rhizosphere and the roots when compared to the amount obtained after seed coating. The re-isolation from the rhizosphere and the inner tissues of surface-sterilized lettuce roots demonstrated that t-ZEA17I is both rhizospheric and endophytic. PMID:25705206

  20. Colonization of lettuce rhizosphere and roots by tagged Streptomyces

    PubMed Central

    Bonaldi, Maria; Chen, Xiaoyulong; Kunova, Andrea; Pizzatti, Cristina; Saracchi, Marco; Cortesi, Paolo

    2015-01-01

    Beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. We studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified Streptomyces spp. Five Streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, Sclerotinia sclerotiorum, were transformed with pIJ8641 plasmid harboring an enhanced green fluorescent protein marker and resistance to apramycin. The fitness of transformants was compared to the wild-type strains and all of them grew and sporulated at similar rates and retained the production of enzymes and selected secondary metabolites as well as in vitro inhibition of S. sclerotiorum. The tagged ZEA17I strain was selected to study the dynamics of lettuce roots and rhizosphere colonization in non-sterile growth substrate. The transformed strain was able to colonize soil, developing roots, and rhizosphere. When the strain was inoculated directly on the growth substrate, significantly more t-ZEA17I was re-isolated both from the rhizosphere and the roots when compared to the amount obtained after seed coating. The re-isolation from the rhizosphere and the inner tissues of surface-sterilized lettuce roots demonstrated that t-ZEA17I is both rhizospheric and endophytic. PMID:25705206

  1. Visualizing Rhizosphere Soil Structure Around Living Roots

    NASA Astrophysics Data System (ADS)

    Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

    2008-12-01

    The rhizosphere, a thin layer of soil (0 to 2 mm) surrounding a living root, is an important interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 ìm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

  2. Enhancing Soybean Rhizosphere Colonization by Rhizobium japonicum

    PubMed Central

    Hossain, A. K. Maqbul; Alexander, Martin

    1984-01-01

    A study was conducted to seek means to increase the colonization of the rhizosphere of soybeans (Glycine max L. Merrill) by Rhizobium japonicum. For this purpose, a strain of R. japonicum that was resistant to benomyl, streptomycin, and erythromycin was used. The numbers of R. japonicum rose quickly in the first 2 days after soybean seeds were planted in soil and then rapidly fell. The decline was slower if the seeds were coated with benomyl. This fungicide reduced the numbers of bacteria and protozoa in the rhizosphere, but the effect became less or disappeared as the plants grew. In sterile soil inoculated with R. japonicum and a mixture of microorganisms, the numbers of R. japonicum were usually lower if protozoa were present than if they were absent. Nodulation and plant yield were increased by the addition of benomyl to soybean seeds sown in sterile soil inoculated with R. japonicum and a mixture of microorganisms. The addition of streptomycin and erythromycin to soil stimulated the growth of R. japonicum but inhibited other bacteria in the presence or absence of soybeans. The data indicate that colonization can be increased by the use of antimicrobial agents and R. japonicum strains resistant to those inhibitors. PMID:16346616

  3. Rhizosphere effect on phosphorus availability in forest soils at different altitudes.

    NASA Astrophysics Data System (ADS)

    De Feudis, Mauro; Cardelli, Valeria; Massaccesi, Luisa; Bol, Roland; Willbold, Sabine; Cocco, Stefania; Corti, Giuseppe; Agnelli, Alberto

    2016-04-01

    Phosphorus (P) is an essential nutrient for plants but it is one of the least available mineral nutrients, and can substantially limit plant growth. Although plants are able to respond to the P shortage, the global warming might modify the soil-plant-microorganisms system and reduce P availability. We evaluated the rhizosphere effect of beech (Fagus sylvatica L.) in forest soils of the Apennines mountains (central Italy) at two altitudes (800 and 1000 m) and along 1° of latitudinal gradient, using latitude and altitude as proxies for temperature change. Specifically, we tested if 1) soil organic C, total N, and organic and available P decrease with increasing latitude and altitude, and 2) the rhizosphere effect on P availability becomes more pronounced when potential nutrient limitations are more severe, as it happens with increasing latitude and altitude. The results suggested that the small latitudinal gradient has no effect on soil properties. Conversely, significant changes occurred between 800 and 1000 m a.s.l., as the soils at higher altitude showed greater TOC, organic and available P contents, and alkaline mono-phosphatases activity than the soils at 800 m a.s.l. Compared to the soils at lower altitude, a marked rhizosphere effect was found at 1000 m a.s.l., and it was mainly attributed to the release of labile organics through rhizodeposition processes. These labile organic compounds were considered able to induce a "priming effect" that fostered the mineralization of the soil organic matter. The enhanced organic carbon cycling, in turn, likely promoted the mineralization of the organic P forms. This was supported by the smaller proportion of orthophosphate monoesters found in the P pool of the rhizosphere than in that of the soil far from the roots, with a consequent increase of the amount of available P. Hence, we speculate that at high altitude the energy supplied by the plants through rhizodeposition to the rhizosphere heterotrophic microbial

  4. Copper accumulation in vineyard soils: Rhizosphere processes and agronomic practices to limit its toxicity.

    PubMed

    Brunetto, Gustavo; Bastos de Melo, George Wellington; Terzano, Roberto; Del Buono, Daniele; Astolfi, Stefania; Tomasi, Nicola; Pii, Youry; Mimmo, Tanja; Cesco, Stefano

    2016-11-01

    Viticulture represents an important agricultural practice in many countries worldwide. Yet, the continuous use of fungicides has caused copper (Cu) accumulation in soils, which represent a major environmental and toxicological concern. Despite being an important micronutrient, Cu can be a potential toxicant at high concentrations since it may cause morphological, anatomical and physiological changes in plants, decreasing both food productivity and quality. Rhizosphere processes can, however, actively control the uptake and translocation of Cu in plants. In particular, root exudates affecting the chemical, physical and biological characteristics of the rhizosphere, might reduce the availability of Cu in the soil and hence its absorption. In addition, this review will aim at discussing the advantages and disadvantages of agronomic practices, such as liming, the use of pesticides, the application of organic matter, biochar and coal fly ashes, the inoculation with bacteria and/or mycorrhizal fungi and the intercropping, in alleviating Cu toxicity symptoms. PMID:27513550

  5. Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

    PubMed Central

    Green, Stefan J.; Prakash, Om; Jasrotia, Puja; Overholt, Will A.; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M.; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

    2012-01-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment. PMID:22179233

  6. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

    PubMed

    Green, Stefan J; Prakash, Om; Jasrotia, Puja; Overholt, Will A; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M; Watson, David B; Schadt, Christopher W; Brooks, Scott C; Kostka, Joel E

    2012-02-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  7. Acceleration of nonylphenol and 4-tert-octylphenol degradation in sediment by Phragmites australis and associated rhizosphere bacteria.

    PubMed

    Toyama, Tadashi; Murashita, Manabu; Kobayashi, Kazutaka; Kikuchi, Shintaro; Sei, Kazunari; Tanaka, Yasuhiro; Ike, Michihiko; Mori, Kazuhiro

    2011-08-01

    We investigated biodegradation of technical nonylphenol (tNP) in Phragmites australis rhizosphere sediment by conducting degradation experiments using sediments spiked with tNP. Accelerated tNP removal was observed in P. australis rhizosphere sediment, whereas tNP persisted in unvegetated sediment without plants and in autoclaved sediment with sterile plants, suggesting that the accelerated tNP removal resulted largely from tNP biodegradation by rhizosphere bacteria. Three bacterial strains, Stenotrophomonas sp. strain IT-1 and Sphingobium spp. strains IT-4 and IT-5, isolated from the rhizosphere were capable of utilizing tNP and 4-tert-octylphenol as a sole carbon source via type II ipso-substitution. Oxygen from P. australis roots, by creating highly oxygenated conditions in the sediment, stimulated cell growth and the tNP-degrading activity of the three strains. Moreover, organic compounds from P. australis roots functioned as carbon and energy sources for two strains, IT-4 and IT-5, supporting cell growth and tNP-degrading activity. Thus, P. australis roots elevated the cell growth and tNP-degrading activity of the three bacterial strains, leading to accelerated tNP removal. These results demonstrate that rhizoremediation of tNP-contaminated sediments using P. australis can be an effective strategy.

  8. Optimizing hydraulic retention times in denitrifying woodchip bioreactors treating recirculating aquaculture system wastewater

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The performance of wood-based denitrifying bioreactors to treat high-nitrate wastewaters from aquaculture systems has not previously been demonstrated. Four pilot-scale woodchip bioreactors (approximately 1:10 scale) were constructed and operated for 268 d to determine the optimal range of design hy...

  9. Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer.

    PubMed

    Santoro, Alyson E; Boehm, Alexandria B; Francis, Christopher A

    2006-03-01

    Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 muM. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program integral-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site. PMID:16517659

  10. Denitrifier Community Composition along a Nitrate and Salinity Gradient in a Coastal Aquifer

    PubMed Central

    Santoro, Alyson E.; Boehm, Alexandria B.; Francis, Christopher A.

    2006-01-01

    Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 μM. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program ∫-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site. PMID:16517659

  11. Assessing the Impact of Denitrifier-Produced Nitric Oxide on Other Bacteria

    PubMed Central

    Choi, Peter S.; Naal, Zeki; Moore, Charles; Casado-Rivera, Emerilis; Abruña, Hector D.; Helmann, John D.; Shapleigh, James P.

    2006-01-01

    A series of experiments was undertaken to learn more about the impact on other bacteria of nitric oxide (NO) produced during denitrification. The denitrifier Rhodobacter sphaeroides 2.4.3 was chosen as a denitrifier for these experiments. To learn more about NO production by this bacterium, NO levels during denitrification were measured by using differential mass spectrometry. This revealed that NO levels produced during nitrate respiration by this bacterium were in the low μM range. This concentration of NO is higher than that previously measured in denitrifiers, including Achromobacter cycloclastes and Paracoccus denitrificans. Therefore, both 2.4.3 and A. cycloclastes were used in this work to compare the effects of various NO levels on nondenitrifying bacteria. By use of bacterial overlays, it was found that the NO generated by A. cycloclastes and 2.4.3 cells during denitrification inhibited the growth of both Bacillus subtilis and R. sphaeroides 2.4.1 but that R. sphaeroides 2.4.3 caused larger zones of inhibition in the overlays than A. cycloclastes. Both R. sphaeroides 2.4.3 and A. cycloclastes induced the expression of the NO stress response gene hmp in B. subtilis. Taken together, these results indicate that there is variability in the NO concentrations produced by denitrifiers, but, irrespective of the NO levels produced, microbes in the surrounding environment were responsive to the NO produced during denitrification. PMID:16517672

  12. Optimization of denitrifying bioreactor performance with agricultural residue-based filter media

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Denitrification bioreactors are a promising technology for mitigation of nitrate-nitrogen (NO3-N) losses in subsurface drainage water. Bioreactors are constructed with carbon substrates, typically wood chips, to provide a substrate for denitrifying microorganisms. Columns were packed with wood chips...

  13. [Effect of carbon source and nitrate concentration on denitrifying dephosphorus removal and variation of ORP].

    PubMed

    Wang, Ya-yi; Peng, Yong-zhen; Wagn, Shu-ying; Song, Xue-qi; Wagn, Shao-po

    2004-07-01

    Effect of added carbon source and nitrate concentration on the denitrifying phosphorus removal by SBR process was systematicaly studied, at the same time the variation of oxidation reductiun potential (ORP) was investigated. The results showed the phosphate release rate and the denitrifying and dephosphorus uptake rate in anoxic phase increased with the high carbon source concentration under anaerobic condition (100-300mg/L). However when the carbon source added in anaerobic phase was high to 300mg/L, the residual COD inhibited the succeed denitrifying dephosphorus uptake. High nitrate concentration (5, 15, 40mg/L) in anoxic phase increased the initial denitrifying dephosphorus rate. Once the nitrate depletes, phosphate uptake changed to phosphate release. Moreover, the time of the turning point occurred later with the higher nitrate addition. ORP can be used as a control parameter of phosphorus release, and it can also indicate the denitrificaiton react degree during the anoxic phosphorus removal but can't be used as control parameter of phosphorus uptake.

  14. Metagenomic analysis of the sludge microbial community in a lab-scale denitrifying phosphorus removal reactor.

    PubMed

    Lv, Xiao-Mei; Shao, Ming-Fei; Li, Ji; Li, Chao-Lin

    2015-04-01

    Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. In the present study, the metagenome of denitrifying phosphorus removal sludge from a lab-scale anaerobic-anoxic SBR was generated by Illumina sequencing to study the microbial community. Compared with the aerobic phosphorus removal sludge, the denitrifying phosphorus removal sludge demonstrated quite similar microbial community profile and microbial diversity with sludge from Aalborg East EBPR WWTP. Proteobacteria was the most dominant phylum; within Proteobacteria, β-Proteobacteria was the most dominant class, followed by α-, γ-, δ-, and ε-Proteobacteria. The genes involved in phosphate metabolism and biofilm formation reflected the selective pressure of the phosphorus removal process. Moreover, ppk sequence from DPAO was outside the Accumulibacter clusters, which suggested different core phosphorus removal bacteria in denitrifying and aerobic phosphorus removal systems. In a summary, putative DPAO might be a novel genus that is closely related between Accumulibacter and Dechloromonas within Rhodocyclus. The microbial community and metabolic profiles achieved in this study will eventually help to improve the understanding of key microorganisms and the entire community in order to improve the phosphorus removal efficiency of EBPR processes.

  15. Denitrifying Bioreactors – An Approach for Reducing Nitrate Loads to Receiving Waters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Low-cost and simple technologies are needed to reduce watershed export of excess nitrogen to sensitive aquatic ecosystems. Denitrifying bioreactors are an approach where solid carbon substrates are added into the flow path of contaminated water. These carbon substrates (often fragmented wood-product...

  16. Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer.

    PubMed

    Santoro, Alyson E; Boehm, Alexandria B; Francis, Christopher A

    2006-03-01

    Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 muM. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program integral-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.

  17. EFFECTS OF MICROCOSM PREPARATION ON RATES OF TOLUENE BIODEGRADATION UNDER DENITRIFYING CONDITIONS

    EPA Science Inventory

    Microcosms were prepared with subsurface material from two aquifers to examine the effects of preparation methods on rates of toluene biodegradation under denitrifying conditions. In both cases, the data fit a zero-order kinetics plot. However, rates of removal were generally pro...

  18. Role of Arbuscular Mycorrhizal Fungi in Phytoremediation of Soil Rhizosphere Spiked with Poly Aromatic Hydrocarbons

    PubMed Central

    2005-01-01

    Results from an innovative approach to improve remediation in the rhizosphere by encouraging healthy plant growth and thus enhancing microbial activity are reported. The effect of arbuscular mycorrhizal fungi (Am) on remediation efficacy of wheat, mungbean and eggplant grown in soil spiked with polyaromatic hydrocarbons (PAH) was assessed in a pot experiment. The results of this study showed that Am inoculation enhanced dissipation amount of PAHs in planted soil, plant uptake PAHs, dissipation amount of PAHs in planted versus unplanted spiked soil and loss of PAHs by the plant-promoted biodegradation. A number of parameters were monitored including plant shoot and root dry weight, plant tissue water content, plant chlorophyll, root lipid content, oxido-reductase enzyme activities in plant and soil rhizosphere and total microbial count in the rhizospheric soil. The observed physiological data indicate that plant growth and tolerance increased with Am, but reduced by PAH. This was reflected by levels of mycorrhizal root colonization which were higher for mungbean, moderate for wheat and low for eggplant. Levels of Am colonization increased on mungbean > wheat > eggplant. This is consistent with the efficacy of plant in dissipation of PAHs in spiked soil. Highly significant positive correlations were shown between of arbuscular formation in root segments (A)) and plant water content, root lipids, peroxidase, catalase polyphenol oxidase and total microbial count in soil rhizosphere as well as PAH dissipation in spiked soil. As consequence of the treatment with Am, the plants provide a greater sink for the contaminants since they are better able to survive and grow. PMID:24049473

  19. Availability of iron to Pseudomonas fluorescens in rhizosphere and bulk soil evaluated with an ice nucleation reporter gene.

    PubMed Central

    Loper, J E; Henkels, M D

    1997-01-01

    The biological availability of iron in the rhizosphere was assessed by evaluating ice nucleation activity (INA) expressed in situ by Pseudomonas fluorescens Pf-5 containing a transcriptional fusion (pvd-inaZ) of an iron-regulated promoter to an ice nucleation reporter gene (inaZ). Pf-5 containing pvd-inaZ expresses INA that is inversely related to the iron availability of a growth medium (J. E. Loper and S. E. Lindow, Appl. Environ. Microbiol. 60:1934-1941, 1994). INA expressed by rhizosphere populations of Pf-5 containing pvd-inaZ was at a maximum within 12 to 24 h following inoculation of the bacterium onto bean roots and typically decreased gradually during the following 4 days. Iron availability in the soil, which was altered by the addition of chelators, influenced INA expressed by rhizosphere populations of Pf-5 containing pvd-inaZ. In soil adjusted to a pH of 7.0 or 8.0 by adding Ca(OH)2, rhizosphere populations of Pf-5 containing pvd-inaZ expressed greater INA, indicating lower iron availability, than they did in the nonamended soil at a pH of 5.4. Similarly, rhizosphere populations of Pf-5 containing pvd-inaZ expressed less INA in an agricultural soil of pH 5.4 than in other agricultural soils ranging in pH from 6.4 to 7.7. These results conform to the predictions of chemical models stating that pH is a major factor influencing iron availability in soil solutions. The results of this study indicate that P. fluorescens Pf-5 encountered an iron-limited environment immediately after it was inoculated onto bean roots planted in agricultural field soils. One to two days after the bacterium was inoculated onto root surfaces, however, iron became more available to rhizosphere populations of Pf-5. We speculate that iron acquisition systems of plants and other rhizosphere organisms may provide available sources of iron to established rhizosphere populations of P. fluorescens. PMID:8979343

  20. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils.

    PubMed

    Pajares, Silvia; Bohannan, Brendan J M

    2016-01-01

    Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research. PMID:27468277

  1. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

    DOE PAGES

    Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; Cole, James R.; Wu, Liyou; Luo, Yiqi; Schuur, E. A. G.; Zhou, Jizhong; Tiedje, James M.

    2015-07-21

    Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

  2. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

    SciTech Connect

    Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; Cole, James R.; Wu, Liyou; Luo, Yiqi; Schuur, E. A. G.; Zhou, Jizhong; Tiedje, James M.

    2015-07-21

    Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

  3. [Distribution Characteristics of Nitrifiers and Denitrifiers in the River Sediments of Tongling City].

    PubMed

    Cheng, Jian-hua; Dou, Zhi-yong; Sun, Qing-ye

    2016-04-15

    Rivers in mining areas were influenced by contaminants such as nitrogen, phosphorus and organic matter due to domestic and agricultural wastewater discharge in addition to pollutants caused by mining activities. In this study, surface sediment samples of rivers in Tongling city were collected to address the effect of season and pollution type on the abundance of nitrifiers and denitrifiers using quantitative polymerase chain reaction (QPCR) technique targeting at the ammonia monooxygenase (amoA) and nitrite reductase (nir) genes. The results showed that the average ahundance of ammonia oxidizing archaea (AGA) (ranging from 1.74 x 10⁵ to 1.45 x 10⁸ copies · g⁻¹) was 4.39 times that of ammonia oxidizing hacteria (AGH) (ranging from 1.39 x 10⁵ to 3.39 x 10⁷ copies · g⁻¹); and the average abundance of nirK gene (ranging from 4.45 x 10⁶ to 1.51 x 10⁸ copies · g) was almost a thirtieth part of nirS gene (ranging from 1.69 x 10⁷ to 8.55 x 10⁹ copies · g⁻¹). The abundance of AOA was higher in spring and autumn, and lower in summer and winter. And sediment AOB abundance was higher in spring and winter than in summer and autumn. Meanwhile, the abundance of nir genes was in the order of spring (nirS )/autumn (nirK) > summer > winter > autumn (nirS )/spring (nirK). Moreover, the abundance of bacterial and archaeal arnoA and nirS genes in sediments influenced by mine pollution was generally higher than that in sediments influenced by agricultural non-point pollution, whereas the abundance of nirK gene showed an opposite trend. PMID:27548957

  4. [Identification and denitrification characteristics of a psychrotolerant facultative basophilic aerobic denitrifier].

    PubMed

    Wang, Zhao-Yang; Chen, Guo-Yao; Jiang, Ke; Xu, Pei-Ya

    2014-06-01

    An aerobic denitrifier was isolated from the activated sludge of landfill leachate through traditional microbiological methods. Based on its morphological feature, physiological and biochemical properties, and 16S rDNA sequence analysis, this strain was identified as Pseudomonas sp., named as GL19 with an accession number of KC710974 in GenBank. Its aerobic denitrification characteristics and nitrification function were studied to show that the factors including carbon source, C/N, pH and cultivation temperature were important for denitrification. The optimized condition for aerobic denitrification was as follows: sodium citrate as the carbon resource, C/N no less than 15, pH of 6-10, DO of 4.8-7.7 mg x L(-1), culture temperature of 15-34 degrees C and the initial nitrate nitrogen of 140 mg x L(-1). Combining these conditions, the removal rate of nitrate nitrogen and average removal rate of TN reached 100% and 96.5%, respectively, without the accumulation of nitrite nitrogen. The strain had the capability to utilize nitrite nitrogen or ammonia nitrogen to achieve high nitrogen removal efficiency: the nitrite nitrogen removal rate reached 100% in 20 hours with an initial nitrite nitrogen of 140 mg x L(-1); the ammonia nitrogen was efficiently removed from 280 mg x L(-1) to 3.11 mg x L(-1) in 28 hours with the removal rate of up to 98.9%. These results suggested that strain GL19 with the function of cold resistance and highly effective aerobic denitrification could achieve simultaneous nitrification and denitrification. Hence, GL19 could have high potential in practical wastewater treatment in winter of south area. PMID:25158516

  5. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

    PubMed Central

    Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; Cole, James R.; Wu, Liyou; Luo, Yiqi; Schuur, E. A. G.; Zhou, Jizhong; Tiedje, James M.

    2015-01-01

    Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations. PMID:26284038

  6. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

    PubMed Central

    Pajares, Silvia; Bohannan, Brendan J. M.

    2016-01-01

    Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research. PMID:27468277

  7. Isolation, characterization, and distribution of denitrifying toluene degraders from a variety of habitats.

    PubMed Central

    Fries, M R; Zhou, J; Chee-Sanford, J; Tiedje, J M

    1994-01-01

    Enrichments capable of toluene degradation under O2-free denitrifying conditions were established with diverse inocula including agricultural soils, compost, aquifer material, and contaminated soil samples from different geographic regions of the world. Successful enrichment was strongly dependent on the initial use of relatively low toluene concentrations, typically 5 ppm. From the enrichments showing positive activity for toluene degradation, 10 bacterial isolates were obtained. Fingerprints generated by PCR-amplified DNA, with repetitive extragenic palindromic sequence primers, showed that eight of these isolates were different. Under aerobic conditions, all eight isolates degraded toluene, five degraded ethylbenzene, three consumed benzene, and one degraded chlorobenzene, meta-Xylene was the only other substrate used anaerobically and was used by only one isolate. All isolates were motile gram-negative rods, produced N2 from denitrification, and did not hydrolyze starch. All strains but one fixed nitrogen as judged by ethylene production from acetylene, but only four strains hybridized to the nifHDK genes. All strains appeared to have heme nitrite reductase since their DNA hybridized to the heme (nirS) but not to the Cu (nirU) genes. Five strains hybridized to a toluene ortho-hydroxylase catabolic probe, and two of those also hybridized to a toluene meta-hydroxylase probe. Partial sequences of the 16S rRNA genes of all isolates showed substantial similarity to 16S rRNA sequences of Azoarcus sp. Physiological, morphological, fatty acid, and 16S rRNA analyses indicated that these strains were closely related to each other and that they belong to the genus Azoarcus.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:8085824

  8. Nitrate reduction by denitrifying anaerobic methane oxidizing microorganisms can reach a practically useful rate.

    PubMed

    Cai, Chen; Hu, Shihu; Guo, Jianhua; Shi, Ying; Xie, Guo-Jun; Yuan, Zhiguo

    2015-12-15

    Methane in biogas has been proposed to be an electron donor to facilitate complete nitrogen removal using denitrifying anaerobic methane oxidizing (DAMO) microorganisms in an anaerobic ammonium oxidation (anammox) reactor, by reducing the nitrate produced. However, the slow growth and the low activity of DAMO microorganisms cast a serious doubt about the practical usefulness of such a process. In this study, a previously established lab-scale membrane biofilm reactor (MBfR), with biofilms consisting of a coculture of DAMO and anammox microorganisms, was operated to answer if the DAMO reactor can achieve a nitrate reduction rate that can potentially be applied for wastewater treatment. Through progressively increasing nitrate and ammonium loading rates to the reactor, a nitrate removal rate of 684 ± 10 mg-N L(-1) d(-1) was achieved after 453 days of operation. This rate is, to our knowledge, by far the highest reported for DAMO reactors, and far exceeds what is predicted to be required for nitrate removal in a sidestream (5.6-135 mg-N L(-1) d(-1)) or mainstream anammox reactor (3.2-124 mg-N L(-1) d(-1)). Mass balance analysis showed that the nitrite produced by nitrate reduction was jointly reduced by anammox bacteria at a rate of 354 ± 3 mg-N L(-1) d(-1), accompanied by an ammonium removal rate of 268 ± 2 mg-N L(-1) d(-1), and DAMO bacteria at a rate of 330 ± 9 mg-N L(-1) d(-1). This study shows that the nitrate reduction rate achieved by the DAMO process can be high enough for removing nitrate produced by anammox process, which would enable complete nitrogen removal from wastewater. PMID:26414889

  9. Accumulation of the Antibiotic Phenazine-1-Carboxylic Acid in the Rhizosphere of Dryland Cereals

    PubMed Central

    Mavrodi, Dmitri V.; Mavrodi, Olga V.; Parejko, James A.; Bonsall, Robert F.; Kwak, Youn-Sig; Paulitz, Timothy C.; Weller, David M.

    2012-01-01

    Natural antibiotics are thought to function in the defense, fitness, competitiveness, biocontrol activity, communication, and gene regulation of microorganisms. However, the scale and quantitative aspects of antibiotic production in natural settings are poorly understood. We addressed these fundamental questions by assessing the geographic distribution of indigenous phenazine-producing (Phz+) Pseudomonas spp. and the accumulation of the broad-spectrum antibiotic phenazine-1-carboxylic acid (PCA) in the rhizosphere of wheat grown in the low-precipitation zone (<350 mm) of the Columbia Plateau and in adjacent, higher-precipitation areas. Plants were collected from 61 commercial wheat fields located within an area of about 22,000 km2. Phz+ Pseudomonas spp. were detected in all sampled fields, with mean population sizes ranging from log 3.2 to log 7.1 g−1 (fresh weight) of roots. Linear regression analysis demonstrated a significant inverse relationship between annual precipitation and the proportion of plants colonized by Phz+ Pseudomonas spp. (r2 = 0.36, P = 0.0001). PCA was detected at up to nanomolar concentrations in the rhizosphere of plants from 26 of 29 fields that were selected for antibiotic quantitation. There was a direct relationship between the amount of PCA extracted from the rhizosphere and the population density of Phz+ pseudomonads (r2 = 0.46, P = 0.0006). This is the first demonstration of accumulation of significant quantities of a natural antibiotic across a terrestrial ecosystem. Our results strongly suggest that natural antibiotics can transiently accumulate in the plant rhizosphere in amounts sufficient not only for inter- and intraspecies signaling but also for the direct inhibition of sensitive organisms. PMID:22138981

  10. Actinomycetes in the rhizosphere of semidesert soils of Mongolia

    NASA Astrophysics Data System (ADS)

    Norovsuren, Zh.; Zenova, G. M.; Mosina, L. V.

    2007-04-01

    The population density of actinomycetes in the desert-steppe soil, rhizosphere, and the above-ground parts of plants varies from tens to hundreds of thousands of colony-forming units (CFU) per gram of substrate. The actinomycetal complexes of the brown desert-steppe soil without plant roots are more diverse in their taxonomic composition than the actinomycetal complexes in the rhizosphere and the aboveground parts of plants. Additionally to representatives of the Streptomyces and Micromonospora genera, actinomycetes from the Nocardia, Saccharopolyspora, Thermomonospora, and Actinomadura genera were identified in the soil. The population density of actinomycetes in the rhizosphere and in the soil reached hundreds of thousand CFU/g; it considerably exceeded the population density of actinomycetes in the aboveground parts of plants. The maximum population density of actinomycetes was determined in the rhizosphere of Asparagus gobicus, Salsola pestifera, and Cleistogenes songorica.

  11. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    PubMed Central

    Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M.; Jun, Se-Ran; Parales, Rebecca E.; Tan, Watumesa A.; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Brown, Steven D.; Ussery, David W.; Schadt, Christopher W.; Tuskan, Gerald A.; Doktycz, Mitchel J.; Weston, David J.; Pelletier, Dale A.

    2015-01-01

    The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates. PMID:26528266

  12. Effect of rhizosphere on soil microbial community and in-situ pyrene biodegradation

    USGS Publications Warehouse

    Su, Y.; Yang, X.; Chiou, C.T.

    2008-01-01

    To access the influence of a vegetation on soil microorganisms toward organic pollutant biogegration, this study examined the rhizospheric effects of four plant species (sudan grass, white clover, alfalfa, and fescue) on the soil microbial community and in-situ pyrene (PYR) biodegradation. The results indicated that the spiked PYR levels in soils decreased substantially compared to the control soil without planting. With equal planted densities, the efficiencies of PYR degradation in rhizosphere with sudan grass, white clover, alfalfa and fescue were 34.0%, 28.4%, 27.7%, and 9.9%, respectively. However, on the basis of equal root biomass the efficiencies were in order of white clover >> alfalfa > sudan > fescue. The increased PYR biodegradation was attributed to the enhanced bacterial population and activity induced by plant roots in the rhizosphere. Soil microbial species and biomasses were elucidated in terms of microbial phospholipid ester-linked fatty acid (PLFA) biomarkers. The principal component analysis (PCA) revealed significant changes in PLFA pattern in planted and non-planted soils spiked with PYR. Total PLFAs in planted soils were all higher than those in non-planted soils. PLFA assemblages indicated that bacteria were the primary PYR degrading microorganisms, and that Gram-positive bacteria exhibited higher tolerance to PYR than Gram-negative bacteria did. ?? 2008 Higher Education Press and Springer-Verlag GmbH.

  13. Molecular detection of catabolic genes for polycyclic aromatic hydrocarbons in the reed rhizosphere of Sunchon Bay.

    PubMed

    Kahng, Hyung-Yeel; Oh, Kye-Heon

    2005-12-01

    This study focused on detecting catabolic genes for polycyclic aromatic hydrocarbons (PAHs) distributed in the reed rhizosphere of Sunchon Bay, Korea. These marsh and mud environments were severely affected by human activities, including agriculture and fisheries. Our previous study on microbial roles in natural decontamination displayed the possibility that PAH-degrading bacteria, such as Achromobacter sp., Alcaligenes sp., Burkholderia sp. and Pseudomonas sp. play an important decontamination role in a reed rhizosphere. In order to gain further fundamental knowledge on the natural decontamination process, catabolic genes for PAH metabolism were investigated through PCR amplification of dioxygenase genes using soil genomic DNA and sequencing. Comparative analysis of predicted amino acid sequences from 50 randomly selected dioxygenase clones capable of hydroxylating inactivated aromatic nuclei indicated that these were divided into three groups, two of which might be originated from PAH-degrading bacteria. Amino acid sequences of each dioxygenase clone were a part of the genes encoding enzymes for initial catabolism of naphthalene, phenanthrene, or pyrene that might be originated from bacteria in the reed rhizosphere of Sunchon Bay.

  14. Correlative Imaging and Analyses of Soil Organic Matter Stabilization in the Rhizosphere

    NASA Astrophysics Data System (ADS)

    Dohnalkova, Alice; Tfaily, Malak; Chu, Rosalie; Crump, Alex; Brislawn, Colin; Varga, Tamas; Chrisler, William

    2016-04-01

    Correlative Imaging and Analyses of Soil Organic Matter Stabilization in the Rhizosphere Understanding the dynamics of carbon (C) pools in soil systems is a critical area for mitigating atmospheric carbon dioxide levels and maintaining healthy soils. Although microbial contributions to stable soil carbon pools have often been regarded as low to negligible, we present evidence that microbes may play a far greater role in the stabilization of soil organic matter (SOM), thus in contributing to soil organic matter pools with longer residence time. The rhizosphere, a zone immediately surrounding the plant roots, represents a geochemical hotspot with high microbial activity and profuse SOM production. Particularly, microbially secreted extracellular polymeric substances (EPS) present a remarkable dynamic entity that plays a critical role in numerous soil processes including mineral weathering. We approach the interface of soil minerals and microbes with a focus on the organic C stabilization mechanisms. We use a suite of high-resolution imaging and analytical methods (confocal, scanning and transmission electron microscopy, Fourier transform ion cyclotron resonance mass spectrometry, DNA sequencing and X-ray diffraction), to study the living and non-living rhizosphere components. Our goal is to elucidate a pathway for the formation, storage, transformation and protection of persistent microbially-produced carbon in soils. Based on our multimodal analytical approach, we propose that persistent microbial necromass in soils accounts for considerably higher soil carbon than previously estimated.

  15. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    SciTech Connect

    Timm, Collin M.; Campbell, Alicia G.; Utturkar, Sagar M.; Jun, Se Ran; Parales, Rebecca E.; Tan, Mesa; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Schadt, Christopher Warren; Doktycz, Mitchel John; Weston, David; Pelletier, Dale A.

    2015-10-14

    The bacterial microbiota of plants is diverse, with ~1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work we investigate how 19 sequenced Pseudomonas fluorescens strains representing a single OTU isolated from Populus deltoides rhizosphere and endosphere differ using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for bacterial-plant interactions are enriched in endosphere isolate genomes and growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways important for bacterial-plant interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria that are enriched in event he most closely related isolates.

  16. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    DOE PAGES

    Timm, Collin M.; Campbell, Alicia G.; Utturkar, Sagar M.; Jun, Se Ran; Parales, Rebecca E.; Tan, Mesa; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Schadt, Christopher Warren; et al

    2015-10-14

    The bacterial microbiota of plants is diverse, with ~1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work we investigate how 19 sequenced Pseudomonas fluorescens strains representing a single OTU isolated from Populus deltoides rhizosphere and endosphere differ using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for bacterial-plant interactions are enriched in endosphere isolate genomes and growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have more metabolic pathwaysmore » for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways important for bacterial-plant interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria that are enriched in event he most closely related isolates.« less

  17. Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture

    PubMed Central

    Wu, Linkun; Wang, Juanying; Huang, Weimin; Wu, Hongmiao; Chen, Jun; Yang, Yanqiu; Zhang, Zhongyi; Lin, Wenxiong

    2015-01-01

    Under consecutive monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during monoculture. Prolonged monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates. PMID:26515244

  18. Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture

    NASA Astrophysics Data System (ADS)

    Wu, Linkun; Wang, Juanying; Huang, Weimin; Wu, Hongmiao; Chen, Jun; Yang, Yanqiu; Zhang, Zhongyi; Lin, Wenxiong

    2015-10-01

    Under consecutive monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during monoculture. Prolonged monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.

  19. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

    PubMed

    Timm, Collin M; Campbell, Alisha G; Utturkar, Sagar M; Jun, Se-Ran; Parales, Rebecca E; Tan, Watumesa A; Robeson, Michael S; Lu, Tse-Yuan S; Jawdy, Sara; Brown, Steven D; Ussery, David W; Schadt, Christopher W; Tuskan, Gerald A; Doktycz, Mitchel J; Weston, David J; Pelletier, Dale A

    2015-01-01

    The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates. PMID:26528266

  20. Nitrogen removal from micro-polluted reservoir water by indigenous aerobic denitrifiers.

    PubMed

    Huang, Ting-Lin; Zhou, Shi-Lei; Zhang, Hai-Han; Zhou, Na; Guo, Lin; Di, Shi-Yu; Zhou, Zi-Zhen

    2015-01-01

    accumulation in either system. Our results show that aerobic denitrifying bacteria remain highly active after domestication and demonstrate the applicability of such organisms in the bioremediation of oligotrophic ecosystems. PMID:25867475

  1. Nitrogen Removal from Micro-Polluted Reservoir Water by Indigenous Aerobic Denitrifiers

    PubMed Central

    Huang, Ting-Lin; Zhou, Shi-Lei; Zhang, Hai-Han; Zhou, Na; Guo, Lin; Di, Shi-Yu; Zhou, Zi-Zhen

    2015-01-01

    accumulation in either system. Our results show that aerobic denitrifying bacteria remain highly active after domestication and demonstrate the applicability of such organisms in the bioremediation of oligotrophic ecosystems. PMID:25867475

  2. The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia.

    PubMed

    Nunes da Rocha, Ulisses; Plugge, Caroline M; George, Isabelle; van Elsas, Jan Dirk; van Overbeek, Leonard Simon

    2013-01-01

    There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.

  3. The Rhizosphere Selects for Particular Groups of Acidobacteria and Verrucomicrobia

    PubMed Central

    Plugge, Caroline M.; George, Isabelle; van Elsas, Jan Dirk

    2013-01-01

    There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence. PMID:24349285

  4. Use of Rhizosphere Metabolomics to Investigate Exudation of Phenolics by Arabidopsis Roots

    NASA Astrophysics Data System (ADS)

    Lee, Yong Jian; Rai, Amit; Reuben, Sheela; Nesati, Victor; Almeida, Reinaldo; Swarup, Sanjay

    2013-04-01

    The rhizosphere is a specialised micro-niche for bacteria that have an active exchange of signals and nutrients with the host plant. Nearly 20% of photosynthates are released as root exudates, which consist of primary metabolites and products of secondary metabolism which are largely phenolic in nature. Previously, using rhizosphere metabolomics, we showed that nearly 50% of organic carbon in the exudates is in the form of phenolic compounds, of which the largest fraction is from the phenylpropanoid synthesis pathway. Using Arabidopsis as a model, we have demonstrated that a biased rhizosphere can be created using plants with varying levels of phenylpropanoids due to mutations in the biosynthetic or regulatory genes. These phenylpropanoids levels are reflected in the exudates, and exudates from lines with regulatory gene mutations, tt8 and ttg, have higher levels of phenylpropanoids, whereas biosynthetic mutant line, tt4, has very low and undetectable levels of phenylpropanoids. The biased rhizosphere of tt8 and ttg lines provides a nutritional advantage to rhizobacteria that can utilize these phenylpropanoids such as quercetin. With such a strategy to increase the competitiveness of plant growth-promoting rhizobacteria (PGPR) such as Pseudomonas putida, this system can be applied to improve plant performance. In order to better understand the metabolic basis of the nutritional advantage behind the competitiveness of the favoured P. putida, we elucidated its quercetin utilization pathway. We have recently cloned the gene for quercetin oxidoreductase (QuoA) and expressed it in transgenic Arabidopsis lines to alter the plant phenylpropanoid metabolism, using a gain of function approach. Since phenylpropanoid biosynthesis in plants involve formation of quercetin from naringenin, we envisaged that QuoA expression in plants will provide us with a genetic tool to "reverse" this biosynthetic step. This perturbation led to a decrease in flavonoids and an increase in lignin

  5. An Apple Fruit Fermentation (AFF) Treatment Improves the Composition of the Rhizosphere Microbial Community and Growth of Strawberry (Fragaria × ananassa Duch ‘Benihoppe’) Seedlings

    PubMed Central

    Bu, Yufen; Shao, Wei; Huang, Weijing; Ji, Qianlong; Yao, Yuncong

    2016-01-01

    Plant growth can be promoted by the application of apple fruit fermentation (AFF), despite unclear of the underlying mechanisms, the effects involved in AFF on rhizosphere microorganisms have been hypothesized. We investigated the consequences of applying AFF alone or in combination with Bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA were performed to determine AFF effects on rhizosphere. Moreover, the growth index and antioxidant enzyme activities were determined 30 days after treatments. We identified five dominant bacteria in AFF: Coprinus atramentarius, Bacillus megaterium, Bacillus licheniformis, Weissella and B. subtilis. The greatest number of bacterial species were observed in the rhizosphere of control matrix (water treated), and the lowest diversity appeared in the rhizosphere soil treated with 108 cfu/mL B. licheniformis alone. Combining AFF plus B. licheniformis in one treatment resulted in the largest leaf area, plant height, root length, plant weight, and the markedly higher activities of antioxidant enzymes. We conclude that a combination of AFF plus B. licheniformis treatment to matrix can increase antioxidant enzymes activities in strawberry seedlings, optimize the status of rhizosphere microbial, and promote plant growth. PMID:27755580

  6. Microbial degradation of mefenoxam in rhizosphere of Zinnia angustifolia.

    PubMed

    Pai, S G; Riley, M B; Camper, N D

    2001-08-01

    The fate of the fungicide mefenoxam was studied in a containerized rhizosphere system. The rhizosphere system used Zinnia angustifolia (Tropic Snow) in a bark/sand potting mix and was compared to bulk potting mix (no plants). Rhizosphere microbial populations were allowed to establish for 3 weeks prior to fungicide addition (20 microg per g mix). Mefenoxam and degradation product concentrations were determined by High HPLC or capillary electrophoresis after extraction. Seventy eight percent of the fungicide originally applied to the rhizosphere was degraded after 21 days compared to 44% in bulk system (no plant). The primary degradation product was the free acid N-(2,6-dimethylphenyl)-N-(methoxyacetyl)-DL-alanine, which accounted for 71% of the applied parent chemical after 30 days. N-(2,6-dimethylphenyl)-acetamide was also detected, but in lesser amounts. Bacterial populations in the rhizosphere increased during the 30-day period, which correlated with an increase in degradation of the parent compound. Pure cultures of Pseudomonas fluorescens and Chrysobacterium indologenes isolated from the rhizosphere system could degrade the applied fungicide (10 microg/ml) almost completely to the free acid within 54 h. PMID:11482644

  7. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    PubMed

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community. PMID:26580738

  8. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    PubMed

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

  9. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

    PubMed Central

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; Zhou, Jizhong

    2015-01-01

    ABSTRACT It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. PMID:26242625

  10. RELATIONSHIP BETWEEN THE CONCENTRATION OF DENITRIFIERS AND PSEUDOMONAS SPP. IN SOILS: IMPLICATIONS FOR BTX BIOREMEDIATION (R823420)

    EPA Science Inventory

    Aquifer microcosms were used to investigate the effect of stimulating denitrification on microbial population shifts and BTX degradation potential. Selective pressure
    for facultative denitrifiers was applied to a treatment set by feeding acetate and nitrate, and cycling electr...

  11. [Transformation and mobility of arsenic in the rhizosphere and non-rhizosphere soils at different growth stages of rice].

    PubMed

    Yang, Wen-Tao; Wang, Ying-Jie; Zhou, Hang; Yi, Kai-Xin; Zeng, Min; Peng, Pei-Qin; Liao, Bo-Han

    2015-02-01

    Speciation and bioavailability of arsenic in the rhizosphere and non-rhizosphere soils at different growth stages (tillering stage, jointing stage, booting stage, filling stage and maturing stage) of rice (Oryza sativa L.) were studied using toxicity characteristic leaching procedure (TCLP) and arsenic speciation analysis. Pot experiments were conducted and the soil samples were taken from a certain paddy soil in Hunan Province contaminated by mining industry. The results showed that: (1) With the extension of rice growth period, pH values and TCLP extractable arsenic levels in the rhizosphere and non-rhizosphere soils increased gradually. Soil pH and TCLP extractable arsenic levels in non-rhizosphere soils were higher than those in the rhizosphere soils at the same growth stage. (2) At the different growth stages of rice, contents of exchangeable arsenic (AE-As) in rhizosphere and non-rhizosphere soils were lower than those before the rice planting, and increased gradually with the extension of the rice growing period. Contents of Al-bound arsenic (Al-As), Fe-bound arsenic (Fe-As) and Ca-bound arsenic (Ca-As) increased gradually after rice planting, but not significantly. Residual arsenic (O-As) and total arsenic (T-As) decreased gradually after rice planting, by 37.30% and 14.69% in the rhizosphere soils and by 31.38% and 8.67% in the non-rhizosphere soils, respectively. (3) At the different growth stages of rice, contents of various forms of arsenic in the soils were in the following order: residual arsenic (O-As) > Fe-bound arsenic ( Fe-As) > Al-bound arsenic (Al-As) > Ca-bound arsenic (Ca-As) > exchangeable arsenic (AE-As). In the pH range of 5.0- 5.8, significant positive linear correlations were found between most forms of arsenic or TCLP extractable arsenic levels and pH values, while the Ca-bound arsenic was poorly correlated with pH values in the rhizosphere soils. PMID:26031100

  12. [Transformation and mobility of arsenic in the rhizosphere and non-rhizosphere soils at different growth stages of rice].

    PubMed

    Yang, Wen-Tao; Wang, Ying-Jie; Zhou, Hang; Yi, Kai-Xin; Zeng, Min; Peng, Pei-Qin; Liao, Bo-Han

    2015-02-01

    Speciation and bioavailability of arsenic in the rhizosphere and non-rhizosphere soils at different growth stages (tillering stage, jointing stage, booting stage, filling stage and maturing stage) of rice (Oryza sativa L.) were studied using toxicity characteristic leaching procedure (TCLP) and arsenic speciation analysis. Pot experiments were conducted and the soil samples were taken from a certain paddy soil in Hunan Province contaminated by mining industry. The results showed that: (1) With the extension of rice growth period, pH values and TCLP extractable arsenic levels in the rhizosphere and non-rhizosphere soils increased gradually. Soil pH and TCLP extractable arsenic levels in non-rhizosphere soils were higher than those in the rhizosphere soils at the same growth stage. (2) At the different growth stages of rice, contents of exchangeable arsenic (AE-As) in rhizosphere and non-rhizosphere soils were lower than those before the rice planting, and increased gradually with the extension of the rice growing period. Contents of Al-bound arsenic (Al-As), Fe-bound arsenic (Fe-As) and Ca-bound arsenic (Ca-As) increased gradually after rice planting, but not significantly. Residual arsenic (O-As) and total arsenic (T-As) decreased gradually after rice planting, by 37.30% and 14.69% in the rhizosphere soils and by 31.38% and 8.67% in the non-rhizosphere soils, respectively. (3) At the different growth stages of rice, contents of various forms of arsenic in the soils were in the following order: residual arsenic (O-As) > Fe-bound arsenic ( Fe-As) > Al-bound arsenic (Al-As) > Ca-bound arsenic (Ca-As) > exchangeable arsenic (AE-As). In the pH range of 5.0- 5.8, significant positive linear correlations were found between most forms of arsenic or TCLP extractable arsenic levels and pH values, while the Ca-bound arsenic was poorly correlated with pH values in the rhizosphere soils.

  13. Impact of Bt corn on rhizospheric and soil eubacterial communities and on beneficial mycorrhizal symbiosis in experimental microcosms.

    PubMed

    Castaldini, M; Turrini, A; Sbrana, C; Benedetti, A; Marchionni, M; Mocali, S; Fabiani, A; Landi, S; Santomassimo, F; Pietrangeli, B; Nuti, M P; Miclaus, N; Giovannetti, M

    2005-11-01

    A polyphasic approach has been developed to gain knowledge of suitable key indicators for the evaluation of environmental impact of genetically modified Bt 11 and Bt 176 corn lines on soil ecosystems. We assessed the effects of Bt corn (which constitutively expresses the insecticidal toxin from Bacillus thuringiensis, encoded by the truncated Cry1Ab gene) and non-Bt corn plants and their residues on rhizospheric and bulk soil eubacterial communities by means of denaturing gradient gel electrophoresis analyses of 16S rRNA genes, on the nontarget mycorrhizal symbiont Glomus mosseae, and on soil respiration. Microcosm experiments showed differences in rhizospheric eubacterial communities associated with the three corn lines and a significantly lower level of mycorrhizal colonization in Bt 176 corn roots. In greenhouse experiments, differences between Bt and non-Bt corn plants were detected in rhizospheric eubacterial communities (both total and active), in culturable rhizospheric heterotrophic bacteria, and in mycorrhizal colonization. Plant residues of transgenic plants, plowed under at harvest and kept mixed with soil for up to 4 months, affected soil respiration, bacterial communities, and mycorrhizal establishment by indigenous endophytes. The multimodal approach utilized in our work may be applied in long-term field studies aimed at monitoring the real hazard of genetically modified crops and their residues on nontarget soil microbial communities.

  14. Mineral Dissolution and Metal Mobility From Rhizosphere and Non-rhizosphere Soils by Low Molecular Weight Organic Acids

    NASA Astrophysics Data System (ADS)

    Little, D. A.; Field, J. B.; Welch, S. A.

    2005-12-01

    This research is part of an ongoing investigation of micro-biogeochemistry in the rhizosphere of co-occurring Eucalyptus mannifera and Acacia falciformis on the Southern Tablelands of New South Wales, Australia. While there is still considerable controversy in the literature regarding the roles of low molecular weight organic acids in soil processes there is growing evidence suggesting low molecular weight compounds, especially di-carboxylic acids, have large impacts on mineral dissolution and metal mobility in the rhizosphere. Rhizosphere and non-rhizosphere samples from adjacent E. mannifera and A. falciformis trees were subjected to four separate treatments in sets of 3 replicates; +oxalic acid, +malic acid, +citric acid or +NaCl control solution. These three acids were chosen because they are produced by rhizosphere species and they form stable complexes with nutrient elements such as Phosphorus (P), Iron (Fe), and Calcium (Ca). Solution samples were collected at day 1, day 8 and day 15 for pH measurement and analysed for major and trace elements by ICP-AES and ICP-MS. The results of the preliminary dissolution experiments show that milli-molar concentrations of individual organic acids, malate and oxalate, and in particular citrate, greatly increase the release of major and trace metals to solution compared to inorganic controls. Concentrations of Al and Fe in organic acid solutions were up to 10 times greater than in the inorganic controls. Si concentrations were a factor of 2-5 greater in the organic acid solutions, suggesting preferential weathering of Fe and Al oxyhydroxide phases rather than primary silicate minerals. Dissolution of elements such as Si, Al and Fe from rhizosphere soils were about twice that observed from non-rhizosphere soils, further supporting this. Interestingly Ti and Zr, which are usually considered to be immobile during chemical weathering and are not usually taken up by plants, were also mobilised from the rhizosphere soils

  15. Bioaugmentation of nitrate-dependent anaerobic ferrous oxidation by heterotrophic denitrifying sludge addition: A promising way for promotion of chemoautotrophic denitrification.

    PubMed

    Wang, Ru; Zheng, Ping; Zhang, Meng; Zhao, He-Ping; Ji, Jun-Yuan; Zhou, Xiao-Xin; Li, Wei

    2015-12-01

    Nitrate-dependent anaerobic ferrous oxidation (NAFO) is a new and valuable bio-process for the treatment of wastewaters with low C/N ratio, and the NAFO process is in state of the art. The heterotrophic denitrifying sludge (HDS), possessing NAFO activity, was used as bioaugmentation to enhance NAFO efficiency. At a dosage of 6% (V/V), the removal of nitrate and ferrous was 2.4 times and 2.3 times of as primary, and the volumetric removal rate (VRR) of nitrate and ferrous was 2.4 times and 2.2 times of as primary. Tracing experiments of HDS indicated that the bioaugmentation on NAFO reactor was resulted from the NAFO activity by HDS itself. The predominant bacteria in HDS were identified as Thauera (52.5%) and Hyphomicrobium (20.0%) which were typical denitrifying bacteria and had potential ability to oxidize ferrous. In conclusion, HDS could serve as bioaugmentation or a new seeding sludge for operating high-efficiency NAFO reactors. PMID:26348287

  16. Selection rhizosphere-competent microbes for development of microbial products as biocontrol agents

    NASA Astrophysics Data System (ADS)

    Mashinistova, A. V.; Elchin, A. A.; Gorbunova, N. V.; Muratov, V. S.; Kydralieva, K. A.; Khudaibergenova, B. M.; Shabaev, V. P.; Jorobekova, Sh. J.

    2009-04-01

    Rhizosphere-borne microorganisms reintroduced to the soil-root interface can establish without inducing permanent disturbance in the microbial balance and effectively colonise the rhizosphere due to carbon sources of plant root exudates. A challenge for future development of microbial products for use in agriculture will be selection of rhizosphere-competent microbes that both protect the plant from pathogens and improve crop establishment and persistence. In this study screening, collection, identification and expression of stable and technological microbial strains living in soils and in the rhizosphere of abundant weed - couch-grass Elytrigia repens L. Nevski were conducted. A total of 98 bacteria isolated from the rhizosphere were assessed for biocontrol activity in vitro against phytopathogenic fungi including Fusarium culmorum, Fusarium heterosporum, Fusarium oxysporum, Drechslera teres, Bipolaris sorokiniana, Piricularia oryzae, Botrytis cinerea, Colletothrichum atramentarium and Cladosporium sp., Stagonospora nodorum. Biocontrol activity were performed by the following methods: radial and parallel streaks, "host - pathogen" on the cuts of wheat leaves. A culture collection comprising 64 potential biocontrol agents (BCA) against wheat and barley root diseases has been established. Of these, the most effective were 8 isolates inhibitory to at least 4 out of 5 phytopathogenic fungi tested. The remaining isolates inhibited at least 1 of 5 fungi tested. Growth stimulating activity of proposed rhizobacteria-based preparations was estimated using seedling and vegetative pot techniques. Seeds-inoculation and the tests in laboratory and field conditions were conducted for different agricultural crops - wheat and barley. Intact cells, liquid culture filtrates and crude extracts of the four beneficial bacterial strains isolated from the rhizosphere of weed were studied to stimulate plant growth. As a result, four bacterial strains selected from rhizosphere of weed

  17. Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China.

    PubMed

    Yi, Neng; Gao, Yan; Zhang, Zhenhua; Wang, Yan; Liu, Xinhong; Zhang, Li; Yan, Shaohua

    2015-01-01

    Streams are an important sink for anthropogenic N owing to their hydrological connections with terrestrial systems, but main factors influencing the community structure and abundance of denitrifiers in stream water remain unclear. To elucidate the potential impact of varying water properties of different streams on denitrifiers, the abundance and community of three denitrifying genes coding for nitrite (nirK, nirS) and nitrous oxide (nosZ) reductase were investigated in 11 streams inlets at the north part of Dianchi Lake. The DGGE results showed the significant pairwise differences in community structure of nirK, nirS, and nosZ genes among different streams. The results of redundancy analysis (RDA) confirmed that nitrogen and phosphorus concentrations, pH, and temperature in waters were the main environmental factors leading to a significant alteration in the community structure of denitrifiers among different streams. The denitrifying community size was assessed by quantitative PCR (qPCR) of the nirS, nirK, and nosZ genes. The abundance of nirK, nirS, and nosZ was positively associated with concentrations of total N (TN) and PO4 (3-) (p < 0.001). The difference in spatial patterns between nirK and nirS community diversity, in combination with the spatial distribution of the nirS/nirK ratio, indicated the occurrence of habitat selection for these two types of denitrifiers in the different streams. The results indicated that the varying of N species and PO4 (3-) together with pH and temperature would be the main factors shaping the community structure of denitrifiers. Meanwhile, the levels of N in water, together with PO4 (3-), tend to affect the abundance of denitrifiers. PMID:26504771

  18. Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China

    PubMed Central

    Yi, Neng; Gao, Yan; Zhang, Zhenhua; Wang, Yan; Liu, Xinhong; Zhang, Li; Yan, Shaohua

    2015-01-01

    Streams are an important sink for anthropogenic N owing to their hydrological connections with terrestrial systems, but main factors influencing the community structure and abundance of denitrifiers in stream water remain unclear. To elucidate the potential impact of varying water properties of different streams on denitrifiers, the abundance and community of three denitrifying genes coding for nitrite (nirK, nirS) and nitrous oxide (nosZ) reductase were investigated in 11 streams inlets at the north part of Dianchi Lake. The DGGE results showed the significant pairwise differences in community structure of nirK, nirS, and nosZ genes among different streams. The results of redundancy analysis (RDA) confirmed that nitrogen and phosphorus concentrations, pH, and temperature in waters were the main environmental factors leading to a significant alteration in the community structure of denitrifiers among different streams. The denitrifying community size was assessed by quantitative PCR (qPCR) of the nirS, nirK, and nosZ genes. The abundance of nirK, nirS, and nosZ was positively associated with concentrations of total N (TN) and PO43− (p < 0.001). The difference in spatial patterns between nirK and nirS community diversity, in combination with the spatial distribution of the nirS/nirK ratio, indicated the occurrence of habitat selection for these two types of denitrifiers in the different streams. The results indicated that the varying of N species and PO43− together with pH and temperature would be the main factors shaping the community structure of denitrifiers. Meanwhile, the levels of N in water, together with PO43−, tend to affect the abundance of denitrifiers. PMID:26504771

  19. Allelochemicals in the rhizosphere soil of Euphorbia himalayensis.

    PubMed

    Liu, Quan; Lu, Dengxue; Jin, Hui; Yan, Zhiqiang; Li, Xiuzhuang; Yang, Xiaoyan; Guo, Hongru; Qin, Bo

    2014-08-27

    Weed infestation has been known to cause considerable reductions in crop yields, thereby hindering sustainable agriculture. Many plants in genus Euphorbia affect neighboring plants and other organisms by releasing chemicals into the environment. In view of the serious threat of weeds to agriculture, the allelochemicals of Euphorbia himalayensis and their allelopathic effects were investigated. The extract of root exudates from rhizosphere soil exhibited allelopathic activities against crops (wheat, rape, and lettuce) and grasses (Poa annua, Festuca rubra, and red clover). Bioassay-guided fractionation and isolation from the root extract of E. himalayensis led to the characterization of two ellagic acid derivatives and a jatrophane diterpene, which observably showed phytotoxic activities against lettuce, Festuca arundinacea, and F. rubra. They were further confirmed by ultra-performance liquid chromatography-tandem mass spectrometry to have concentrations of 3.6, 3.8, and 8.99 nmol/g in the rhizospere soil, respectively. Bioassay indicated that the combination of the allelochemicals could be selective plant growth regulator in agriculture.

  20. Allelochemicals in the rhizosphere soil of Euphorbia himalayensis.

    PubMed

    Liu, Quan; Lu, Dengxue; Jin, Hui; Yan, Zhiqiang; Li, Xiuzhuang; Yang, Xiaoyan; Guo, Hongru; Qin, Bo

    2014-08-27

    Weed infestation has been known to cause considerable reductions in crop yields, thereby hindering sustainable agriculture. Many plants in genus Euphorbia affect neighboring plants and other organisms by releasing chemicals into the environment. In view of the serious threat of weeds to agriculture, the allelochemicals of Euphorbia himalayensis and their allelopathic effects were investigated. The extract of root exudates from rhizosphere soil exhibited allelopathic activities against crops (wheat, rape, and lettuce) and grasses (Poa annua, Festuca rubra, and red clover). Bioassay-guided fractionation and isolation from the root extract of E. himalayensis led to the characterization of two ellagic acid derivatives and a jatrophane diterpene, which observably showed phytotoxic activities against lettuce, Festuca arundinacea, and F. rubra. They were further confirmed by ultra-performance liquid chromatography-tandem mass spectrometry to have concentrations of 3.6, 3.8, and 8.99 nmol/g in the rhizospere soil, respectively. Bioassay indicated that the combination of the allelochemicals could be selective plant growth regulator in agriculture. PMID:25088250

  1. Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates.

    PubMed

    Ghequire, Maarten G K; Dillen, Yörg; Lambrichts, Ivo; Proost, Paul; Wattiez, Ruddy; De Mot, René

    2015-09-26

    Bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. Such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated DNA. A subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. Functional characterization of bactericidal tailocins of two Pseudomonas putida rhizosphere isolates revealed not only extensive similarity with the tail assembly module of the Pseudomonas aeruginosa R-type pyocins but also differences in genomic integration site, regulatory genes, and lytic release modules. Conversely, these three features are quite similar between strains of the P. putida and Pseudomonas fluorescens clades, although phylogenetic analysis of tail genes suggests them to have evolved separately. Unlike P. aeruginosa R pyocin elements, the tailocin gene clusters of other pseudomonads frequently carry cargo genes, including bacteriocins. Compared with P. aeruginosa, the tailocin tail fiber sequences that act as specificity determinants have diverged much more extensively among the other pseudomonad species, mostly isolates from soil and plant environments. Activity of the P. putida antibacterial particles requires a functional lipopolysaccharide layer on target cells, but contrary to R pyocins from P. aeruginosa, strain susceptibilities surpass species boundaries.

  2. Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates

    PubMed Central

    Ghequire, Maarten G.K.; Dillen, Yörg; Lambrichts, Ivo; Proost, Paul; Wattiez, Ruddy; De Mot, René

    2015-01-01

    Bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. Such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated DNA. A subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. Functional characterization of bactericidal tailocins of two Pseudomonas putida rhizosphere isolates revealed not only extensive similarity with the tail assembly module of the Pseudomonas aeruginosa R-type pyocins but also differences in genomic integration site, regulatory genes, and lytic release modules. Conversely, these three features are quite similar between strains of the P. putida and Pseudomonas fluorescens clades, although phylogenetic analysis of tail genes suggests them to have evolved separately. Unlike P. aeruginosa R pyocin elements, the tailocin gene clusters of other pseudomonads frequently carry cargo genes, including bacteriocins. Compared with P. aeruginosa, the tailocin tail fiber sequences that act as specificity determinants have diverged much more extensively among the other pseudomonad species, mostly isolates from soil and plant environments. Activity of the P. putida antibacterial particles requires a functional lipopolysaccharide layer on target cells, but contrary to R pyocins from P. aeruginosa, strain susceptibilities surpass species boundaries. PMID:26412856

  3. Microbial carbon turnover in the plant-rhizosphere-soil continuum

    NASA Astrophysics Data System (ADS)

    Malik, Ashish; Dannert, Helena; Griffiths, Robert; Thomson, Bruce; Gleixner, Gerd

    2014-05-01

    Soil microbial biomass contributes significantly to maintenance of soil organic matter (SOM). It is well known that biochemical fractions of soil microorganisms have varying turnover and therefore contribute differentially to soil C storage. Here we compare the turnover rates of different microbial biochemical fractions using a pulse chase 13CO2 plant labelling experiment. The isotope signal was temporally traced into rhizosphere soil microorganisms using the following biomarkers: DNA, RNA, fatty acids and chloroform fumigation extraction derived microbial biomass size classes. C flow into soil microbial functional groups was assessed through phospholipid and neutral lipid fatty acid (PLFA/NLFA) analyses. Highest 13C enrichment was seen in the low molecular weight (LMW) size class of microbial biomass (Δδ13C =151) and in nucleic acids (DNA: 38o RNA: 66) immediately after the pulse followed by a sharp drop. The amount of 13C in the high molecular weight (HMW) microbial biomass (17-81) and total fatty acids (32-54) was lower initially and stayed relatively steady over the 4 weeks experimental period. We found significant differences in turnover rates of different microbial biochemical and size fractions. We infer that LMW cytosolic soluble compounds are rapidly metabolized and linked to respiratory C fluxes, whereas mid-sized products of microbial degradation and HMW polymeric compounds have lower renewal rate in that order. The turnover of cell wall fatty acids was also very slow. DNA and RNA showed faster turnover rate; and as expected RNA renewal was the fastest due to its rapid production by active microorganisms independent of cell replication. 13C incorporation into different functional groups confirmed that mutualistic arbuscular mycorrhizal fungi rely on root C and are important in the initial plant C flux. We substantiated through measurements of isotope incorporation into bacterial RNA that rhizosphere bacteria are also important in the initial C conduit

  4. [Construction of a landscaping-type wetland system for wastewater treatment construction of a landscaping-type wetland system for wastewater treatment and analysis of plant denitrifying effect].

    PubMed

    Chen, Ming-li; Wu, Xiao-fu; Chen, Yong-hua; Jiang, Li-juan; Ji, Zhi-hui; Ma, Qun

    2010-03-01

    A pilot landscaping-type wetland system for wastewater treatment was constructed by introduction of 15 selected ornamental plant species (including 4 terrestrial plant species). The pilot system consists of 2 sequenced treatment units and 12 sub-units, i.e., a primary treatment unit with 4 parallel cells and a secondary treatment unit with 8 subsurface flow cells. Designed experiments were conducted in the established system to investigate the characteristics of nitrogen accumulation in different plants and the contribution of plant nitrogen uptake to total nitrogen removal of the constructed wetland system. The result shows that the direct contribution by plant uptake to the total nitrogen removal is low, ca. 1%-3% within the nitrogen concentration range 37.5-55.6 mg/L in the influent. Plant uptake does not fully reflect the important role of the plant species in the constructed wetland system for wastewater treatment as the function of the plant should include further its interaction with microorganisms and wetland fillers by enhancing microbial activities and filler adsorption capacities. The plant denitrifying effect, defined as the difference in nitrogen removal rates between units with and without plants, has been used to represent the contribution in nitrogen removal due to presence of plant in the system. The plant denitrifying effect thus includes both the plant nitrogen uptake and the interaction effect of plant with microorganisms and wetland fillers, the later being found to account for more than 80% of the total nitrogen removal in the established treatment system.

  5. Two-step nitrification in a pure moving bed biofilm reactor-membrane bioreactor for wastewater treatment: nitrifying and denitrifying microbial populations and kinetic modeling.

    PubMed

    Leyva-Díaz, J C; González-Martínez, A; Muñío, M M; Poyatos, J M

    2015-12-01

    The moving bed biofilm reactor-membrane bioreactor (MBBR-MBR) is a novel solution to conventional activated sludge processes and membrane bioreactors. In this study, a pure MBBR-MBR was studied. The pure MBBR-MBR mainly had attached biomass. The bioreactor operated with a hydraulic retention time (HRT) of 9.5 h. The kinetic parameters for heterotrophic and autotrophic biomasses, mainly nitrite-oxidizing bacteria (NOB), were evaluated. The analysis of the bacterial community structure of the ammonium-oxidizing bacteria (AOB), NOB, and denitrifying bacteria (DeNB) from the pure MBBR-MBR was carried out by means of pyrosequencing to detect and quantify the contribution of the nitrifying and denitrifying bacteria in the total bacterial community. The relative abundance of AOB, NOB, and DeNB were 5, 1, and 3%, respectively, in the mixed liquor suspended solids (MLSS), and these percentages were 18, 5, and 2%, respectively, in the biofilm density (BD) attached to carriers. The pure MBBR-MBR had a high efficiency of total nitrogen (TN) removal of 71.81±16.04%, which could reside in the different bacterial assemblages in the fixed biofilm on the carriers. In this regard, the kinetic parameters for autotrophic biomass had values of YA=2.3465 mg O2 mg N(-1), μm, A=0.7169 h(-1), and KNH=2.0748 mg NL(-1).

  6. Utilization of alkylbenzenes during anaerobic growth of pure cultures of denitrifying bacteria on crude oil

    SciTech Connect

    Rabus, R.; Widdel, F.

    1996-04-01

    Leakage from oil pipelines and underground fuel tanks may result in contamination of soils and deeper horizons. Even though the equilibrium partitioning of BTEX (benzene, toluene, ethylbenzene, and xylenes) between oil and water is largely on the side of the hydrophobic phase, BTEX exhibit a certain water solubility higher than other oil hydrocarbons. This study evaluates the growth of four strains of denitrifying bacteria on crude oil and the resulting, strain-specific depletion of alkylbenzenes.

  7. [Analysis on Diversity of Denitrifying Microorganisms in Sequential Batch Bioreactor Landfill].

    PubMed

    Li, Wei-Hua; Sun, Ying-Jie; Liu, Zi-Liang; Ma, Qiang; Yang, Qiang

    2016-01-15

    A denitrification functional microorganism gene clone library (amoA, nosZ) and the PCR-RFLP technology was constructed to investigate the microbial diversity of denitrifying microorganisms in the late period of stabilization of sequential batch bioreactor landfill. The results indicated that: the bacterial diversity of ammonia oxidizing bacteria in the aged refuse reactor was very high, and most of them were unknown groups, also, all bacteria were unculturable or had not been isolated. The phylogenetic analysis suggested that the dominant ammonia oxidizing bacteria were presumably Nitrosomonas of 6-Proteobacteria. The diversity of denitrifying bacteria in fresh refuse reactor was abundant, which mainly included Thauera and Thiobacillus of 6-Proteobacteria. As Thauera sp. has the denitrification characteristics under the condition of aerobic while Thiobacillus denitrificans has the autotrophic denitrification characteristics, it was speculated that aerobic denitrification and autotrophic denitrification might be the main pathways for nitrogen removal in the fresh refuse reactor at the late period of stabilization. Additionally, another group in the gene clone library of denitrifying bacteria may be classified as Bradyrhizobiaceae of alpha-Proteobacteria.

  8. Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

    NASA Technical Reports Server (NTRS)

    Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

    2013-01-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  9. [Analysis on Diversity of Denitrifying Microorganisms in Sequential Batch Bioreactor Landfill].

    PubMed

    Li, Wei-Hua; Sun, Ying-Jie; Liu, Zi-Liang; Ma, Qiang; Yang, Qiang

    2016-01-15

    A denitrification functional microorganism gene clone library (amoA, nosZ) and the PCR-RFLP technology was constructed to investigate the microbial diversity of denitrifying microorganisms in the late period of stabilization of sequential batch bioreactor landfill. The results indicated that: the bacterial diversity of ammonia oxidizing bacteria in the aged refuse reactor was very high, and most of them were unknown groups, also, all bacteria were unculturable or had not been isolated. The phylogenetic analysis suggested that the dominant ammonia oxidizing bacteria were presumably Nitrosomonas of 6-Proteobacteria. The diversity of denitrifying bacteria in fresh refuse reactor was abundant, which mainly included Thauera and Thiobacillus of 6-Proteobacteria. As Thauera sp. has the denitrification characteristics under the condition of aerobic while Thiobacillus denitrificans has the autotrophic denitrification characteristics, it was speculated that aerobic denitrification and autotrophic denitrification might be the main pathways for nitrogen removal in the fresh refuse reactor at the late period of stabilization. Additionally, another group in the gene clone library of denitrifying bacteria may be classified as Bradyrhizobiaceae of alpha-Proteobacteria. PMID:27078976

  10. A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes.

    PubMed

    Lv, Xiao-Mei; Shao, Ming-Fei; Li, Chao-Lin; Li, Ji; Gao, Xin-Lei; Sun, Fei-Yun

    2014-09-17

    Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. Two lab-scale sequencing batch reactors (SBRs) were operated in alternating anaerobic-anoxic (A-A) or anaerobic-oxic (A-O) conditions to achieve denitrifying enhanced biological phosphate removal (EBPR) and traditional EBPR. No significant differences were observed in phosphorus removal efficiencies between A-A SBR and A-O SBR, with phosphorus removal rates being 87.9% and 89.0% respectively. The community structures in denitrifying and traditional EBPR processes were evaluated by high-throughput sequencing of the PCR-amplified partial 16S rRNA genes from each sludge. The results obtained showed that the bacterial community was more diverse in A-O sludge than in A-A sludge. Taxonomy and β-diversity analyses indicated that a significant shift occurred in the dominant microbial community in A-A sludge compared with the seed sludge during the whole acclimation phase, while a slight fluctuation was observed in the abundance of the major taxonomies in A-O sludge. One Dechloromonas-related OTU outside the 4 known Candidatus "Accumulibacter" clades was detected as the main OTU in A-A sludge at the stationary operation, while Candidatus "Accumulibacter" dominated in A-O sludge.

  11. Formation of diclofenac and sulfamethoxazole reversible transformation products in aquifer material under denitrifying conditions: batch experiments.

    PubMed

    Barbieri, Manuela; Carrera, Jesús; Ayora, Carlos; Sanchez-Vila, Xavier; Licha, Tobias; Nödler, Karsten; Osorio, Victoria; Pérez, Sandra; Köck-Schulmeyer, Marianne; López de Alda, Miren; Barceló, Damià

    2012-06-01

    Soil-aquifer processes have proven to work as a natural treatment for the attenuation of numerous contaminants during artificial recharge of groundwater. Nowadays, significant scientific effort is being devoted to understanding the fate of pharmaceuticals in subsurface environments, and to verify if such semipersistent organic micropollutants could also be efficiently removed from water. In this context we carried out a series of batch experiments involving aquifer material, selected drugs (initial concentration of 1 μg/L and 1 mg/L), and denitrifying conditions. Diclofenac and sulfamethoxazole exhibited an unreported and peculiar behavior. Their concentrations consistently dropped in the middle of the tests but recovered toward the end, which suggest a complex effect of denitrifying conditions on aromatic amines. The transformation products Nitro-Diclofenac and 4-Nitro-Sulfamethoxazole were detected in the biotic experiments, while nitrite was present in the water. Their concentrations developed almost opposite to those of their respective parent compounds. We conjecture that this temporal and reversible effect of denitrifying conditions on the studied aromatic amines could have significant environmental implications, and could explain at least partially the wide range of removals in subsurface environments reported in literature for DCF and SMX, as well as some apparent discrepancies on SMX behavior. PMID:22534360

  12. A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes.

    PubMed

    Lv, Xiao-Mei; Shao, Ming-Fei; Li, Chao-Lin; Li, Ji; Gao, Xin-Lei; Sun, Fei-Yun

    2014-09-17

    Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. Two lab-scale sequencing batch reactors (SBRs) were operated in alternating anaerobic-anoxic (A-A) or anaerobic-oxic (A-O) conditions to achieve denitrifying enhanced biological phosphate removal (EBPR) and traditional EBPR. No significant differences were observed in phosphorus removal efficiencies between A-A SBR and A-O SBR, with phosphorus removal rates being 87.9% and 89.0% respectively. The community structures in denitrifying and traditional EBPR processes were evaluated by high-throughput sequencing of the PCR-amplified partial 16S rRNA genes from each sludge. The results obtained showed that the bacterial community was more diverse in A-O sludge than in A-A sludge. Taxonomy and β-diversity analyses indicated that a significant shift occurred in the dominant microbial community in A-A sludge compared with the seed sludge during the whole acclimation phase, while a slight fluctuation was observed in the abundance of the major taxonomies in A-O sludge. One Dechloromonas-related OTU outside the 4 known Candidatus "Accumulibacter" clades was detected as the main OTU in A-A sludge at the stationary operation, while Candidatus "Accumulibacter" dominated in A-O sludge. PMID:24964811

  13. Nanoparticle-based measurements of pH and O2 dynamics in the rhizosphere of Zostera marina L.: effects of temperature elevation and light-dark transitions.

    PubMed

    Elgetti Brodersen, Kasper; Koren, Klaus; Lichtenberg, Mads; Kühl, Michael

    2016-07-01

    Seagrasses can modulate the geochemical conditions in their immediate rhizosphere through the release of chemical compounds from their below-ground tissue. This is a vital chemical defence mechanism, whereby the plants detoxify the surrounding sediment. Using novel nanoparticle-based optical O2 and pH sensors incorporated in reduced and transparent artificial sediment, we investigated the spatio-temporal dynamics of pH and O2 within the entire rhizosphere of Zostera marina L. during experimental manipulations of light and temperature. We combined such measurements with O2 microsensor measurements of the photosynthetic productivity and respiration of seagrass leaves. We found pronounced pH and O2 microheterogeneity within the immediate rhizosphere of Z. marina, with higher below-ground tissue oxidation capability and rhizoplane pH levels during both light exposure of the leaf canopy and elevated temperature, where the temperature-mediated stimuli of biogeochemical processes seemed to predominate. Low rhizosphere pH microenvironments appeared to correlate with plant-derived oxic microzones stimulating local sulphide oxidation and thus driving local proton generation, although the rhizoplane pH levels generally where much higher than the bulk sediment pH. Our data show that Z. marina can actively alter its rhizosphere pH microenvironment alleviating the local H2 S toxicity and enhancing nutrient availability in the adjacent sediment via geochemical speciation shift. PMID:27003238

  14. Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.

    PubMed

    Ding, Jing; Fu, Liang; Ding, Zhao-Wei; Lu, Yong-Ze; Cheng, Shuk H; Zeng, Raymond J

    2016-01-01

    The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage.

  15. Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology

    PubMed Central

    Bisht, Sandeep; Pandey, Piyush; Bhargava, Bhavya; Sharma, Shivesh; Kumar, Vivek; Sharma, Krishan D.

    2015-01-01

    The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective. PMID:26221084

  16. Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology.

    PubMed

    Bisht, Sandeep; Pandey, Piyush; Bhargava, Bhavya; Sharma, Shivesh; Kumar, Vivek; Sharma, Krishan D

    2015-03-01

    The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective.

  17. Rhizosphere remediation of chlorpyrifos in mycorrhizospheric soil using ryegrass.

    PubMed

    Korade, Deepali L; Fulekar, M H

    2009-12-30

    The potential of ryegrass for rhizosphere bioremediation of chlorpyrifos in mycorrhizal soil was investigated by the green house pot culture experiments. The pot cultured soil amended at initial chlorpyrifos concentration of 10mg/kg was observed to be degraded completely within 7 days where the rest amended concentrations (25-100mg/kg) decreased rapidly under the influence of ryegrass mycorrhizosphere as the incubation progressed till 28 days. This bioremediation of chlorpyrifos in soil is attributed to the microorganisms associated with the roots in the ryegrass rhizosphere, therefore the microorganisms surviving in the rhizospheric soil spiked at highest concentration (100mg/kg) was assessed and used for isolation of chlorpyrifos degrading microorganisms. The potential degrader identified by 16s rDNA analysis using BLAST technique was Pseudomonas nitroreducens PS-2. Further, bioaugmentation for the enhanced chlorpyrifos biodegradation was performed using PS-2 as an inoculum in the experimental set up similar to the earlier. The heterotrophic bacteria and fungi were also enumerated from the inoculated and non-inoculated rhizospheric soils. In bioaugmentation experiments, the percentage dissipation of chlorpyrifos was 100% in the inoculated rhizospheric soil as compared to 76.24, 90.36 and 90.80% in the non-inoculated soil for initial concentrations of 25, 50 and 100mg/kg at the 14th, 21st and 28th day intervals respectively.

  18. Significance of rhizosphere microorganisms in reclaiming water in a CELSS.

    PubMed

    Greene, C; Bubenheim, D L; Wignarajah, K

    1997-01-01

    Plant-microbe interactions, such as those of the rhizosphere, may be ideally suited for recycling water in a Controlled Ecological Life Support System (CELSS). The primary contaminant of waste hygiene water will be surfactants or soaps. We identified changes in the microbial ecology in the rhizosphere of hydroponical1y grown lettuce during exposure to surfactant. Six week old lettuce plants were transferred into a chamber with a recirculating hydroponic system. Microbial density and population composition were determined for the nutrient solution prior to introduction of plants and then again with plants prior to surfactant addition. The surfactant Igepon was added to the recirculating nutrient solution to a final concentration of 1.0 g L-1. Bacteria density and species diversity of the solution were monitored over a 72-h period following introduction of Igepon. Nine distinct bacterial types were identified in the rhisosphere; three species accounted for 87% of the normal rhizosphere population. Microbial cell number increased in the presence of Igepon, however species diversity declined. At the point when Igepon was degraded from solution, diversity was reduced to only two species. Igepon was found to be degraded directly by only one species found in the rhizosphere. Since surfactants are degraded from the waste hygiene water within 24 h, the potential for using rhizosphere bacteria as a waste processor in a CELSS is promising.

  19. Significance of rhizosphere microorganisms in reclaiming water in a CELSS

    NASA Astrophysics Data System (ADS)

    Greene, C.; Bubenheim, D. L.; Wignarajah, K.

    1997-01-01

    Plant-microbe interactions, such as those of the rhizosphere, may be ideally suited for recycling water in a Controlled Ecological Life Support System (CELSS). The primary contaminant of waste hygiene water will be surfactants or soaps. We identified changes in the microbial ecology in the rhizosphere of hydroponically grown lettuce during exposure to surfactant. Six week old lettuce plants were transferred into a chamber with a recirculating hydroponic system. Microbial density and population composition were determined for the nutrient solution prior to introduction of plants and then again with plants prior to surfactant addition. The surfactant Igepon was added to the recirculating nutrient solution to a final concentration of 1.0 g L^-1. Bacteria density and species diversity of the solution were monitored over a 72-h period following introduction of Igepon. Nine distinct bacterial types were identified in the rhisosphere; three species accounted for 87% of the normal rhizosphere population. Microbial cell number increased in the presence of Igepon, however species diversity declined. At the point when Igepon was degraded from solution, diversity was reduced to only two species. Igepon was found to be degraded directly by only one species found in the rhizosphere. Since surfactants are degraded from the waste hygiene water within 24 h, the potential for using rhizosphere bacteria as a waste processor in a CELSS is promising.

  20. Significance of rhizosphere microorganisms in reclaiming water in a CELSS

    NASA Astrophysics Data System (ADS)

    1997-01-01

    Plant-microbe interactions, such as those of the rhizosphere, may be ideally suited for recycling water in a Controlled Ecological Life Support System (CELSS). The primary contaminant of waste hygiene water will be surfactants or soaps. We identified changes in the microbial ecology in the rhizosphere of hydroponically grown lettuce during exposure to surfactant. Six week old lettuce plants were transferred into a chamber with a recirculating hydroponic system. Microbial density and population composition were determined for the nutrient solution prior to introduction of plants and then again with plants prior to surfactant addition. The surfactant Igepon was added to the recirculating nutrient solution to a final concentration of 1.0 g L-1. Bacteria density and species diversity of the solution were monitored over a 72-h period following introduction of Igepon. Nine distinct bacterial types were identified in the rhisosphere; three species accounted for 87% of the normal rhizosphere population. Microbial cell number increased in the presence of Igepon, however species diversity declined. At the point when Igepon was degraded from solution, diversity was reduced to only two species. Igepon was found to be degraded directly by only one species found in the rhizosphere. Since surfactants are degraded from the waste hygiene water within 24 h, the potential for using rhizosphere bacteria as a waste processor in a CELSS is promising.

  1. Cyanogenic Pseudomonads Influence Multitrophic Interactions in the Rhizosphere

    PubMed Central

    Rudrappa, Thimmaraju; Splaine, Robert E.; Biedrzycki, Meredith L.; Bais, Harsh P.

    2008-01-01

    In the rhizosphere, plant roots cope with both pathogenic and beneficial bacterial interactions. The exometabolite production in certain bacterial species may regulate root growth and other root-microbe interactions in the rhizosphere. Here, we elucidated the role of cyanide production in pseudomonad virulence affecting plant root growth and other rhizospheric processes. Exposure of Arabidopsis thaliana Col-0 seedlings to both direct (with KCN) and indirect forms of cyanide from different pseudomonad strains caused significant inhibition of primary root growth. Further, we report that this growth inhibition was caused by the suppression of an auxin responsive gene, specifically at the root tip region by pseudomonad cyanogenesis. Additionally, pseudomonad cyanogenesis also affected other beneficial rhizospheric processes such as Bacillus subtilis colonization by biofilm formation on A. thaliana Col-0 roots. The effect of cyanogenesis on B. subtilis biofilm formation was further established by the down regulation of important B. subtilis biofilm operons epsA and yqxM. Our results show, the functional significance of pseudomonad cyanogenesis in regulating multitrophic rhizospheric interactions. PMID:18446201

  2. Stable Nitrogen and Oxygen Isotope Analysis of Nitrate using Denitrifying Bacteria

    NASA Astrophysics Data System (ADS)

    Edenburn, L.; Michalski, G. M.

    2009-12-01

    The total isotopic composition of nitrate is used for identifying the origin and fate of nitrate in atmospheric, terrestrial and aquatic systems. The analysis of δ 18O, δ15N, and Δ17O values each give important and unique information about the sources and sinks of nitrate in these systems. Currently, there is no published method that allows for the simultaneous determination of δ18O, δ15N, and Δ17O of nitrate. Cascotti designed a novel method for measurement of δ18O and δ15N in nitrate but not Δ17O. This denitrifier method is based on the isotope ratio analysis of nitrous oxide generated by reduction of nitrate by cultured denitrifying bacteria. Kaiser then altered Cascotti's denitrifier method by converting N2O into O2 followed by the quantitative measurement δ18O and Δ17O, however δ15N was not measured. Here we present preliminary data on δ15N, δ18O, Δ17O values of N2 and O2 generated by the disproportionation of bacterial produced N2O. During the process of denitrification, nitrates are converted to nitrogen gas via a series of intermediate gaseous nitrogen oxide products. This is possible due to the presence of heterotrophic bacteria or autotrophic denitrifiers in select bacteria. Thus, we have chosen three distinct bacteria for the investigation of nitrate reduction for this study: Pseudomonas aureofaciens, Bacillus halodenitrificans, and Achromobacter cycloclastes. They each contain the copper-containing nitrite reductase necessary for the catalyzation of nitrate in order to complete the nitrogen cycle by returning N2 to the atmosphere. Bacillus halodenitrificans has the advantage of being an anaerobic halotolerant (salt-tolerant) denitrifier. Many of our samples have a high saline content; also, pre-concentration techniques using anion resin require elution using high ionic strength solutions. Further, high saline growth solutions limit contamination from other bacteria or organisms. Our efforts also focus on the conversion of N2O over a gold

  3. Enhanced Nitrogen Availability in Karst Ecosystems by Oxalic Acid Release in the Rhizosphere.

    PubMed

    Pan, Fujing; Liang, Yueming; Zhang, Wei; Zhao, Jie; Wang, Kelin

    2016-01-01

    In karst ecosystems, a high level of CaCO3 enhances the stabilization of soil organic matter (SOM) and causes nitrogen (N) and/or phosphorus (P) limitation in plants. Oxalic acid has been suggested to be involved in the nutrient-acquisition strategy of plants because its addition can temporarily relieve nutrient limitation. Therefore, understanding how oxalic acid drives N availability may help support successful vegetation restoration in the karst ecosystems of southwest China. We tested a model suggested by Clarholm et al. (2015) where oxalate reacts with Ca bridges in SOM, thus exposing previously protected areas to enzymatic attacks in a way that releases N for local uptake. We studied the effects of oxalic acid, microbial biomass carbon (MBC), and β-1,4-N-acetylglucosaminidase (NAG) on potential N mineralization rates in rhizosphere soils of four plant species (two shrubs and two trees) in karst areas. The results showed that rhizosphere soils of shrubs grown on formerly deforested land had significantly lower oxalic acid concentrations and NAG activity than that of trees in a 200-year-old forest. The levels of MBC in rhizosphere soils of shrubs were significantly lower than those of trees in the growing season, but the measure of shrubs and trees were similar in the non-growing season; the potential N mineralization rates showed a reverse pattern. Positive relationships were found among oxalic acid, MBC, NAG activity, and potential N mineralization rates for both shrubs and trees. This indicated that oxalic acid, microbes, and NAG may enhance N availability for acquisition by plants. Path analysis showed that oxalic acid enhanced potential N mineralization rates indirectly through inducing microbes and NAG activities. We found that the exudation of oxalic acid clearly provides an important mechanism that allows plants to enhance nutrient acquisition in karst ecosystems.

  4. Enhanced Nitrogen Availability in Karst Ecosystems by Oxalic Acid Release in the Rhizosphere

    PubMed Central

    Pan, Fujing; Liang, Yueming; Zhang, Wei; Zhao, Jie; Wang, Kelin

    2016-01-01

    In karst ecosystems, a high level of CaCO3 enhances the stabilization of soil organic matter (SOM) and causes nitrogen (N) and/or phosphorus (P) limitation in plants. Oxalic acid has been suggested to be involved in the nutrient-acquisition strategy of plants because its addition can temporarily relieve nutrient limitation. Therefore, understanding how oxalic acid drives N availability may help support successful vegetation restoration in the karst ecosystems of southwest China. We tested a model suggested by Clarholm et al. (2015) where oxalate reacts with Ca bridges in SOM, thus exposing previously protected areas to enzymatic attacks in a way that releases N for local uptake. We studied the effects of oxalic acid, microbial biomass carbon (MBC), and β-1,4-N-acetylglucosaminidase (NAG) on potential N mineralization rates in rhizosphere soils of four plant species (two shrubs and two trees) in karst areas. The results showed that rhizosphere soils of shrubs grown on formerly deforested land had significantly lower oxalic acid concentrations and NAG activity than that of trees in a 200-year-old forest. The levels of MBC in rhizosphere soils of shrubs were significantly lower than those of trees in the growing season, but the measure of shrubs and trees were similar in the non-growing season; the potential N mineralization rates showed a reverse pattern. Positive relationships were found among oxalic acid, MBC, NAG activity, and potential N mineralization rates for both shrubs and trees. This indicated that oxalic acid, microbes, and NAG may enhance N availability for acquisition by plants. Path analysis showed that oxalic acid enhanced potential N mineralization rates indirectly through inducing microbes and NAG activities. We found that the exudation of oxalic acid clearly provides an important mechanism that allows plants to enhance nutrient acquisition in karst ecosystems. PMID:27252713

  5. Enhanced Nitrogen Availability in Karst Ecosystems by Oxalic Acid Release in the Rhizosphere.

    PubMed

    Pan, Fujing; Liang, Yueming; Zhang, Wei; Zhao, Jie; Wang, Kelin

    2016-01-01

    In karst ecosystems, a high level of CaCO3 enhances the stabilization of soil organic matter (SOM) and causes nitrogen (N) and/or phosphorus (P) limitation in plants. Oxalic acid has been suggested to be involved in the nutrient-acquisition strategy of plants because its addition can temporarily relieve nutrient limitation. Therefore, understanding how oxalic acid drives N availability may help support successful vegetation restoration in the karst ecosystems of southwest China. We tested a model suggested by Clarholm et al. (2015) where oxalate reacts with Ca bridges in SOM, thus exposing previously protected areas to enzymatic attacks in a way that releases N for local uptake. We studied the effects of oxalic acid, microbial biomass carbon (MBC), and β-1,4-N-acetylglucosaminidase (NAG) on potential N mineralization rates in rhizosphere soils of four plant species (two shrubs and two trees) in karst areas. The results showed that rhizosphere soils of shrubs grown on formerly deforested land had significantly lower oxalic acid concentrations and NAG activity than that of trees in a 200-year-old forest. The levels of MBC in rhizosphere soils of shrubs were significantly lower than those of trees in the growing season, but the measure of shrubs and trees were similar in the non-growing season; the potential N mineralization rates showed a reverse pattern. Positive relationships were found among oxalic acid, MBC, NAG activity, and potential N mineralization rates for both shrubs and trees. This indicated that oxalic acid, microbes, and NAG may enhance N availability for acquisition by plants. Path analysis showed that oxalic acid enhanced potential N mineralization rates indirectly through inducing microbes and NAG activities. We found that the exudation of oxalic acid clearly provides an important mechanism that allows plants to enhance nutrient acquisition in karst ecosystems. PMID:27252713

  6. Biodegradation of phenol, 2,4-DCP, 2,4-D, and 2,4,5-T in field-collected rhizosphere and nonrhizosphere soils

    SciTech Connect

    Boyle, J.J.; Shann, J.R.

    1995-07-01

    This study investigated xenobiotic biodegradation in rhizosphere soil collected from field-grown plants, grouped for analysis as monocots or dicots. Microbial activity was highest in monocot rhizosphere soils, No differences were seen between these soils in the mineralization of phenol or 2,4-dichlorophenol (2,4-DCP), but there were differences in 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) mineralization. The rate constants for 2,4-D or 2,4,5-T mineralization in nonrhizosphere soil. Thus, soils that had a prior association with a plant showed significantly increased rates o mineralization for the more recalcitrant compounds tested. In addition, this enhanced mineralization in the rhizosphere appeared to be dependent on the type of plant involved. 20 refs., 4 figs., 2 tabs.

  7. Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication.

    PubMed

    van Dam, Nicole M; Bouwmeester, Harro J

    2016-03-01

    The rhizosphere is densely populated with a variety of organisms. Interactions between roots and rhizosphere community members are mostly achieved via chemical communication. Root exudates contain an array of primary and secondary plant metabolites that can attract, deter, or kill belowground insect herbivores, nematodes, and microbes, and inhibit competing plants. Metabolomics of root exudates can potentially help us to better understand this chemical dialogue. The main limitations are the proper sampling of the exudate, the sensitivity of the metabolomics platforms, and the multivariate data analysis to identify causal relations. Novel technologies may help to generate a spatially explicit metabolome of the root and its exudates at a scale that is relevant for the rhizosphere community.

  8. Denitrifying phosphorus removal from municipal wastewater and dynamics of "Candidatus Accumulibacter" and denitrifying bacteria based on genes of ppk1, narG, nirS and nirK.

    PubMed

    Zeng, Wei; Zhang, Jie; Wang, Anqi; Peng, Yongzhen

    2016-05-01

    Relevance of clade-level population dynamics of "Candidatus Accumulibacter" to performance of denitrifying phosphorus (P) removal from municipal wastewater was investigated. Stable denitrifying P removal in anoxic zone of continuous-flow reactor was achieved, accounting for 90% of total P removal. Clades IIC and IIF affiliated with Accumulibacter lineage were the dominant clades during denitrifying P removal, reaching 90% of ppk1 clone library. NarG gene library indicated Gamma and Beta-proteobacteria played an important role in nitrate reduction. Diversity and abundance of nirS library was much more than nirK, and thus became the main functional gene to execute nitrite reduction. Based on abundance of nirS, nirK and ppk1, the ratio of Accumulibacter capable of denitrifying P removal to total Accumulibacter was 22%. No matter whether Accumulibacter had narG gene or not, high abundance of narG at a level of 10(9)cells/(g dried-sludge) promoted nitrate reduced to nitrite, ensuring performance of denitrifying P removal. PMID:26896717

  9. Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes.

    PubMed

    Vollack, K U; Härtig, E; Körner, H; Zumft, W G

    1999-03-01

    Pseudomonas stutzeri is a facultative anaerobic bacterium with the capability of denitrification. In searching for regulators that control the expression of this trait in response to oxygen withdrawal, we have found an unprecedented multiplicity of four genes encoding transcription factors of the FNR family. The fnrA gene encodes a genuine FNR-type regulator, which is expressed constitutively and controls the cytochrome cbb3-type terminal oxidase (the cco operon), cytochrome c peroxidase (the ccp gene) and the oxygen-independent coproporphyrinogen III oxidase (the hemN gene), in addition to its previously demonstrated role in arginine catabolism (the arc operon). The fnr homologues dnrD, dnrE and dnrS encode regulators of a new subgroup within the FNR family. Their main distinctive feature is the lack of cysteine residues for complexing the [4Fe-4S] centre of redox-active FNR-type regulators. However, they form a phylogenetic lineage separate from the FixK branch of FNR proteins, which also lack this cysteine signature. We have studied the expression of the dnr genes under aerobic, oxygen-limited and denitrifying conditions. DnrD is a key regulator of denitrification by selective activation of the genes for cytochrome cd1 nitrite reductase and NO reductase. The dnrD gene is part of the 30 kb region carrying denitrification genes of P. stutzeri. Transcription of dnrD was activated in O2-limited cells and particularly strongly in denitrifying cells, but was not under the control of FnrA. In response to denitrifying growth conditions, dnrD was transcribed as part of an operon together with genes downstream and upstream of dnrD. dnrS was found about 9 kb upstream of dnrD, next to the nrdD gene for anaerobic ribonucleotide reductase. The transcription of dnrS required FnrA in O2-limited cells. Mutation of dnrS affected nrdD and the expression of ferredoxin I as an element of the oxidative stress response. The dnrE gene is part of the nar region encoding functions for

  10. Understanding the role of agricultural practices in the potential colonization and contamination by Escherichia coli in the rhizospheres of fresh produce.

    PubMed

    Habteselassie, Mussie Y; Bischoff, Marianne; Applegate, Bruce; Reuhs, Bradley; Turco, Ronald F

    2010-11-01

    To better protect consumers from exposure to produce contaminated with Escherichia coli, the potential transfer of E. coli from manure or irrigation water to plants must be better understood. We used E. coli strains expressing bioluminescence (E. coli O157:H7 lux) or multiantibiotic resistance (E. coli²(+)) in this study. These marked strains enabled us to visualize in situ rhizosphere colonization and metabolic activity and to track the occurrence and survival of E. coli in soil, rhizosphere, and phyllosphere. When radish and lettuce seeds were treated with E. coli O157:H7 lux and grown in an agar-based growth system, rapid bacterial colonization of the germinating seedlings and high levels of microbial activity were seen. Introduction of E. coli²(+) to soil via manure or via manure in irrigation water showed that E. coli could establish itself in the lettuce rhizosphere. Regardless of introduction method, 15 days subsequent to its establishment in the rhizosphere, E. coli²(+) was detected on the phyllosphere of lettuce at an average number of 2.5 log CFU/g. When E. coli²(+) was introduced 17 and 32 days postseeding to untreated soil (rather than the plant surface) via irrigation, it was detected at low levels (1.4 log CFU/g) on the lettuce phyllosphere 10 days later. While E. coli²(+) persisted in the bulk and rhizosphere soil throughout the study period (day 41), it was not detected on the external portions of the phyllosphere after 27 days. Overall, we find that E. coli is mobile in the plant system and responds to the rhizosphere like other bacteria.

  11. Water repellency in the rhizosphere of maize: measurements and modelling

    NASA Astrophysics Data System (ADS)

    Ahmed, Mutez; Kroener, Eva; Carminati, Andrea

    2016-04-01

    Although maize roots have been extensively studied, there is limited information on the effect of root exudates on the hydraulic properties of maize rhizosphere. Recent experiments suggested that the mucilaginous fraction of root exudates may cause water repellency of the rhizosphere. Our objectives were: 1) to investigate whether maize rhizosphere turns hydrophobic after drying and subsequent rewetting; 2) to develop a new method to collect root mucilage and test whether maize mucilage is hydrophobic; and 3) to find a quantitative relation between rhizosphere rewetting, particle size, soil matric potential and mucilage concentration. Maize plants were grown in aluminum containers filled with a sandy soil. When the plants were three-weeks-old, the soil was let dry and then it was irrigated. The soil water content during irrigation was imaged using neutron radiography. In a parallel experiment, ten maize plants were grown in sandy soil for five weeks. Mucilage was collected from young brace roots using a new developed method. Mucilage was placed on glass slides and let dry. The contact angle was measured with the sessile drop method for varying mucilage concentration. Additionally, we used neutron radiography to perform capillary rise experiments in soils of varying particle size mixed with maize mucilage. We then used a pore-network model in which mucilage was randomly distributed in a cubic lattice. The general idea was that rewetting of a pore is impeded when the concentration of mucilage on the pore surface (g cm-2) is higher than a given threshold value. The threshold value depended on soil matric potential, pore radius and contact angle. Then, we randomly distributed mucilage in the pore network and we calculated the percolation of water across a cubic lattice for varying soil particle size, mucilage concentration and matric potential. Our results showed that: 1) the rhizosphere of maize stayed temporarily dry after irrigation; 2) mucilage became water

  12. [Responses of rhizosphere nitrogen and phosphorus transformations to different acid rain intensities in a hilly red soil tea plantation].

    PubMed

    Chen, Xi; Chen, Fu-sheng; Ye, Su-qiong; Yu, Su-qin; Fang, Xiang-min; Hu, Xiao-fei

    2015-01-01

    Tea (Camellia sinensis) plantation in hilly red soil region has been long impacted by acid deposition, however its effects on nitrogen (N) and phosphorus (P) transformations in rhizosphere soils remain unclear. A 25-year old tea plantation in a typical hilly red soil region was selected for an in situ simulation experiment treated by pH 4.5, pH 3.5, pH 2.5 and control. Rhizosihere and bulk soils were collected in the third year from the simulated acid deposition experiment. Soil mineral N, available P contents and major enzyme activities were analyzed using the chemical extraction and biochemical methods, and N and P mineralization rates were estimated using the indoor aerobic incubation methods. Our results showed that compared to the control, the treatments of pH 4.5, pH 3.5 and pH 2.5, respectively decreased 7.1%, 42.1% and 49.9% NO3(-)-N, 6.4%, 35.9% and 40.3% mineral N, 10.5%, 41.1% and 46.9% available P, 18.7%, 30.1% and 44.7% ammonification rate, 3.6%, 12.7% and 38.8% net N-mineralization rate, and 31.5%, 41.8% and 63.0% P mineralization rate in rhizosphere soils; however, among the 4 treatments, rhizosphere soil nitrification rate was not significantly different, the rhizosphere soil urease and acid phosphatase activities generally increased with the increasing intensity of acid rain (P<0.05). In bulk soil, compared with the control, the treatments of pH 4.5, pH 3.5 and pH 2.5 did not cause significant changes in NO3(-)-N, mineral N, available P as well as in the rates of nitrification, ammonification, net N-mineralization and P mineralization. With increasing the acid intensity, the rhizosphere effects of NH4+-N, NO3(-)-N, mineral N, ammonification and net N-mineralization rates were altered from positive to negative effects, those of urease and acid phosphatease showed the opposite trends, those of available P and P mineralization were negative and that of nitrification was positive. In sum, prolonged elevated acid rain could reduce N and P transformation

  13. [Responses of rhizosphere nitrogen and phosphorus transformations to different acid rain intensities in a hilly red soil tea plantation].

    PubMed

    Chen, Xi; Chen, Fu-sheng; Ye, Su-qiong; Yu, Su-qin; Fang, Xiang-min; Hu, Xiao-fei

    2015-01-01

    Tea (Camellia sinensis) plantation in hilly red soil region has been long impacted by acid deposition, however its effects on nitrogen (N) and phosphorus (P) transformations in rhizosphere soils remain unclear. A 25-year old tea plantation in a typical hilly red soil region was selected for an in situ simulation experiment treated by pH 4.5, pH 3.5, pH 2.5 and control. Rhizosihere and bulk soils were collected in the third year from the simulated acid deposition experiment. Soil mineral N, available P contents and major enzyme activities were analyzed using the chemical extraction and biochemical methods, and N and P mineralization rates were estimated using the indoor aerobic incubation methods. Our results showed that compared to the control, the treatments of pH 4.5, pH 3.5 and pH 2.5, respectively decreased 7.1%, 42.1% and 49.9% NO3(-)-N, 6.4%, 35.9% and 40.3% mineral N, 10.5%, 41.1% and 46.9% available P, 18.7%, 30.1% and 44.7% ammonification rate, 3.6%, 12.7% and 38.8% net N-mineralization rate, and 31.5%, 41.8% and 63.0% P mineralization rate in rhizosphere soils; however, among the 4 treatments, rhizosphere soil nitrification rate was not significantly different, the rhizosphere soil urease and acid phosphatase activities generally increased with the increasing intensity of acid rain (P<0.05). In bulk soil, compared with the control, the treatments of pH 4.5, pH 3.5 and pH 2.5 did not cause significant changes in NO3(-)-N, mineral N, available P as well as in the rates of nitrification, ammonification, net N-mineralization and P mineralization. With increasing the acid intensity, the rhizosphere effects of NH4+-N, NO3(-)-N, mineral N, ammonification and net N-mineralization rates were altered from positive to negative effects, those of urease and acid phosphatease showed the opposite trends, those of available P and P mineralization were negative and that of nitrification was positive. In sum, prolonged elevated acid rain could reduce N and P transformation

  14. Linking roots and rhizospheres to hydrological processes

    NASA Astrophysics Data System (ADS)

    Dawson, T. E.

    2007-12-01

    There is ample evidence that shows how plants can exert very significant and often dominant -controls" over the manner and magnitude by which water and other soil-borne resources cycle through diverse ecosystems on Earth. The use and redistribution of soil water resources by root systems has been a particularly important addition to our understanding of how the movement of soil water resources can impact hydrological processes at a range of scales. When soil and plant water relations data are coupled with land-use and climatic change data and predictive models for seasonally-dry ecosystems they have revealed new insights into how the water cycle is also changing and the role that plant root functions plays in shaping fundamental aspects of the hydrological cycle. I will highlight the ways my research group as well as the work of others have used a range of methods to explore the links between roots and rhizospheres and hydrological processes. The detailed analyses of the stable isotope composition of plant and soil water and precipitation and the temporal and spatial patterns of water use by diverse trees in temperate and tropical biomes when coupled with ongoing modeling research has revealed new insights into how belowground and aboveground plant water use behaviors can impact the manned and magnitude of water cycling on local and regional scales. Further, new results clearly show the impacts that plant water uptake and use have on ecosystem carbon fixation and both temperature and precipitation patterns over vast regions like the Amazon as well as other parts of the globe covered by trees and deeply rooted woody vegetation. The combination of empirical and theoretical research results shows that plants can help sustain water recycling, can significantly impact carbon and nutrient cycles, and impact regional climate, drought and its seasonality thereby establishing a direct link between plant functioning, resource movement and the climate system across the globe.

  15. Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning.

    PubMed

    Liu, Xian; Chen, Chengrong; Wang, Weijin; Hughes, Jane M; Lewis, Tom; Hou, Enqing; Shen, Jupei

    2015-11-01

    Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH(4)(+)), and nitrate (NO(3)(-)), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime.

  16. Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning.

    PubMed

    Liu, Xian; Chen, Chengrong; Wang, Weijin; Hughes, Jane M; Lewis, Tom; Hou, Enqing; Shen, Jupei

    2015-11-01

    Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH(4)(+)), and nitrate (NO(3)(-)), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime. PMID:26066514

  17. [Rapid enrichment and cultivation of denitrifying phosphate-removal bacteria and its identification by fluorescence in situ hybridization technology].

    PubMed

    Liu, Li; Tang, Bing; Huang, Shao-Song; Fu, Feng-Lian; Zhang, Qi-Qin; Li, Jian-Bin; Luo, Jian-Zhong

    2013-07-01

    The present work focused on a rapid enrichment and cultivation of denitrifying phosphate-removal bacteria (DPB) in a membrane bio-reactor(MBR) by using A2/O anaerobic sludge from a wastewater treatment plant as seed, as well as providing an identification method. In the experiments, sodium acetate was used as the carbon source and a certain amount of nitrate was added to the MBR in the anoxic stage. Results showed that, with the efficient trap of the hollow-fiber membrane module, the proportion of DPB in all the phosphate-accumulating organisms (PAOs) increased from 24% to 93% within 35 days after two-stage's cultivation including anaerobic/aerobic and anaerobic/anoxic, during which the removal efficiency of nitrogen and phosphorus reached more than 90%. The activated sludge was identified by combining a regular method and the fluorescence in situ hybridization (FISH) technique, which demonstrated that Pseudomonas sp. and Rhodocyclus sp. were the dominant bacteria in the used bioreactor.

  18. Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor.

    PubMed

    Hwang, C; Wu, W-M; Gentry, T J; Carley, J; Carroll, S L; Schadt, C; Watson, D; Jardine, P M; Zhou, J; Hickey, R F; Criddle, C S; Fields, M W

    2006-08-01

    High levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the Y-12 National Security Complex in Oak Ridge, TN. A field-scale denitrifying fluidized bed reactor (FBR) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. After inoculation, biofilms developed on the granular activated carbon particles. Changes in the bacterial community of the FBR were evaluated with clone libraries (n = 500 partial sequences) of the small-subunit rRNA gene for samples taken over a 4-month start-up period. Early phases of start-up operation were characterized by a period of selection, followed by low diversity and predominance by Azoarcus-like sequences. Possible explanations were high pH and nutrient limitations. After amelioration of these conditions, diversification increased rapidly, with the appearance of Dechloromonas, Pseudomonas, and Hydrogenophaga sequences. Changes in NO3, SO4, and pH also likely contributed to shifts in community composition. The detection of sulfate-reducing-bacteria-like sequences closely related to Desulfovibrio and Desulfuromonas in the FBR have important implications for downstream applications at the field site.

  19. Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor

    SciTech Connect

    Carley, Jack M; Carroll, Sue L; Schadt, Christopher Warren; Watson, David B; Jardine, Philip M; Zhou, Jizhong; Hickey, Robert; Criddle, Craig; Fields, Matthew Wayne

    2006-05-01

    High levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the Y-12 National Security Complex in Oak Ridge, TN. A field-scale denitrifying fluidized bed reactor (FBR) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. After inoculation, biofilms developed on the granular activated carbon particles. Changes in the bacterial community of the FBR were evaluated with clone libraries (n=500 partial sequences) of the small-subunit rRNA gene for samples taken over a 4-month start-up period. Early phases of start-up operation were characterized by a period of selection, followed by low diversity and predominance by Azoarcus-like sequences. Possible explanations were high pH and nutrient limitations. After amelioration of these conditions, diversification increased rapidly, with the appearance of Dechloromonas, Pseudomonas, and Hydrogenophaga sequences. Changes in NO{sub 3}, SO{sub 4}, and pH also likely contributed to shifts in community composition. The detection of sulfate-reducing-bacteria-like sequences closely related to Desulfovibrio and Desulfuromonas in the FBR have important implications for downstream applications at the field site.

  20. Changes in bacterial community structure correlate with initialoperating conditions of a field-scale denitrifying fluidized bedreactor

    SciTech Connect

    Hwang, C.; Wu, W.-M.; Gentry, T.J.; Carley, J.; Carroll, S.L.; Schadt, C.; Watson, D.; Jardine, P.M.; Zhou, J.; Hickey, R.F.; Criddle,C.S.; Fields, M.W.

    2007-04-02

    High levels of nitrate are present in groundwater migratingfrom the former waste disposal ponds at the Y-12 National SecurityComplex in Oak Ridge, TN. A field-scale denitrifying fluidized bedreactor (FBR) was designed, constructed, and operated with ethanol as anelectron donor for the removal of nitrate. After inoculation, biofilmsdeveloped on the granular activated carbon particles. Changes in thebacterial community of the FBR were evaluated with clone libraries (n=500partial sequences) of the small-subunit rRNA gene for samples taken overa 4-month start-up period. Early phases of start-up operationwerecharacterized by a period of selection, followed by low diversity andpredominance by Azoarcus-like sequences. Possible explanations were highpH and nutrient limitations. After amelioration of these conditions,diversification increased rapidly, with the appearance of Dechloromonas,Pseudomonas, and Hydrogenophaga sequences. Changes in NO3, SO4, and pHalso likely contributed to shifts in community composition. The detectionof sulfate-reducing-bacteria-like sequences closely related toDesulfovibrio and Desulfuromonas in the FBR have important implicationsfor downstream applications at the field site.

  1. Functional patterns of microbial communities of rhizospheric soils across the development stages of a young mangrove in French Guiana.

    PubMed

    Luglia, Mathieu; Criquet, Stéven; Sarrazin, Max; Ziarelli, Fabio; Guiral, Daniel

    2014-02-01

    The functional patterns of microbial communities (microbial respiration, enzyme activities, functional diversity) and the relevant physico-chemical characteristics of rhizospheric soils were studied during the process of mudflat colonization by mangrove. The study site is a fringe mangrove stand located in Montabo Bay at Cayenne (French Guiana). It is characterized by different vegetation development stages dominated by an assemblage of Avicennia germinans and Laguncularia racemosa. Rhizospheric and surface soils were collected from three stations based on successional stages of mangrove colonization: pioneer (P), coppice (C), and young forest (F). The microbial functional patterns showed significant progressive shifts along the mangrove vegetation profile. The P stages, those most influenced by tide currents, were macroscopically characterized by hydro-sedimentary instability and micro-phytobenthic colonization of mudflat. This stage, characterized by low total organic carbon (TOC) content and quality, showed the lowest extracellular enzymatic activities and the highest functional metabolic diversities. TOC quality analyses by (13)C CPMAS NMR provided evidence of progressive TOC enrichment and an increasing imprint of aboveground vegetation on C quality as succession occurs. These differences in the origin, amount, and quality of soil organic matter (SOM) of older stages exerted both a quantitative and qualitative control over microbial functional responses. This indicated the enhancement of aboveground-belowground functional linkages, leading to the expression of high decomposition activities and a functional loss and specialization of rhizospheric microbial communities. PMID:24141938

  2. Functional patterns of microbial communities of rhizospheric soils across the development stages of a young mangrove in French Guiana.

    PubMed

    Luglia, Mathieu; Criquet, Stéven; Sarrazin, Max; Ziarelli, Fabio; Guiral, Daniel

    2014-02-01

    The functional patterns of microbial communities (microbial respiration, enzyme activities, functional diversity) and the relevant physico-chemical characteristics of rhizospheric soils were studied during the process of mudflat colonization by mangrove. The study site is a fringe mangrove stand located in Montabo Bay at Cayenne (French Guiana). It is characterized by different vegetation development stages dominated by an assemblage of Avicennia germinans and Laguncularia racemosa. Rhizospheric and surface soils were collected from three stations based on successional stages of mangrove colonization: pioneer (P), coppice (C), and young forest (F). The microbial functional patterns showed significant progressive shifts along the mangrove vegetation profile. The P stages, those most influenced by tide currents, were macroscopically characterized by hydro-sedimentary instability and micro-phytobenthic colonization of mudflat. This stage, characterized by low total organic carbon (TOC) content and quality, showed the lowest extracellular enzymatic activities and the highest functional metabolic diversities. TOC quality analyses by (13)C CPMAS NMR provided evidence of progressive TOC enrichment and an increasing imprint of aboveground vegetation on C quality as succession occurs. These differences in the origin, amount, and quality of soil organic matter (SOM) of older stages exerted both a quantitative and qualitative control over microbial functional responses. This indicated the enhancement of aboveground-belowground functional linkages, leading to the expression of high decomposition activities and a functional loss and specialization of rhizospheric microbial communities.

  3. Dynamic changes of rhizosphere properties and antioxidant enzyme responses of wheat plants (Triticum aestivum L.) grown in mercury-contaminated soils.

    PubMed

    Li, Yonghua; Sun, Hongfei; Li, Hairong; Yang, Linsheng; Ye, Bixiong; Wang, Wuyi

    2013-10-01

    A pot experiment was conducted to investigate the dynamic changes in the rhizosphere properties and antioxidant enzyme responses of wheat plants (Triticum aestivum L.) grown in three levels of Hg-contaminated soils. The concentrations of soluble Hg and dissolved organic carbon (DOC) in the rhizosphere soil solutions of the wheat plants were characterised by the sequence before sowing>trefoil stage>stooling stage, whereas the soil solution pH was found to follow an opposite distribution pattern. The activities of antioxidant enzymes in wheat plants under Hg stress were substantially altered. Greater superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities were observed in the wheat plants grown in a highly polluted soil than in a slightly polluted soil (with increases of 11-27% at the trefoil stage and 26-70% at the stooling stage); however, increasing concentrations of Hg up to seriously polluted level led to reduced enzyme activities. The present results suggest that wheat plants could positively adapt to environmental Hg stress, with rhizosphere acidification, the enhancement of DOC production and greater antioxidant enzyme activities perhaps being three important mechanisms involved in the metal uptake/tolerance in the rhizospheres of wheat plants grown in Hg-contaminated soils.

  4. Effect of Rhizosphere Enzymes on Phytoremediation in PAH-Contaminated Soil Using Five Plant Species

    PubMed Central

    Liu, Rui; Dai, Yuanyuan; Sun, Libo

    2015-01-01

    A pot experiment was performed to study the effectiveness of remediation using different plant species and the enzyme response involved in remediating PAH-contaminated soil. The study indicated that species Echinacea purpurea, Festuca arundinacea Schred, Fire Phoenix (a combined F. arundinacea), and Medicago sativa L. possess the potential for remediation in PAH-contaminated soils. The study also determined that enzymatic reactions of polyphenol oxidase (except Fire Phoenix), dehydrogenase (except Fire Phoenix), and urease (except Medicago sativa L.) were more prominent over cultivation periods of 60d and 120d than 150d. Urease activity of the tested species exhibited prominently linear negative correlations with alkali-hydrolyzable nitrogen content after the tested plants were cultivated for 150d (R2 = 0.9592). The experiment also indicated that alkaline phosphatase activity in four of the five tested species (Echinacea purpurea, Callistephus chinensis, Festuca arundinacea Schred and Fire Phoenix) was inhibited during the cultivation process (at 60d and 120d). At the same time, the study determined that the linear relationship between alkaline phosphatase activity and effective phosphorus content in plant rhizosphere soil exhibited a negative correlation after a growing period of 120d (R2 = 0.665). Phytoremediation of organic contaminants in the soil was closely related to specific characteristics of particular plant species, and the catalyzed reactions were the result of the action of multiple enzymes in the plant rhizosphere soil. PMID:25822167

  5. Speciation of arsenic in bulk and rhizosphere soils from artisanal cooperative mines in Bolivia.

    PubMed

    Acosta, Jose A; Arocena, Joselito M; Faz, Angel

    2015-11-01

    Soils near artisanal and small-scale gold mines (ASGM) have high arsenic (As) contents due to the presence of arsenopyrite in gold ores and accelerated accumulations due to mine wastes disposal practices and other mining activities. We determined the content and speciation to understand the fate and environmental risks of As accumulations in 24 bulk and 12 rhizosphere soil samples collected in the Virgen Del Rosario and the Rayo Rojo cooperative mines in the highlands of Bolivia. Mean total As contents in bulk and rhizosphere soils ranged from 13 to 64 mg kg(-1) and exceeded the soil environmental quality guidelines of Canada. Rhizosphere soils always contained at least twice the As contents in the bulk soil. Elemental mapping using 4×5 μm synchrotron-generated X-ray micro-beam revealed As accumulations in areas enriched with Fe. Results of As-X-ray Absorption Near Edge Spectroscopy (As-XANES) showed that only As(V) species was detectable in all samples regardless of As contents, size fractions and types of vegetation. Although the toxicity of As(V) is less than As(III), we suggest that As uptake of commonly-grazed vegetation by alpaca and llama must be determined to fully understand the environmental risks of high As in soils near ASGM in Bolivia. In addition, knowledge on the speciation of the As bio-accessible fraction will provide another useful information to better understand the fate and transfer of As from soils into the food chain in environments associated with the ASGM in Bolivia and other parts of the world.

  6. Effect of immobilized rhizobacteria and organic amendment in bulk and rhizospheric soil of Cistus albidus L.

    NASA Astrophysics Data System (ADS)

    Mengual, Carmen Maria; del Mar Alguacil, Maria; Roldan, Antonio; Schoebitz, Mauricio

    2013-04-01

    A field experiment was carried out to assess the effectiveness of the immobilized microbial inoculant and the addition of organic olive residue. The microbial inoculant contained two rhizobacterial species identified as Azospirillum brasilense and Pantoea dispersa immobilized in a natural inert support. Bacterial population densities were 3.5×109 and 4.1×109 CFU g-1 of A. brasilense M3 and P. dispersa C3, respectively. The amendment used was the organic fraction extracted with KOH from composted "alperujo". The raw material was collected from an olive-mill and mixed with fresh cow bedding as bulking agent for composting. The inoculation of rhizobacteria and the addition of organic residue were employed for plant growth promotion of Cistus albidus L. and enhancement of soil physicochemical, biochemical and biological properties in a degraded semiarid Mediterranean area. One year after planting, the available phosphorus and potassium content in the amended soils was about 100 and 70% respectively higher than in the non-amended soil. Microbial inoculant and their interaction with organic residue increased the aggregate stability of the rhizosphere soil of C. albidus (by 12% with respect to control soil) while the organic residue alone not increased the aggregate stability of the rhizosphere of C. albidus. Microbial biomass C content and enzyme activities (dehydrogenase, urease, protease-BAA and alkaline phosphatase) of the rhizosphere of C. albidus were increased by microbial inoculant and organic residue interaction but not by microbial inoculation alone. The microbial inoculant and organic residue interaction were the most effective treatment for stimulating the roots dry weight of C. albidus (by 133% with respect to control plants) and microbial inoculant was the most effective treatment for increase the shoot dry weigh of plants (by 106% with respect to control plants). The combined treatment, involving microbial inoculant and addition of the organic residue

  7. Speciation of arsenic in bulk and rhizosphere soils from artisanal cooperative mines in Bolivia.

    PubMed

    Acosta, Jose A; Arocena, Joselito M; Faz, Angel

    2015-11-01

    Soils near artisanal and small-scale gold mines (ASGM) have high arsenic (As) contents due to the presence of arsenopyrite in gold ores and accelerated accumulations due to mine wastes disposal practices and other mining activities. We determined the content and speciation to understand the fate and environmental risks of As accumulations in 24 bulk and 12 rhizosphere soil samples collected in the Virgen Del Rosario and the Rayo Rojo cooperative mines in the highlands of Bolivia. Mean total As contents in bulk and rhizosphere soils ranged from 13 to 64 mg kg(-1) and exceeded the soil environmental quality guidelines of Canada. Rhizosphere soils always contained at least twice the As contents in the bulk soil. Elemental mapping using 4×5 μm synchrotron-generated X-ray micro-beam revealed As accumulations in areas enriched with Fe. Results of As-X-ray Absorption Near Edge Spectroscopy (As-XANES) showed that only As(V) species was detectable in all samples regardless of As contents, size fractions and types of vegetation. Although the toxicity of As(V) is less than As(III), we suggest that As uptake of commonly-grazed vegetation by alpaca and llama must be determined to fully understand the environmental risks of high As in soils near ASGM in Bolivia. In addition, knowledge on the speciation of the As bio-accessible fraction will provide another useful information to better understand the fate and transfer of As from soils into the food chain in environments associated with the ASGM in Bolivia and other parts of the world. PMID:25577694

  8. [Effects of growth years of Paeonia lactiflora on bacterial community in rhizosphere soil and paeoniflorin content].

    PubMed

    Yuan, Xiao-Feng; Peng, San-Mei; Wang, Bo-Lin; Ding, Zhi-Shan

    2014-08-01

    To explore the relationship between microecological environment and Paeonia lactiflora the effects of growth years of P. lactillora on rhizosphere bacterial communities were studied by PCR-DGGE and the paeoniflorin content determined by HPLC. Results showed that the soil pH increased with growing years of P. lactillora. In the fourth year, soil pH and enzyme activity reached the highest level, while organic matter content was the lowest. The bacterial diversity had a positive correlation with growing years varied from 3.38 to 3.61. Sequencing results demonstrated that Gamm