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

    PubMed Central

    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. PMID:11536820

  3. Assessment of denitrifying bacterial composition in activated sludge.

    PubMed

    Srinandan, C S; Shah, Mrinal; Patel, Bhavita; Nerurkar, Anuradha S

    2011-10-01

    The abundance and structure of denitrifying bacterial community in different activated sludge samples were assessed, where the abundance of denitrifying functional genes showed nirS in the range of 10(4)-10(5), nosZ with 10(4)-10(6) and 16S rRNA gene in the range 10(9)-10(10) copy number per ml of sludge. The culturable approach revealed Pseudomonas sp. and Alcaligenes sp. to be numerically high, whereas culture independent method showed betaproteobacteria to dominate the sludge samples. Comamonas sp. and Pseudomonas fluorescens isolates showed efficient denitrification, while Pseudomonas mendocina, Pseudomonas stutzeri and Brevundimonas diminuta accumulated nitrite during denitrification. Numerically dominant RFLP OTUs of the nosZ gene from the fertilizer factory sludge samples clustered with the known isolates of betaproteobacteria. The data also suggests the presence of different truncated denitrifiers with high numbers in sludge habitat. PMID:21868215

  4. [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. PMID:16471342

  5. 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

  6. Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems.

    PubMed

    McIlroy, Simon Jon; Starnawska, Anna; Starnawski, Piotr; Saunders, Aaron Marc; Nierychlo, Marta; Nielsen, Per Halkjaer; Nielsen, Jeppe Lund

    2016-01-01

    Denitrification is essential to the removal of nitrogen from wastewater during treatment, yet an understanding of the diversity of the active denitrifying bacteria responsible in full-scale wastewater treatment plants (WWTPs) is lacking. In this study, stable-isotope probing (SIP) was applied in combination with microautoradiography (MAR)-fluorescence in situ hybridization (FISH) to identify previously unrecognized active denitrifying phylotypes in a full-scale WWTP with biological N and P removal. Acknowledging that different denitrifiers will have specific carbon source preferences, a fully (13)C-labelled complex substrate was used for SIP incubations, under nitrite-reducing conditions, in order to maximize the capture of the potentially metabolically diverse denitrifiers likely present. Members of the Rhodoferax, Dechloromonas, Sulfuritalea, Haliangium and Thermomonas were represented in the 16S rRNA gene clone libraries from DNA enriched in (13)C, with FISH probes optimized here for their in situ characterization. FISH and MAR confirmed that they were all active denitrifiers in the community. The combined approach of SIP and MAR-FISH represents an excellent approach for identifying and characterizing an un-described diversity of active denitrifiers in full-scale systems. PMID:25181571

  7. Effect of electro-stimulation on activity of heterotrophic denitrifying bacteria and denitrification performance.

    PubMed

    Liu, Hengyuan; Tong, Shuang; Chen, Nan; Liu, Ying; Feng, Chuanping; Hu, Qili

    2015-11-01

    The effects of electro-stimulation on heterotrophic denitrifying bacterial activity and nitrate removal were investigated using a bench-scale bio-electrochemical reactor in this study. Results showed that the maximum nitrate removal efficiency was 100% at the optimum current density of 200mA/m(2), at which low nitrite production and high ATP aggregate level were obtained. The activity of denitrifying bacteria was highest at the range densities of 200-250mA/m(2), although the terminative pH increased to 8.62 at 200mA/m(2) and 9.63 at 250mA/m(2). This demonstrates that suitable current densities could improve the activity of denitrifying bacteria. Therefore, this study provides a number of useful information to improve the bio-electrochemical reactor designs and promote the removal efficiency of pollutants. PMID:26231132

  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. Microbial Community Composition and Denitrifying Enzyme Activities in Salt Marsh Sediments▿

    PubMed Central

    Cao, Yiping; Green, Peter G.; Holden, Patricia A.

    2008-01-01

    Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh. PMID:18978080

  12. 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

  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. PMID:25429458

  14. 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

  15. 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.

  16. [Chemical properties and enzyme activities of rhizosphere and non-rhizosphere soils under six Chinese herbal medicines on Mt. Taibai of Qinling Mountains, Northwest China].

    PubMed

    Meng, Ling-Jun; Geng, Zeng-Chao; Yin, Jin-Yan; Wang, Hai-Tao; Ji, Peng-Fei

    2012-10-01

    This paper studied the chemical properties and enzyme activities of rhizosphere and non-rhizosphere soils in different habitats of six Chinese herbal medicines, including Pyrola decorata, Cephalotaxus fortunei, Polygonatum odoratum, Potentilla glabra, Polygonum viviparum, and Potentilla fruticosa, on the Mt. Taibai of Qinling Mountains. In the rhizosphere soils of the herbs, the contents of soil organic matter, total nitrogen, available nitrogen, and available phosphorus and the soil cation exchange capacity (CEC) were higher, presenting an obvious rhizosphere aggregation, and the soil enzyme activities also showed an overall stronger characteristics, compared with those in non-rhizosphere soils. The soil organic matter, total nitrogen, and total phosphorus contents in the rhizosphere soils had significant positive correlations with soil neutral phosphatase activity, and the soil CEC had significant positive correlations with the activities of soil neutral phosphatase and acid phosphatase. In the non-rhizosphere soils, the soil organic matter and total nitrogen contents had significant positive correlations with the activities of soil urease, catalase and neutral phosphatase, and the soil CEC showed a significant positive correlation with the activities of soil urease, catalase, neutral phosphatase and acid phosphatase. The comprehensive fertility level of the rhizosphere soils was higher than that of the non-rhizosphere soils, and the rhizosphere and non-rhizosphere soils of P. fruticosa, P. viviparum, and P. glabra had higher comprehensive fertility level than those of P. decorata, P. odoratum and C. fortunei. In the evaluation of the fertility levels of rhizosphere and non-rhizosphere soils under the six Chinese herbal medicines, soil organic matter content and CEC played important roles, and soil neutral phosphatase could be the preferred soil enzyme indicator. PMID:23359927

  17. 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

  18. 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. PMID:24480748

  19. Rhizosphere activity and methane oxidation in a temperate forest soil

    NASA Astrophysics Data System (ADS)

    Moody, Catherine S.; Subke, Jens-Arne; Voke, Naomi R.; Holden, Robert D.; Ineson, Phil; Arn Teh, Yit

    2010-05-01

    Methane (CH4) concentrations in the Earth's atmosphere have increased dramatically over recent decades. An abundance of studies indicate that the magnitude of natural methane efflux from wetlands is likely to increase due to climate change. However, the role of vegetation and soils in upland methane oxidation are less well understood. Well-aerated soils are known to be sites of methane oxidation, and amongst a range of abiotic environmental parameters, soil moisture has been identified as critical regulator of the methane oxidation rates. However, the role of microbial activity within the soil, particularly C turnover in the plant rhizosphere, has not been investigated as a means for regulating methanotrophy. We combined a continuous soil CO2 efflux system (Li-Cor Biosciences, LI-8100) with a Cavity-Ringdown-Spectroscopy Fast Greenhouse Gas Analyser (Los Gatos Research Inc.) to measure soil CH4 oxidation in a pine forest in NE England. The soil has a shallow organic layer overlaying a well-draining sandy gley soil. Fluxes were measured from three different collar treatments: (1) excluding both root and ectomycorrhizal (EM) hyphae by trenching using deep collars, (2) excluding roots but allowing access by EM hyphae, and (3) unmodified forest soil (i.e. including both roots and EM hyphae). All collars were protected from natural throughfall, and received weekly-averaged amounts of throughfall based on collections in the stand. Data from two months in early summer 2009 indicate that CH4 oxidation in collars with an intact rhizosphere is more than twice that of either of the exclusion treatments (averaging approx. 90 g ha-1 d-1 in that period). We observed higher fluxes when soils were dryer (i.e. with increasing time since watering), indicating a significant influence of moisture. Despite the confounding effects of soil moisture associated with root water uptake in the unmodified soil collars, we argue that rhizosphere activity is an overlooked component in

  20. 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.

  1. 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.

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

    PubMed Central

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

    2006-01-01

    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. N2O emissions were not significantly different among treatments; however, N2 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 N2 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

  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. Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1

    PubMed Central

    Cua, Lynnie S.; Stein, Lisa Y.

    2014-01-01

    Sphingomonas wittichii RW1 has no reported denitrifying activity yet encodes nitrite and nitric oxide reductases. The aims of this study were to determine conditions under which S. wittichii RW1 consumes nitrite (NO−2) and produces nitrous oxide (N2O), examine expression of putative genes for N-oxide metabolism, and determine the functionality of chromosomal (ch) and plasmid (p) encoded quinol-dependent nitric oxide reductases (NorZ). Batch cultures of wildtype (WT) and a norZch mutant of S. wittichii RW1 consumed NO−2 and produced N2O during stationary phase. The norZch mutant produced N2O, although at significantly lower levels (c.a. 66–87%) relative to the WT. Rates of N2O production were 2–3 times higher in cultures initiated at low relative to atmospheric O2 per unit biomass, although rates of NO−2 consumption were elevated in cultures initiated with atmospheric O2 and 1 mM NaNO2. Levels of mRNA encoding nitrite reductase (nirK), plasmid-encoded nitric oxide dioxygenase (hmpp) and plasmid-encoded nitric oxide reductase (norZp) were significantly higher in the norZch mutant over a growth curve relative to WT. The presence of NO−2 further increased levels of nirK and hmpp mRNA in both the WT and norZch mutant; levels of norZp mRNA compensated for the loss of norZch expression in the norZch mutant. Together, the results suggest that S. wittichii RW1 denitrifies NO−2 to N2O and expresses gene products predicted to detoxify N-oxides. So far, only S. wittichii strains within four closely related taxa have been observed to encode both nirK and norZ genes, indicating a species-specific lateral gene transfer that may be relevant to the niche preference of S. wittichii. PMID:25147547

  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. 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

  9. 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

  10. EFFECTS OF GLYPHOSATE AND FOLIAR AMENDMENTS ON ACTIVITY OF MICROORGANISMS IN THE SOYBEAN RHIZOSPHERE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 to GR soybean at the V4 - V5 development stages. Check tre...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 co-culture against A. flav...

  12. 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

  13. 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

  14. Diaphorobacter nitroreducens gen nov, sp nov, a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge.

    PubMed

    Khan, Shams Tabrez; Hiraishi, Akira

    2002-12-01

    Three denitrifying strains of bacteria capable of degrading poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were isolated from activated sludge and characterized. All of the isolates had almost identical phenotypic characteristics. They were motile gram-negative rods with single polar flagella and grew well with simple organic compounds, as well as with PHB and PHBV, as carbon and energy sources under both aerobic and anaerobic denitrifying conditions. However, none of the sugars tested supported their growth. The cellular fatty acid profiles showed the presence of C16:1omega7cis and C16:0 as the major components and of 3-OH-C10:0 as the sole component of hydroxy fatty acids. Ubiquinone-8 was detected as the major respiratory quinone. A 16S rDNA sequence-based phylogenetic analysis showed that all the isolates belonged to the family Comamonadaceae, a major group of beta-Proteobacteria, but formed no monophyletic cluster with any previously known species of this family. The closest relative to our strains was an unidentified bacterium strain LW1 (=DSM 13225) (99.9% similarity), reported previously as a 1-chloro-4-nitrobenzene degrading bacterium. DNA-DNA hybridization levels among the new isolates were more than 60%, whereas those between our isolates and strain DSM 13225 were less than 50%. The G+C content of genomic DNA of the new strains was 64 to 65 mol%. Based on these results, we concluded that the PHBV-degrading denitrifying isolates should be classified as a new genus and a new species, for which we propose the name Diaphorobacter nitroreducens. The type strain is strain NA10B (=JCM 11421=CIP 107294). We also propose to classify strain DSM 13225 as a genospecies of Diaphorobacter. PMID:12682868

  15. 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

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

    PubMed

    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 (pH H2O = 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

  18. 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

  19. Root carbon inputs to the rhizosphere stimulate extracellular enzyme activity and increase nitrogen availability in temperate forest soils

    NASA Astrophysics Data System (ADS)

    Brzostek, E. R.; Phillips, R.; Dragoni, D.; Drake, J. E.; Finzi, A. C.

    2011-12-01

    The mobilization of nitrogen (N) from soil organic matter in temperate forest soils is controlled by the microbial production and activity of extracellular enzymes. The exudation of carbon (C) by tree roots into the rhizosphere may subsidize the microbial production of extracellular enzymes in the rhizosphere and increase the access of roots to N. The objective of this research was to investigate whether rates of root exudation and the resulting stimulation of extracellular enzyme activity in the rhizosphere (i.e., rhizosphere effect) differs between tree species that form associations with ectomycorrhizal (ECM) or arbuscular mycorrhizal (AM) fungi. This research was conducted at two temperate forest sites, the Harvard Forest (HF) in Central MA and the Morgan Monroe State Forest (MMSF) in Southern IN. At the HF, we measured rates of root exudation and the rhizosphere effects on enzyme activity, N cycling, and C mineralization in AM and ECM soils. At the MMSF, we recently girdled AM and ECM dominated plots to examine the impact of severing belowground C allocation on rhizosphere processes. At both sites, the rhizosphere effect on proteolytic, chitinolytic and ligninolytic enzyme activities was greater in ECM soils than in AM soils. In particular, higher rates of proteolytic enzyme activity increased the availability of amino acid-N in ECM rhizospheres relative to the bulk soils. Further, this stimulation of enzyme activity was directly correlated with higher rates of C mineralization in the rhizosphere than in the bulk soil. Although not significantly different between species, root exudation of C comprised 3-10% of annual gross primary production at the HF. At the MMSF, experimental girdling led to a larger decline in soil respiration and enzyme activity in ECM plots than in AM plots. In both ECM and AM soils, however, girdling resulted in equivalent rates of enzyme activity in rhizosphere and corresponding bulk soils. The results of this study contribute to the

  20. Denitrifying kinetics and nitrous oxide emission under different copper concentrations.

    PubMed

    Wu, Guangxue; Zhai, Xiaofeng; Jiang, Chengai; Guan, Yuntao

    2014-01-01

    Denitrifying activities and nitrous oxide (N2O) emission during denitrification can be affected by copper concentrations. Different denitrifiers were acclimated in sequencing batch reactors with acetate or methanol as the electron donor and nitrate as the electron acceptor. The effect of copper concentrations on the denitrifying activity and N2O emission for the acclimated denitrifiers was examined in batch experiments. Denitrifying activities of the acclimated denitrifiers declined with increasing copper concentrations, and the copper concentration exhibited a higher effect on denitrifiers acclimated with acetate than those acclimated with methanol. Compared with the control without the addition of copper, at the copper concentration of 1 mg/L, the acetate utilization rate reduced by 89% for acetate-acclimated denitrifiers, while the methanol utilization rate only reduced by 15% for methanol-acclimated denitrifiers. Copper also had different effects on N2O emission during denitrification carried out by various types of denitrifiers. For the acetate-acclimated denitrifiers, N2O emission initially increased and then decreased with increasing copper concentrations, while for the methanol-acclimated denitrifiers, N2O emission decreased with increasing copper concentrations. PMID:24569272

  1. [Effects of saltwater incursion on the microbiological characteristics and denitrification in a riparian rhizosphere soil in Chongming Island of Shanghai, East China].

    PubMed

    Yang, Chang-Ming; Cai, Wen-Juan; Li, Jian-Hua

    2012-04-01

    A simulation test was conducted to study the effects of saltwater incursion on the microbiological characteristics and denitrification in the riparian rhizosphere soils vegetated with different plants in Chongming Island of Shanghai. Saltwater incursion changed the microflora in the rhizospheric soils. Except for actinomycete whose quantity had slight increase, the quantities of bacteria, fungi, nitrifiers, and denitrifiers all decreased to some extent by saltwater incursion, with the denitrifiers decreased by 51.8%, suggesting that the riparian soil microflora responded differentially to saltwater incursion. The activities of soil nitrogen-transforming enzymes were significantly inhibited by saltwater incursion, and the inhibitory effects differed with the enzymes. Nitrite reductase activity was most sensitive to saltwater incursion, with an inhibition rate of 43.5%, followed by urease activity, with 37.4% inhibition, and by dehydrogenase (29.5% inhibition). Saltwater incursion inhibited the denitrification, with the average denitrification rate decreased by 34.9%. There existed significant differences in the eco-physiological responses of the microbes in the rhizosphere soils vegetated with different plants to the saltwater incursion. The microbial quantities and enzyme activities showed the highest inhibition percentages in the rhizosphere soil of Zizania aquatica, followed by in the rhizosphere soils of Acorus calamus and Phragmites australis. Under saltwater incursion, the inhibition percentages of microbial quantities, enzyme activities, and denitrification rate in the rhizosphere soil of A. calamus-P. australis were significantly lower, as compared with those in the rhizosphere soils vegetated with Z. aquatica, A. calamus, and P. australis, respectively, suggesting that mixed vegetation showed a better buffer effect on the responses of riparian rhizosphere soil microbiological processes and denitrification to saltwater incursion. PMID:22803478

  2. Community structures and activity of denitrifying microbes in a forested catchment in central Japan: survey using nitrite reductase genes

    NASA Astrophysics Data System (ADS)

    Ohte, N.; Aoki, M.; Katsuyama, C.; Suwa, Y.; Tange, T.

    2012-12-01

    To elucidate the mechanisms of denitrification processes in the forested catchment, microbial ecological approaches have been applied in an experimental watershed that has previously investigated its hydrological processes. The study catchment is located in the Chiba prefecture in central Japan under the temperate Asian monsoon climate. Potential activities of denitrification of soil samples were measured by incubation experiments under anoxic condition associated with Na15NO3 addition. Existence and variety of microbes having nitrite reductase genes were investigated by PCR amplification, cloning and sequencings of nirK and nirS fragments after DNA extraction. Contrary to our early expectation that the potential denitrification activity was higher at deeper soil horizon with consistent groundwater residence than that in the surface soil, denitrification potential was higher in shallower soil horizons than deeper soils. This suggested that the deficiency of NO3- as a respiratory substrate for denitrifier occurred in deeper soils especially in the summer. However, high denitrification activity and presence of microbes having nirK and nirS in surface soils usually under aerobic condition was explainable by the fact that the majority of denitrifying bacteria have been recognized as a facultative anaerobic bacterium. This also suggests the possibility of that denitrification occurs even in the surface soils if the wet condition is provided by rainwater during and after a storm event. Community structures of microbes having nirK were different between near surface and deeper soil horizons, and ones having nirS was different between saturated zone (under groundwater table) and unsaturated soil horizons. These imply that microbial communities with nisK are sensitive to the concentration of soil organic matters and ones with nirS is sensitive to soil moisture contents.

  3. 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

  4. Insights into the Effect of Soil pH on N2O and N2 Emissions and Denitrifier Community Size and Activity

    PubMed Central

    Čuhel, Jiří; Šimek, Miloslav; Laughlin, Ronnie J.; Bru, David; Chèneby, Dominique; Watson, Catherine J.; Philippot, Laurent

    2010-01-01

    The objective of this study was to investigate how changes in soil pH affect the N2O and N2 emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H2SO4 solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N2O and N2 emissions using the 15N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N2O/(N2O + N2) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N2O production were observed. Denitrification activity and N2O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N2O/(N2O + N2) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification. PMID:20118356

  5. 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...

  6. Enrichment of denitrifying glycogen-accumulating organisms in anaerobic/anoxic activated sludge system.

    PubMed

    Zeng, Raymond J; Yuan, Zhiguo; Keller, Jürg

    2003-02-20

    Denitrifying glycogen-accumulating organisms (DGAO) were successfully enriched in a lab-scale sequencing batch reactor (SBR) running with anaerobic/anoxic cycles and acetate feeding during the anaerobic period. Acetate was completely taken up anaerobically, which was accompanied by the consumption of glycogen and the production of poly-beta-hydroxy-alkanoates (PHA). In the subsequent anoxic stage, nitrate or nitrite was utilized as electron acceptor for the oxidation of PHA, resulting in glycogen replenishment and cell growth. The above phenotype showed by the enrichment culture demonstrates the existence of DGAO. Further, it was found that the anaerobic behavior of DGAO could be predicted well by the anaerobic GAO model of Filipe et al. (2001) and Zeng et al. (2002a). The final product of denitrification during anoxic stage was mainly nitrous oxide (N(2)O) rather than N(2). The data strongly suggests that N(2)O production may be caused by the inhibition of nitrous oxide reductase by an elevated level of nitrite accumulated during denitrification. The existence of these organisms is a concern in biological nutrient removal systems that typically have an anaerobic/anoxic/aerobic reactor sequence since they are potential competitors to the polyphosphate-accumulating organisms. PMID:12491525

  7. Lettuce Cultivar Mediates Both Phyllosphere and Rhizosphere Activity of Escherichia coli O157:H7

    PubMed Central

    Quilliam, Richard S.; Williams, A. Prysor; Jones, Davey L.

    2012-01-01

    Plant roots and leaves can be colonized by human pathogenic bacteria, and accordingly some of the largest outbreaks of foodborne illness have been associated with salad leaves contaminated by E. coli O157. Integrated disease management strategies often exploit cultivar resistance to provide a level of protection from economically important plant pathogens; however, there is limited evidence of whether the genotype of the plant can also influence the extent of E. coli O157 colonization. To determine cultivar-specific effects on colonization by E. coli O157, we used 12 different cultivars of lettuce inoculated with a chromosomally lux-marked strain of E. coli O157:H7. Lettuce seedlings grown gnotobiotically in vitro did exhibit a differential cultivar-specific response to E. coli O157 colonization, although importantly there was no relationship between metabolic activity (measured as bioluminescence) and cell numbers. Metabolic activity was highest and lowest on the cultivars Vaila-winter gem and Dazzle respectively, and much higher in endophytic and tightly bound cells than in epiphytic and loosely bound cells. The cultivar effect was also evident in the rhizosphere of plants grown in compost, which suggests that cultivar-specific root exudate influences E. coli O157 activity. However, the influence of cultivar in the rhizosphere was the opposite to that in the phyllosphere, and the higher number and activity of E. coli O157 cells in the rhizosphere may be a consequence of them not being able to gain entry to the plant as effectively. If metabolic activity in the phyllosphere corresponds to a more prepared state of infectivity during human consumption, leaf internalization of E. coli O157 may pose more of a public health risk than leaf surface contamination alone. PMID:22439006

  8. 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

  9. 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...

  10. 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

  11. The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

    PubMed

    Lee, Seung-Hoon; Kang, Hojeong

    2016-02-01

    The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain

  12. Metabolic activity and genetic diversity of microbial communities inhabiting the rhizosphere of halophyton plants.

    PubMed

    Bárány, Agnes; Szili-Kovács, Tibor; Krett, Gergely; Füzy, Anna; Márialigeti, Károly; Borsodi, Andrea K

    2014-09-01

    A preliminary study was conducted to compare the community level physiological profile (CLPP) and genetic diversity of rhizosphere microbial communities of four plant species growing nearby Kiskunság soda ponds, namely Böddi-szék, Kelemen-szék and Zab-szék. CLPP was assessed by MicroResp method using 15 different substrates while Denaturing Gradient Gel Electrophoresis (DGGE) was used to analyse genetic diversity of bacterial communities. The soil physical and chemical properties were quite different at the three sampling sites. Multivariate statistics (PCA and UPGMA) revealed that Zab-szék samples could be separated according to their genetic profile from the two others which might be attributed to the geographical location and perhaps the differences in soil physical properties. Böddi-szék samples could be separated from the two others considering the metabolic activity which could be explained by their high salt and low humus contents. The number of bands in DGGE gels was related to the metabolic activity, and positively correlated with soil humus content, but negatively with soil salt content. The main finding was that geographical location, soil physical and chemical properties and the type of vegetation were all important factors influencing the metabolic activity and genetic diversity of rhizosphere microbial communities. PMID:25261946

  13. 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

  14. 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. PMID:26315595

  15. Enzymatic activity in the rhizosphere of Spartina maritima: potential contribution for phytoremediation of metals.

    PubMed

    Reboreda, Rosa; Caçador, Isabel

    2008-02-01

    Extracellular enzymatic activity (EEA) of five enzymes (peroxidase, phenol oxidase, beta-glucosidase, beta-N-acetylglucosaminidase and acid phosphatase) was analysed in sediments colonised by Spartina maritima in two salt marshes (Rosário and Pancas) of the Tagus estuary (Portugal) with different characteristics such as sediment parameters and metal contaminant levels. Our aim was a better understanding of the influence of the halophyte on microbial activity in the rhizosphere under different site conditions, and its potential consequences for metal cycling and phytoremediation in salt marshes. Acid phosphatase and beta-N-acetylglucosaminidase presented significantly higher EEA in Rosário than in Pancas, whereas the opposite occurred for peroxidase. This was mainly attributed to differences in organic matter between the two sites. A positive correlation between root biomass and EEA of hydrolases (beta-glucosidase, beta-N-acetylglucosaminidase and acid phosphatase) was found, indicating a possible influence of the halophyte in sediment microbial function. This would potentially affect metal cycling in the rhizosphere through microbial reactions. PMID:17935772

  16. 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

  17. 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

  18. 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

  19. Selection pressure, cropping system and rhizosphere proximity affect atrazine degrader populations and activity in s-triazine adapted soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Atrazine degrader populations and activity in s-triazine adapted soils are likely affected by interactions among and (or) between s-triazine application frequency, crop production system, and proximity to the rhizosphere. A field study was conducted on an s-triazine adapted soil to determine the ef...

  20. 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

  1. RHIZOSPHERE ECOLOGY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rhizosphere is defined as the region of soil surrounding plant roots that is under the influence of the root. This region is centered around the root, and is best defined by the biotic response to the influence of the root. Thus, the spatial limits of the rhizosphere are determined by the soil...

  2. 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

  3. 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

  4. Denitrification activity of a remarkably diverse fen denitrifier community in finnish lapland is N-oxide limited.

    PubMed

    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

  5. 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)

  6. 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

  7. 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

  8. Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities.

    PubMed

    Ahmad, Farah; Ahmad, Iqbal; Khan, M S

    2008-01-01

    Plant growth promoting rhizobacteria (PGPR) are known to influence plant growth by various direct or indirect mechanisms. In search of efficient PGPR strains with multiple activities, a total of 72 bacterial isolates belonging to Azotobacter, fluorescent Pseudomonas, Mesorhizobium and Bacillus were isolated from different rhizospheric soil and plant root nodules in the vicinity of Aligarh. These test isolates were biochemically characterized. These isolates were screened in vitro for their plant growth promoting traits like production of indoleacetic acid (IAA), ammonia (NH(3)), hydrogen cyanide (HCN), siderophore, phosphate solubilization and antifungal activity. More than 80% of the isolates of Azotobacter, fluorescent Pseudomonas and Mesorhizobium ciceri produced IAA, whereas only 20% of Bacillus isolates was IAA producer. Solubilization of phosphate was commonly detected in the isolates of Bacillus (80%) followed by Azotobacter (74.47%), Pseudomonas (55.56%) and Mesorhizobium (16.67%). All test isolates could produce ammonia but none of the isolates hydrolyzed chitin. Siderophore production and antifungal activity of these isolates except Mesorhizobium were exhibited by 10-12.77% isolates. HCN production was more common trait of Pseudomonas (88.89%) and Bacillus (50%). On the basis of multiple plant growth promoting activities, eleven bacterial isolates (seven Azotobacter, three Pseudomonas and one Bacillus) were evaluated for their quantitative IAA production, and broad-spectrum (active against three test fungi) antifungal activity. Almost at all concentration of tryptophan (50-500 microg/ml), IAA production was highest in the Pseudomonas followed by Azotobacter and Bacillus isolates. Azotobacter isolates (AZT(3), AZT(13), AZT(23)), Pseudomonas (Ps(5)) and Bacillus (B(1)) showed broad-spectrum antifungal activity on Muller-Hinton medium against Aspergillus, one or more species of Fusarium and Rhizoctonia bataticola. Further evaluation of the isolates

  9. 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.

  10. 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

  11. 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

  12. ¹³C pulse-chase labeling comparative assessment of the active methanogenic archaeal community composition in the transgenic and nontransgenic parental rice rhizospheres.

    PubMed

    Zhu, Weijing; Lu, Haohao; Hill, Jaclyn; Guo, Xiaohui; Wang, Hailong; Wu, Weixiang

    2014-03-01

    More and more investigations indicate that genetic modification has no significant or persistent effects on microbial community composition in the rice rhizosphere. Very few studies, however, have focused on its impact on functional microorganisms. This study completed a ¹³C-CO₂ pulse-chase labeling experiment comparing the potential effects of cry1Ab gene transformation on ¹³C tissue distribution and rhizosphere methanogenic archaeal community composition with its parental rice variety (Ck) and a distant parental rice variety (Dp). Results showed that ¹³C partitioning in aboveground biomass (mainly in stems) and roots of Dp was significantly lower than that of Ck. However, there were no significant differences in ¹³C partitioning between the Bt transgenic rice line (Bt) and Ck. RNA-stable isotope probing combined with clone library analyses inferred that the group Methanosaetaceae was the predominant methanogenic Archaea in all three rice rhizospheres. The active methanogenic archaeal community in the Bt rhizosphere was dominated by Methanosarcinaceae, Methanosaetaceae, and Methanomicrobiaceae, while there were only two main methanogenic clusters (Methanosaetaceae and Methanomicrobiaceae) in the Ck and Dp rhizospheres. These results indicate that the insertion of cry1Ab gene into the rice genome has the potential to result in the modification of methanogenic community composition in its rhizosphere. PMID:24266498

  13. Antimicrobial Activities of Some Actinomycetes Isolated from Different Rhizospheric Soils in Tunisia.

    PubMed

    Trabelsi, Ines; Oves, Daniel; Manteca, Angel; Genilloud, Olga; Altalhi, Abdullah; Nour, Mohamed

    2016-08-01

    Fifty four isolates of actinomycetes were collected from four different rhizospheric soils: 18 strains from palm tree bark and soil, 12 strains from an olive field soil, 9 strains from a coastal forest, and 15 strains from an agriculture soil situated in the Algerian-Tunisian border (Oum Tboul). Based on morphological and cultural characters, the isolates were classified as Streptomyces (42 strains), Micromonospora (4 strains), Pseudonocardia (1 strain), Actinomadura (1 strain), Nocardia (1 strain), and non-Streptomyces (5 strains). More than half of the isolates inhibited at least one tested pathogenic microorganisms in liquid culture. In addition, antimicrobial activities of some strains were tested on solid culture. Several bioactive compounds were identified by liquid chromatography joined with low-resolution mass spectroscopy (LC/MS) and analysed by MEDINA's database and by the dictionary of natural products Chapman & Hall. An interesting chlorinated compound with the molecular formula C20H37ClN2O4, produced by three different strains (SF1, SF2, and SF5), was subject of an attempted purification. However, it was demonstrated using confocal microscopy and LC/MS high resolution that this compound is produced only on solid culture. These three potential antimicrobial isolates showed high similarity with Streptomyces thinghirensis and Streptomyces lienomycini, in terms of morphological characteristics and 16S rRNA gene sequences (bootstrap 97 %). All these findings prove the high antimicrobial diversity of the studied soils. The potential of the selected and other relatively unexplored extreme environments constitute a source of interesting actinomycete strains producing several biologically active secondary metabolites. PMID:27139253

  14. [Research advances in aerobic denitrifiers].

    PubMed

    Wang, Wei; Cai, Zu-cong; Zhong, Wen-hui; Wang, Guo-xiang

    2007-11-01

    This paper reviewed the varieties and characteristics of aerobic denitrifiers, their action mechanisms, and the factors affecting aerobic denitrification. Aerobic denitrifiers mainly include Pseudomonas, Alcaligenes, Paracoccus and Bacillus, which are either aerobic or facultative aerobic, and heterotrophic. They can denitrify under aerobic conditions, with the main product being N2O. They can also convert NH4+ -N to gas product. The nitrate reductase which catalyzes the denitrification is periplasmic nitrate reductase rather than membrane-bound nitrate reductase. Dissolved oxygen concentration and C/N ratio are the main factors affecting aerobic denitrification. The main methods for screening aerobic denitrifiers, such as intermittent aeration and selected culture, were also introduced. The research advances in the application of aerobic denitrifiers in aquaculture, waste water processing, and bio-degradation of organic pollutants, as well as the contributions of aerobic denitrifiers to soil nitrogen emission were summarized. PMID:18260473

  15. 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

  16. 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

  17. 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.

  18. 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

  19. [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

  20. [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

  1. Bacterial Activity in the Rhizosphere Analyzed at the Single-Cell Level by Monitoring Ribosome Contents and Synthesis Rates

    PubMed Central

    Ramos, Cayo; Mølbak, Lars; Molin, Søren

    2000-01-01

    The growth activity of Pseudomonas putida cells colonizing the rhizosphere of barley seedlings was estimated at the single-cell level by monitoring ribosomal contents and synthesis rates. Ribosomal synthesis was monitored by using a system comprising a fusion of the ribosomal Escherichia coli rrnBP1 promoter to a gene encoding an unstable variant of the green fluorescent protein (Gfp). Gfp expression in a P. putida strain carrying this system inserted into the chromosome was strongly dependent on the growth phase and growth rate of the strain, and cells growing exponentially at rates of ≥0.17 h−1 emitted growth rate-dependent green fluorescence detectable at the single-cell level. The single-cell ribosomal contents were very heterogeneous, as determined by quantitative hybridization with fluorescently labeled rRNA probes in P. putida cells extracted from the rhizosphere of 1-day-old barley seedlings grown under sterile conditions. After this, cells extracted from the root system had ribosomal contents similar to those found in starved cells. There was a significant decrease in the ribosomal content of P. putida cells when bacteria were introduced into nonsterile bulk or rhizosphere soil, and the Gfp monitoring system was not induced in cells extracted from either of the two soil systems. The monitoring system used permitted nondestructive in situ detection of fast-growing bacterial microcolonies on the sloughing root sheath cells of 1- and 2-day-old barley seedlings grown under sterile conditions, which demonstrated that it may be possible to use the unstable Gfp marker for studies of transient gene expression in plant-microbe systems. PMID:10653754

  2. 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

  3. 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

  4. 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(-).

  5. Draft Genome Sequence of Bacillus amyloliquefaciens Strain RHNK22, Isolated from Rhizosphere with Biosurfactant (Surfactin, Iturin, and Fengycin) and Antifungal Activity.

    PubMed

    Narendra Kumar, Papathoti; Swapna, T H; Sathi Reddy, Koppula; Archana, K; Nageshwar, Lingampalli; Nalini, S; Khan, Mohamed Yahya; Hameeda, Bee

    2016-01-01

    Bacillus amyloliquefaciens strain RHNK22 isolated from groundnut rhizosphere showed direct and indirect plant growth-promoting traits along with biosurfactant activity and reduction in surface tension of water. Biosurfactants were identified as lipopeptides (surfactin, iturin, and fengycin) by molecular and biochemical analysis in our studies. PMID:26823600

  6. Draft Genome Sequence of Bacillus amyloliquefaciens Strain RHNK22, Isolated from Rhizosphere with Biosurfactant (Surfactin, Iturin, and Fengycin) and Antifungal Activity

    PubMed Central

    Narendra Kumar, Papathoti; Swapna, T. H.; Sathi Reddy, Koppula; Archana, K.; Nageshwar, Lingampalli; Nalini, S.; Khan, Mohamed Yahya

    2016-01-01

    Bacillus amyloliquefaciens strain RHNK22 isolated from groundnut rhizosphere showed direct and indirect plant growth-promoting traits along with biosurfactant activity and reduction in surface tension of water. Biosurfactants were identified as lipopeptides (surfactin, iturin, and fengycin) by molecular and biochemical analysis in our studies. PMID:26823600

  7. 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.

  8. 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

  9. 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

  10. 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

  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. PMID:23448242

  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 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.

  14. 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

  15. 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

  16. Fungal invasion of the rhizosphere microbiome.

    PubMed

    Chapelle, Emilie; Mendes, Rodrigo; Bakker, Peter A H M; Raaijmakers, Jos M

    2016-01-01

    The rhizosphere is the infection court where soil-borne pathogens establish a parasitic relationship with the plant. To infect root tissue, pathogens have to compete with members of the rhizosphere microbiome for available nutrients and microsites. In disease-suppressive soils, pathogens are strongly restricted in growth by the activities of specific rhizosphere microorganisms. Here, we sequenced metagenomic DNA and RNA of the rhizosphere microbiome of sugar beet seedlings grown in a soil suppressive to the fungal pathogen Rhizoctonia solani. rRNA-based analyses showed that Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae and Sphingomonadaceae were significantly more abundant in the rhizosphere upon fungal invasion. Metatranscriptomics revealed that stress-related genes (ppGpp metabolism and oxidative stress) were upregulated in these bacterial families. We postulate that the invading pathogenic fungus induces, directly or via the plant, stress responses in the rhizobacterial community that lead to shifts in microbiome composition and to activation of antagonistic traits that restrict pathogen infection. PMID:26023875

  17. Identification of actinomycetes from plant rhizospheric soils with inhibitory activity against Colletotrichum spp., the causative agent of anthracnose disease

    PubMed Central

    2011-01-01

    Background Colletotrichum is one of the most widespread and important genus of plant pathogenic fungi worldwide. Various species of Colletotrichum are the causative agents of anthracnose disease in plants, which is a severe problem to agricultural crops particularly in Thailand. These phytopathogens are usually controlled using chemicals; however, the use of these agents can lead to environmental pollution. Potential non-chemical control strategies for anthracnose disease include the use of bacteria capable of producing anti-fungal compounds such as actinomycetes spp., that comprise a large group of filamentous, Gram positive bacteria from soil. The aim of this study was to isolate actinomycetes capable of inhibiting the growth of Colletotrichum spp, and to analyze the diversity of actinomycetes from plant rhizospheric soil. Results A total of 304 actinomycetes were isolated and tested for their inhibitory activity against Colletotrichum gloeosporioides strains DoA d0762 and DoA c1060 and Colletotrichum capsici strain DoA c1511 which cause anthracnose disease as well as the non-pathogenic Saccharomyces cerevisiae strain IFO 10217. Most isolates (222 out of 304, 73.0%) were active against at least one indicator fungus or yeast. Fifty four (17.8%) were active against three anthracnose fungi and 17 (5.6%) could inhibit the growth of all three fungi and S. cerevisiae used in the test. Detailed analysis on 30 selected isolates from an orchard at Chanthaburi using the comparison of 16S rRNA gene sequences revealed that most of the isolates (87%) belong to the genus Streptomyces sp., while one each belongs to Saccharopolyspora (strain SB-2) and Nocardiopsis (strain CM-2) and two to Nocardia (strains BP-3 and LK-1). Strains LC-1, LC-4, JF-1, SC-1 and MG-1 exerted high inhibitory activity against all three anthracnose fungi and yeast. In addition, the organic solvent extracts prepared from these five strains inhibited conidial growth of the three indicator fungi

  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. PMID:25541320

  19. The rhizosphere revisited: root microbiomics

    PubMed Central

    Bakker, Peter A. H. M.; Berendsen, Roeland L.; Doornbos, Rogier F.; Wintermans, Paul C. A.; Pieterse, Corné M. J.

    2013-01-01

    The rhizosphere was defined over 100 years ago as the zone around the root where microorganisms and processes important for plant growth and health are located. Recent studies show that the diversity of microorganisms associated with the root system is enormous. This rhizosphere microbiome extends the functional repertoire of the plant beyond imagination. The rhizosphere microbiome of Arabidopsis thaliana is currently being studied for the obvious reason that it allows the use of the extensive toolbox that comes with this model plant. Deciphering plant traits that drive selection and activities of the microbiome is now a major challenge in which Arabidopsis will undoubtedly be a major research object. Here we review recent microbiome studies and discuss future research directions and applicability of the generated knowledge. PMID:23755059

  20. Denitrification and the denitrifier community in coastal microbial mats.

    PubMed

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

    2015-03-01

    Denitrification was measured in three structurally different coastal microbial mats by using the stable isotope technique. The composition of the denitrifying community was determined by analyzing the nitrite reductase (nirS and nirK) genes using clone libraries and the GeoChip. The highest potential rate of denitrification (7.0 ± 1.0 mmol N m(-2) d(-1)) was observed during summer at station 1 (supra-littoral). The rates of denitrification were much lower in the stations 2 (marine) and 3 (intermediate) (respectively 0.1 ± 0.05 and 0.7 ± 0.2 mmol N m(-2) d(-1)) and showed less seasonality when compared to station 1. The denitrifying community at station 1 was also more diverse than that at station 2 and 3, which were more similar to each other than either of these stations to station 1. In all three stations, the diversity of both nirS and nirK denitrifiers was higher in summer when compared to winter. The location along the tidal gradient seems to determine the composition, diversity and activity of the denitrifier community, which may be driven by salinity, nitrate/nitrite and organic carbon. Both nirS and nirK denitrifiers are equally present and therefore they are likely to play a role in the denitrification of the microbial mats studied. PMID:25764561

  1. 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.

  2. 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). PMID:22195426

  3. [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

  4. 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

  5. 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

  6. 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

  7. Inhibition of alkylbenzene biodegradation under denitrifying conditions by using the acetylene block technique.

    PubMed Central

    Hutchins, S R

    1992-01-01

    Addition of acetylene to microcosms simultaneously amended with nitrate and alkylbenzenes resulted in inhibition of the rate of alkylbenzene biodegradation under denitrifying conditions. Toluene, xylenes, and 1,2,4-trimethylbenzene were recalcitrant, whereas ethylbenzene was degraded at a slower rate than usual. Benzene was not degraded in either case. Addition of acetylene to microcosms preexposed to nitrate and alkylbenzenes produced similar inhibition. These data indicate that the activities of microorganisms that degrade alkylbenzenes under denitrifying conditions may be suppressed if the standard acetylene block technique is used to verify denitrifying activity. PMID:1444371

  8. Enrichment of denitrifying anaerobic methane oxidizing microorganisms.

    PubMed

    Hu, Shihu; Zeng, Raymond J; Burow, Luke C; Lant, Paul; Keller, Jurg; Yuan, Zhiguo

    2009-10-01

    The microorganisms responsible for anaerobic oxidation of methane (AOM) coupled to denitrification have not been clearly elucidated. Three recent publications suggested it can be achieved by a denitrifying bacterium with or without the involvement of anaerobic methanotrophic archaea. A key factor limiting the progress in this research field is the shortage of enrichment cultures performing denitrifying anaerobic methane oxidation (DAMO). In this study, DAMO cultures were enriched from mixed inoculum including sediment from a freshwater lake, anaerobic digester sludge and return activated sludge from a sewage treatment plant. Two reactors, operated at 35°C and at 22°C, respectively, showed simultaneous methane oxidation and nitrate reduction after several months of operation. Analysis of 16S rRNA gene clone libraries from the 35°C enrichment showed the presence of an archaeon closely related to other DAMO archaea and a dominated bacterium belonging to the yet uncultivated NC10 phylum. This culture preferred nitrite to nitrate as the electron acceptor. The present study suggests that the archaea are rather methanotrophs than methanogens. The highest denitrification rate achieved was 2.35 mmol NO3 (-) -N gVSS(-1)  day(-1) . The culture enriched at 22°C contained the same NC10 bacterium observed in the culture enriched at 35°C but no archaea. PMID:23765890

  9. 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

  10. Enhanced performance of denitrifying sulfide removal process under micro-aerobic condition.

    PubMed

    Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

    2010-07-15

    The denitrifying sulfide removal (DSR) process with bio-granules comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide and acetate into di-nitrogen gas, elementary sulfur and carbon dioxide, respectively, at high loading rates. This study determines the reaction rate of sulfide oxidized into sulfur, as well as the reduction of nitrate to nitrite, would be enhanced under a micro-aerobic condition. The presence of limited oxygen mitigated the inhibition effects of sulfide on denitrifier activities, and enhanced the performance of DSR granules. The advantages and disadvantages of applying the micro-aerobic condition to the DSR process are discussed. PMID:20233637

  11. GacS-dependent regulation of enzymic and antifungal activities and synthesis of N-acylhomoserine lactones in rhizospheric strain Pseudomonas chlororaphis 449.

    PubMed

    Veselova, M; Lipasova, V; Protsenko, M A; Buza, N; Khmel, I A

    2009-09-01

    Pseudomonas chlororaphis strain 449 isolated from the rhizosphere of maize suppresses numerous plant pathogens in vitro. The strain produces phenazine antibiotics and synthesizes at least three types of quorum sensing signaling molecules, N-acylhomoserine lactones. Here we have shown that the rhizospheric P. chlororaphis strains 449, well known strain 30-84 as well as two other P. chlororaphis strains exhibit polygalacturonase activity. Using mini-Tn5 transposon mutagenesis, four independent mutants of strain P. chlororaphis 449 with insertion of mini-Tn5 Km2 in gene gacS of two-component GacA-GacS system of global regulation were selected. All these mutant strains were deficient in production of extracellular proteinase(s), phenazines, N-acylhomoserine lactones synthesis, and did not inhibit the growth of G(+) bacteria in comparison with the wild type strain. The P. chlororaphis 449-06 gacS (-) mutant studied in greater detail was deficient in polygalacturonase, pectin methylesterase activities, swarming motility and antifungal activity. It is the first time the involvement of GacA-GacS system in the regulation of enzymes of pectin metabolism, polygalacturonase and pectin methylesterase, was demonstrated in fluorescent pseudomonads. PMID:19937212

  12. 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.

  13. 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

  14. Antifungal activity of selected indigenous pseudomonas and bacillus from the soybean rhizosphere.

    PubMed

    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

  15. 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. PMID:24271005

  16. 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

  17. 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

  18. 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

    2014-01-01

    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. PMID:25062484

  19. 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

  20. 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

  1. 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.

  2. 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...

  3. 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

  4. [Research advances in denitrogenation characteristics of aerobic denitrifiers].

    PubMed

    Liang, Shu-Cheng; Zhao, Min; Lu, Lei; Zhao, Li-Yan

    2010-06-01

    The discovery of aerobic denitrifiers is the enrichment and breakthrough of traditional denitrification theory. Owing to their unique superiority in denitrogenation, aerobic denitrifiers have become a hotspot in the study of bio-denitrogenation of waste water. Under aerobic conditions, the aerobic denitrifiers can utilize organic carbon sources for their growth, and produce N2 from nitrate and nitrite. Most of the denitrifiers can also proceed with heterotrophic nitrification simultaneously, transforming NH4(+)-N to gaseous nitrogen. In this paper, the denitrogenation characteristics and action mechanisms of some isolated aerobic denitrifiers were discussed from the aspects of electron theory and denitrifying enzyme system. The effects of the environmental factors DO, carbon sources, and C/N on the denitrogenation process of aerobic denitrifiers were analyzed, and the screening methods as well as the present and potential applications of aerobic denitrifiers in wastewater treatment were described and discussed. PMID:20873638

  5. 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 ...

  6. Microbial expression profiles in the rhizosphere of willows depend on soil contamination

    PubMed Central

    Yergeau, Etienne; Sanschagrin, Sylvie; Maynard, Christine; St-Arnaud, Marc; Greer, Charles W

    2014-01-01

    The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation. PMID:24067257

  7. 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

  8. Accessible mixotrophic growth of denitrifying sulfide removal consortium.

    PubMed

    Juang, Ruey-Shin; Wong, Biing-Teo; Lee, Duu-Jong

    2015-06-01

    Nitrate, sulfide and organic matters in wastewaters can be removed simultaneously by denitrifying sulfide removal (DSR) process. Complicated interactions between different microbial groups in the DSR medium render the process design and control difficult to implement. A consortium with DSR activity was grown mixotrophically at varying concentrations of nitrate, acetate or ammonium. The kinetic diagram previously proposed was adopted to quantitatively represent DSR performance with accessible regimes of the diagram being identified. Example on the use of the so-yielded accessible regime was provided. PMID:25795451

  9. 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

  10. 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.

  11. Influence of copper on expression of nirS, norB and nosZ and the transcription and activity of NIR, NOR and N2 OR in the denitrifying soil bacteria Pseudomonas stutzeri.

    PubMed

    Black, Amanda; Hsu, Pei-Chun L; Hamonts, Kelly E; Clough, Tim J; Condron, Leo M

    2016-05-01

    Reduction of the potent greenhouse gas nitrous oxide (N2 O) occurs in soil environments by the action of denitrifying bacteria possessing nitrous oxide reductase (N2 OR), a dimeric copper (Cu)-dependent enzyme producing environmentally benign dinitrogen (N2 ). We examined the effects of increasing Cu concentrations on the transcription and activity of nitrite reductase (NIR), nitric oxide reductase (NOR) and N2 OR in Pseudomonas stutzeri grown anaerobically in solution over a 10-day period. Gas samples were taken on a daily basis and after 6 days, bacterial RNA was recovered to determine the expression of nirS, norB and nosZ encoding NIR, NOR and N2 OR respectively. Results revealed that 0.05 mM Cu caused maximum conversion of N2 O to N2 via bacterial reduction of N2 O. As soluble Cu generally makes up less than 0.001% of total soil Cu, extrapolation of 0.05 mg l(-l) soluble Cu would require soils to have a total concentration of Cu in the range of, 150-200 μg g(-1) to maximize the proportion of N2 O reduced to N2 . Given that many intensively farmed agricultural soils are deficient in Cu in terms of plant nutrition, providing a sufficient concentration of biologically accessible Cu could provide a potentially useful microbial-based strategy of reducing agricultural N2 O emissions. PMID:26935976

  12. 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. PMID:23749248

  13. 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

  14. 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. PMID:25851442

  15. 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

  16. 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

  17. 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.

  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. New Methods To Unravel Rhizosphere Processes.

    PubMed

    Oburger, Eva; Schmidt, Hannes

    2016-03-01

    Root-triggered processes (growth, uptake and release of solutes) vary in space and time, and interact with heterogeneous soil microenvironments that provide habitats for (micro)biota on various scales. Despite tremendous progress in method development in the past decades, finding a suitable experimental set-up to investigate processes occurring at the dynamic conjunction of biosphere, hydrosphere, and pedosphere in the close vicinity of active plant roots still represents a major challenge. We discuss recent methodological developments in rhizosphere research with a focus on imaging techniques. We further review established concepts that have been updated with novel techniques, highlighting the need for combinatorial approaches to disentangle rhizosphere processes on relevant scales. PMID:26776474

  20. Characterization of a phenazine-producing strain Pseudomonas chlororaphis GP72 with broad-spectrum antifungal activity from green pepper rhizosphere

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new Pseudomonas strain, designated GP72, was isolated from green pepper rhizosphere and identified as a member of species Pseudomonas chlororaphis based on morphology; conventional biochemical and physiologic tests; Biolog GN system (Biolog Inc., Hayward, CA); and 16S rDNA sequence analysis. The s...

  1. 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.

  2. 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

  3. Dechlorination of polychlorinated methanes by a sequential methanogenic-denitrifying bioreactor system.

    PubMed

    Yu, Z; Smith, G B

    2000-04-01

    A two-stage bioreactor has been developed to link dechlorination of halogenated methane compounds to the anaerobic processes of methanogenesis and denitrification. A digester methanogenic consortium was shown to dechlorinate chloroform (CF) and carbon tetrachloride (CT) to dichloromethane (DCM), and DCM was then mineralized by an acclimated denitrifying biological activated carbon consortium. Combining these two processes, a sequential methanogenic-denitrifying bioreactor (SMDB) system that completely degraded polychlorinated methanes including CT, CF, and DCM was developed. More than 95% of the added CT and CF was dechlorinated in the methanogenic bioreactor with methanol as the primary substrate, and the resultant DCM was biodegraded in the denitrifying bioreactor with nitrate as the electron acceptor. In the denitrifying bioreactor, the residual CF was completely removed, and the DCM removal efficiency was more than 95%. This novel bioreactor system eliminates the need for aeration and so avoids the air contamination associated with aerobic biotreatment of volatile chlorinated pollutants. This SMDB system provides an alternative to conventional biotreatment of wastewaters and other matrices contaminated with polychlorinated methanes and is, to our knowledge, the first report on such a sequential anoxic system. PMID:10803908

  4. [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

  5. The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rhizosphere is a hot spot of microbial interactions as exudates released by plant roots are a main food source for microorganisms and a driving force of their population density and activities. The rhizosphere harbors many organisms that have a neutral effect on the plant, but also attracts orga...

  6. 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

  7. 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

  8. 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

  9. 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

  10. A novel denitrifying bacterial isolate that degrades trimethylamine both aerobically and anaerobically via two different pathways.

    PubMed

    Kim, S G; Bae, H S; Lee, S T

    2001-10-01

    The aerobic and anaerobic degradation of trimethylamine by a newly isolated denitrifying bacterium from an enrichment culture with trimethylamine inoculated with activated sludge was studied. Based on 16S rDNA analysis, this strain was identified as a Paracoccus sp. The isolate, strain T231, aerobically degraded trimethylamine, dimethylamine and methylamine and released a stoichiometric amount of ammonium ion into the culture fluid as a metabolic product, indicating that these methylated amines were completely degraded to formaldehyde and ammonia. The strain degraded trimethylamine also under denitrifying conditions and consumed a stoichiometric amount of nitrate, demonstrating that complete degradation of trimethylamine was coupled with nitrate reduction. Cell-free extract prepared from cells grown aerobically on trimethylamine exhibited activities of trimethylamine mono-oxygenase, trimethylamine N-oxide demethylase, dimethylamine mono-oxygenase, and methylamine mono-oxygenase. Cell-free extract from cells grown anaerobically on trimethylamine and nitrate exhibited activities of trimethylamine dehydrogenase and dimethylamine dehydrogenase. These results indicate that strain T231 had two different pathways for aerobic and anaerobic degradation of trimethylamine. This is a new feature for trimethylamine metabolism in denitrifying bacteria. PMID:11685371

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

    PubMed

    Anderson, I C; Levine, J S

    1986-05-01

    Biogenic emissions of nitric and nitrous oxides have important impacts on the photochemistry and chemistry of the atmosphere. Although biogenic production appears to be the overwhelming source of N(2)O, the magnitude of the biogenic emission of NO is very uncertain. In soils, possible sources of NO and N(2)O include nitrification by autotrophic and heterotrophic nitrifiers, denitrification by nitrifiers and denitrifiers, nitrate respiration by fermenters, and chemodenitrification. The availability of oxygen determines to a large extent the relative activities of these various groups of organisms. To better understand this influence, we investigated the effect of the partial pressure of oxygen (pO(2)) on the production of NO and N(2)O by a wide variety of common soil nitrifying, denitrifying, and nitrate-respiring bacteria under laboratory conditions. The production of NO per cell was highest by autotrophic nitrifiers and was independent of pO(2) in the range tested (0.5 to 10%), whereas N(2)O production was inversely proportional to pO(2). Nitrous oxide production was highest in the denitrifier Pseudomonas fluorescens, but only under anaerobic conditions. The molar ratio of NO/N(2)O produced was usually greater than unity for nitrifiers and much less than unity for denitrifiers. Chemodenitrification was the major source of both the NO and N(2)O produced by the nitrate respirer Serratia marcescens. Chemodenitrification was also a possible source of NO and N(2)O in nitrifier cultures but only when high concentrations of nitrite had accumulated or were added to the medium. Although most of the denitrifiers produced NO and N(2)O only under anaerobic conditions, chemostat cultures of Alcaligenes faecalis continued to emit these gases even when the cultures were sparged with air. Based upon these results, we predict that aerobic soils are primary sources of NO and that N(2)O is produced only when there is sufficient soil moisture to provide the anaerobic microsites

  12. Microbial degradation of trichloroethylene in the rhizosphere: potential application to biological remediation of waste sites.

    PubMed Central

    Walton, B T; Anderson, T A

    1990-01-01

    The possibility that vegetation may be used to actively promote microbial restoration of chemically contaminated soils was tested by using rhizosphere and nonvegetated soils collected from a trichloroethylene (TCE)-contaminated field site. Biomass determinations, disappearance of TCE from the headspace of spiked soil slurries, and mineralization of [14C]TCE to 14CO2 all showed that microbial activity is greater in rhizosphere soils and that TCE degradation occurs faster in the rhizosphere than in the edaphosphere. Thus, vegetation may be an important variable in the biological restoration of surface and near-surface soils. PMID:2339867

  13. 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

  14. 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.

  15. Denitrifying sulfide removal process on high-salinity wastewaters.

    PubMed

    Liu, Chunshuang; Zhao, Chaocheng; Wang, Aijie; Guo, Yadong; Lee, Duu-Jong

    2015-08-01

    Denitrifying sulfide removal (DSR) process comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide, and acetate into nitrogen gas, elemental sulfur (S(0)), and carbon dioxide, respectively. Sulfide- and nitrate-laden wastewaters at 2-35 g/L NaCl were treated by DSR process. A C/N ratio of 3:1 was proposed to maintain high S(0) conversion rate. The granular sludge with a compact structure and smooth outer surface was formed. The microbial communities of DSR consortium via high-throughput sequencing method suggested that salinity shifts the predominating heterotrophic denitrifiers at <10 g/L NaCl to autotrophic denitrifiers at >10 g/L NaCl. PMID:25773977

  16. Soil nitrifying and denitrifying capacities are altered by global change factors in a California annual grassland

    NASA Astrophysics Data System (ADS)

    Niboyet, A.; Le Roux, X.; Barthes, L.; Hungate, B.; Dijkstra, P.; Blankinship, J. C.; Brown, J. R.; Field, C. B.; Leadley, P. W.

    2009-12-01

    Nitrification and denitrification are key mediators of nitrogen (N) cycling, especially N losses, in terrestrial ecosystems, yet little is known about the long-term, in situ responses of these two microbial processes to the simultaneous and interacting global changes likely to occur this century. We investigated the responses of the two steps of nitrification - ammonia oxidation and nitrite oxidation - and of denitrification to the interactive effects of elevated CO2, warming, increased precipitation and N deposition as part of the Jasper Ridge Global Change Experiment. We followed these responses over two growing seasons of the experiment using measures of potential rates of ammonia oxidation, nitrite oxidation, and denitrification, along with key correlates of these activities (gross N mineralization, gross nitrification, soil moisture, soil NH4+ and NO3- concentrations, soil pH, soil temperature, soil CO2 and N2O effluxes, and root and shoot biomass). Across all dates, soil ammonia and nitrite oxidizing capacities responded very differently to global change treatments: soil ammonia oxidizing capacities were increased by 59% in the high N deposition treatment (likely as a result of higher substrate availability for ammonia-oxidizers), while soil nitrite oxidizing capacities did not respond to the N deposition treatment but were reduced by 10% in the increased precipitation treatment. Soil denitrifying capacities were increased by 26% in the high N deposition treatment (likely as a result of higher substrate availability for denitrifiers) and by 15% in the increased precipitation treatment (likely as a result of higher soil water content). Overall, elevated CO2 and warming were found to have little effects on soil nitrifying and denitrifying capacities, and interactive effects between global change components were rare when analyzed across multiple sampling dates. Thus, our results suggest that increased atmospheric N deposition and changes in precipitation

  17. Insight into the short- and long-term effects of Cu(II) on denitrifying biogranules.

    PubMed

    Chen, Hui; Chen, Qian-Qian; Jiang, Xiao-Yan; Hu, Hai-Yan; Shi, Man-Ling; Jin, Ren-Cun

    2016-03-01

    This study aimed to investigate the short- and long-term effects of Cu(2+) on the activity and performance of denitrifying bacteria. The short-term effects of various concentrations of Cu(2+) on the denitrifying bacteria were evaluated using batch assays. The specific denitrifying activity (SDA) decreased from 14.3 ± 2.2 (without Cu(2+)) to 6.1 ± 0.1 mg N h(-1)g(-1) VSS (100 mg Cu(2+)L(-1)) when Cu(2+) increased from 0 to 100 mg L(-1) with an increment of 10 mg Cu(2+)L(-1). A non-competitive inhibition model was used to calculate the 50% inhibition concentration (IC50) of Cu(2+) on denitrifying sludge (30.6 ± 2.5 mg L(-1)). Monod and Luong models were applied to investigate the influence of the initial substrate concentration, and the results suggested that the maximum substrate removal rate would be reduced with Cu(2+) supplementation. Pre-exposure to Cu(2+) could lead to an 18.2-46.2% decrease in the SDA and decreasing percentage of the SDA increased with both exposure time and concentration. In the continuous-flow test, Cu(2+) concentration varied from 1 to 75 mg L(-1); however, no clear deterioration was observed in the reactor, and the reactor was kept stable, with the total nitrogen removal efficiency and total organic carbon efficiency greater than 89.0 and 85.0%, respectively. The results demonstrated the short-term inhibition of Cu(2+) upon denitrification, and no notable adversity was observed during the continuous-flow test after long-term acclimation. PMID:26610098

  18. 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.

  19. Algal exudates and stream organic matter influence the structure and function of denitrifying bacterial communities.

    PubMed

    Kalscheur, Kathryn N; Rojas, Miguel; Peterson, Christopher G; Kelly, John J; Gray, Kimberly A

    2012-11-01

    Within aquatic ecosystems, periphytic biofilms can be hot spots of denitrification, and previous work has suggested that algal taxa within periphyton can influence the species composition and activity of resident denitrifying bacteria. This study tested the hypothesis that algal species composition within biofilms influences the structure and function of associated denitrifying bacterial communities through the composition of organic exudates. A mixed population of bacteria was incubated with organic carbon isolated from one of seven algal species or from one of two streams that differed in anthropogenic inputs. Pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) revealed differences in the organic composition of algal exudates and stream waters, which, in turn, selected for distinct bacterial communities. Organic carbon source had a significant effect on potential denitrification rates (DNP) of the communities, with organics isolated from a stream with high anthropogenic inputs resulting in a bacterial community with the highest DNP. There was no correlation between DNP and numbers of denitrifiers (based on nirS copy numbers), but there was a strong relationship between the species composition of denitrifier communities (as indicated by tag pyrosequencing of nosZ genes) and DNP. Specifically, the relative abundance of Pseudomonas stutzeri-like nosZ sequences across treatments correlated significantly with DNP, and bacterial communities incubated with organic carbon from the stream with high anthropogenic inputs had the highest relative abundance of P. stutzeri-like nosZ sequences. These results demonstrate a significant relationship between bacterial community composition and function and provide evidence of the potential impacts of anthropogenic inputs on the structure and function of stream microbial communities. PMID:22828897

  20. Evidence for degradation of 2-chlorophenol by enrichment cultures under denitrifying conditions.

    PubMed

    Bae, Hee-Sung; Yamagishi, Takao; Suwa, Yuichi

    2002-01-01

    Although chlorophenol (CP) degradation has been studied, no bacterium responsible for degradation of CP under denitrifying conditions has been isolated. Moreover, little substantial evidence for anaerobic degradation of CPs coupled with denitrification is available even for mixed cultures. Degradation of CP [2-CP, 3-CP, 4-CP, 2,4-dichlorophenol (DCP) or 2,6-DCP] under denitrifying conditions was examined in anaerobic batch culture inoculated with activated sludge. Although 3-CP, 4-CP, 2,4-DCP and 2,6-DCP were not stably degraded, 2-CP was degraded and its degradation capability was sustained in a subculture. However, the rate of 2-CP degradation was not significantly enhanced by subculturing. In 2-CP-degrading cultures, nitrate was consumed stoichiometrically and concomitantly during 2-CP degradation, and a dechlorination intermediate was not detected, suggesting that 2-CP degradation was coupled with nitrate reduction. A 2-CP-degrading enrichment culture degraded 2-CP in the presence of nitrate, but did not in the absence of nitrate or the presence of sulfate. This suggests that the enrichment culture strictly requires nitrate for degradation of 2-CP. The apparent specific growth rate of the 2-CP degrading species was 0.0139 d(-1). Thus the apparent doubling time of the 2-CP-degrading population in the enrichment culture was greater than 50 d, which may explain difficulty in enrichment and isolation of micro-organisms responsible for CP degradation under denitrifying conditions. PMID:11782514

  1. 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

  2. Influence of temperature and soil water content on bacterial, archaeal and denitrifying microbial communities in drained fen grassland soil microcosms.

    PubMed

    Stres, Blaz; Danevcic, Tjasa; Pal, Levin; Fuka, Mirna Mrkonjić; Resman, Lara; Leskovec, Simona; Hacin, Janez; Stopar, David; Mahne, Ivan; Mandic-Mulec, Ines

    2008-10-01

    In this study, microcosms were used to investigate the influence of temperature (4 and 28 degrees C) and water content (45% and 90% WHC) on microbial communities and activities in carbon-rich fen soil. Bacterial, archaeal and denitrifier community composition was assessed during incubation of microcosms for 12 weeks using terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA and nitrous oxide reductase (nosZ) genes. In addition, microbial and denitrifier abundance, potential denitrification activity and production of greenhouse gases were measured. No detectable changes were observed in prokaryote or denitrifier abundance. In general, cumulatively after 12 weeks more carbon was respired at the higher temperature (3.7 mg CO(2) g(-1) soil), irrespective of the water content, whereas nitrous oxide production was greater under wet conditions (98-336 microg N(2)O g(-1) soil). After an initial lag phase, methane emissions (963 microg CH(4) g(-1) soil) were observed only under warm and wet conditions. T-RFLP analyses of bacterial 16S rRNA and nosZ genes revealed small or undetectable community changes in response to temperature and water content, suggesting that bacterial and denitrifying microbial communities are stable and do not respond significantly to seasonal changes in soil conditions. In contrast, archaeal microbial community structure was more dynamic and was strongly influenced by temperature. PMID:18710395

  3. Bio-active composts from rice straw enriched with rock phosphate and their effect on the phosphorous nutrition and microbial community in rhizosphere of cowpea.

    PubMed

    Zayed, Gaber; Abdel-Motaal, Heba

    2005-05-01

    Composts were produced from rice straw enriched with rock phosphate and inoculated with Aspergillus niger, Trichoderma viride and/or farmyard manure (FYM). The resulting composts were evaluated as organic phosphate fertilizers for cowpea plants in pot experiments. The results showed that the maximum amount of soluble phosphorous (1000 ppm) was produced in composts inoculated with A. niger+T. viride with or without FYM. Any of the produced composts was much better than superphosphate fertilizer in providing the growing cowpea plants with phosphorous. Fertilization of the cowpea plants with the compost inoculated with FYM+A. niger+T. viride resulted in maximum amount of phosphorous uptake (295 ppm). The highest phosphate dissolving fungi numbers in rhizosphere soils of cowpea plants were obtained after fertilization with composts which received A. niger and T. viride treatments, while the highest phosphate dissolving bacterial numbers were found after fertilization with composts which received FYM treatments. PMID:15627564

  4. 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. PMID:26085172

  5. Genetic characterization of denitrifier communities with contrasting intrinsic functional traits.

    PubMed

    Braker, Gesche; Dörsch, Peter; Bakken, Lars R

    2012-02-01

    Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes (DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N(2) O/N(2) ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes (nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N(2) O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N(2) O/N(2) ) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N(2) O/N(2) ). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N(2) O emission of the soils. PMID:22092293

  6. 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.

  7. Biological changes in the rhizosphere of wheat after foliar application of chlorocholinechloride, urea and 4-chloro-2-methylphenoxyacetic acid.

    PubMed

    Vraný, J

    1975-01-01

    In field experiments wheat in the phase of shooting was sprayed with solutions of chlorocholinechloride (CCC) and urea, CCC and ammonium salt MCPA (Aminex) or CCC, urea and Aminex. The effect of the treatment on dry weight of overground parts of wheat, number of bacteria, production of carbon dioxide, urease activity and content of ammonium in the rhizosphere soil was investigated. In all cases evolution of carbon dioxide in the rhizosphere soil was higher than that in the control soil. Highest numbers of bacteria were found in the rhizosphere soil of plants treated with urea, the herbicide and their mixtures. Content of ammonium was higher in the control soil than in the rhizosphere soils, the urease activity was highest in the rhizosphere soil of plants treated with the solution of the herbicide and with the combination of the herbicide with urea. PMID:1193493

  8. Anaerobic oxidation of cholesterol by a denitrifying enrichment.

    PubMed

    Barrandeguy, E; Tarlera, S

    2001-01-01

    Sterols (e.g. cholesterol) present in wool scouring effluent represent the most recalcitrant fraction in anaerobic treatment. This study was conducted to examine the feasibility of removal of this organic load through a denitrifying post-treatment stage. A stable cholesterol-denitrifying enrichment (CHOL-1) was obtained from sludge of a bench-scale upflow sludge bed (USB) denitrifying reactor integrated to a carbon and nitrogen removal system for sanitary landfill leachate. According to the amounts of cholesterol degraded and of nitrite and nitrogen gas formed, the capacity for complete cholesterol oxidation under anaerobic conditions by CHOL-1 can be assumed. Nitrite accumulation observed at a low C/N ratio outlines the importance of determining the optimal C/N ratio for adequate denitrifying reactor performance. The enrichment was partly identified with molecular analysis of cloned 16S rDNA sequences revealing the presence of two groups of bacteria belonging to the beta subclass of the Proteobacteria. According to analysis of sequences, it can be inferred that a yet uncultivated new bacterium is the one responsible for cholesterol oxidation. Results of this study suggest that sludge from a denitrifying reactor treating leachate is potentially useful in a combined anaerobic-anoxic system for degradation of cholesterol that remains after methanogenic treatment. PMID:11575077

  9. Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

    PubMed Central

    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

  10. Impact of Plant Species and Site on Rhizosphere-Associated Fungi Antagonistic to Verticillium dahliae Kleb.

    PubMed Central

    Berg, Gabriele; Zachow, Christin; Lottmann, Jana; Götz, Monika; Costa, Rodrigo; Smalla, Kornelia

    2005-01-01

    Fungi with antagonistic activity toward plant pathogens play an essential role in plant growth and health. To analyze the effects of the plant species and the site on the abundance and composition of fungi with antagonistic activity toward Verticillium dahliae, fungi were isolated from oilseed rape and strawberry rhizosphere and bulk soil from three different locations in Germany over two growing seasons. A total of 4,320 microfungi screened for in vitro antagonism toward Verticillium resulted in 911 active isolates. This high proportion of fungi antagonistic toward the pathogen V. dahliae was found for bulk and rhizosphere soil at all sites. A plant- and site-dependent specificity of the composition of antagonistic morphotypes and their genotypic diversity was found. The strawberry rhizosphere was characterized by preferential occurrence of Penicillium and Paecilomyces isolates and low numbers of morphotypes (n = 31) and species (n = 13), while Monographella isolates were most frequently obtained from the rhizosphere of oilseed rape, for which higher numbers of morphotypes (n = 41) and species (n = 17) were found. Trichoderma strains displayed high diversity in all soils, but a high degree of plant specificity was shown by BOX-PCR fingerprints. The diversity of rhizosphere-associated antagonists was lower than that of antagonists in bulk soil, suggesting that some fungi were specifically enriched in each rhizosphere. A broad spectrum of new Verticillium antagonists was identified, and the implications of the data for biocontrol applications are discussed. PMID:16085804

  11. Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae kleb.

    PubMed

    Berg, Gabriele; Zachow, Christin; Lottmann, Jana; Götz, Monika; Costa, Rodrigo; Smalla, Kornelia

    2005-08-01

    Fungi with antagonistic activity toward plant pathogens play an essential role in plant growth and health. To analyze the effects of the plant species and the site on the abundance and composition of fungi with antagonistic activity toward Verticillium dahliae, fungi were isolated from oilseed rape and strawberry rhizosphere and bulk soil from three different locations in Germany over two growing seasons. A total of 4,320 microfungi screened for in vitro antagonism toward Verticillium resulted in 911 active isolates. This high proportion of fungi antagonistic toward the pathogen V. dahliae was found for bulk and rhizosphere soil at all sites. A plant- and site-dependent specificity of the composition of antagonistic morphotypes and their genotypic diversity was found. The strawberry rhizosphere was characterized by preferential occurrence of Penicillium and Paecilomyces isolates and low numbers of morphotypes (n = 31) and species (n = 13), while Monographella isolates were most frequently obtained from the rhizosphere of oilseed rape, for which higher numbers of morphotypes (n = 41) and species (n = 17) were found. Trichoderma strains displayed high diversity in all soils, but a high degree of plant specificity was shown by BOX-PCR fingerprints. The diversity of rhizosphere-associated antagonists was lower than that of antagonists in bulk soil, suggesting that some fungi were specifically enriched in each rhizosphere. A broad spectrum of new Verticillium antagonists was identified, and the implications of the data for biocontrol applications are discussed. PMID:16085804

  12. 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

  13. Nitrogen Fixation in Denitrified Marine Waters

    PubMed Central

    Fernandez, Camila; Farías, Laura; Ulloa, Osvaldo

    2011-01-01

    Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m−2 d−1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m−2 d−1) than the oxic euphotic layer (48±68 µmol m−2 d−1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions. PMID:21687726

  14. 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. PMID:25273518

  15. Comparison of rhizosphere bacterial communities in Arabidopsis thaliana mutants for systemic acquired resistance.

    PubMed

    Hein, John W; Wolfe, Gordon V; Blee, Kristopher A

    2008-02-01

    Systemic acquired resistance (SAR) is an inducible systemic plant defense against a broad spectrum of plant pathogens, with the potential to secrete antimicrobial compounds into the soil. However, its impact on rhizosphere bacteria is not known. In this study, we examined fingerprints of bacterial communities in the rhizosphere of the model plant Arabidopsis thaliana to determine the effect of SAR on bacterial community structure and diversity. We compared Arabidopsis mutants that are constitutive and non-inducible for SAR and verified SAR activation by measuring pathogenesis-related protein activity via a beta-glucoronidase (GUS) reporter construct driven by the beta-1-3 glucanase promoter. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of MspI- and HaeIII-digested 16S rDNA to estimate bacterial rhizosphere community diversity, with Lactobacillus sp. added as internal controls. T-RFLP analysis showed a clear rhizosphere effect on community structure, and diversity analysis of both rhizosphere and bulk soil operational taxonomic units (as defined by terminal restriction fragments) using richness, Shannon-Weiner, and Simpson's diversity indices and evenness confirmed that the presence of Arabidopsis roots significantly altered bacterial communities. This effect of altered soil microbial community structure by plants was also seen upon multivariate cluster analysis of the terminal restriction fragments. We also found visible differences in the rhizosphere community fingerprints of different Arabidopsis SAR mutants; however, there was no clear decrease of rhizosphere diversity because of constitutive SAR expression. Our study suggests that SAR can alter rhizosphere bacterial communities, opening the door to further understanding and application of inducible plant defense as a driving force in structuring soil bacterial assemblages. PMID:17619212

  16. Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments

    NASA Astrophysics Data System (ADS)

    Huang, S.; Chen, C.; Wu, Q.; Zhang, R.; Yang, X.

    2011-05-01

    Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0-25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5-15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78-94 %) between the nirS sequences recovered from Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic N (DIN: NH4+, NO2denitrifying genes and the nirS-encoding denitrifier community in the river sediment. Our results also reveal a variety of novel denitrifying bacteria in the river sediment.

  17. 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.

  18. 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

  19. 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

  20. Organic acids, sugars, and L-tryptophane in exudates of vegetables growing on stonewool and their effects on activities of rhizosphere bacteria.

    PubMed

    Kamilova, Faina; Kravchenko, Lev V; Shaposhnikov, Alexander I; Azarova, Tatiyana; Makarova, Nataliya; Lugtenberg, Ben

    2006-03-01

    The influence of stonewool substrate on the exudation of the major soluble carbon nutrients and of the auxin precursor tryptophane for Pseudomonas biocontrol agents was studied. To this end, the composition of the organic acids and sugars, as well that of tryptophane, of axenically collected exudates of seed, seedlings, and roots of tomato, cucumber, and sweet pepper was determined. The major results were as follows. i) The total amount of organic acid is much higher than that of total sugar. ii) Exudation of both organic acids and sugars increases during plant growth. iii) Citric, succinic, and malic acids represent the major organic acids, whereas fructose and glucose are the major sugars. iv) Compared with glass beads as a neutral substrate, stonewool substantially stimulates exudation of organic acids and sugars. v) It appeared that enhanced root-tip-colonizing bacteria isolated previously from the rhizosphere of tomato and cucumber grow much better in minimal medium with citrate as the sole carbon source than other, randomly selected rhizobacteria do. This indicates that the procedure which selects for excellent root-tip colonizers enriches for strains which utilize the major exudate carbon source citrate. vi) The content of L-tryptophane, the direct precursor of auxin, is approximately 60-fold higher in seedling exudates of tomato and sweet pepper than in cucumber seedling exudates, indicating a higher possibility of plant growth stimulation after inoculation with auxin-producing rhizobacteria for tomato and sweet pepper crops than for cucumber. However, the biocontrol strain Pseudomonas fluorescens WCS365, which is able to convert tryptophane into auxin, did not stimulate growth of these three crops. In contrast, this strain did stimulate growth of roots of radish, a plant which exudes nine times more tryptophane than tomato does. PMID:16570655

  1. 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

  2. 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.

  3. 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. PMID:23847815

  4. 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...

  5. 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 ...

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. Purple phototrophic bacterium enhances stevioside yield by Stevia rebaudiana Bertoni via foliar spray and rhizosphere irrigation.

    PubMed

    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

  12. 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

  13. Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea.

    PubMed

    Haldar, Shyamalina; Choudhury, Susanta Roy; Sengupta, Sanghamitra

    2011-06-01

    Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system. PMID:21380504

  14. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

    PubMed Central

    Hu, Ziye; Meng, Han; Shi, Jin-Huan; Bu, Nai-Shun; Fang, Chang-Ming; Quan, Zhe-Xue

    2014-01-01

    Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition. PMID:25101072

  15. 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.

  16. 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

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

    PubMed

    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

  18. A possible role of NADPH-dependent cytochrome P450nor isozyme in glycolysis under denitrifying conditions.

    PubMed

    Watsuji, Tomo-o; Takaya, Naoki; Nakamura, Akira; Shoun, Hirofumi

    2003-05-01

    The denitrifying fungus Cylindrocarpon tonkinense contains two isozymes of cytochrome P450nor. One isozyme, P450nor1, uses NADH specifically as its electron donor whereas the other isozyme P450nor2 prefers NADPH to NADH. Here we show that P450nor1 is localized in both cytosol and mitochondria, like P450nor of Fusarium oxysporum, while P450nor2 is exclusively in cytosol. We also found that the addition of glucose as a carbon source to the culture media leads to the production of much more P450nor2 in the fungal cells than a non-fermentable substrate (glycerol or acetate) does. These results suggest that the NADP-dependent pentose phosphate cycle acts predominantly in C. tonkinense as the glycolysis pathway under the denitrifying conditions, which was confirmed by the observation that glucose induced enzyme activities involved in the cycle. These results showed that P450nor2 should act as the electron sink under anaerobic, denitrifying conditions to regenerate NADP+ for the pentose phosphate cycle. PMID:12834289

  19. 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.

  20. 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

  1. Denitrification characteristics of a marine origin psychrophilic aerobic denitrifying bacterium.

    PubMed

    Zheng, Haiyan; Liu, Ying; Sun, Guangdong; Gao, Xiyan; Zhang, Qingling; Liu, Zhipei

    2011-01-01

    A psychrophilic aerobic denitrifying bacterium, strain S1-1, was isolated from a biological aerated filter conducted for treatment of recirculating water in a marine aquaculture system. Strain S1-1 was preliminarily identified as Psychrobacter sp. based on the analysis of its 16S rRNA gene sequence, which showed 100% sequence similarity to that of Psychrobacter sp. TSBY-70. Strain S1-1 grew well either in high nitrate or high nitrite conditions with a removal of 100% nitrate or 63.50% nitrite, and the total nitrogen removal rates could reach to 46.48% and 31.89%, respectively. The results indicated that nitrate was mainly reduced in its logarithmic growth phase with a very low level accumulation of nitrite, suggesting that the aerobic denitrification process of strain S1-1 occurred mainly in this phase. The GC-MS results showed that N2O was formed as the major intermediate during the aerobic denitrifying process of strain S1-1. Finally, factors affecting the growth of strain S1-1 and its aerobic denitrifying ability were also investigated. Results showed that the optimum aerobic denitrification conditions for strain S1-1 were sodium succinate as carbon source, C/N ratio15, salinity 10 g/L NaCl, incubation temperature 20 degrees C and initial pH 6.5. PMID:22432315

  2. Diversity of Denitrifying Bacteria in the San Francisco Bay

    NASA Astrophysics Data System (ADS)

    Atluri, A.; Lee, J.; Francis, C. A.

    2012-12-01

    We compared the diversity of communities of denitrifying bacteria from the San Francisco Bay to investigate whether environmental factors affect diversity. To do this, we studied the sequence diversity of the marker gene nirK. nirK codes for the enzyme nitrite reductase which helps reduce nitrite to nitric oxide, an important step in denitrification. Sediment samples were collected spatially from five different locations and temporally during the four different seasons along a salinity gradient in the bay. After collecting samples and extracting DNA from them, we used PCR to amplify our gene of interest, created clone libraries for sequencing, and compared phylogenetic trees from the different communities. Based on several phylogenetic analyses on our tree and environments, we saw that denitrifying bacteria from the North and Central Bay form distinct spatial clusters; Central Bay communities are very similar to each other, while communities from the North Bay are more distinct from each other and from communities in the Central Bay. Bacteria from site 8.1M (Carquinez Strait) showed the most cm-scale spatial diversity, and there was the most species richness during the winter. All this suggests that diversity of communities of denitrifying bacteria may be affected by spatial and temporal environmental factors.

  3. 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

  4. 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

  5. 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

  6. 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. PMID:27177464

  7. 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

  8. [Denitrifying and phosphorus accumulating mechanisms of denitrifying phosphorus accumulating organisms (DPAOs) for wastewater treatment--a review].

    PubMed

    Yu, Hongting; Li, Min

    2015-03-01

    Eutrophication has raised increasing concerns due to its adverse effects on creatures. It is widely accepted that microbes are capable of removing nitrogen (N) and phosphate (P) via denitrification and P accumulation. So far, several strains can do this work. Therefore, more studies are focused on looking for micro-organisms that have both denitrification and P accumulation ability. Whether exposed to aerobic or anaerobic environment, microbial N and P removal mechanisms differ. Proton Motive Force and Electron Acceptor Theory are involved in the chemical process, whereas denitrifying enzymes polyphosphate kinases are regarded as the leading participators in the enzymatic systems. Studies have shown the influences of N on P accumulation, but further investigation should identify the influences of P on N removal. Here we reviewed the aspects of N and P removal mechanisms in denitrifying phosphorus accumulating organisms (DPAOs) and their potential to remove N and P from water system. Moreover, future works on clarifying denitrifying phosphorus accumulating mechanisms in depth and improving efficiency of removing N and P by DPAOs are provided. PMID:26065268

  9. The seasonal dynamics of yeast communities in the rhizosphere of soddy-podzolic soils

    NASA Astrophysics Data System (ADS)

    Golubtsova, Yu. V.; Glushakova, A. M.; Chernov, I. Yu.

    2007-08-01

    The annual dynamics of the number and taxonomic composition of yeast was studied in the rhizosphere of two plant species (Ajuga reptans L. and Taraxacum officinale Wigg.) in a forb-birch forest on soddy-podzolic soil. Eurybiont phyllobasidial cryptococci and red-pigmented phytobionts Rhodotorula glutinis were found to predominate in the phyllosphere of these plants, whereas the typical pedobionts Cryptococcus terricola and Cr. podzolicus occurred on the surface of roots and in the rhizosphere. The seasonal changes in the number and species composition of the yeast communities in the rhizosphere were more smooth as compared to those in the phyllosphere. In the period of active vegetation of the plants, the phytobiont yeasts develop over their whole surface, including the rhizoplane. Their number on the aboveground parts of the plants was significantly lower than that of the pedobiont forms. Thus, the above-and underground parts of the plants significantly differed in the composition of the dominant species of epiphytic yeasts.

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

    PubMed

    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

  11. 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

  12. 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

  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. Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments

    NASA Astrophysics Data System (ADS)

    Huang, S.; Chen, C.; Yang, X.; Wu, Q.; Zhang, R.

    2011-10-01

    Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0-25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5-15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78-94 %) between the nirS sequences recovered from the Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that the nitrogen source in the Pearl River sediment was affected by domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic nitrogen (including NH4+, NO2- and NO3-) concentrations in sediment. It was concluded that the difference in dissolved inorganic nitrogen concentrations along the sediment profile influenced the distribution of denitrifying genes and the nirS-encoding denitrifier community in the river sediment. In addition, a variety of novel denitrifying bacteria were revealed in the river sediment.

  15. Characterization of a marine origin aerobic nitrifying-denitrifying bacterium.

    PubMed

    Zheng, Hai-Yan; Liu, Ying; Gao, Xi-Yan; Ai, Guo-Min; Miao, Li-Li; Liu, Zhi-Pei

    2012-07-01

    The bacterial strain F6 was isolated from a biological aerated filter that is used for purifying recirculating water in a marine aquaculture system and was identified as Marinobacter sp. based on the analysis of its 16S rRNA gene sequence. Strain F6 showed efficient aerobic denitrifying ability. One hundred percent of nitrates and 73.10% of nitrites were removed, and the total nitrogen (TN) removal rates reached 50.08% and 33.03% under a high nitrate and nitrite concentration in the medium, respectively. N(2)O and (15)N(2), as revealed by GC-MS and GC-IRMS, were the products of aerobic denitrification. Factors affecting the growth and aerobic denitrifying performance of strain F6 were investigated. The results showed that the optimum aerobic denitrification conditions for strain F6 were the presence of sodium succinate as a carbon source, a C/N ratio of 15, salinity ranging from 32-35 g/L of NaCl, incubation temperature of 30°C, an initial pH of 7.5, and rotation speed of 150 rpm [dissolved oxygen (DO) 6.75 mg/L]. In addition, strain F6 was confirmed to be a heterotrophic nitrifier through its NO(2)(-) generation and 25.96% TN removal when NH(4)(+) was used as the sole N source. Therefore, strain F6, the first reported member of genus Marinobacter with aerobic heterotrophic nitrifying-denitrifying ability, is an excellent candidate for facilitating simultaneous nitrification and denitrification (SND) in industry and aquaculture wastewater. PMID:22578593

  16. Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes

    PubMed Central

    Saarenheimo, Jatta; Tiirola, Marja Annika; Rissanen, Antti J.

    2015-01-01

    Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of nirS, nirK, and nosZ genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations (nirS and nosZ genes) correlated with coupled nitrification-denitrification (Dn), and the denitrification of the overlying water NO3- (Dw) correlated with the nirS/nirK ratio. The number of core nirS, nirK, and nosZ operational taxonomical units (OTUs) was low (6, 7, and 3, respectively), and most of these core OTUs were shared among the lakes. Dominant nirK sequences matched best with those of the order Rhizobiales, which was one of the main bacterial orders present in the sediment microbiomes, whereas the dominant nirS sequences were affiliated with the order Burkholderiales. Over half of the nosZ sequences belonged to a single OTU of the order Burkholderiales, but coupled nitrification–denitrification rate correlated with another dominant nosZ OTU assigned to the order Rhodospirillales. The study indicates that a few core proteobacterial clusters may drive denitrification in boreal lake sediments, as the same Alpha- and Betaproteobacteria denitrifier clusters were present in different lakes and seasons. PMID:26191058

  17. 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

  18. 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…

  19. 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.

  20. 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.

  1. [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

  2. Community dynamics of denitrifying bacteria in full-scale wastewater treatment plants.

    PubMed

    Zielińska, Magdalena; Rusanowska, Paulina; Jarząbek, Joanna; Nielsen, Jeppe Lund

    2016-09-01

    Effective and stable nitrogen removal from wastewater requires abundant and active denitrifying populations. In this study, a one-year investigation of the population dynamics of phylogenetic groups known to harbor nitrate reducers was conducted in three municipal wastewater treatment plants (WWTPs). The bacterial community composition was determined by amplicon sequencing of the 16S rRNA gene, and putative nitrate reducers were identified by sequencing narG and napA genes. Fluorescence in situ hybridization with oligonucleotide probes targeting known nitrate reducers in wastewater revealed that certain bacteria predominated in the WWTPs: Curvibacter-related bacteria, Comamonadaceae, Azoarcus, Thauera, Dechloromonas, and Candidatus Accumulibacter within Rhodocyclaceae. The data showed high diversity in the nitrate-reducing community and a large degree of redundancy, with a relatively stable core group of bacteria in each plant that ensured small yearly variation in nitrate reduction rates. PMID:26932371

  3. 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

  4. 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. PMID:25348688

  5. Denitrifying Bioreactors for Nitrate Removal: A Meta-Analysis.

    PubMed

    Addy, Kelly; Gold, Arthur J; Christianson, Laura E; David, Mark B; Schipper, Louis A; Ratigan, Nicole A

    2016-05-01

    Meta-analysis approaches were used in this first quantitative synthesis of denitrifying woodchip bioreactors. Nitrate removal across environmental and design conditions was assessed from 26 published studies, representing 57 separate bioreactor units (i.e., walls, beds, and laboratory columns). Effect size calculations weighted the data based on variance and number of measurements for each bioreactor unit. Nitrate removal rates in bed and column studies were not significantly different, but both were significantly higher than wall studies. In denitrifying beds, wood source did not significantly affect nitrate removal rates. Nitrate removal (mass per volume) was significantly lower in beds with <6-h hydraulic retention times, which argues for ensuring that bed designs incorporate sufficient time for nitrate removal. Rates significantly declined after the first year of bed operation but then stabilized. Nitrogen limitation significantly affected bed nitrate removal. Categorical and linear assessments found significant nitrate removal effects with bed temperature; a of 2.15 was quite similar to other studies. Lessons from this meta-analysis can be incorporated into bed designs, especially extending hydraulic retention times to increase nitrate removal under low temperature and high flow conditions. Additional column studies are warranted for comparative assessments, as are field-based studies for assessing in situ conditions, especially in aging beds, with careful collection and reporting of design and environmental data. Future assessment of these systems might take a holistic view, reviewing nitrate removal in conjunction with other processes, including greenhouse gas and other unfavorable by-product production. PMID:27136153

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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. PMID:23717427

  11. 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

  12. Rhizosphere priming effects on soil N availability in forests exposed to elevated atmospheric CO2

    NASA Astrophysics Data System (ADS)

    Phillips, R. P.; Bernhardt, E. S.

    2008-12-01

    The progressive nitrogen (N) limitation hypothesis suggests that the uptake of N due to rapid tree growth under elevated CO2 depletes pools of available N resulting in short-term increases in productivity under elevated CO2. To date however, a down-regulation of forest productivity under elevated CO2 has not been observed among the four forest FACE experiments suggesting that our understanding of the mechanisms by which trees influence soil N cycling needs further refinement. We sought to test the hypothesis that trees exposed to elevated CO2 increase soil N availability by 'priming' rhizosphere microbes via the release of root exudates. At the Duke Forest FACTS-1 site, NC, we collected exudates bi-monthly from intact fine roots of 25 year-old loblolly pine Pinus taeda trees exposed to elevated CO2 and N fertilization. In addition, we collected rhizosphere and bulk soil from the same plots in order to develop a time-integrated estimate of the plant- microbial response to the CO2 and N treatments. In general, there were strong interactive effects between CO2 and N fertilization on exudation and rhizosphere microbial activity. In non-fertilized plots, mass-specific exudation rates were 15% greater with CO2 enrichment. In fertilized soils the opposite patterns were detected, as CO2 decreased mass specific rates by 40% (relative to the ambient rates). In the soil, treatment effects on rhizosphere microbial activity were similar: elevated CO2 increased microbial activity in non-fertilized plots (29%) but decreased it in fertilized plots (15%). However, we found no differences in net N mineralization rates in the rhizosphere in response to either CO2 or N fertilization. Collectively, these results suggest that although changes in exudation and microbial activity are likely mediated by soil N availability, the degree to which such processes are responsible for increased soil N cycling in forests exposed to elevated CO2 remains unclear.

  13. Using sludge fermentation liquid to improve wastewater short-cut nitrification-denitrification and denitrifying phosphorus removal via nitrite.

    PubMed

    Ji, Zhouying; Chen, Yinguang

    2010-12-01

    Wastewater biological nutrient removal (BNR) by short-cut nitrification-denitrification (SCND) and denitrifying phosphorus removal via nitrite (DPRN) has several advantages, such as organic carbon source saving. In this paper, a new method, i.e., by using waste activated sludge alkaline fermentation liquid as BNR carbon source, for simultaneously improving SCND and DPRN was reported. First, the performance of SCND and DPRN with sludge fermentation liquid as carbon source was compared with acetic acid, which was commonly used in literatures. Sludge fermentation liquid showed much higher nitrite accumulation during aerobic nitrification than acetic acid (81.8% versus 40.9%), and the former had significant anoxic denitrification and phosphorus uptake. The soluble phosphorus and total nitrogen removal efficiencies with sludge fermentation liquid were much higher than with acetic acid (97.6% against 73.4% and 98.7% versus 79.2%). Then the mechanisms for sludge fermentation liquid showed higher SCND and DPRN than acetic acid were investigated from the aspects of wastewater composition, microorganisms assayed by 16S rRNA gene clone library, and fluorescence in situ hybridization. More NO(2)(-)-N accumulated by the use of sludge fermentation liquid was attributed to be more humic acids in the influent, which inhibited nitrite oxidizing bacteria (NOB) more serious than ammonia oxidizing bacteria (AOB), and more AOB but less NOB were observed in the BNR system. The reasons for sludge fermentation liquid BNR system exhibiting greater short-cut denitrifying phosphorus removal were that there were less glycogen accumulating organisms and more phosphorus accumulating organisms and anoxic denitrifying phosphorus removal bacteria with higher nitrite reductase activity. PMID:21053972

  14. Mathematical Modeling of Nitrous Oxide Production during Denitrifying Phosphorus Removal Process.

    PubMed

    Liu, Yiwen; Peng, Lai; Chen, Xueming; Ni, Bing-Jie

    2015-07-21

    A denitrifying phosphorus removal process undergoes frequent alternating anaerobic/anoxic conditions to achieve phosphate release and uptake, during which microbial internal storage polymers (e.g., Polyhydroxyalkanoate (PHA)) could be produced and consumed dynamically. The PHA turnovers play important roles in nitrous oxide (N2O) accumulation during the denitrifying phosphorus removal process. In this work, a mathematical model is developed to describe N2O dynamics and the key role of PHA consumption on N2O accumulation during the denitrifying phosphorus removal process for the first time. In this model, the four-step anoxic storage of polyphosphate and four-step anoxic growth on PHA using nitrate, nitrite, nitric oxide (NO), and N2O consecutively by denitrifying polyphosphate accumulating organisms (DPAOs) are taken into account for describing all potential N2O accumulation steps in the denitrifying phosphorus removal process. The developed model is successfully applied to reproduce experimental data on N2O production obtained from four independent denitrifying phosphorus removal study reports with different experimental conditions. The model satisfactorily describes the N2O accumulation, nitrogen reduction, phosphate release and uptake, and PHA dynamics for all systems, suggesting the validity and applicability of the model. The results indicated a substantial role of PHA consumption in N2O accumulation due to the relatively low N2O reduction rate by using PHA during denitrifying phosphorus removal. PMID:26114730

  15. 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. PMID:22565253

  16. 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

  17. 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. PMID:20937516

  18. Implications of non-specific strigolactone signaling in the rhizosphere.

    PubMed

    Koltai, Hinanit

    2014-08-01

    Strigolactones produced by various plant species are involved in the development of different plant parts. They are also exuded by plant roots to the rhizosphere, where they are involved in the induction of seed germination of the parasitic plants Striga and Orobanche, hyphal branching of the symbiotic arbuscular mycorrhizal fungi (AMF), and the symbiotic interaction with Rhizobium. In the present discussion paper, the essentialness of strigolactones as communication signals in these plant interactions is discussed in view of the existence of other plant-derived substances that are able to promote these plant interactions. In addition, the importance of strigolactones for determination of interaction specificity is discussed based on current knowledge on strigolactone composition, perception and delivery. The different activities of strigolactones in plant development and in the rhizosphere suggest their possible use in agriculture. However, despite efforts made in this direction, there is no current, practical implementation. Possible reasons for the encountered difficulties and suggested solutions to promote strigolactone use in agriculture are discussed. PMID:25017154

  19. 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. PMID:24580822

  20. Elemental sulfur formation and nitrogen removal from wastewaters by autotrophic denitrifiers and anammox bacteria.

    PubMed

    Liu, Chunshuang; Zhao, Dongfeng; Yan, Laihong; Wang, Aijie; Gu, Yingying; Lee, Duu-Jong

    2015-09-01

    Elemental sulfur (S(0)) formation from and nitrogen removal on sulfide, nitrate and ammonium-laden wastewaters were achieved by denitrifying ammonium oxidation (DEAMOX) reactor with autotrophic denitrifiers and anaerobic ammonium oxidation (anammox) bacteria. The sulfide to nitrate ratio is a key process parameter for excess accumulation of S(0) and a ratio of 1.31:1 is a proposed optimum. The Alishewanella, Thauera and Candidatus Anammoximicrobium present respectively the autotrophic denitrifiers and anammox bacteria for the reactor. DEAMOX is demonstrated promising biological process for treating organics-deficient (S+N) wastewaters with excess S(0) production. PMID:26022701

  1. 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

  2. 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

  3. 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

  4. Characterizing and handling different kinds of AM fungal spores in the rhizosphere.

    PubMed

    Sun, Xueguang; Hu, Wentao; Tang, Ming; Chen, Hui

    2016-06-01

    Spores are important propagules as well as the most reliable species-distinguishing traits of arbuscular mycorrhizal (AM) fungi. During surveys of AM fungal communities, spore enumeration and spore identification are frequently conducted, but generally little attention is given to the age and viability of the spores. In this study, AM fungal spores in the rhizosphere were characterized as live or dead by vital staining and by performing a germination assay. A considerable proportion of the spores in the rhizosphere were dead despite their intact appearance. Furthermore, morphological and molecular analyses of spores to determine species identity revealed that both viable spores and dead spores with contents were identified. The accurate identification of spores at different developmental stages on the basis of morphology requires considerable experience. Our findings suggest that surveys of AM fungal communities based on spore enumeration and morphological and molecular identification are likely to be inaccurate, primarily because of the large proportion of dead spores in the rhizosphere. A viability check is recommended prior to spore molecular identification, and the use of trap cultures would give more reliable morphological identification results. We show that the abundance and activity of AM fungi in the rhizosphere can be determined by calculating the density of viable spores and the density of spores that could germinate. The adoption of these methods should provide a more reliable basis for further AM fungal community analysis. PMID:27116963

  5. Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles.

    PubMed

    Finzi, Adrien C; Abramoff, Rose Z; Spiller, Kimberly S; Brzostek, Edward R; Darby, Bridget A; Kramer, Mark A; Phillips, Richard P

    2015-05-01

    While there is an emerging view that roots and their associated microbes actively alter resource availability and soil organic matter (SOM) decomposition, the ecosystem consequences of such rhizosphere effects have rarely been quantified. Using a meta-analysis, we show that multiple indices of microbially mediated C and nitrogen (N) cycling, including SOM decomposition, are significantly enhanced in the rhizospheres of diverse vegetation types. Then, using a numerical model that combines rhizosphere effect sizes with fine root morphology and depth distributions, we show that root-accelerated mineralization and priming can account for up to one-third of the total C and N mineralized in temperate forest soils. Finally, using a stoichiometrically constrained microbial decomposition model, we show that these effects can be induced by relatively modest fluxes of root-derived C, on the order of 4% and 6% of gross and net primary production, respectively. Collectively, our results indicate that rhizosphere processes are a widespread, quantitatively important driver of SOM decomposition and nutrient release at the ecosystem scale, with potential consequences for global C stocks and vegetation feedbacks to climate. PMID:25421798

  6. Diversity analysis of type I ketosynthase in rhizosphere soil of cucumber.

    PubMed

    Zhao, Baixia; Gao, Zenggui; Shao, Yang; Yan, Jianfang; Hu, Yingchang; Yu, Jicheng; Liu, Qiu; Chen, Fei

    2012-04-01

    Fusarium wilt [Fusarium oxysporum (Sch1.) f.sp. cucumerinum Owen.] is a major soil-borne disease of cucumber worldwide, and can cause huge yield losses. Biological control of Fusarium wilt of cucumber has received considerable attention. Many bacteria, particularly actinomycetes, are known to produce secondary metabolites synthesized by Polyketide synthases (PKSs) with a diverse range of biological activities. Ketosynthase (KS) gene diversity was analyzed in samples which were collected from rhizosphere soil of both diseased cucumber and healthy cucumber in Dalian, China. The phylogenetic analysis amino acid (AA) sequences indicated that the KS genes in the rhizosphere soil samples were clustered into diverse seven clades, including Sorangium cellulosum, Anabaena variabilis, Nostoc punctiforme, Xanthobacter autotrophicus, Streptomyces, myxobacteria and uncultured bacteria. Among seven major clades in the phylogenetic tree, two clades were peculiar to rhizosphere soil of diseased cucumber and one was peculiar to healthy cucumber. Among the 182 cloned KS genes, 147 KS genes were clustered with the uncultured bacteria group. Most of the KS genes showed about 80% similarity at the AA level to sequences known in GenBank. These results revealed the great diversity and novelty of KS genes in rhizosphere soil of cucumber. PMID:21780139

  7. Salt tolerant SUV3 overexpressing transgenic rice plants conserve physicochemical properties and microbial communities of rhizosphere.

    PubMed

    Sahoo, Ranjan K; Ansari, Mohammad W; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Key concerns in the ecological evaluation of GM crops are undesirably spread, gene flow, other environmental impacts, and consequences on soil microorganism's biodiversity. Numerous reports have highlighted the effects of transgenic plants on the physiology of non-targeted rhizospheric microbes and the food chain via causing adverse effects. Therefore, there is an urgent need to develop transgenics with insignificant toxic on environmental health. In the present study, SUV3 overexpressing salt tolerant transgenic rice evaluated in New Delhi and Cuttack soil conditions for their effects on physicochemical and biological properties of rhizosphere. Its cultivation does not affect soil properties viz., pH, Eh, organic C, P, K, N, Ca, Mg, S, Na and Fe(2+). Additionally, SUV3 rice plants do not cause any change in the phenotype, species characteristics and antibiotic sensitivity of rhizospheric bacteria. The population and/or number of soil organisms such as bacteria, fungi and nematodes were unchanged in the soil. Also, the activity of bacterial enzymes viz., dehydrogenase, invertase, phenol oxidases, acid phosphatases, ureases and proteases was not significantly affected. Further, plant growth promotion (PGP) functions of bacteria such as siderophore, HCN, salicylic acid, IAA, GA, zeatin, ABA, NH3, phosphorus metabolism, ACC deaminase and iron tolerance were, considerably, not influenced. The present findings suggest ecologically pertinent of salt tolerant SUV3 rice to sustain the health and usual functions of the rhizospheric organisms. PMID:25303666

  8. 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.

  9. 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

  10. Taxonomical and functional microbial community selection in soybean rhizosphere.

    PubMed

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

    2014-08-01

    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

  11. 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

  12. 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

  13. Metabolic Status of Bacteria and Fungi in the Rhizosphere of Ponderosa Pine Seedlings

    PubMed Central

    Norton, Jeanette M.; Firestone, Mary K.

    1991-01-01

    We 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. Determination of total and INT-active biomass has increased our understanding of the role of spatial compartmentalization of bacteria and fungi in rhizosphere carbon flow. PMID:16348461

  14. Deciphering the rhizosphere microbiome for disease-suppressive bacteria.

    PubMed

    Mendes, Rodrigo; Kruijt, Marco; de Bruijn, Irene; Dekkers, Ester; van der Voort, Menno; Schneider, Johannes H M; Piceno, Yvette M; DeSantis, Todd Z; Andersen, Gary L; Bakker, Peter A H M; Raaijmakers, Jos M

    2011-05-27

    Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections. PMID:21551032

  15. 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...

  16. 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

  17. 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

  18. Microbial Community Dynamics Associated with Rhizosphere Carbon Flow

    PubMed Central

    Butler, Jessica L.; Williams, Mark A.; Bottomley, Peter J.; Myrold, David D.

    2003-01-01

    Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a 13C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1ω5 PLFA were more active in utilizing 13C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2ω6,9 was the most highly labeled. These results demonstrate the effectiveness of using 13C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved. PMID:14602642

  19. 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

  20. 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...

  1. Draft Genome Sequence of Bacillus methylotrophicus FKM10, a Plant Growth-Promoting Rhizobacterium Isolated from Apple Rhizosphere

    PubMed Central

    Wang, Chengqiang; Hu, Xiuna; Liu, Kai; Hou, Qihui; Yang, Qianqian

    2016-01-01

    Bacillus methylotrophicus FKM10 is a strain of plant growth-promoting rhizobacterium with antimicrobial activity, which was isolated from apple rhizosphere. Here, we present the genome sequence of B. methylotrophicus FKM10. Two scaffolds were finally assembled, and several functional genes related to its antimicrobial activity were discovered. PMID:26868409

  2. Draft Genome Sequence of Bacillus methylotrophicus FKM10, a Plant Growth-Promoting Rhizobacterium Isolated from Apple Rhizosphere.

    PubMed

    Wang, Chengqiang; Hu, Xiuna; Liu, Kai; Hou, Qihui; Yang, Qianqian; Ding, Yanqin; Du, Binghai

    2016-01-01

    Bacillus methylotrophicus FKM10 is a strain of plant growth-promoting rhizobacterium with antimicrobial activity, which was isolated from apple rhizosphere. Here, we present the genome sequence of B. methylotrophicus FKM10. Two scaffolds were finally assembled, and several functional genes related to its antimicrobial activity were discovered. PMID:26868409

  3. 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

  4. 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

  5. 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

  6. 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

  7. Analysis of denitrifier community in a bioaugmented sequencing batch reactor for the treatment of coking wastewater containing pyridine and quinoline.

    PubMed

    Bai, Yaohui; Sun, Qinghua; Xing, Rui; Wen, Donghui; Tang, Xiaoyan

    2011-05-01

    The denitrifier community and associated nitrate and nitrite reduction in the bioaugmented and general sequencing batch reactors (SBRs) during the treatment of coking wastewater containing pyridine and quinoline were investigated. The efficiency and stability of nitrate and nitrite reduction in SBR was considerably improved after inoculation with four pyridine- or quinoline-degrading bacterial strains (including three denitrifying strains). Terminal restriction fragment length polymorphism (T-RFLP) based on the nosZ gene revealed that the structures of the denitrifier communities in bioaugmented and non-bioaugmented reactors were distinct and varied during the course of the experiment. Bioaugmentation protected indigenous denitrifiers from disruptions caused by pyridine and quinoline. Clone library analysis showed that one of the added denitrifiers comprised approximately 6% of the denitrifier population in the bioaugmented sludge. PMID:21327410

  8. 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

  9. 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

  10. 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.

  11. 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

  12. STRESS ETHYLENE: A BIOASSAY FOR RHIZOSPHERE-APPLIED PHYTOTOXICANTS

    EPA Science Inventory

    A bioassay for rhizosphere-applied phytotoxicants was developed and evaluated with a broad range of chemicals. Test substances were applied to the rhizosphere of whole, intact bush bean plants (Phaseolus vulgaris L. cv. Bush Blue Lake 290) grown in a solid support medium and the ...

  13. 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

  14. RHIZOSPHERE MICROBIOLOGY OF CHLORINATED ETHENE CONTAMINATED SOILS: EFFECTS ON PHOSPHOLIPID FATTY ACID CONTENT

    SciTech Connect

    Brigmon, R. L.; Stanhopc, A.; Franck, M. M.; McKinsey, P. C.; Berry, C. J.

    2005-05-26

    Microbial degradation of chlorinated ethenes (CE) in rhizosphere soils was investigated at seepline areas impacted by CE plumes. Successful bioremediation of CE in rhizosphere soils is dependent on microbial activity, soil types, plant species, and groundwater CE concentrations. Seepline soils were exposed to trichloroethylene (TCE) and perchloroethylene (PCE) in the 10-50 ppb range. Greenhouse soils were exposed to 2-10 ppm TCE. Plants at the seepline were poplar and pine while the greenhouse contained sweet gum, willow, pine, and poplar. Phospholipid fatty acid (PLFA) analyses were performed to assess the microbial activity in rhizosphere soils. Biomass content was lowest in the nonvegetated control soil and highest in the Sweet Gum soil. Bacterial rhizhosphere densities, as measured by PLFA, were similar in different vegetated soils while fungi biomass was highly variable. The PLFA soil profiles showed diverse microbial communities primarily composed of Gram-negative bacteria. Adaptation of the microbial community to CE was determined by the ratio of {omega}7t/{omega}7c fatty acids. Ratios (16:1{omega}7v16:1{omega}7c and 18:l{omega}7t/18:1{omega}7c) greater than 0.1 were demonstrated in soils exposed to higher CE concentrations (10-50 ppm), indicating an adaptation to CE resulting in decreased membrane permeability. Ratios of cyclopropyl fatty acids showed that the vegetated control soil sample contained the fastest microbial turnover rate and least amount of environmental stress. PLFA results provide evidence that sulfate reducing bacteria (SRB) are active in these soils. Microcosm studies with these soils showed CE dechlorinating activity was occurring. This study demonstrates microbial adaptation to environmental contamination and supports the application of natural soil rhizosphere activity as a remedial strategy.

  15. 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

  16. 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.

  17. 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.

  18. 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. PMID:26573667

  19. 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

  20. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    DOE PAGESBeta

    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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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. PMID:24873702

  9. 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.

  10. 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

  11. Effect of some sulphur compounds on soil microflora of spruce rhizosphere.

    PubMed

    Lettl, A

    1981-01-01

    The effect of a long-term application of sulphite, thiosulphate and sodium sulphate on the soil microflora and spruce seedlings was investigated in a pot experiment. Sulphur compounds decreased the concentration of bacteria, including thiobacilli, increased the concentration of microscopic fungi and sulphate-reducing bacteria; they inhibited respiration, nitrification and oxidation of thiosulphate, stimulated ammonification and oxidation of elemental sulphur. In certain cases the spruce rhizosphere exhibited just the opposite effect. In the rhizosphere the sulphate-reducing bacteria was suppressed together with thiobacilli, whose unit oxidative activity increased substantially. Growth of seedlings was inhibited by sulphite and stimulated by thiosulphate and sulphate. Sulphite, the effects of which were similar to those of sulphur dioxide immissions, was the most effective compound. In regions influenced by immissions the soil is apparently intoxicated by the absorbed sulphite. PMID:7274844

  12. 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. PMID:25910602

  13. Heterotrophic nitrifying and oxygen tolerant denitrifying bacteria from greenwater system of coastal aquaculture.

    PubMed

    Velusamy, Kathiravan; Krishnani, Kishore Kumar

    2013-03-01

    In this work, herbivorous fish Mugil cephalus has been cultured to secrete protein rich green slime, which helps nitrifying and oxygen tolerant denitrifying bacteria to grow and colonize. Four strains representing Alcaligenaceae family have been isolated from greenwater system and characterized using biochemical test, fatty acid methyl ester (GC-FAME) analysis, 16S rRNA and functional gene approaches. They were tested for an ability to nitrify ammonia and nitrite aerobically. Two strains showed notable nitrification activity, when grown in a mineral salts medium containing ammonium sulfate and potassium nitrite. Functional gene analysis confirmed the presence of nitrous oxide reductase (nosZ) gene showing that they have an oxygen-tolerant denitrification system. It has been proposed that Alcaligenes faecalis strains heterotrophically nitrify ammonia into nitrite via formation of hydroxyl amine, which is oxidized to nitrous oxide using oxygen or nitrite as electron acceptor. These results provide a possible advantage of having nitrification and denitrification capabilities in the same organism, which plays an important role in biological wastewater system. PMID:23354499

  14. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment.

    PubMed

    Kampman, Christel; Hendrickx, Tim L G; Luesken, Francisca A; van Alen, Theo A; Op den Camp, Huub J M; Jetten, Mike S M; Zeeman, Grietje; Buisman, Cees J N; Temmink, Hardy

    2012-08-15

    Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to 'Candidatus Methylomirabilis oxyfera' were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO(2)(-)-N/Ld (using synthetic medium) and 37.8 mg NO(2)(-)-N/Ld (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass retention. PMID:22657102

  15. [Screening, denitrification characteristics, and anaerobic ammonium oxidation ability of denitrifying bacterium aHD7].

    PubMed

    Chu, Shu-Yi; Jiang, Hui-Xia; Xiao, Ji-Bo; Shan, Sheng-Dao

    2012-11-01

    A highly efficient denitrifying bacterium aHD7 was screened from activated sludge. After static culture at 30 degrees C for 3 days, the denitrification rate of the aHD7 reached 91.7%, and during denitrification, nitrite had lower accumulation, with its concentration basically maintained at 1.8 mg x L(-1). The microscopy observation demonstrated that the aHD7 was a gram-negative bacillus, with an average size of 0.5 microm x (1.5-2.5) microm. Based on its biochemical/morphological characteristics and homologic analysis of 16S rDNA sequence, the aHD7 was identified as Pseudomonas mendocina. The investigation on the factors affecting the denitrification capacity of aHD7 showed that at the initial concentration of nitrate nitrogen being less than 276.95 mg x L(-1), the denitrification rate was almost 100%, and when the initial concentration of nitrate nitrogen was as high as 553.59 mg x L(-1), the denitrification rate could reach 66.8%, with little nitrite accumulated. Ethanol was the most suitable carbon source. C/N ratio 6-8 and pH value 6-9 benefited the denitrification. The aHD7 had a good ability of anaerobic ammonium oxidation, and its average ammonium utilization rate reached 4.56 mg x L(-1) x d(-1). PMID:23431796

  16. The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs depending on plant species and site.

    PubMed

    Berg, Gabriele; Opelt, Katja; Zachow, Christin; Lottmann, Jana; Götz, Monika; Costa, Rodrigo; Smalla, Kornelia

    2006-05-01

    Rhizobacteria with antagonistic activity towards plant pathogens play an essential role in root growth and plant health and are influenced by plant species in their abundance and composition. To determine the extent of the effect of the plant species and of the site on the abundance and composition of bacteria with antagonistic activity towards Verticillium dahliae, bacteria isolated from the rhizosphere of two Verticillium host plants, oilseed rape and strawberry, and from bulk soil were analysed at three different locations in Germany over two growing seasons. A total of 6732 bacterial isolates screened for in vitro antagonism towards Verticillium resulted in 560 active isolates, among which Pseudomonas (77%) and Serratia (6%) were the most dominant genera. The rhizosphere effect on the antagonistic bacterial community was shown by an enhanced proportion of antagonistic isolates, by enrichment of specific amplified ribosomal DNA restriction analysis types, species and genotypes, and by a reduced diversity in the rhizosphere in comparison to bulk soil. Such an effect was influenced by the plant species and by the site of its cultivation. Altogether, 16S rRNA gene sequencing of 66 isolates resulted in the identification of 22 different species. Antagonists of the genus Serratia were preferentially isolated from oilseed rape rhizosphere, with the exception of one site. For isolates of Pseudomonas and Serratia, plant-specific and site-specific genotypes were found. PMID:16629754

  17. Simulating root-induced rhizosphere deformation and its effect on water flow

    NASA Astrophysics Data System (ADS)

    Aravena, J. E.; Ruiz, S.; Mandava, A.; Regentova, E. E.; Ghezzehei, T.; Berli, M.; Tyler, S. W.

    2011-12-01

    Soil structure in the rhizosphere is influenced by root activities, such as mucilage production, microbial activity and root growth. Root growth alters soil structure by moving and deforming soil aggregates, affecting water and nutrient flow from the bulk soil to the root surface. In this study, we utilized synchrotron X-ray micro-tomography (XMT) and finite element analysis to quantify the effect of root-induced compaction on water flow through the rhizosphere to the root surface. In a first step, finite element meshes of structured soil around the root were created by processing rhizosphere XMT images. Then, soil deformation by root expansion was simulated using COMSOL Multiphysics° (Version 4.2) considering the soil an elasto-plastic porous material. Finally, fluid flow simulations were carried out on the deformed mesh to quantify the effect of root-induced compaction on water flow to the root surface. We found a 31% increase in water flow from the bulk soil to the root due to a 56% increase in root diameter. Simulations also show that the increase of root-soil contact area was the dominating factor with respect to the calculated increase in water flow. Increase of inter-aggregate contacts in size and number were observed within a couple of root diameters away from the root surface. But their influence on water flow was, in this case, rather limited compared to the immediate soil-root contact.

  18. Pseudomonas aeruginosa PAO1 virulence factors and poplar tree response in the rhizosphere

    PubMed Central

    Attila, Can; Ueda, Akihiro; Cirillo, Suat L. G.; Cirillo, Jeffrey D.; Chen, Wilfred; Wood, Thomas K.

    2008-01-01

    Summary Whole‐transcriptome analysis was used here for the first time in the rhizosphere to discern the genes involved in the pathogenic response of Pseudomonas aeruginosa PAO1 as well as to discern the response of the poplar tree. Differential gene expression shows that 185 genes of the bacterium and 753 genes of the poplar tree were induced in the rhizosphere. Using the P. aeruginosatranscriptome analysis, isogenic knockout mutants, and two novel plant assays (poplar and barley), seven novel PAO1 virulence genes were identified (PA1385, PA2146, PA2462, PA2463, PA2663, PA4150 and PA4295). The uncharacterized putative haemolysin repressor, PA2463, upon inactivation, resulted in greater poplar virulence and elevated haemolysis while this mutant remained competitive in the rhizosphere. In addition, disruption of the haemolysin gene itself (PA2462) reduced the haemolytic activity of P. aeruginosa, caused less cytotoxicity and reduced barley virulence, as expected. Inactivating PA1385, a putative glycosyl transferase, reduced both poplar and barley virulence. Furthermore, disrupting PA2663, a putative membrane protein, reduced biofilm formation by 20‐fold. Inactivation of PA3476 (rhlI) increased virulence with barley as well as haemolytic activity and cytotoxicity, so quorum sensing is important in plant pathogenesis. Hence, this strategy is capable of elucidating virulence genes for an important pathogen. PMID:21261818

  19. 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

  20. Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus spp. in methanol-fed biofilms.

    PubMed Central

    Neef, A; Zaglauer, A; Meier, H; Amann, R; Lemmer, H; Schleifer, K H

    1996-01-01

    The microbial community of a denitrifying sand filter in a municipal wastewater treatment plant was examined by conventional and molecular techniques to identify the bacteria actively involved in the removal of nitrate. In this system, denitrification is carried out as the last step of water treatment by biofilms growing on quartz grains with methanol as a supplemented carbon source. The biofilms are quite irregular, having a median thickness of 13 to 20 microns. Fatty acid analysis of 56 denitrifying isolates indicated the occurrence of Paracoccus spp. in the sand filter. 16S rRNA-targeted probes were designed for this genus and the species cluster Paracoccus denitrificans-Paracoccus versutus and tested for specificity by whole-cell hybridization. Stringency requirements for the probes were adjusted by use of a formamide concentration gradient to achieve complete discrimination of even highly similar target sequences. Whole-cell hybridization confirmed that members of the genus Paracoccus were abundant among the isolates. Twenty-seven of the 56 isolates hybridized with the genus-specific probes. In situ hybridization identified dense aggregates of paracocci in detached biofilms. Probes complementary to the type strains of P. denitrificans and P. versutus did not hybridize to cells in the biofilms, suggesting the presence of a new Paracoccus species in the sand filter. Analysis using confocal laser scanning microscopy detected spherical aggregates of morphologically identical cells exhibiting a uniform fluorescence. Cell quantification was performed after thorough disruption of the biofilms and filtration onto polycarbonate filters. An average of 3.5% of total cell counts corresponded to a Paracoccus sp., whereas in a parallel sand filter with no supplemented methanol, and no measurable denitrification, only very few paracocci (0.07% of cells stained with 4',6-diamidino-2-phenylindole) could be detected. Hyphomicrobium spp. constituted approximately 2% of all cells

  1. Differential Isotopic Fractionation during Cr(VI) Reduction by an Aquifer-Derived Bacterium under Aerobic versus Denitrifying Conditions

    PubMed Central

    Han, Ruyang; Qin, Liping; Brown, Shaun T.; Christensen, John N.

    2012-01-01

    We studied Cr isotopic fractionation during Cr(VI) reduction by Pseudomonas stutzeri strain RCH2. 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). PMID:22286991

  2. 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).

  3. 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. PMID:26036704

  4. Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana.

    PubMed

    Doornbos, Rogier F; Geraats, Bart P J; Kuramae, Eiko E; Van Loon, L C; Bakker, Peter A H M

    2011-04-01

    Systemically induced resistance is a promising strategy to control plant diseases, as it affects numerous pathogens. However, since induced resistance reduces one or both growth and activity of plant pathogens, the indigenous microflora may also be affected by an enhanced defensive state of the plant. The aim of this study was to elucidate how much the bacterial rhizosphere microflora of Arabidopsis is affected by induced systemic resistance (ISR) or systemic acquired resistance (SAR). Therefore, the bacterial microflora of wild-type plants and plants affected in their defense signaling was compared. Additionally, ISR was induced by application of methyl jasmonate and SAR by treatment with salicylic acid or benzothiadiazole. As a comparative model, we also used wild type and ethylene-insensitive tobacco. Some of the Arabidopsis genotypes affected in defense signaling showed altered numbers of culturable bacteria in their rhizospheres; however, effects were dependent on soil type. Effects of plant genotype on rhizosphere bacterial community structure could not be related to plant defense because chemical activation of ISR or SAR had no significant effects on density and structure of the rhizosphere bacterial community. These findings support the notion that control of plant diseases by elicitation of systemic resistance will not significantly affect the resident soil bacterial microflora. PMID:21171889

  5. 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. PMID:26762934

  6. 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

  7. 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.

  8. Quantifying rhizosphere respiration for two cool-season perennial forages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the regulation of ecosystem carbon dioxide flux from forage production systems requires knowledge of component fluxes, including photosynthetic uptake and respiratory loss. Experimental separation of soil respiration into its heterotrophic (free-living soil organisms) and rhizosphere c...

  9. 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.

  10. 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.

  11. ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants.

    PubMed

    Bal, Himadri Bhusan; Das, Subhasis; Dangar, Tushar K; Adhya, Tapan K

    2013-12-01

    Beneficial plant-associated bacteria play a key role in supporting and/or promoting plant growth and health. Plant growth promoting bacteria present in the rhizosphere of crop plants can directly affect plant metabolism or modulate phytohormone production or degradation. We isolated 355 bacteria from the rhizosphere of rice plants grown in the farmers' fields in the coastal rice field soil from five different locations of the Ganjam district of Odisha, India. Six bacteria producing both ACC deaminase (ranging from 603.94 to 1350.02 nmol α-ketobutyrate mg(-1)  h(-1) ) and indole acetic acid (IAA; ranging from 10.54 to 37.65 μM ml(-1) ) in pure cultures were further identified using polyphasic taxonomy including BIOLOG((R)) , FAME analysis and the 16S rRNA gene sequencing. Phylogenetic analyses of the isolates resulted into five major clusters to include members of the genera Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Seed inoculation of rice (cv. Naveen) by the six individual PGPR isolates had a considerable impact on different growth parameters including root elongation that was positively correlated with ACC deaminase activity and IAA production. The cultures also had other plant growth attributes including ammonia production and at least two isolates produced siderophores. Study indicates that presence of diverse rhizobacteria with effective growth-promoting traits, in the rice rhizosphere, may be exploited for a sustainable crop management under field conditions. PMID:23681643

  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. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    DOE PAGESBeta

    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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. [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

  1. 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. PMID:16269702

  2. 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

  3. Effects of long term rice straw application on the microbial communities of rapeseed rhizosphere in a paddy-upland rotation system.

    PubMed

    Peng, Caijuan; Lai, Songsong; Luo, Xuesong; Lu, Jianwei; Huang, Qiaoyun; Chen, Wenli

    2016-07-01

    The influence of the rice straw application on rhizosphere microbial communities in the long-term rotation system remains unclear. Two experimental sites (Jingzhou and Wuxue) with the same straw fertilization have been cultivated under the rapeseed-rice rotation mode for 7years. Eco-plate data indicated that the microbial metabolic potential at both sites was enhanced in the cores applied with rice straw. Rhizosphere microbial communities at the two fields could be well distinguished by phospholipid fatty acid data. Redundancy analysis showed that the rapeseed rhizosphere microbial communities in Jingzhou were influenced by soil moisture content, available potassium and available nitrogen, whereas those in Wuxue were influenced by soil available phosphorous, available potassium, total soil carbon and available nitrogen. Variation in soil enzyme activities could be mainly explained by available potassium in Jingzhou, and it was significantly affected by total soil carbon, available nitrogen, available potassium, available phosphorous, total soil nitrogen, moisture content and total phosphorous in Wuxue. The two rapeseed rhizosphere microbial communities are differently affected by the rice-straw application. Rhizosphere with more fungi was passively influenced by the rice-straw, while that with more Gram-negative bacteria was actively in response to the treatment. PMID:26994810

  4. Root-induced changes in pH and dissolved organic matter binding capacity affect copper dynamic speciation in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Bravin, Matthieu N.; Garnier, Cédric; Lenoble, Véronique; Gérard, Frédéric; Dudal, Yves; Hinsinger, Philippe

    2012-05-01

    Due to only few experimental evidences, the importance of root-induced alteration of metal dynamic speciation in the rhizosphere in the determination of metal bioavailability to plants is still a matter for debate. The present study thus investigated how root-induced changes in pH and dissolved organic matters (DOM) altered copper (Cu) dynamic speciation in the rhizosphere of durum wheat (Triticum turgidum durum L.). Plants were exposed to a Cu-contaminated soil previously alkalised by liming to cover soil pH values ranging from 4.8 to 7.5. A range of analytical techniques was deployed on soil exposed (i.e. in the rhizosphere) or not (i.e. in the bulk soil) to plant roots, including the measurement and the modelling (using the Humic Ion-Binding Model VI) of Cu2+ activity, the measurement of labile Cu concentration and Cu lability by Differential Pulse Anodic Stripping Voltammetry (DPASV) and Diffusive Gradients in Thin films (DGT). Due to root-induced alkalisation, pH reached about 7.3 in the rhizosphere whatever the initial bulk soil pH. Compared to the most acidic bulk soil (pH ≈ 4.8), Cu2+ activity decreased by three orders of magnitude in the rhizosphere while DPASV-Cu concentration decreased by 6-fold. DOM became the key driver of Cu dynamic speciation in the rhizosphere, where roots induced up to an order of magnitude increase in DOM concentration compared to bulk soils. This resulted in an increase in labile-Cu (both DPASV and DGT) concentrations, in spite of a decrease in Cu2+ activity. Model VI calculations supported a decrease in DOM binding capacity towards Cu in the rhizosphere. DPASV measurements unequivocally demonstrated that the increase in Cu lability in the rhizosphere solution can be attributed to a greater lability of organically-bound Cu. Collectively, our data introduce a consistent picture of root-induced changes of Cu dynamic speciation in the rhizosphere that were notably related to substantial alterations of DOM binding capacity.

  5. 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. PMID:22179233

  6. Comparison of endogenous metabolism during long-term anaerobic starvation of nitrite/nitrate cultivated denitrifying phosphorus removal sludges.

    PubMed

    Wang, Yayi; Zhou, Shuai; Wang, Hong; Ye, Liu; Qin, Jian; Lin, Ximao

    2015-01-01

    Denitrifying phosphorus removal (DPR) by denitrifying phosphorus-accumulating organisms (DPAOs) is a promising approach for reducing energy and carbon usage. However, influent fluctuations or interruptions frequently expose the DPAOs biomass to starvation conditions, reducing biomass activity and amount, and ultimately degrading the performance of DPR. Therefore, a better understanding of the endogenous metabolism and recovery ability of DPAOs is urgently required. In the present study, anaerobic starvation (12 days) and recovery were investigated in nitrite- and nitrate-cultivated DPAOs at 20 ± 1 °C. The cell decay rates in nitrite-DPAOs sludges from the end of the anaerobic and aerobic phase were 0.008 day⁻¹ and 0.007 day⁻¹, respectively, being 64% and 68% lower than those of nitrate-DPAOs sludges. Nitrite-DPAOs sludges also recovered more rapidly than nitrate-DPAOs sludge after 12 days of starvation. The maintenance energy of nitrite-DPAOs sludges from the end of the anaerobic and aerobic phase were approximately 31% and 34% lower, respectively, than those of nitrate-DPAOs sludges. Glycogen and polyphosphate (poly-P) sequentially served as the main maintenance energy sources in both nitrite-and nitrate-DPAOs sludges. However, the transformation pathway of the intracellular polymers during starvation differed between them. Nitrate-DPAOs sludge used extracellular polymeric substances (EPS) (mainly polysaccharides) as an additional maintenance energy source during the first 3 days of starvation. During this phase, EPS appeared to contribute to 19-27% of the ATP production in nitrate-DPAOs, but considerably less to the cell maintenance of nitrite-DPAOs. The high resistance of nitrite-DPAOs to starvation might be attributable to frequent short-term starvation and exposure to toxic substances such as nitrite/free nitrous acids in the parent nitrite-fed reactor. The strong resistance of nitrite-DPAOs sludge to anaerobic starvation may be exploited in P removal

  7. 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

  8. Comparing spatial and temporal dynamics of anammox and denitrifying communities at Cape Fear River Estuary and New River Estuary, North Carolina

    NASA Astrophysics Data System (ADS)

    Lisa, J. A.; Hirsch, M. D.; Duernberger, K. A.; Tobias, C. R.; Song, B.

    2010-12-01

    Anaerobic ammonium oxidation (anammox) and denitrification are two main microbial processes capable of removing fixed nitrogen by conversion into a gaseous species. Both microbial processes are known to occur in anoxic estuarine sediments and are capable of remediating excess nitrogen loadings from anthropogenic activities. In order to understand the importance of anammox and denitrification in estuarine ecosystems, we investigated both processes in two different estuaries of North Carolina to compare sedimentary nitrogen removal capacity and to identify key players of N2 production pathways. Both Cape Fear River Estuary (CFRE) and New River Estuary (NRE) are highly enriched with nitrogen from anthropogenic sources in spite of distinct geomorphological and geochemical characteristics. We conducted seasonal samplings to collect sediments across transects at fifteen stations along each estuary. 15N tracer techniques were used to measure spatial and temporal variations of N2 production by denitrification and anammox in estuarine sediments. Molecular analysis of nitrous oxide reductase (nosZ) and hydrazine oxidase (hzo) genes was conducted to examine community structures of denitrifying and anammox bacteria, respectively. Denitrification was found to be the dominant N2 production processes in both estuaries. Anammox contributed up to 19% and 15 % of total N2 productions in the CFEE and the NRE, respectively. Phylogenetic analysis of hzo genes identified that the anammox bacteria at both estuaries are closely associated with five known genera in the order Brocadiales. Anammox communities at the CFRE showed biogeographical distribution along the estuarine gradients while high seasonal variations were observed in the NRE communities. Spatial and temporal variations of denitrifying communities at both estuaries were also found based on nosZ gene analysis. Multivariate analysis was conducted to define key biogeochemical parameters influencing the community dynamics and

  9. 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

  10. 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...

  11. [Denitrifying phosphate uptake of biological phosphorous removal granular sludge in SBR].

    PubMed

    Liu, Xiao-ying; Zhao, Hong-mei; Peng, Dang-cong; Sui, Xian-jie

    2008-08-01

    The denitrification and excessive P removal can be realized by denitrifying phosphate-accumulating organisms (DNPAOs) under low carbon condition. DNPAOs use poly-3-hydroxy- butyrate (PHB) as electron donor, and use nitrate and nitrite as electron acceptor during the denitrifying phosphate uptake. In this study the biological phosphorus removal granular sludge was induced into the denitrifying and phosphate uptake granular sludge under an anaerobic/anoxic/aerobic alternating operation (referred to as an A/A/O) in a sequencing batch reactor (SBR). When the system is stable, the P and N removal ratio is over 90% and 93% respectively; the release phosphorus is 25-33 mg/L at anaerobic stage; 1g NOx-N approximately takes up P 1.3 g at anoxic stage. In the typical cycle the anaerobic maximum specific release phosphorus rate (max. SRPR) is 18.39 mg/(g x h); the anoxic max. specific uptake phosphorus rate (SUPR) and the max. specific denitrification rate (SDNR) is 23.72 mg/(g x h) and 18.19 mg/(g x h) respectively; the aerobic max. SUPR is 17.15 mg/(g x h). The fraction of DNPAOs rises from 14.9% to 80.7%. Compared with the physical-chemical property of the biological phosphorus removal granular sludge, the settling velocity and the specific gravity of the denitrifying phosphate uptake granular sludge is elevated 0.16-0.7 times and 0.0031 respectively. PMID:18839581

  12. 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

  13. 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

  14. 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...

  15. 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...

  16. Isolation and Characterization of a New Denitrifying Spirillum Capable of Anaerobic Degradation of Phenol

    PubMed Central

    Shinoda, Yoshifumi; Sakai, Yasuyoshi; Ué, Makiko; Hiraishi, Akira; Kato, Nobuo

    2000-01-01

    Two kinds of phenol-degrading denitrifying bacteria, Azoarcus sp. strain CC-11 and spiral bacterial strain CC-26, were isolated from the same enrichment culture after 1 and 3 years of incubation, respectively. Both strains required ferrous ions for growth, but strain CC-26 grew better than strain CC-11 grew under iron-limited conditions, which may have resulted in the observed change in the phenol-degrading bacteria during the enrichment process. Strain CC-26 grew on phenol, benzoate, and other aromatic compounds under denitrifying conditions. Phylogenetic analysis of 16S ribosomal DNA sequences revealed that this strain is most closely related to a Magnetospirillum sp., a member of the α subclass of the class Proteobacteria, and is the first strain of a denitrifying aromatic compound-degrading bacterium belonging to this group. Unlike previously described Magnetospirillum strains, however, this strain did not exhibit magnetotaxis. It grew on phenol only under denitrifying conditions. Other substrates, such as acetate, supported aerobic growth, and the strain exhibited microaerophilic features. PMID:10742201

  17. 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...

  18. 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. PMID:25820294

  19. 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

  20. 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

  1. 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

  2. [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

  3. 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

  4. 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.

  5. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

    DOE PAGESBeta

    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

  6. 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

  7. 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

  8. 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

  9. 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

  10. Microbial Biomass in the Rhizosphere: Model Development and Column Experiments

    NASA Astrophysics Data System (ADS)

    Sung, K.; Corapcioglu, M.; Kim, J.

    2001-12-01

    Microorganisms are important factor in the major contribution to degradation of organic contaminants in bioremediation as well as in phytoremediation. Enhanced biodegradation takes place in soils if there are increased numbers of microorganisms stimulated by additional substrates such as root exudates, exogenous substrate addition, and indigenous substrate conversion. Roots can thus greatly affect the concentration and distribution of microbial biomass in soils. A mathematical model is presented that can be applied to various bioremediation methods, especially phytoremediation, for simulating microbial biomass changes in soils. Experiments were conducted in field lysimeters containing freshly contaminated soil and sown with Johnsongrass. The microbial biomass concentrations from rhizosphere soil, bulk soil, and unplanted soil were estimated for one year using an incubation-fumigation method. The mathematical model was applied to the field data on microbial biomass. To investigate the model behavior, numerical experiments were conducted before applying the model to actual field data. The results show good correlation between simulated and experimental data. Microbial effects on contaminant degradation in phytoremediation can be smaller than that resulting from additional substrates due to indigenous conversion or exogenous supply. However, the addition of exogenous substrates in phytoremediation can increase remediation efficiency in the early period when the roots may not produce exudates rapidly. Cultivation before planting may also increase microbial activity to accelerate degradation of contaminants in soil.

  11. 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

  12. Diversity and heritability of the maize rhizosphere microbiome under field conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant....

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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...

  19. 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

  20. 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. PMID:26832948

  1. Dechlorination of PCBs in the rhizosphere of Switchgrass and Poplar

    PubMed Central

    Meggo, Richard E.; Schnoor, Jerald L.; Hu, Dingfei

    2014-01-01

    Polychlorinated biphenyl (PCB) congeners (PCB 52, 77, and 153) singly and in mixture were spiked and aged in soil microcosms and subsequently planted with switchgrass (Panicum virgatum) or poplar (Populus deltoids x nigra DN34). The planted reactors showed significantly greater reductions in PCB parent compounds when compared to unplanted systems after 32 weeks. There was evidence of reductive dechlorination in both planted and unplanted systems, but the planted microcosms with fully developed roots and rhizospheres showed greater biotransformation than the unplanted reactors. These dechlorination products accounted for approximately all of the molar mass of parent compound lost. Based on the transformation products, reductive dechlorination pathways are proposed for rhizospheric biotransformation of PCB 52, 77, and 153. This is the first report of rhizosphere biotransformation pathways for reductive dechlorination in marginally aerobic, intermittently flooded soil as evidenced by a mass balance on transformation products. PMID:23603468

  2. 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. PMID:21219711

  3. 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

  4. 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

  5. [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

  6. 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.

  7. Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1.

    PubMed Central

    Ball, H A; Johnson, H A; Reinhard, M; Spormann, A M

    1996-01-01

    Initial reactions in anaerobic oxidation of ethylbenzene were investigated in a denitrifying bacterium, strain EB1. Cells of strain EB1 mineralized ethylbenzene to CO2 under denitrifying conditions, as demonstrated by conversion of 69% of [14C]ethylbenzene to 14CO2. In anaerobic suspensions of strain EB1 cells metabolizing ethylbenzene, the transient formation and consumption of 1-phenylethanol, acetophenone, and an as yet unidentified compound were observed. On the basis of growth experiments and spectroscopic data, the unknown compound is proposed to be benzoyl acetate. Cell suspension experiments using H2(18)O demonstrated that the hydroxyl group of the first product of anoxic ethylbenzene oxidation, 1-phenylethanol, is derived from water. A tentative pathway for anaerobic ethylbenzene mineralization by strain EB1 is proposed. PMID:8824622

  8. 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

  9. 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). PMID:26264139

  10. Experimental and model-based evaluation of the role of denitrifying polyphosphate accumulating organisms at two large scale WWTPs in northern Poland.

    PubMed

    Makinia, J; Rosenwinkel, K H; Swinarski, M; Dobiegala, E

    2006-01-01

    The capabilities of denitrifying Polyphosphate Accumulating Organisms (DPAOs) in two large-scale plants in northern Poland performing enhanced biological phosphorus removal (EBPR) were evaluated in this study. A series of batch tests with the process biomass aimed at the measurements of phosphate release (with artificial substrate and real wastewater) and subsequent phosphate uptake under anoxic/aerobic conditions. The process kinetics were predicted using ASM2d implemented in the GPS-X ver. 4.0.2 simulation package. The results from one experimental series (summer) were used for the model calibration, whereas the results from another series (spring) were used for the model validation. The model parameters were also accurately confirmed by predictions of the accompanying field measurements in the full-scale bioreactors. The experimental and simulation results revealed that a relatively small fraction of PAO could denitrify (eta(NO3,PAO) = 0.32). The denitrification rates associated with the anoxic storage of PP and the anoxic growth of PAO only constituted 16.0-21.0% of the denitrification rates associated with the anoxic activity of "ordinary" heterotrophs. PMID:17163015

  11. 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.

  12. Impact of Flood Spates on Denitrifying Bacteria in Low Order Streams

    NASA Astrophysics Data System (ADS)

    Herrman, K.; Stokdyk, J.

    2011-12-01

    The impact of flood events on channel design, macroinvertebrates, and periphyton in stream ecosystems has been well studied. Little is known, however, about how flood spates affect microorganisms found in stream sediments. Denitrifying bacteria are beneficial organisms because they convert nitrates to nitrogen gas. Providing data that describes the impact of flood events on denitrifiers and the time required after the disturbance for the bacteria to recover are crucial in understanding nitrogen dynamics in stream ecosystems. Three low order streams in central Wisconsin, USA are being monitored during several flood spates during July and August of 2011. Discharge is being continuously monitored in all three streams and sediments are being collected before and after several flood events for laboratory assays. Specifically, sediments are being processed for denitrification rates using the acetylene inhibition technique, microbial biomass carbon using chloroform fumigation, and the quantification of denitrifying bacteria (i.e., nirS, nirK, and nosZ genes) using real-time quantitative PCR. Preliminary data show that within 36 hours after a 90 mm rain event, microbial biomass carbon in all three streams (580 μg C g sediment-1) significantly increased (F1,23 = 650 ± 140; p < 0.001) compared to microbial biomass during baseflow (200 ± 27 μg C g sediment-1). These initial results suggest that contrary to our expectations flood events enhance bacteria in stream sediments. Denitrification rates and quantification of denitrifying bacteria still need to be analyzed to determine if these specific bacteria follow a similar pattern or if the bacterial recolonization of stream sediments follows a unique pattern.

  13. 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

  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. PMID:26394860

  15. 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

  16. Biodegradation of Free Phytol by Bacterial Communities Isolated from Marine Sediments under Aerobic and Denitrifying Conditions

    PubMed Central

    Rontani, Jean-François; Bonin, Patricia C.; Volkman, John K.

    1999-01-01

    Biodegradation of (E)-phytol [3,7,11,15-tetramethylhexadec-2(E)-en-1-ol] by two bacterial communities isolated from recent marine sediments under aerobic and denitrifying conditions was studied at 20°C. This isoprenoid alcohol is metabolized efficiently by these two bacterial communities via 6,10,14-trimethylpentadecan-2-one and (E)-phytenic acid. The first step in both aerobic and anaerobic bacterial degradation of (E)-phytol involves the transient production of (E)-phytenal, which in turn can be abiotically converted to 6,10,14-trimethylpentadecan-2-one. Most of the isoprenoid metabolites identified in vitro could be detected in a fresh sediment core collected at the same site as the sediments used for the incubations. Since (E)-phytenal is less sensitive to abiotic degradation at the temperature of the sediments (15°C), the major part of (E)-phytol appeared to be biodegraded in situ via (E)-phytenic acid. (Z)- and (E)-phytenic acids are present in particularly large quantities in the upper section of the core, and their concentrations quickly decrease with depth in the core. This degradation (which takes place without significant production of phytanic acid) is attributed to the involvement of alternating β-decarboxymethylation and β-oxidation reaction sequences induced by denitrifiers. Despite the low nitrate concentration of marine sediments, denitrifying bacteria seem to play a significant role in the mineralization of (E)-phytol. PMID:10584007

  17. 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

  18. [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

  19. Nitrous oxide generation in denitrifying phosphorus removal process: main causes and control measures.

    PubMed

    Li, Cong; Zhang, Jian; Liang, Shuang; Ngo, Huu Hao; Guo, Wenshan; Zhang, Yingying; Zou, Yina

    2013-08-01

    Despite the many benefits of denitrifying phosphorus removal process, the significant generation of nitrous oxide (N2O), a potent greenhouse gas, remains a problem for this innovative and promising process. To better understand and more effectively control N2O generation in denitrifying phosphorus removal process, batch experiments were carried out to investigate the main causes of N2O generation, based on which the control measures were subsequently proposed. The results showed that N2O generation accounted for 0.41 % of the total nitrogen removal in denitrifying phosphorus removal process, whereas, in contrast, almost no N2O was generated in conventional denitrification process. It was further demonstrated that the weak competition of N2O reductase for electrons and the high nitrite accumulation were the two main causes for N2O generation, evidenced by N2O production and reduction rates under different conditions. Accordingly, the reduction of N2O generation was successfully achieved via two control measures: (1) the use of continuous nitrate addition reducing N2O generation by around 91.4 % and (2) the use of propionate as the carbon source reducing N2O generation by around 69.8 %. PMID:23407928

  20. 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

  1. 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

  2. The effect of mulching and soil compaction on fungi composition and microbial communities in the rhizosphere of soybean

    NASA Astrophysics Data System (ADS)

    Frac, M.; Siczek, A.; Lipiec, J.

    2009-04-01

    The soil environment is the habitat of pathogenic and saprotrophic microorganisms. The composition of the microbial community are related to biotic and abiotic factors, such as root exudates, crop residues, climate factors, mulching, mineral fertilization, pesticides introduction and soil compaction. The aim of the study was to determine the effect of the mulching and soil compaction on the microorganism communities in the rhizosphere soil of soybean. The studies were carried out on silty loam soil (Orthic Luvisol) developed from loess (Lublin, Poland). The experiment area was 192m2 divided into 3 sections consisted of 6 micro-plots (7m2). Three levels of soil compaction low, medium and heavy obtained through tractor passes were compared. The soil was compacted and loosened within seedbed layer 2 weeks before sowing. Soybean "Aldana" seeds were inoculated with Bradyrhizobium japonicum and were sown with interrow spacing of 0.3m. Wheat straw (as mulch) was uniformly spread on the half of each micro-plot at an amount of 0.5kg m-1 after sowing. Rhizosphere was collected three times during growing season of soybean. Microbiological analyses were conducted in 3 replications and included the determination of: the total number of bacteria and fungi, the number of bacteria Pseudomonas sp. and Bacillus sp., the genus identification of fungi isolated from rhizosphere of soybean. Results indicated a positive effect of mulching on the increase number of all groups of examined rhizosphere microorganisms (fungi, bacteria, Pseudomonas sp., Bacillus sp.). The highest number of the microorganisms was found in the low and medium compacted soil and markedly decreased in the most compacted soil. Relatively high number of antagonistic fungi (Penicillium sp., Trichoderma sp.) was recorded in the rhizosphere of low and medium compacted soil, particularly in mulched plots. The presence of these fungi can testify to considerable biological activity, which contributes to the improvement of

  3. Plant growth-promoting and rhizosphere-competent Acinetobacter rhizosphaerae strain BIHB 723 from the cold deserts of the Himalayas.

    PubMed

    Gulati, Arvind; Vyas, Pratibha; Rahi, Praveen; Kasana, Ramesh Chand

    2009-04-01

    A phosphate-solubilizing bacterial strain BIHB 723 isolated from the rhizosphere of Hippophae rhamnoides was identified as Acinetobacter rhizosphaerae on the basis of phenotypic characteristics, carbon source utilization pattern, fatty acid methyl esters analysis, and 16S rRNA gene sequence. The strain exhibited the plant growth-promoting attributes of inorganic and organic phosphate solubilization, auxin production, 1-aminocyclopropane-1-carboxylate deaminase activity, ammonia generation, and siderophore production. A significant increase in the growth of pea, chickpea, maize, and barley was recorded for inoculations under controlled conditions. Field testing with the pea also showed a significant increment in plant growth and yield. The rifampicin mutant of the bacterial strain effectively colonized the pea rhizosphere without adversely affecting the resident microbial populations. PMID:19137371

  4. Rhizosphere microbiome assemblage is affected by plant development

    PubMed Central

    Chaparro, Jacqueline M; Badri, Dayakar V; Vivanco, Jorge M

    2014-01-01

    There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P<0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage. PMID:24196324

  5. IMPACT OF SOIL MANAGEMENT ON COTTON RHIZOSPHERE BACTERIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil dwelling bacteria and fungi are responsible for a number of ecosystem services critical to agriculture. In particular, bacteria living in the rhizosphere (portion of soil directly influenced by plant roots) and arbuscular mycorrhizal fungi have been shown to improve nutrient and water uptake an...

  6. PSEUDOMONAS GENE EXPRESSION DURING GROWTH IN THE RHIZOSPHERE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The plant rhizosphere is a nutrient rich oasis for soil dwelling microbes, both benevolent and pathogenic. Perhaps one of the best-studied groups of bacteria that live in this niche are the fluorescent pseudomonads. This due to the variety of traits they display, such as secondary metabolite produ...

  7. Accelerated aromatic compounds degradation in aquatic environment by use of interaction between Spirodela polyrrhiza and bacteria in its rhizosphere.

    PubMed

    Toyama, Tadashi; Yu, Ning; Kumada, Hirohide; Sei, Kazunari; Ike, Michihiko; Fujita, Masanori

    2006-04-01

    Accelerated degradation of organic chemicals by aquatic plant-bacterial associations was reported for the first time with elucidation of the role and contribution of aquatic plant and bacteria in its rhizosphere using a fast-growing giant duckweed, Spirodela polyrrhiza. The results clearly showed the accelerated degradation of all the three aromatic compounds (phenol, aniline and 2,4-dichlorophenol [2,4-DCP]) tested by aquatic plant-bacterial associations. In phenol degradation system, phenol-degrading bacteria indigenous to the rhizosphere fraction of S. polyrrhiza mainly contributed, while in aniline degradation system S. polyrrhiza mainly contributed by stimulating aniline-degrading bacteria both in the rhizosphere and balk water fraction. On the other hand in 2,4-DCP degradation system, S. polyrrhiza itself mainly contributed to its removal by uptake and degradation. Thus, the mechanisms for accelerated removal of aromatic compounds were quite different depending on the substrates. S. polyrrhiza showed selective accumulation of phenol-degrading bacteria in its rhizosphere fraction, while aniline- and 2,4-DCP-degrading bacteria were not much accumulated. S. polyrrhiza secreted peroxidase and laccase. However, both of the enzymatic activities increased with the addition of aromatic compounds, degrading ability of S. polyrrhiza itself should be owing to the production of peroxidase rather than laccase because the change of peroxidase activity and concentration of each aromatic compound well concurred. From the results obtained in the present study, it can be concluded that the feasibility of the use of aquatic plant-bacterial associations to accelerate the degradation of organic chemicals especially recalcitrant compounds in aquatic environment was shown. PMID:16716944

  8. Does the rhizosphere hydrophobicity limit root water uptake?

    NASA Astrophysics Data System (ADS)

    Zare, Mohsen; Ahmed, Mutez; Kroener, Eva; Carminati, Andrea

    2015-04-01

    The ability of plants to extract water from the soil is influenced by the hydraulic conductivity of roots and their rhizosphere. Recent experiments showed that the rhizosphere turned hydrophobic after drying and it remained dry after rewetting [1]. Our objective was to investigate whether rhizosphere hydrophobicity is a limit to root water uptake after drying. To quantify the effect of rhizosphere hydrophobicity on root water uptake, we used neutron radiography to trace the transport of deuterated water (D2O) in the roots of lupines experiencing a severe, local soil drying. The plants were grown in aluminum containers (30×30×1 cm) filled with sandy soil. The soil was partitioned into nine compartments using three horizontal and three vertical layers of coarse sand (thickness of 1cm) as capillary barrier. When the plants were 28 days old, we let one of the upper lateral compartments dry to a water content of 2-4%, while keeping the other compartments to a water content of 20%. Then we injected 10 ml of D2O in the dry compartment and 10 ml in the symmetric location. The radiographs showed that root water uptake in the soil region that was let dry and then irrigated was 4-8 times smaller than in the wet soil region[2]. In a parallel experiment, we used neutron radiography to monitor the rehydration of lupine roots that were irrigated after a severe drying experiment. Based on root swelling and additional data on the xylem pressure, we calculated the hydraulic conductivity of the root-rhizosphere continuum. We found that the hydraulic conductivity of the root-rhizosphere continuum was initially 5.75×10-14 m s-1and it increased to 4.26×10-12 m s-1after four hours. Both experiments show that rhizosphere hydrophobicity after drying is associated with a reduction in root water uptake and a big decrease in hydraulic conductivity of the soil-root system. [1] Carminati et al (2010) Plant and Soil. Vol. 332: 163-176. [2] Zarebanadkouki and Carmianti (2013) Journal of Plant

  9. 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

  10. Characterization of mineral phosphate solubilization traits from a barley rhizosphere soil functional metagenome.

    PubMed

    Chhabra, Sagar; Brazil, Dina; Morrissey, John; Burke, James I; O'Gara, Fergal; N Dowling, David

    2013-10-01

    Mineral phosphate solubilization (MPS) microorganisms are important for their provision of orthophosphate anions for plant growth promotion activity in soil. In this study, we applied a functional metagenomic approach to identify this trait directly from the microbiome in barley rhizosphere soil that had not received P fertilizer over a 15-year period. A fosmid system was used to clone the metagenome of which 18,000 clones (~666 Mb of DNA) was screened for MPS. Functional assays and High Performance Liquid Chromatography analysis recognized gluconic acid production and MPS activity in the range 24.8-77.1 mmol/L and 27.6-38.16 μg/mL, respectively, when screened in an Escherichia coli host (at frequency of one MPS-positive clone hit per 114 Mb DNA tested). The MPS clones (with average insert size of ~37 kb) were analysed by 454 Roche sequencing and annotated. A number of genes/operons with homology to Phosphorous (P) uptake, regulatory and solubilization mechanisms were identified, linking the MPS function to the uncultivated microbiome present in barley rhizosphere soil. PMID:23894099

  11. Population densities and genetic diversity of actinomycetes associated to the rhizosphere of Theobroma cacao

    PubMed Central

    Barreto, Tâmara R.; da Silva, Augusto C.M.; Soares, Ana Cristina F.; de Souza, Jorge T.

    2008-01-01

    In spite of the acknowledged importance of growth-promoting bacteria, only a reduced number of studies were conducted with these microorganisms on Theobroma cacao. The objectives of this work were to study the population densities and genetic diversity of actinomycetes associated with the rhizosphere of cacao as a first step in their application in plant growth promotion and biological control. The populations densities of actinomycetes in soil and cacao roots were similar, with mean values of 1,0 x 106 CFU/g and 9,6 x 105 CFU/g, respectively. All isolates selected and used in this study were identified through sequencing analyses of a fragment of the rpoB gene that encodes the β-subunit of the RNA polymerase as species of the genus Streptomyces. In vitro cellulolytic, xilanolytic and chitinolytic activity, indolacetic acid production and phosphate solubilization activities were observed in most of the isolates tested. The data obtained in this study demonstrate that actinomycetes account for a higher percentage of the total population of culturable bacteria in soil than on cacao roots. Additionally, actinomycetes from the cacao rhizosphere are genetically diverse and have potential applications as agents of growth promotion. PMID:24031247

  12. Bacteriocins from the rhizosphere microbiome - from an agriculture perspective.

    PubMed

    Subramanian, Sowmyalakshmi; Smith, Donald L

    2015-01-01

    most effective at 100 mM NaCl. The 48 h post germination proteome suggested efficient and speedier partitioning of storage proteins, activation of carbon, nitrogen and energy metabolisms in Th17 treated seeds both under optimal and 100 mM NaCl. This review focuses on the bacteriocins produced by plant-rhizosphere colonizers and plant-pathogenic bacteria, that might have uses in agriculture, veterinary, and human medicine. PMID:26579159

  13. Bacteriocins from the rhizosphere microbiome – from an agriculture perspective

    PubMed Central

    Subramanian, Sowmyalakshmi; Smith, Donald L.

    2015-01-01

    most effective at 100 mM NaCl. The 48 h post germination proteome suggested efficient and speedier partitioning of storage proteins, activation of carbon, nitrogen and energy metabolisms in Th17 treated seeds both under optimal and 100 mM NaCl. This review focuses on the bacteriocins produced by plant-rhizosphere colonizers and plant-pathogenic bacteria, that might have uses in agriculture, veterinary, and human medicine. PMID:26579159

  14. Population Dynamics of Soil Pseudomonads in the Rhizosphere of Potato (Solanum tuberosum L.).

    PubMed

    Loper, J E; Haack, C; Schroth, M N

    1985-02-01

    Rhizosphere population dynamics of seven Pseudomonas fluorescens and Pseudomonas putida strains isolated from rhizospheres of various agricultural plants were studied on potato (Solanum tuberosum L.) in field soil under controlled environmental conditions. Rhizosphere populations of two strains (B10 and B4) were quantitatively related to initial seed piece inoculum levels when plants were grown at -0.3 bar matric potential. At a given inoculum level, rhizosphere populations of strain B4 were consistently greater than those of strain B10. In vivo growth curves on 4-cm root tip-proximal segments indicated that both strains grew at similar rates in the potato rhizosphere, but large populations of strain B10 were not maintained at 24 degrees C after 7 h, whereas those of strain B4 were maintained for at least 40 h. Although both strains grew more rapidly in the rhizosphere at 24 degrees C than at 12 degrees C, their rhizosphere populations after seed piece inoculation were generally greater at 12 or 18 degrees C, indicating that in vivo growth did not solely determine rhizosphere populations in these studies. In vitro osmotolerance of seven Pseudomonas strains (including strains B4 and B10) was correlated with their abilities to establish stable populations in the rhizosphere of potato. Stability of rhizosphere populations of the Pseudomonas strains studied here was maximized at low (i.e., 12 degrees C) soil temperatures. These results indicate that Pseudomonas strains differ in their capacity to maintain stable rhizosphere populations in association with potato. This capacity, distinct from the ability to grow in the rhizosphere, may limit the establishment of rhizosphere populations under some environmental conditions. PMID:16346729

  15. 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

  16. Isolation of plant-growth-promoting rhizobacteria from rhizospheric soil of halophytes and their impact on maize (Zea mays L.) under induced soil salinity.

    PubMed

    Ullah, Sami; Bano, Asghari

    2015-04-01

    The present investigation was aimed to scrutinize the salt tolerance potential of plant-growth-promoting rhizobacteria (PGPR) isolated from rhizospheric soil of selected halophytes (Atriplex leucoclada, Haloxylon salicornicum, Lespedeza bicolor, Suaeda fruticosa, and Salicornica virginica) collected from high-saline fields (electrical conductivity 4.3-5.5) of District Mardan, Pakistan. Five PGPR strains were identified using 16S rRNA amplification and sequence analysis. Bacillus sp., isolated from rhizospheric soil of Atriplex leucoclada, and Arthrobacter pascens, isolated from rhizospheric soil of Suaeda fruticosa, are active phosphate solubilizers and bacteriocin and siderophore producers; hence, their inoculation and co-inoculation on maize ('Rakaposhi') under induced salinity stress enhanced shoot and root length and shoot and root fresh and dry mass. The accumulation of osmolytes, including sugar and proline, and the elevation of antioxidant enzymes activity, including superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase, were enhanced in the maize variety when inoculated and co-inoculated with Bacillus sp. and Arthrobacter pascens. The PGPR (Bacillus sp. and A. pascens) isolated from the rhizosphere of the mentioned halophytes species showed reliability in growth promotion of maize crop in all the physiological parameters; hence, they can be used as bio-inoculants for the plants growing under salt stress. PMID:25776270

  17. Rhizosphere microbial community composition affects cadmium and zinc uptake by the metal-hyperaccumulating plant Arabidopsis halleri.

    PubMed

    Muehe, E Marie; Weigold, Pascal; Adaktylou, Irini J; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas; Behrens, Sebastian

    2015-03-01

    The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a "native" and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, "Candidatus Chloracidobacterium") of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

  18. Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

    PubMed Central

    Muehe, E. Marie; Weigold, Pascal; Adaktylou, Irini J.; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

    2015-01-01

    The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

  19. Bacterial rhizosphere and endosphere populations associated with grasses and trees to be used for phytoremediation of crude oil contaminated soil.

    PubMed

    Fatima, Kaneez; Afzal, Muhammad; Imran, Asma; Khan, Qaiser M

    2015-03-01

    Different grasses and trees were tested for their growth in a crude oil contaminated soil. Three grasses, Lolium perenne, Leptochloa fusca, Brachiaria mutica, and two trees, Lecucaena leucocephala and Acacia ampliceps, were selected to investigate the diversity of hydrocarbon-degrading rhizospheric and endophytic bacteria. We found a higher number of hydrocarbon degrading bacteria associated with grasses than trees and that the endophytic bacteria were taxonomically different from rhizosphere associated bacteria showing their spatial distribution with reference to plant compartment as well as genotype. The rhizospheric soil yielded 22 (59.45 %), root interior yielded 9 (24.32 %) and shoot interior yielded 6 (16.21 %) hydrocarbon-degrading bacteria. These bacteria possessed genes encoding alkane hydroxylase and showed multiple plant growth-promoting activities. Bacillus (48.64 %) and Acinetobacter (18.91 %) were dominant genera found in this study. At 2 % crude oil concentration, all bacterial isolates exhibited 25 %-78 % oil degradation and Acinetobacter sp. strain BRSI56 degraded maximum. Our study suggests that for practical application, support of potential bacteria combined with the grasses is more effective approach than trees to remediate oil contaminated soils. PMID:25661008

  20. 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

  1. Rice Bran Amendment Suppresses Potato Common Scab by Increasing Antagonistic Bacterial Community Levels in the Rhizosphere.

    PubMed

    Tomihama, Tsuyoshi; Nishi, Yatsuka; Mori, Kiyofumi; Shirao, Tsukasa; Iida, Toshiya; Uzuhashi, Shihomi; Ohkuma, Moriya; Ikeda, Seishi

    2016-07-01

    Potato common scab (PCS), caused by pathogenic Streptomyces spp., is a serious disease in potato production worldwide. Cultural practices, such as optimizing the soil pH and irrigation, are recommended but it is often difficult to establish stable disease reductions using these methods. Traditionally, local farmers in southwest Japan have amended soils with rice bran (RB) to suppress PCS. However, the scientific mechanism underlying disease suppression by RB has not been elucidated. The present study showed that RB amendment reduced PCS by repressing the pathogenic Streptomyces population in young tubers. Amplicon sequencing analyses of 16S ribosomal RNA genes from the rhizosphere microbiome revealed that RB amendment dramatically changed bacterial composition and led to an increase in the relative abundance of gram-positive bacteria such as Streptomyces spp., and this was negatively correlated with PCS disease severity. Most actinomycete isolates derived from the RB-amended soil showed antagonistic activity against pathogenic Streptomyces scabiei and S. turgidiscabies on R2A medium. Some of the Streptomyces isolates suppressed PCS when they were inoculated onto potato plants in a field experiment. These results suggest that RB amendment increases the levels of antagonistic bacteria against PCS pathogens in the potato rhizosphere. PMID:27050572

  2. Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria

    PubMed Central

    Ballhausen, Max-Bernhard; van Veen, Johannes A.; Hundscheid, Maria P. J.; de Boer, Wietse

    2015-01-01

    Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae. PMID:26733962

  3. A cytochrome cd1-type nitrite reductase isolated from the marine denitrifier Pseudomonas nautica 617: purification and characterization.

    PubMed

    Besson, S; Carneiro, C; Moura, J J; Moura, I; Fauque, G

    1995-08-01

    Nitrite reductase (cytochrome cd1) was purified to electrophoretic homogeneity from the soluble extract of the marine denitrifying bacterium Pseudomonas nautica strain 617. Cells were anaerobically grown with 10 mM nitrate as final electron acceptor. The soluble fraction was purified by four successive chromatographic steps and the purest cytochrome cd1 exhibited an A280 nm(oxidized)/A410nm(oxidized) coefficient of 0.90. In the course of purification, cytochrome cd1 specific activity presented a maximum value of 0.048 units/mg of protein. This periplasmic enzyme is a homodimer and each 60 kDa subunit contains one heme c and one heme d1 as prosthetic moieties, both in a low spin state. Redox potentials of hemes c and d1 were determined at three different pH values (6.6, 7.6 and 8.6) and did not show any pH dependence. The first 20 amino acids of the NH2-terminal region of the protein were identified and the sequence showed 45% identity with the corresponding region of Pseudomonas aeruginosa nitrite reductase but no homology to Pseudomonas stutzeri and Paracoccus denitrificans enzymes. Spectroscopic properties of Pseudomonas nautica 617 cytochrome cd1 in the ultraviolet-visible range and in electron paramagnetic resonance are described. The formation of a heme d1 -nitric-oxide complex as an intermediate of nitrite reduction was demonstrated by electron paramagnetic resonance experiments. PMID:16887530

  4. Rhizosphere mycoflora of healthy and yellow vein mosaic virus infected okra (Abelmoschus esculentus) plants.

    PubMed

    Singh, S J; Tewari, R P

    1979-01-01

    Investigations on the rhizosphere mycoflora of healthy and virus (YVMV) infected okra plants showed a higher fungal population in the rhizosphere of healthy plants at preflowering and post-flowering stages than in that of diseased ones. Maximum population was observed during flowering both in healthy and diseased plant rhizosphere as well as in non-rhizosphere soil. However, virus infected plants showed a higher population at the flowering stage than healthy ones. The quantitative differences in the rhizosphere of healthy and diseased plants during flowering seem to be due to a change in C/N ratio and amino acids. The drastic reduction in diseased plant rhizospheres during the post-flowering stage may be due to either change in C/N ratio unfavourable to mycoflora or production of some toxic substances inhibiting multiplication of the mycoflora. PMID:94749

  5. Novel Biochar-Plant Tandem Approach for Remediating Hexachlorobenzene Contaminated Soils: Proof-of-Concept and New Insight into the Rhizosphere.

    PubMed

    Song, Yang; Li, Yang; Zhang, Wei; Wang, Fang; Bian, Yongrong; Boughner, Lisa A; Jiang, Xin

    2016-07-13

    Volatilization of semi/volatile persistent organic pollutants (POPs) from soils is a major source of global POPs emission. This proof-of-concept study investigated a novel biochar-plant tandem approach to effectively immobilize and then degrade POPs in soils using hexachlorobenzene (HCB) as a model POP and ryegrass (Lolium perenne L.) as a model plant growing in soils amended with wheat straw biochar. HCB dissipation was significantly enhanced in the rhizosphere and near rhizosphere soils, with the greatest dissipation in the 2 mm near rhizosphere. This enhanced HCB dissipation likely resulted from (i) increased bioavailability of immobilized HCB and (ii) enhanced microbial activities, both of which were induced by ryegrass root exudates. As a major component of ryegrass root exudates, oxalic acid suppressed HCB sorption to biochar and stimulated HCB desorption from biochar and biochar-amended soils, thus increasing the bioavailability of HCB. High-throughput sequencing results revealed that the 2 mm near rhizosphere soil showed the lowest bacterial diversity due to the increased abundance of some genera (e.g., Azohydromonas, Pseudomonas, Fluviicola, and Sporocytophaga). These bacteria were likely responsible for the enhanced degradation of HCB as their abundance was exponentially correlated with HCB dissipation. The results from this study suggest that the biochar-plant tandem approach could be an effective strategy for remediating soils contaminated with semi/volatile organic contaminants. PMID:27327363

  6. Altitudinal Gradient of Microbial Biomass Phosphorus and Its Relationship with Microbial Biomass Carbon, Nitrogen, and Rhizosphere Soil Phosphorus on the Eastern Slope of Gongga Mountain, SW China

    PubMed Central

    Sun, Hongyang; Wu, Yanhong; Yu, Dong; Zhou, Jun

    2013-01-01

    Microbial biomass phosphorus (MBP) is one of the most active forms of phosphorus (P) in soils. MBP plays an important role in the biogeochemical P cycle. To explore MBP distribution and its relationship with other factors, the MBP and rhizosphere soil P concentrations and fractions in six vegetation zones on the eastern slope of Gongga Mountain in SW China were investigated. The MBP distribution followed a parabolic pattern with altitude and the concentration was highest in the subalpine dark coniferous forest (SDC) zone, which was approximately 3500 m above sea level (asl). Below 3500 m asl, the MBP distribution was controlled by precipitation and vegetation type. In addition, temperature, precipitation and vegetation type controlled the MBP distribution at elevations above 3500 m asl. No specific distribution pattern was determined regarding rhizosphere soil P fractions. However, MBP was significantly correlated with the unavailable P fraction in the rhizosphere rather than with the available P fraction. This result suggests that the relationships between the rhizosphere soil P fractions and the MBP depend on time. The microbial biomass element ratios were relatively consistent on the eastern slope of Gongga Mountain. However, variations in the microbial biomass element rations were observed in six of the vegetation zones. The mean C:N:P ratio was 9.0∶1.3∶1. Overall, vegetation type resulted in the observed fluctuations of the microbial biomass element ratio. PMID:24039830

  7. The "Biased Rhizosphere" Concept: Bacterial Competitiveness and Persistence in the Rhizosphere

    NASA Astrophysics Data System (ADS)

    de Bruijn, Frans J.

    2013-04-01

    The association of plant surfaces with microorganisms has been the subject of intense investigations. Numerous processes have been shown to be important in plant-associative bacteria including attachment, motility, chemotaxis, nutrition, and production of signaling molecules and secondary metabolites. One strategy to favor the competitiveness and persistence of bacteria in the plant environment relies upon manipulation of nutritional compounds secreted into the phytosphere, which comprises the rhizosphere (root surface/zone influenced by secretions) and the phyllosphere (leaf surface/zone influenced by secretions). The pattern of plant host exudate can be bred or engineered to establish "biased phytospheres" with bacteria that can naturally, or by engineering, use metabolic resources produced by the host plant. Over the last two decades, natural biases, generated by opine-like molecules of Agrobacterium-plant interactions and by rhizopine-like molecules of the Rhizobium-legume interactions, have provided tactics based on unique metabolites produced by plants to favor the competitiveness and persistence of bacteria that can catabolize the host-produced novel nutrients. An overview of this field or research will be presented.

  8. Distribution of root exudates and mucilage in the rhizosphere: combining 14C imaging with neutron radiography

    NASA Astrophysics Data System (ADS)

    Holz, Maire; Carminati, Andrea; Kuzyakov, Yakov

    2015-04-01

    Water and nutrients will be the major factors limiting food production in future. Plant roots employ various mechanisms to increase the access to limited soil resources. Low molecular weight organic substances released by roots into the rhizosphere increase nutrient availability by interactions with microorganisms, while mucilage improves water availability under low moisture conditions. Though composition and quality of these substances have intensively been investigated, studies on the spatial distribution and quantification of exudates in soil are scarce. Our aim was to quantify and visualize root exudates and mucilage distribution around growing roots using neutron radiography and 14C imaging depending on drought stress. Plants were grown in rhizotrons well suited for neutron radiography and 14C imaging. Plants were exposed to various soil water contents experiencing different levels of drought stress. The water content in the rhizosphere was imaged during several drying/wetting cycles by neutron radiography. The radiographs taken a few hours after irrigation showed a wet region around the root tips showing the allocation and distribution of mucilage. The increased water content in the rhizosphere of the young root segments was related to mucilage concentrations by parameterization described in Kroener et al. (2014). In parallel 14C imaging of root after 14CO2 labeling of shoots (Pausch and Kuzyakov 2011) showed distribution of rhizodeposits including mucilage. Three days after setting the water content, plants were labeled in 14CO2 atmosphere. Two days later 14C distribution in soil was imaged by placing a phosphor-imaging plate on the rhizobox. To quantify rhizodeposition, 14C activity on the image was related to the absolute 14C activity in the soil and root after destructive sampling. By comparing the amounts of mucilage (neutron radiography) with the amount of total root derived C (14C imaging), we were able to differentiate between mucilage and root

  9. Feasibility of enhancing the DEnitrifying AMmonium OXidation (DEAMOX) process for nitrogen removal by seeding partial denitrification sludge.

    PubMed

    Cao, Shenbin; Peng, Yongzhen; Du, Rui; Wang, Shuying

    2016-04-01

    The recently proposed DEnitrifying AMmonium OXidation (DEAMOX) process combined anaerobic ammonia oxidation (ANAMMOX) with denitrification to convert nitrate to nitrite, which was a promising way for treating wastewater containing nitrate and ammonia. This study investigated the feasibility of establishing DEAMOX process by seeding partial denitrification sludge (NO3(-) → NO2(-)) using sodium acetate as an electron donor in a sequencing batch reactor. Results showed that the DEAMOX process was established successfully and operated stably in 114-days operation. The average effluent total nitrogen concentration was below 5 mg L(-1) and TN removal efficiency reached up to 97% at COD/NO3(-) ratio of 3.0 under initial NH4(+) concentration of 25 mg L(-1) and NO3(-) of 30 mg L(-1). It suggested that the presence of NO2(-) in the system supplied for ANAMMOX and the relatively long sludge retention time (SRT) for denitrifiers were attributed to commendable coexistence of ANAMMOX and denitrifying bacteria. PMID:26829308

  10. Fecal Bacteria, Bacteriophage, and Nutrient Reductions in a Full-Scale Denitrifying Woodchip Bioreactor.

    PubMed

    Rambags, Femke; Tanner, Chris C; Stott, Rebecca; Schipper, Louis A

    2016-05-01

    Denitrifying bioreactors using woodchips or other slow-release carbon sources can be an effective method for removing nitrate (NO) from wastewater and tile drainage. However, the ability of these systems to remove fecal microbes from wastewater has been largely uninvestigated. In this study, reductions in fecal indicator bacteria () and viruses (F-specific RNA bacteriophage [FRNA phage]) were analyzed by monthly sampling along a longitudinal transect within a full-scale denitrifying woodchip bioreactor receiving secondary-treated septic tank effluent. Nitrogen, phosphorus, 5-d carbonaceous biochemical oxygen demand (CBOD), and total suspended solids (TSS) reduction were also assessed. The bioreactor demonstrated consistent and substantial reduction of (2.9 log reduction) and FRNA phage (3.9 log reduction) despite receiving highly fluctuating inflow concentrations [up to 3.5 × 10 MPN (100 mL) and 1.1 × 10 plaque-forming units (100 mL) , respectively]. Most of the removal of fecal microbial contaminants occurred within the first meter of the system (1.4 log reduction for ; 1.8 log reduction for FRNA phage). The system was also efficient at removing NO (>99.9% reduction) and TSS (89% reduction). There was no evidence of consistent removal of ammonium, organic nitrogen, or phosphorus. Leaching of CBOD occurred during initial operation but decreased and stabilized at lower values (14 g O m) after 9 mo. We present strong evidence for reliable microbial contaminant removal in denitrifying bioreactors, demonstrating their broader versatility for wastewater treatment. Research on the removal mechanisms of microbial contaminants in these systems, together with the assessment of longevity of removal, is warranted. PMID:27136150

  11. Performance of Agricultural Residue Media in Laboratory Denitrifying Bioreactors at Low Temperatures.

    PubMed

    Feyereisen, Gary W; Moorman, Thomas B; Christianson, Laura E; Venterea, Rodney T; Coulter, Jeffrey A; Tschirner, Ulrike W

    2016-05-01

    Denitrifying bioreactors can be effective for removing nitrate from agricultural tile drainage; however, questions about cold springtime performance persist. The objective of this study was to improve the nitrate removal rate (NRR) of denitrifying bioreactors at warm and cold temperatures using agriculturally derived media rather than wood chips (WC). Corn ( L.) cobs (CC), corn stover (CS), barley ( L.) straw (BS), WC, and CC followed by a compartment of WC (CC+WC) were tested in laboratory columns for 5 mo at a 12-h hydraulic residence time in separate experiments at 15.5 and 1.5°C. Nitrate-N removal rates ranged from 35 to 1.4 at 15.5°C and from 7.4 to 1.6 g N m d at 1.5°C, respectively; NRRs were ranked CC > CC+WC > BS = CS > WC and CC ≥ CC+WC = CS ≥ BS > WC for 15.5 and 1.5°C, respectively. Although NRRs for CC were increased relative to WC, CC released greater amounts of carbon. Greater abundance of nitrous oxide (NO) reductase gene () was supported by crop residues than WC at 15.5°C, and CS and BS supported greater abundance than WC at 1.5°C. Production of NO relative to nitrate removal (NO) was consistently greater at 1.5°C (7.5% of nitrate removed) than at 15.5°C (1.9%). The NO was lowest in CC (1.1%) and CC-WC (0.9%) and greatest in WC (9.7%). Using a compartment of agricultural residue media in series before wood chips has the potential to improve denitrifying bioreactor nitrate removal rates, but field-scale verification is needed. PMID:27136142

  12. Moving Denitrifying Bioreactors beyond Proof of Concept: Introduction to the Special Section.

    PubMed

    Christianson, Laura E; Schipper, Louis A

    2016-05-01

    Denitrifying bioreactors are organic carbon-filled excavations designed to enhance the natural process of denitrification for the simple, passive treatment of nitrate-nitrogen. Research on and installation of these bioreactors has accelerated within the past 10 years, particularly in watersheds concerned about high nonpoint-source nitrate loads and also for tertiary wastewater treatment. This special section, inspired by the meeting of the Managing Denitrification in Agronomic Systems Community at the 2014 Annual Meeting of the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, aims to firmly establish that denitrifying bioreactors for treatment of nitrate in drainage waters, groundwater, and some wastewaters have moved beyond the proof of concept. This collection of 14 papers expands the peer-reviewed literature of denitrifying bioreactors into new locations, applications, and environmental conditions. There is momentum behind the pairing of wood-based bioreactors with other media (biochar, corn cobs) and in novel designs (e.g., use within treatment trains or use of baffles) to broaden applicability into new kinds of waters and pollutants and to improve performance under challenging field conditions such as cool early season agricultural drainage. Concerns about negative bioreactor by-products (nitrous oxide and hydrogen sulfide emissions, start-up nutrient flushing) are ongoing, but this translates into a significant research opportunity to develop more advanced designs and to fine tune management strategies. Future research must think more broadly to address bioreactor impacts on holistic watershed health and greenhouse gas balances and to facilitate collaborations that allow investigation of mechanisms within the bioreactor "black box." PMID:27136139

  13. Relating Phylogenetic and Functional Diversity among Denitrifiers and Quantifying their Capacity to Predict Community Functioning

    PubMed Central

    Salles, Joana Falcão; Le Roux, Xavier; Poly, Franck

    2012-01-01

    Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear to what extent functional diversity (FD), gene sequence diversity and community functioning are linked. For a range of denitrifying bacteria, we analyzed the relationships between (i) the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates) or from N2O accumulation patterns on different carbon sources and (ii) the similarity of phylogenetic (16S rRNA gene) or functional (nir gene) markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic (16S rRNA gene) or functional similarities (based either on metabolic profiles or N2O accumulation patterns), and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence was weakly correlated with the variation in metabolic patterns (ρ = 0.35) and was not related to N2O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analyzed separately, the similarity in amino acids coded by the nirS genes was highly correlated with the observed patterns of N2O accumulation (ρ = 0.62), whereas nirK amino acid residues were unrelated to N2O accumulation. For bacterial assemblages, phylogenetic diversity (average similarity among species in a community) and mean community dissimilarity (average distance between species) calculated using 16S rRNA gene sequences, and FD measures associated with metabolic profiles, poorly predicted the variation in the functioning of assembled communities (≤15%). In contrast, the proxies of FD based on N2O accumulation patterns performed better and explained from 23 to 42% of the variation in denitrification. Amongst those, community niche was the best metric, indicating the importance of complementarity for

  14. Acetate enhances the specific consumption rate of toluene under denitrifying conditions.

    PubMed

    Martínez-Hernández, Sergio; Olguín, Eugenia J; Gómez, Jorge; Cuervo-López, Flor de María

    2009-11-01

    Toluene is usually present in the environment as a contaminant along with other carbon sources which may influence its removal. In this work we studied the effect of a readily consumable carbon source such as acetate on toluene mineralization under denitrifying conditions. Continuous and batch cultures with stabilized denitrifying sludge were carried out. An upflow anaerobic sludge blanket reactor (UASB) was fed with several ratios of acetate-C/toluene-C loading rates (mg C/L-day: 100/0, 75/25, 50/50, and 0/100). Batch assays with different acetate-C/toluene-C ratios (10/70, 30/50, 50/30, and 65/20 mg C/L) were also done. As the acetate loading rate decreased in the culture, the carbon and nitrate consumption efficiency decreased by 40% and 34%, respectively. HCO(3) (-) and N(2) yields also decreased by 43%. Analysis of the denitrifying community using the denaturing gradient gel electrophoresis technique indicated that there was no clear relationship between its population profile and the metabolic pattern. In batch assays, when the acetate concentration was higher than that of toluene (65 mg acetate-C/L vs 20 mg toluene-C/L), the specific consumption rate of toluene (q(T)) was two times higher than in assays with 20 mg toluene-C/L as the sole electron source (0.006 mg C/mg volatile suspended solids-day). It is proposed that acetate can act by enhancing the growth of microbial populations and as a biochemical enhancer. The results show that acetate addition can be useful to improve the consumption rate of toluene in contaminated water. PMID:19387525

  15. The Impact of Rhizosphere Processes on Water Flow and Root Water Uptake

    NASA Astrophysics Data System (ADS)

    Schwartz, Nimrod; Kroener, Eva; Carminati, Andrea; Javaux, Mathieu

    2015-04-01

    For many years, the rhizosphere, which is the zone of soil in the vicinity of the roots and which is influenced by the roots, is known as a unique soil environment with different physical, biological and chemical properties than those of the bulk soil. Indeed, in recent studies it has been shown that root exudate and especially mucilage alter the hydraulic properties of the soil, and that drying and wetting cycles of mucilage result in non-equilibrium water dynamics in the rhizosphere. While there are experimental evidences and simplified 1D model for those concepts, an integrated model that considers rhizosphere processes with a detailed model for water and roots flow is absent. Therefore, the objective of this work is to develop a 3D physical model of water flow in the soil-plant continuum that take in consideration root architecture and rhizosphere specific properties. Ultimately, this model will enhance our understanding on the impact of processes occurring in the rhizosphere on water flow and root water uptake. To achieve this objective, we coupled R-SWMS, a detailed 3D model for water flow in soil and root system (Javaux et al 2008), with the rhizosphere model developed by Kroener et al (2014). In the new Rhizo-RSWMS model the rhizosphere hydraulic properties differ from those of the bulk soil, and non-equilibrium dynamics between the rhizosphere water content and pressure head is also considered. We simulated a wetting scenario. The soil was initially dry and it was wetted from the top at a constant flow rate. The model predicts that, after infiltration the water content in the rhizosphere remained lower than in the bulk soil (non-equilibrium), but over time water infiltrated into the rhizosphere and eventually the water content in the rhizosphere became higher than in the bulk soil. These results are in qualitative agreement with the available experimental data on water dynamics in the rhizosphere. Additionally, the results show that rhizosphere processes

  16. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms.

    PubMed

    Mendes, Rodrigo; Garbeva, Paolina; Raaijmakers, Jos M

    2013-09-01

    Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health. PMID:23790204

  17. Tracing the flow of plant carbohydrates into the rhizosphere

    NASA Astrophysics Data System (ADS)

    Gleixner, Gerd

    2016-04-01

    We investigated the flow of 13C labeled CO2 from plant sugars in leaves, stems and roots into rhizospheric organisms, respired CO2 and soil organic matter in order to better understand the role of the plant-microorganism-soil-continuum for ecosystem carbon cycling. We compared trees and grassland species that had different sugar transport strategies, storage compartments, community compositions and environmental stresses. We used short but highly enriched 13C pulses at controlled CO2 concentrations and temperatures that avoided non-physiological plant responses. We used compound specific 13C measurements of sugars and phospholipids (PLFA) to calculate the carbon turnover of plant sugars and rhizospheric microorganisms. Our results unexpectedly identified transport limitations in the root-shoot carbohydrate transfer, diurnal variations in label respiration and community effects in the carbon transfer to microbial groups. Our results highlight that sophisticated experimental setups and analytical techniques are necessary to gain new knowledge on ecosystem carbon cycling under climate change.

  18. Assessment of functional and genetic diversity of aerobic endospore forming Bacilli from rhizospheric soil of Phyllanthus amarus L.

    PubMed

    Kadyan, Sangeeta; Panghal, Manju; Kumar, Sandeep; Singh, Khushboo; Yadav, Jaya Parkash

    2013-09-01

    Fifty two aerobic and endospore forming Bacilli (AEFB) strains were recovered from rhizospheric soil of Phyllanthus amarus. Morphological, biochemical and molecular characterization by 16S rDNA gene sequencing has shown that these bacterial strains belong to six different genera of AEFB i.e. Bacillus, Brevibacillus, Lysinibacillus, Paenibacillus, Terribacillus and Jeotgalibacillus. Analysis of their PGP activities has shown that 92.30 % strains produced indole acetic acid hormone, 86.53 % of the strains solubilized Phosphate and 44.23 % strains produced siderophore. Chitinase production activity was shown by 42.30 % of the strains and 21.15 % of the strains produced 1-amino cyclopropane-1-carboxylate (ACC) deaminase. 46.15 % of isolates have shown antagonistic activity against common fungal pathogen of the plant i.e. Corynespora cassiicola. Among all of the isolated strains B. Cereus JP44SK22 and JP44SK42 have shown all of the six plant growth promoting traits tested. B. megaterium strains (JP44SK18 and JP44SK35), Lysinibacillus sphaericus strains (JP44SK3 and JP44SK4) and Brevibacillus laterosporus strain JP44SK51 have also shown multiple PGP activities except ACC deaminase production activity. In the present study bacterial strain belonging to genera Jeotgalibacillus sp. JP44SK37 has been reported first time as a member of rhizospheric soil habitat and has also shown PGP activities. It can be concluded that Rhizosphere of P. amarus has harboured a good diversity of AEFB bacterial strains having a lot of biofertilizing and biocontrol abilities. PMID:23526192

  19. The Dynamics of Sediment Oxygenation in Marsh Rhizospheres

    NASA Astrophysics Data System (ADS)

    Koop-Jakobsen, K.

    2014-12-01

    Many marsh grasses are capable of internal oxygen transport from aboveground sources to belowground roots and rhizomes, where oxygen may leak across the rhizodermis and oxygenate the surrounding sediment. In the field, the extent of sediment oxygenation in marshes was assessed in the rhizosphere of the marsh grass; Spartina anglica, inserting 70 optical fiber oxygen sensors into the rhizosphere. Two locations with S. anglica growing in different sediment types were investigated. No oxygen was detected in the rhizospheres indicating that belowground sediment oxygenation in S. anglica has a limited effect on the bulk anoxic sediment and is restricted to sediment in the immediate vicinity of the roots. In the laboratory, the presence of 1.5mm wide and 16mm long oxic root zones was demonstrated around root tips of S. anglica growing in permeable sandy sediment using planar optodes recording 2D-images of the oxygen distribution. Oxic root zones in S. anglica growing in tidal flat deposits were significantly smaller. The size of oxic roots zones was highly dynamic and affected by tidal inundations as well as light availability. Atmospheric air was the primary oxygen source for belowground sediment oxygenation, whereas photosynthetic oxygen production only played a minor role for the size of the oxic root zones during air-exposure of the aboveground biomass. During tidal inundations (1.5 h) completely submerging the aboveground biomass cutting off access to atmospheric oxygen, the size of oxic root zones were reduced significantly in the light and oxic root zones were completely eliminated in darkness. Sediment oxygenation in the rhizospheres of marsh grasses is of significant importance for marshes ability to retain inorganic nitrogen before it reaches the coastal waters. The presence of oxic roots zones promotes coupled nitrification-denitrification at depth in the sediment, which can account for more than 80% of the total denitrification in marshes.

  20. Aerobic and anaerobic metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium isolated from marine sediments.

    PubMed Central

    Rontani, J F; Gilewicz, M J; Michotey, V D; Zheng, T L; Bonin, P C; Bertrand, J C

    1997-01-01

    This report describes the metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium (Marinobacter sp. strain CAB) isolated from marine sediments. Under aerobic and denitrifying conditions, this strain efficiently degraded this ubiquitous isoprenoid ketone. Several bacterial metabolites, 4,8,12-trimethyl-tridecan-1-ol, 4,8,12-trimethyltridecanal, 4,8,12-trimethyltridecanoic acid, Z-3,7-dimethylocten-2-oic acid, Z-3,7,11-trimethyldodecen-2-oic acid, and 6,10,14-trimethylpentadecan-2-ol, were formally identified, and different pathways were proposed to explain the formation of such isoprenoid compounds. PMID:9023941

  1. Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

    PubMed Central

    Wang, Xiao-Hui; Li, Jian-Gui; Qin, Wei; Xiao, Cheng-Ze; Zhao, Xu; Jiang, Hong-Xia; Sui, Jun-Kang; Sa, Rong-Bo; Wang, Wei-Yan; Liu, Xun-Li

    2015-01-01

    Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research. PMID:25685820

  2. Biodegradation of polycyclic aromatic hydrocarbons in rhizosphere soil

    SciTech Connect

    Schwab, A.P.; Banks, M.K.; Arunachalam, M.

    1995-12-31

    Increased contaminant biodegradation in soil in the presence of plants has been demonstrated for several classes of organic compounds. Although enhanced dissipation of polycyclic aromatic hydrocarbons (PAHs) was observed previously in the rhizosphere of several plant species, the mechanism of this effect has not been assessed. A laboratory experiment was conducted to test the importance of cometabolism and the presence of common rhizosphere organic acids on the loss of PAHs (pyrene and phenanthrene) from soil. The role of cometabolism in the mineralization of pyrene was tested by observing the impact of adding phenanthrene to soil containing {sup 14}C-pyrene and observing the effects on {sup 14}CO{sub 2} generation. Adding phenanthrene apparently induced cometabolism of pyrene, particularly in the presence of organic acids. In a subsequent experiment, mineralization of pyrene to {sup 14}CO{sub 2} was significantly greater in soil from the rhizospheres of warm-season grasses, sorghum (Sorghum bicolor L.) and bermuda grass (Cynodon dactylon L.), compared to soil from alfalfa (Medicago sativa L.), which did not differ from sterilized control soil. A highly branched, fine root system appears to be more effective in enhancing biodegradation than taproots, and the presence of organic acids increases rates of PAH mineralization.

  3. Microscale effects on denitrification: does the ability of denitrifying bacteria to reduce N2O depend on their position in the soil matrix?

    NASA Astrophysics Data System (ADS)

    Dörsch, Peter; Nadeem, Shahid; Almås, Åsgeir; Bakken, Lars R.

    2013-04-01

    oxygen depletion, both denitrifying communities expressed similar apparent growth rates, both produced a mixture of NO, N2O and N2, but the relative amount of N2O produced was much higher for LAC than SAC. This reemphasizes the significance of soil structure, habitable pore space, predation and bacteria-mineral interactions as regulating factors for N2O emission in mineral soils and has implications for the understanding of selection pressures for sustained N2O-reductase activity in soil.

  4. Clonal integration ameliorates the carbon accumulation capacity of a stoloniferous herb, Glechoma longituba, growing in heterogenous light conditions by facilitating nitrogen assimilation in the rhizosphere

    PubMed Central

    Chen, Jin-Song; Li, Jun; Zhang, Yun; Zong, Hao; Lei, Ning-Fei

    2015-01-01

    Background and Aims Enhanced availability of photosynthates increases nitrogen (N) mineralization and nitrification in the rhizosphere via rhizodeposition from plant roots. Under heterogeneous light conditions, photosynthates supplied by exposed ramets may promote N assimilation in the rhizosphere of shaded, connected ramets. This study was conducted to test this hypothesis. Methods Clonal fragments of the stoloniferous herb Glechoma longituba with two successive ramets were selected. Mother ramets were subjected to full sunlight and offspring ramets were subjected to 80 % shading, and the stolon between the two successive ramets was either severed or left intact. Measurements were taken of photosynthetic and growth parameters. The turnover of available soil N was determined together with the compostion of the rhizosphere microbial community. Key Results The microbial community composition in the rhizosphere of shaded offspring ramets was significantly altered by clonal integration. Positive effects of clonal integration were observed on NAGase activity, net soil N mineralization rate and net soil N nitrification rate. Increased leaf N and chlorophyll content as well as leaf N allocation to the photosynthetic machinery improved the photosynthetic capability of shaded offspring ramets when the stolon was left intact. Clonal integration improved the growth performance of shaded, connected offspring ramets and whole clonal fragments without any cost to the exposed mother ramets. Conclusions Considerable differences in microbial community composition caused by clonal integration may facilitate N assimilation in the rhizosphere of shaded offspring ramets. Increased N content in the photosynthetic machinery may allow pre-acclimation to high light conditions for shaded offspring ramets, thus promoting opportunistic light capture. In accordance with the theory of the division of labour, it is suggested that clonal integration may ameliorate the carbon assimilation

  5. 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

  6. Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA.

    PubMed

    Duineveld, B M; Kowalchuk, G A; Keijzer, A; van Elsas, J D; van Veen, J A

    2001-01-01

    The effect of developing chrysanthemum roots on the presence and activity of bacterial populations in the rhizosphere was examined by using culture-independent methods. Nucleic acids were extracted from rhizosphere soil samples associated with the bases of roots or root tips of plants harvested at different stages of development. PCR and reverse transcriptase (RT) PCR were used to amplify 16S ribosomal DNA (rDNA) and 16S rRNA, respectively, and the products were subjected to denaturing gradient gel electrophoresis (DGGE). Prominent DGGE bands were excised and sequenced to gain insight into the identities of predominantly present (PCR) and predominantly active (RT-PCR) bacterial populations. The majority of DGGE band sequences were related to bacterial genera previously associated with the rhizosphere, such as Pseudomonas, Comamonas, Variovorax, and Acetobacter, or typical of root-free soil environments, such as Bacillus and Arthrobacter. The PCR-DGGE patterns observed for bulk soil were somewhat more complex than those obtained from rhizosphere samples, and the latter contained a subset of the bands present in bulk soil. DGGE analysis of RT-PCR products detected a subset of bands visible in the rDNA-based analysis, indicating that some dominantly detected bacterial populations did not have high levels of metabolic activity. The sequences detected by the RT-PCR approach were, however, derived from a wide taxonomic range, suggesting that activity in the rhizosphere was not determined at broad taxonomic levels but rather was a strain- or species-specific phenomenon. Comparative analysis of DGGE profiles grouped all DNA-derived root tip samples together in a cluster, and within this cluster the root tip samples from young plants formed a separate subcluster. Comparison of rRNA-derived bacterial profiles showed no grouping of root tip samples versus root base samples. Rather, all profiles derived from 2-week-old plant rhizosphere soils grouped together regardless of

  7. Full-scale post denitrifying biofilters: sinks of dissolved N2O?

    PubMed

    Bollon, Julien; Filali, Ahlem; Fayolle, Yannick; Guerin, Sabrina; Rocher, Vincent; Gillot, Sylvie

    2016-09-01

    In this study, nitrous oxide (N2O) emissions from a full-scale denitrifying biofilter plant were continuously monitored over two periods (summer campaign in September 2014 and winter campaign in February 2015). Results of the summer campaign showed that the major part (>99%) of N2O flux was found in the liquid phase and was discharged with the effluent. N2O emissions were highly variable and represented in average 1.28±1.99% and 0.22±0.31% of the nitrate uptake rate during summer and winter campaigns, respectively. Denitrification was able to consume a large amount of dissolved N2O coming from the upstream nitrification stage. In the absence of methanol injection failure and with an influent BOD/NO3-N ratio higher than 3, average reduction of N2O was estimated to be of 93%. The control of exogenous carbon dosage is essential to minimize N2O production from denitrifying biofilters, in correlation to NO2-N concentrations in the filter. PMID:27139304

  8. Optimizing and real-time control of biofilm formation, growth and renewal in denitrifying biofilter.

    PubMed

    Liu, Xiuhong; Wang, Hongchen; Long, Feng; Qi, Lu; Fan, Haitao

    2016-06-01

    A pilot-scale denitrifying biofilter (DNBF) with a treatment capacity of 600m(3)/d was used to study real-time control of biofilm formation, removal and renewal. The results showed biofilm formation, growth and removal can be well controlled using on-line monitored turbidity. The status of filter layer condition can be well indicated by Turb break points on turbidity profile. There was a very good linear relationship between biofilm growth degree (Xbiof) and filter clogging degree (Cfilter) with R(2) higher than 0.99. Filter layer clogging coefficient (Yc) lower than 0.27 can be used to determine stable filter layer condition. Since variations of turbidity during backwash well fitted normal distribution with R(2) higher than 0.96, biofilm removal during backwash also can be well optimized by turbidity. Although biofilm structure and nirK-coding denitrifying communities using different carbon sources were much more different, DNBF was still successfully and stably optimized and real-time controlled via on-line turbidity. PMID:26994461

  9. Efficiency and detrimental side effects of denitrifying bioreactors for nitrate reduction in drainage water.

    PubMed

    Weigelhofer, Gabriele; Hein, Thomas

    2015-09-01

    A laboratory column experiment was conducted to test the efficiency of denitrifying bioreactors for the nitrate (NO3-N) removal in drainage waters at different flow rates and after desiccation. In addition, we investigated detrimental side effects in terms of the release of nitrite (NO2-N), ammonium (NH4-N), phosphate (PO4-P), dissolved organic carbon (DOC), methane (CH4), and dinitrogen oxide (N2O). The NO3-N removal efficiency decreased with increasing NO3-N concentrations, increasing flow rates, and after desiccation. Bioreactors with purely organic fillings showed higher NO3-N removal rates (42.6-55.7 g NO3-N m(-3) day(-1)) than those with organic and inorganic fillings (6.5-21.4 g NO3-N m(-3) day(-1)). The release of NO2-N and DOC was considerable and resulted in concentrations of up to 800 μg NO2-N L(-1)and 25 mg DOC L(-1) in the effluent water. N2O concentrations increased by 4.0 to 15.3 μg N2O-N L(-1) between the influent and the effluent, while CH4 production rates were low. Our study confirms the high potential of denitrifying bioreactors to mitigate NO3-N pollution in drainage waters, but highlights also the potential risks for the environment. PMID:25943519

  10. Controls Influencing the Treatment of Excess Agricultural Nitrate with Denitrifying Bioreactors.

    PubMed

    Pluer, William T; Geohring, Larry D; Steenhuis, Tammo S; Walter, M Todd

    2016-05-01

    Denitrifying bioreactors have been suggested as effective best management practices to reduce nitrate and nitrite (NO) in large-scale agricultural tile drainage. This study combines experiments in flow-through laboratory reactors with in situ continuous monitoring and experiments in a pair of field reactors to determine the effectiveness of reactors for small-scale agriculture in New York. It also compares the use of a typical woodchip media with a woodchip and biochar mixture. Laboratory results showed linear increase in NO removal with both increased inflow concentration and increased residence time. Average removal of NO in weekly monitoring of field reactors over the course of two growing seasons was 3.23 and 4.00 g N m d for woodchip and woodchip/biochar reactors, respectively. Removal of NO during two field experimental runs was similar to in situ monitoring and did not correlate with laboratory experiments. Factors that are uncontrollable at the field scale, such as temperature and inflow water chemistry, may result in more complex and resilient microbial communities that are less specialized for denitrification. Further study of other controlling variables, other field sites, and other parameters, including microbial communities and trace gas emissions, will help elucidate function and applicability of denitrifying bioreactors. PMID:27136141

  11. Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium.

    PubMed

    Li, Rongpeng; Zi, Xiaoli; Wang, Xinfeng; Zhang, Xia; Gao, Haofeng; Hu, Nan

    2013-01-01

    The isolation and characterization of a novel halophilic denitrifying marine bacterium is described. The halophilic bacterium, designated as NY-4, was isolated from soil in Yancheng City, China, and identified as Marinobacter hydrocarbonoclasticus by 16S rRNA gene sequence phylogenetic analysis. This organism can grow in NaCl concentrations ranging from 20 to 120 g/L. Optimum growth occurs at 80 g/L NaCl and pH 8.0. The organism can grow on a broad range of carbon sources and demonstrated efficient denitrifying ability (94.2% of nitrate removal and 80.9% of total nitrogen removal in 48 h). During denitrification by NY-4, no NO2 (-)-N was accumulated, N2 was the only gaseous product and no harmful N2O was produced. Because of its rapid denitrification ability, broad carbon use range and ability to grow under high salinity and pH conditions, NY-4 holds promise for the treatment of saline waste waters. PMID:25538872

  12. INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium.

    PubMed

    Araujo Granda, Pablo; Gras, Anna; Ginovart, Marta; Moulton, Vincent

    2016-08-21

    We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request. PMID:27179457

  13. Salt requirements in the denitrifying bacterium Pseudomonas nautica 617.

    PubMed

    Bonin, P; Gilewicz, M; Denis, M; Bertrand, J C

    1989-02-01

    Pseudomonas nautica 617, which was isolated from superficial marine sediment, was found to require sodium for growth. Growth also appeared to be sensitive to the divalent cation, Mg2+, the presence of which, together with that of Na+, was necessary for achieving maximal growth. We investigated cell capacity to resist lysis after washing with either 0.05 M MgCl2 or 0.5 M NaCl, by monitoring suspension optical density changes as well as the release of ultraviolet absorbing material. Mg2+ turned out to play a significant role in stabilizing the structure of the cell envelope. Respiratory activity was also sensitive to ionic environment. With cells washed with 0.05 M MgCl2 and suspended in 0.05 M Tris buffer, the respiration rate, assessed by N2O evolution, was 15% of that measured in artificial sea water. Upon addition of 0.5 M Na+, nitrous oxide production rose to 32% of the reference level. The dinitrification rate was fully restored by further addition of 0.05 M Mg2+. K+ alone had almost no effect, but when added with Na+, the rate of denitrification increased to 45%. PMID:2799064

  14. [Suppression of three soil-borne diseases of cucumber by a rhizosphere fungal strain].

    PubMed

    Lyu, Heng; Niu, Yong-chun; Deng, Hui; Lin, Xiao-min; Jin, Chun-li

    2015-12-01

    To understand the effect of rhizosphere fungi on soil-borne diseases of cucumber, 16 fungal, strains from rhizosphere soil were investigated for the antagonistic activity to three soilborne pathogenic fungi with dual culture method and for suppression of cucumber diseases caused by the pathogens in pot experiments. Four strains showed antagonism to one or more pathogenic fungi tested. The strain JCL143, identified as Aspergillus terreus, showed strong antagonistic activity to the three pathogenic fungi Fusarium oxysporum f. sp. cucumerinum, Rhizoctonia solani and Sclerotinia sclerotiorum. In greenhouse pot experiments, inoculation with strain JCL143 provided 74% or more of relative control effect to all the three diseases of cucumber seedling caused by the above three pathogenic fungi, and provided 85% or more of relative control effect to Rhizoctonia root rot and Sclerotinia root and stem rot in pot experiment with non-sterilized substrate. In pot experiment with natural soil as substrate, inoculation with strain JCL143 provided average 84.1% of relative control effect to Fusarium wilt of cucumber at vine elongation stage. The fermentation broth of strain JCL143 showed inhibitory effect in different degrees on the colonial growth of the three pathogenic fungi tested, and reached 63.3% of inhibitory rate of colonial growth to S. sclerotiorum. The inhibitory activity of the fermentation broth decreased with increasing treatment temperature, was liable to decrease to alkaline pH than acid pH, and stable to protease treatment. The results indicated that A. terreus is an important factor in suppression of plant soil-borne diseases, and strain JCL143 with stable disease suppression is potential in biocontrol application. PMID:27112016

  15. Denitrifying Alphaproteobacteria from the Arabian Sea That Express nosZ, the Gene Encoding Nitrous Oxide Reductase, in Oxic and Suboxic Waters

    PubMed Central

    Hodgson, Sylvia; Bird, Clare

    2013-01-01

    Marine ecosystems are significant sources of the powerful greenhouse gas nitrous oxide (N2O). A by-product of nitrification and an intermediate in the denitrification pathway, N2O is formed primarily in oxygen-deficient waters and sediments. We describe the isolation of a group of alphaproteobacteria from the suboxic waters of the Arabian Sea that are phylogenetically affiliated with Labrenzia spp. and other denitrifiers. Quantitative PCR assays revealed that these organisms were very broadly distributed in this semienclosed ocean basin. Their biogeographical range extended from the productive, upwelling region off the Omani shelf to the clear, oligotrophic waters that are found much further south and also included the mesotrophic waters overlying the oxygen minimum zone (OMZ) in the northeastern sector of the Arabian Sea. These organisms actively expressed NosZ (N2O reductase, the terminal step in the denitrification pathway) within the OMZ, an established region of pelagic denitrification. They were found in greatest numbers outside the OMZ, however, and nosZ mRNAs were also readily detected near the base of the upper mixed layer in nutrient-poor, oxic regions. Our findings provide firm molecular evidence of a potential sink for N2O within well-ventilated, oceanic surface waters in this biogeochemically important region. We show that the Labrenzia-like denitrifiers and their close relatives are habitual colonizers of the pseudobenthic environment provided by Trichodesmium spp. We develop the conjecture that the O2-depleted microzones that occur within the colonies of these filamentous, diazotrophic cyanobacteria might provide unexpected niches for the reduction of nitrogen oxides in tropical and subtropical surface waters. PMID:23396348

  16. Involvement of NarK1 and NarK2 Proteins in Transport of Nitrate and Nitrite in the Denitrifying Bacterium Pseudomonas aeruginosa PAO1

    PubMed Central

    Sharma, Vandana; Noriega, Chris E.; Rowe, John J.

    2006-01-01

    Two transmembrane proteins were tentatively classified as NarK1 and NarK2 in the Pseudomonas genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in Pseudomonas aeruginosa. The narK1 and narK2 genes are located in a cluster along with the structural genes for the nitrate reductase complex. Our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex narK1K2GHJI constitutes an operon. Utilizing an isogenic narK1 mutant, a narK2 mutant, and a narK1K2 double mutant, we explored their effect on growth under denitrifying conditions. While the ΔnarK1::Gm mutant was only slightly affected in its ability to grow under denitrification conditions, both the ΔnarK2::Gm and ΔnarK1K2::Gm mutants were found to be severely restricted in nitrate-dependent, anaerobic growth. All three strains demonstrated wild-type levels of nitrate reductase activity. Nitrate uptake by whole-cell suspensions demonstrated both the ΔnarK2::Gm and ΔnarK1K2::Gm mutants to have very low yet different nitrate uptake rates, while the ΔnarK1::Gm mutant exhibited wild-type levels of nitrate uptake. Finally, Escherichia coli narK rescued both the ΔnarK2::Gm and ΔnarK1K2::Gm mutants with respect to anaerobic respiratory growth. Our results indicate that only the NarK2 protein is required as a nitrate/nitrite transporter by Pseudomonas aeruginosa under denitrifying conditions. PMID:16391109

  17. Phosphorus Depletion From Rhizosphere Solution by Maize Grown in Compost-amended Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of rhizosphere processes is essential for characterizing soil nutrient availability. Our objective in this controlled-climate study was to evaluate phosphorus (P) dynamics in the rhizosphere of juvenile maize (Zea mays L.) grown in soil amended with compost. Maize seedlings were transplant...

  18. Nitrogen fertilizer rate affects root exudation, the rhizosphere microbiome and nitrogen-use-efficiency of maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The composition and function of microbial communities present in the rhizosphere of crops has been linked to edaphic factors and root exudate composition. In this paper, we examined the effect of N fertilizer rate on maize root exudation, the associated rhizosphere community, and nitrogen-use-effici...

  19. Book Review: "The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface, Second Edition"

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complexity of the biological, chemical, and physical interactions occurring in the volume of soil surrounding the root of a growing plant dictates that a multidisciplinary approach must be taken to improve our understanding of this rhizosphere. Hence, "The Rhizosphere: Biochemistry and Organic S...

  20. Cucumber rhizosphere microbial community response to biocontrol agent Bacillus subtilis B068150

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gram-positive bacteria Bacillus subtilis B068150 has been used as a biocontrol agent against the pathogen Fusarium oxysporum f. sp. Cucumerinum. However, their survival ability in cucumber rhizosphere and non-rhizosphere as well as their influence on native microbial communities has not been fully i...

  1. Rice rhizosphere soil and root surface bacterial community response to water management changes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Different water management practices could affect microbial populations in the rice rhizosphere. A field-scale study was conducted to evaluate microbial populations in the root plaque and rhizosphere of rice in response to continuous and intermittent flooding conditions. Microbial populations in rhi...

  2. Effects of different quinoid redox mediators on the simultaneous removal of p-cresol and sulphide in a denitrifying process.

    PubMed

    Meza-Escalante, Edna R; Texier, Anne-Claire; Cuervo-López, Flor; Gómez, Jorge; Cervantes, Francisco J

    2009-01-01

    The catalytic effects of different quinoid redox mediators (RM) on the simultaneous removal of sulphide and p-cresol in a denitrifying process were evaluated in batch studies. 2-Hydroxy-1,4-naphthoquinone (LAW) and anthraquinone-2,6-disulphonate (AQDS) did not significantly affect the sulphide oxidation rate, which, in contrast, was increased 14% in the presence of 1,2-naphthoquinone-4-sulphonate (NQS). The input of NQS on the oxidation of sulphide was also favourably reflected in a 13% higher sulphate production. All RM promoted a higher (up to 34% compared to the control lacking RM) degree of mineralization of p-cresol. LAW also supported a 47% higher denitrifying yield (Y(N2)), compared to the control lacking quinones. Nevertheless, AQDS and NQS decreased the Y(N2) by 12-13%. Our results suggest that a proper scrutiny should be conducted before deciding the sort of quinone to be applied in denitrifying processes. The heterogeneous effects observed also advise to consider both the respiratory rates and the yields as important parameters for deciphering the impact of RM on denitrifying processes. PMID:19474488

  3. EFFECTS OF A PERMEABLE REACTIVE BARRIER ON DENITRIFYING BACTERIA COMMUNITIES AND METHYLMERCURY CONCENTRATIONS IN WAQUOIT BAY, MA

    EPA Science Inventory

    It is expected that microbial denitrifying bacterial communities in the barrier will be distinct from those at control sites due to the high amount of degradable carbon and the unique redox conditions present within the barrier. It also is expected that toxic methylmercury ...

  4. Water Properties Influencing the Abundance and Diversity of Denitrifiers on Eichhornia crassipes Roots: A Comparative Study from Different Effluents around Dianchi Lake, China

    PubMed Central

    Yi, Neng; Gao, Yan; Zhang, Zhenhua; Shao, Hongbo; Yan, Shaohua

    2015-01-01

    To evaluate effects of environmental conditions on the abundance and communities of three denitrifying genes coding for nitrite (nirK, nirS) reductase and nitrous oxide (nosZ) reductase on the roots of Eichhornia crassipes from 11 rivers flowing into the northern part of Dianchi Lake. The results showed that the abundance and community composition of denitrifying genes on E. crassipes root varied with different rivers. The nirK gene copies abundance was always greater than that of nirS gene on the roots of E. crassipes, suggesting that the surface of E. crassipes roots growth in Dianchi Lake was more suitable for the growth of nirK-type denitrifying bacteria. The DGGE results showed significant differences in diversity of denitrifying genes on the roots of E. crassipes among the 11 rivers. Using redundancy analysis (RDA), the correlations of denitrifying microbial community compositions with environmental factors revealed that water temperature (T), dissolved oxygen (DO), and pH were relatively important environmental factors to modifying the community structure of the denitrifying genes attached to the root of E. crassipes. The results indicated that the specific environmental conditions related to different source of rivers would have a stronger impact on the development of denitrifier communities on E. crassipes roots. PMID:26495277

  5. Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity1[C

    PubMed Central

    De-la-Peña, Clelia; Loyola-Vargas, Víctor M.

    2014-01-01

    Microbes and plants have evolved biochemical mechanisms to communicate with each other. The molecules responsible for such communication are secreted during beneficial or harmful interactions. Hundreds of these molecules secreted into the rhizosphere have been identified, and their functions are being studied in order to understand the mechanisms of interaction and communication among the different members of the rhizosphere community. The importance of root and microbe secretion to the underground habitat in improving crop productivity is increasingly recognized, with the discovery and characterization of new secreting compounds found in the rhizosphere. Different omic approaches, such as genomics, transcriptomics, proteomics, and metabolomics, have expanded our understanding of the first signals between microbes and plants. In this review, we highlight the more recent discoveries related to molecules secreted into the rhizosphere and how they affect plant productivity, either negatively or positively. In addition, we include a survey of novel approaches to studying the rhizosphere and emerging opportunities to direct future studies. PMID:25118253

  6. Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth

    PubMed Central

    Singh, Mangal; Awasthi, Ashutosh; Soni, Sumit K.; Singh, Rakshapal; Verma, Rajesh K.; Kalra, Alok

    2015-01-01

    An assessment of roles of rhizospheric microbial diversity in plant growth is helpful in understanding plant-microbe interactions. Using random combinations of rhizospheric bacterial species at different richness levels, we analysed the contribution of species richness, compositions, interactions and identity on soil microbial respiration and plant biomass. We showed that bacterial inoculation in plant rhizosphere enhanced microbial respiration and plant biomass with complementary relationships among bacterial species. Plant growth was found to increase linearly with inoculation of rhizospheric bacterial communities with increasing levels of species or plant growth promoting trait diversity. However, inoculation of diverse bacterial communities having single plant growth promoting trait, i.e., nitrogen fixation could not enhance plant growth over inoculation of single bacteria. Our results indicate that bacterial diversity in rhizosphere affect ecosystem functioning through complementary relationship among plant growth promoting traits and may play significant roles in delivering microbial services to plants. PMID:26503744

  7. Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes.

    PubMed

    Saleem, Muhammad; Law, Audrey D; Moe, Luke A

    2016-02-01

    Root-associated microbes have a profound impact on plant health, yet little is known about the distribution of root-associated microbes among different root morphologies or between rhizosphere and root environments. We explore these issues here with two commercial varieties of burley tobacco (Nicotiana tabacum) using 16S rRNA gene amplicon sequencing from rhizosphere soil, as well as from primary, secondary, and fine roots. While rhizosphere soils exhibited a fairly rich and even distribution, root samples were dominated by Proteobacteria. A comparison of abundant operational taxonomic units (OTUs) between rhizosphere and root samples indicated that Nicotiana roots select for rare taxa (predominantly Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Acidobacteria) from their corresponding rhizosphere environments. The majority of root-inhabiting OTUs (~80 %) exhibited habitat generalism across the different root morphological habitats, although habitat specialists were noted. These results suggest a specific process whereby roots select rare taxa from a larger community. PMID:26391804

  8. Biocontrol and Plant Growth Promotion Characterization of Bacillus Species Isolated from Calendula officinalis Rhizosphere.

    PubMed

    Ait Kaki, Asma; Kacem Chaouche, Noreddine; Dehimat, Laid; Milet, Asma; Youcef-Ali, Mounia; Ongena, Marc; Thonart, Philippe

    2013-12-01

    The phenotypic and genotypic diversity of the plant growth promoting Bacillus genus have been widely investigated in the rhizosphere of various agricultural crops. However, to our knowledge this is the first report on the Bacillus species isolated from the rhizosphere of Calendula officinalis. 15 % of the isolated bacteria were screened for their important antifungal activity against Fusarium oxysporum, Botrytis cinerea, Aspergillus niger, Cladosporium cucumerinium and Alternaria alternata. The bacteria identification based on 16S r-RNA and gyrase-A genes analysis, revealed strains closely related to Bacillus amyloliquefaciens, B. velezensis, B. subtilis sub sp spizezenii and Paenibacillus polymyxa species. The electro-spray mass spectrometry coupled to liquid chromatography (ESI-LC MS) analysis showed that most of the Bacillus isolates produced the three lipopeptides families. However, the P. polymyxa (18SRTS) didn't produce any type of lipopeptides. All the tested Bacillus isolates produced cellulase but the protease activity was observed only in the B. amyloliquefaciens species (9SRTS). The Salkowsky colorimetric test showed that the screened bacteria synthesized 6-52 μg/ml of indole 3 acetic acid. These bacteria produced siderophores with more than 10 mm wide orange zones on chromazurol S. The greenhouse experiment using a naturally infested soil with Sclerotonia sclerotiorum showed that the B. amyloliquefaciens (9SRTS) had no significant (P > 0.05) effect on the pre-germination of the chickpea seeds. However, it increased the size of the chickpea plants and reduced the stem rot disease (P < 0.05).These results suggested that the Bacillus strains isolated in this work may be further used as bioinoculants to improve the production of C. officinalis and other crop systems. PMID:24426149

  9. Plant inter-species effects on rhizosphere priming effect and nitrogen acquisition by plants

    NASA Astrophysics Data System (ADS)

    Sun, Yue; Xu, Xingliang; Yang, Baijie; Kuzyakov, Yakov

    2015-04-01

    Rhizosphere interactions play a central role linking roots-soil system and regulate various aspects of nutrient cycling. Rhizodeposition inputs are known to change soil organic matter (SOM) decomposition via rhizosphere priming effects (RPEs) through enhancing soil biological activity and altering microbial community structure. The magnitude of RPEs varies widely among plant-species and root biomass possibly due to different quality and quantity of rhizodeposits. However, it is virtually unknown whether the RPEs are influenced by plant inter-species interactions and how these processes affect N mineralization and available N for plants. Monocultures of maize (M) and soybean (S), and mixed cultures of maize/maize (MM), soybean/soybean (SS), maize/soybean (MS) were grown over a 45-day greenhouse experiment. We labeled them with plant litter that was enriched in13C and 15N. The 15N distributions in plants and microbial biomass were measured at 14, 35, and 45days after labeling. The RPEs were positive under all plants, ranging from 11.7% to 138.3% and gradually decreased with plant growth. The RPE in the SS was significantly higher than these in others treatments at 14 days, while at 45 days it was higher in the MS than these from their monocultures, suggesting that the RPE was enhanced by the inter-species effects of maize and soybean. The litter decomposition ratio and 15N recovery of plants and microorganism increased with the root growth across all plants. The 15N recovery of plants in the MS (14.2%) was higher than these in the MM (12.3%) and SS(9.7%) at 45 days. Similarly, the 15N recovery of microorganism in the corresponding treatments was 6.7%, 2.2%, and 6.8%, respectively. The MS showed higher soil organic N mineralization amount than that from all soybean and maize monocultures at 45 days. We conclude that plant inter-species interactions may have significant effect on rhizosphere priming and modify the plant N uptake from litter resource and SOM.

  10. Association of Novel and Highly Diverse Acid-Tolerant Denitrifiers with N2O Fluxes of an Acidic Fen▿ †

    PubMed Central

    Palmer, Katharina; Drake, Harold L.; Horn, Marcus A.

    2010-01-01

    Wetlands are sources of denitrification-derived nitrous oxide (N2O). Thus, the denitrifier community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitrifiers approximated 1011 cells·gDW−1 (where DW is dry weight) and 108 cells·gDW−1, respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (vmax) values for denitrification in anoxic microcosms ranged from 1 to 24 and −19 to −105 nmol N2O h−1· gDW−1, with maximal values occurring in the upper soil layers. Denitrification was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitrification. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomic units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifier diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifier community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifier communities capable of complete denitrification and consumption of atmospheric N2O at in situ pH. PMID:20023077

  11. Towards engineering degradation of the explosive pollutant hexahydro-1,3,5-trinitro-1,3,5-triazine in the rhizosphere.

    PubMed

    Lorenz, Astrid; Rylott, Elizabeth L; Strand, Stuart E; Bruce, Neil C

    2013-03-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a serious environmental pollutant on military land. This compound is the most widely used explosive and pollution has arisen primarily as the result of military training, along with munition manufacturing and disassembly processes. This toxic explosive is recalcitrant to degradation in the environment and leaches rapidly into groundwater, where accumulation in aquifers is threatening drinking water supplies (Clausen, et al., 2004). While plants have only limited degradative activity towards RDX, microorganisms, including Rhodococcus rhodochrous 11Y, have been isolated from contaminated land. Despite the presence of microbial RDX-metabolising activity in contaminated soils, the persistence of RDX in leachate from contaminated soil indicates that this activity or biomass is insufficient, limiting its use to remediate polluted soils. Bacterial activity in the rhizosphere is of magnitudes greater than in the surrounding soil, and the roots of grass species on training ranges in the United States are known to penetrate deeply into the soil, producing a compact root system and providing an ideal environment to support the capture of RDX by microorganisms in the rhizosphere. Here, we have investigated the ability of the root-colonising bacterium Pseudomonas fluorescens, engineered to express XplA, to degrade RDX in the rhizosphere. PMID:23289483

  12. Actinobacterial Nitrate Reducers and Proteobacterial Denitrifiers Are Abundant in N2O-Metabolizing Palsa Peat

    PubMed Central

    Palmer, Katharina

    2012-01-01

    Palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (N2O). Palsa peats are predicted to react sensitively to global warming. The acidic palsa peat Skalluvaara (approximate pH 4.4) is located in the discontinuous permafrost zone in northwestern Finnish Lapland. In situ N2O fluxes were spatially variable, ranging from 0.01 to −0.02 μmol of N2O m−2 h−1. Fertilization with nitrate stimulated in situ N2O emissions and N2O production in anoxic microcosms without apparent delay. N2O was subsequently consumed in microcosms. Maximal reaction velocities (vmax) of nitrate-dependent denitrification approximated 3 and 1 nmol of N2O per h per gram (dry weight [gDW]) in soil from 0 to 20 cm and below 20 cm of depth, respectively. vmax values of nitrite-dependent denitrification were 2- to 5-fold higher than the vmax nitrate-dependent denitrification, and vmax of N2O consumption was 1- to 6-fold higher than that of nitrite-dependent denitrification, highlighting a high N2O consumption potential. Up to 12 species-level operational taxonomic units (OTUs) of narG, nirK and nirS, and nosZ were retrieved. Detected OTUs suggested the presence of diverse uncultured soil denitrifiers and dissimilatory nitrate reducers, hitherto undetected species, as well as Actino-, Alpha-, and Betaproteobacteria. Copy numbers of nirS always outnumbered those of nirK by 2 orders of magnitude. Copy numbers of nirS tended to be higher, while copy numbers of narG and nosZ tended to be lower in 0- to 20-cm soil than in soil below 20 cm. The collective data suggest that (i) the source and sink functions of palsa peat soils for N2O are associated with denitrification, (ii) actinobacterial nitrate reducers and nirS-type and nosZ-harboring proteobacterial denitrifiers are important players, and (iii) acidic soils like palsa peats represent

  13. Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived Pseudomonad

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Han, R.; Geller, J. T.

    2009-12-01

    Chromium contamination of groundwater is widespread within the Department of Energy (DOE) complex. For example, at DOE’s Hanford 100 Area in Washington state, the volume of Cr-contaminated groundwater is estimated to be 1.5 billion gallons. Bioremediation (in situ reductive immobilization) studies involving injection of a lactate-containing polymer have been conducted in the Hanford 100H area, where we have observed sequential use of the dissolved electron acceptors present in groundwater, namely, oxygen, nitrate, and sulfate. As part of an effort to explore Cr(VI) reduction under relevant electron-accepting conditions and with relevant bacteria, we have conducted studies with strain RCH2, a denitrifying bacterium similar to Pseudomonas stutzeri that was isolated from the Hanford 100H aquifer. Cell suspension studies with lactate demonstrated that Cr(VI) reduction could occur under either denitrifying or aerobic conditions (at comparable rates), and that reduction was much more rapid when the terminal electron acceptor (i.e., nitrate or O2) was present. It appears that, under both aerobic and denitrifying conditions, the chromate reductase gene(s) are not inducible by Cr; this conclusion is based on the fact that these cell suspension studies were conducted with cells grown in the absence of Cr and resuspended in a buffer that included chloramphenicol, which inhibits protein synthesis. As our studies indicate that anaerobic Cr(VI) reduction by strain RCH2 is much more rapid in the presence of nitrate (i.e., during denitrification) than in its absence, we explored molecular methods that could readily assess in situ denitrification. Specifically, we investigated whether the gene and transcript copy number of diagnostic denitrification genes (nirS and narG) in groundwater could be used to estimate in situ denitrification rates. Continuous culture (chemostat) studies showed strong correlations (r2 values > 0.93) between denitrification rate and either nirS or nar

  14. Granulation of susceptible sludge under carbon deficient conditions: A case of denitrifying sulfur conversion-associated EBPR process.

    PubMed

    Guo, Gang; Wu, Di; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Lu, Hui; Chen, Guanghao

    2016-10-15

    Sludge granulation has been recognized as a promising biotechnology in wastewater treatment. Whereas the granulation of susceptible sludge in particular with a very low organic loading rate (OLR) (≤0.6 kg COD/m(3)/day or ≤ 120 mg COD/g VSS/day) is a difficult task that has not been achieved in activated sludge systems yet. This study was aimed at exploring an effective strategy for sludge granulation in the recently developed Denitrifying Sulfur conversion-associated Enhanced Biological Phosphorus Removal (DS-EBPR) process using a sequencing batch pump-lift reactor. Four strategies were studied by manipulating the factors of organic loading rate (OLR), superficial upflow velocity and sludge settling time individually or collectively. Increasing both the OLR and the superficial upflow velocity effectively promoted granule formation but at the same time led to unstable and even deteriorated reactor performance. The development of granules proceeded via several stages: formation, dispersion, reformation and stabilization. Gradually increasing the superficial upflow velocity from 5.1 to 6.8 m/h and keeping the OLR at 112.4 mg COD/g VSS/day proved to be most effective strategy for accelerating granulation while simultaneously achieving stable reactor performance. Under these conditions, the granules became stable with a diameter of 375-400 μm and displayed excellent settleability. The two major microbial groups, sulfate-reducing bacteria and sulfide-oxidizing bacteria, in the microbial community of the DS-EBPR granular sludge were enriched to 17.7% and 15.8% respectively. The newly developed DS-EBPR granular system was able to achieve an almost threefold improvement in phosphorus removal efficiency and 25% reduction in the operating cycle time compared with a flocculent DS-EBPR system. PMID:27498252

  15. Autecology in Rhizospheres and Nodulating Behavior of Indigenous Rhizobium trifolii†

    PubMed Central

    Demezas, David H.; Bottomley, Peter J.

    1986-01-01

    Indigenous serotype 1-01 of Rhizobium trifolii occupied significantly fewer nodules (6%) on plants of soil-grown noninoculated subterranean clover (Trifolium subterraneum L.) cv. Woogenellup than on cv. Mt. Barker (36%) sampled at the flowering stage of growth. Occupancy by indigenous serotype 2-01, was not significantly different on the two cultivars (16 and 26%)