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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. Effect of nitrogen and waterlogging on denitrifier gene abundance, community structure and activity in the rhizosphere of wheat.

    PubMed

    Hamonts, Kelly; Clough, Tim J; Stewart, Alison; Clinton, Peter W; Richardson, Alan E; Wakelin, Steven A; O'Callaghan, Maureen; Condron, Leo M

    2013-03-01

    Microbial denitrification plays a key role in determining the availability of soil nitrogen (N) to plants. However, factors influencing the structure and function of denitrifier communities in the rhizosphere remain unclear. Waterlogging can result in root anoxia and increased denitrification, leading to significant N loss from soil and potential nitrous oxide (N(2)O) emissions. This study investigated denitrifier gene abundance, community structure and activity in the rhizosphere of wheat in response to anoxia and N limitation. Denitrifier community structure in the rhizosphere differed from that in bulk soil, and denitrifier gene copy numbers (nirS, nirK, nosZ) and potential denitrification activity were greater in the rhizosphere. Anoxia and N limitation, and in particular a combination of both, reduced the magnitude of this effect on gene abundance (in particular nirS) and activity, with N limitation having greater impact than waterlogging in rhizosphere soil, in contrast to bulk soil where the impact of waterlogging was greater. Increased N supply to anoxic plants improved plant health and increased rhizosphere soil pH, which resulted in enhanced reduction of N(2)O. Both anoxia and N limitation significantly influenced the structure and function of denitrifier communities in the rhizosphere, with reduced root-derived carbon postulated to play an important role.

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

    PubMed

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

    2012-06-01

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

  4. Diversity and activity of denitrifiers of chilean arid soil ecosystems.

    PubMed

    Orlando, Julieta; Carú, Margarita; Pommerenke, Bianca; Braker, Gesche

    2012-01-01

    The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility, and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS) genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of denitrifiers in particular.

  5. Diversity and Activity of Denitrifiers of Chilean Arid Soil Ecosystems

    PubMed Central

    Orlando, Julieta; Carú, Margarita; Pommerenke, Bianca; Braker, Gesche

    2012-01-01

    The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility, and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS) genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of denitrifiers in particular

  6. Microbial community composition and denitrifying enzyme activities in salt marsh sediments.

    PubMed

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

    2008-12-01

    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.

  7. 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.

  8. 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.

  9. 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

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

    PubMed

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

    2016-01-07

    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.

  11. 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

  12. [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.

  13. Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India.

    PubMed

    Jaiswal, Shubham K; Saxena, Rituja; Mittal, Parul; Gupta, Ankit; Sharma, Vineet K

    2017-02-02

    The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification.

  14. Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India

    PubMed Central

    Jaiswal, Shubham K.; Saxena, Rituja; Mittal, Parul; Gupta, Ankit

    2017-01-01

    ABSTRACT The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification. PMID:28153890

  15. Draft Genome Sequence of Marinobacter hydrocarbonoclasticus Strain STW2, a Polycyclic Aromatic Hydrocarbon-Degrading and Denitrifying Bacterium from the Rhizosphere of Seagrass Enhalus acodoides

    PubMed Central

    Ling, Juan; Lin, Liyun; Zhang, Yanying; Lin, Xiancheng; Ahamad, Manzoor; Zhou, Weiguo

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of Marinobacter hydrocarbonoclasticus strain STW2, which was isolated from the rhizosphere of seagrass Enhalus acodoides. This study will facilitate future studies on the genetic pathways of marine microbes capable of both polycyclic aromatic hydrocarbon degradation and nitrate reduction. PMID:28232431

  16. 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.

  17. Effect of Bacteria and Amoebae on Rhizosphere Phosphatase Activity

    PubMed Central

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

    1979-01-01

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

  18. 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

  19. 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

  20. Calibration of denitrifying activity of polyphosphate accumulating organisms in an extended ASM2d model.

    PubMed

    García-Usach, F; Ribes, J; Ferrer, J; Seco, A

    2010-10-01

    This paper presents the results of an experimental study for the modelling and calibration of denitrifying activity of polyphosphate accumulating organisms (PAOs) in full-scale WWTPs that incorporate simultaneous nitrogen and phosphorus removal. The convenience of using different yields under aerobic and anoxic conditions for modelling biological phosphorus removal processes with the ASM2d has been demonstrated. Thus, parameter η(PAO) in the model is given a physical meaning and represents the fraction of PAOs that are able to follow the DPAO metabolism. Using stoichiometric relationships, which are based on assumed biochemical pathways, the anoxic yields considered in the extended ASM2d can be obtained as a function of their respective aerobic yields. Thus, this modification does not mean an extra calibration effort to obtain the new parameters. In this work, an off-line calibration methodology has been applied to validate the model, where general relationships among stoichiometric parameters are proposed to avoid increasing the number of parameters to calibrate. The results have been validated through a UCT scheme pilot plant that is fed with municipal wastewater. The good concordance obtained between experimental and simulated values validates the use of anoxic yields as well as the calibration methodology. Deterministic modelling approaches, together with off-line calibration methodologies, are proposed to assist in decision-making about further process optimization in biological phosphate removal, since parameter values obtained by off-line calibration give valuable information about the activated sludge process such as the amount of DPAOs in the system.

  1. Influence of soil reaction on diversity and antifungal activity of fluorescent pseudomonads in crop rhizospheres.

    PubMed

    Verma, Rajni; Naosekpam, Ajit Singh; Kumar, Sanjay; Prasad, Ramdeen; Shanmugam, V

    2007-05-01

    The diversity and antifungal activity of fluorescent pseudomonads isolated from rhizospheres of tea, gladiolus, carnation and black gram grown in acidic soils with similar texture and climatic conditions were studied. Biochemical characterisation including antibiotic resistance assay, RAPD and PCR-RFLP studies revealed a largely homogenous population. At soil pH (5.2), the isolates exhibited growth with varying levels of siderophore production, irrespective of crop rhizospheres. Two isolates with maximum chitinase production showed antagonism. The bacterial populations in general lacked the ability to produce deleterious traits such as cellulase, pectinase and hydrogen cyanide. However, increased pH levels beyond 5.2 caused reduction in metabolite production with reduced antifungal activity. The homogeneity of the bacterial population irrespective of crop rhizospheres together with decreased secondary metabolite production at higher pH levels reinstated the importance of soil over host plant in influencing rhizosphere populations. The studies also yielded acid tolerant chitinase producing antagonistic fluorescent pseudomonads.

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

    PubMed

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

    2014-12-01

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

  3. 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

  4. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.

    PubMed

    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.

  5. Activation of the Jasmonic Acid Plant Defence Pathway Alters the Composition of Rhizosphere Bacterial Communities

    PubMed Central

    Carvalhais, Lilia C.; Dennis, Paul G.; Badri, Dayakar V.; Tyson, Gene W.; Vivanco, Jorge M.; Schenk, Peer M.

    2013-01-01

    Jasmonic acid (JA) signalling plays a central role in plant defences against necrotrophic pathogens and herbivorous insects, which afflict both roots and shoots. This pathway is also activated following the interaction with beneficial microbes that may lead to induced systemic resistance. Activation of the JA signalling pathway via application of methyl jasmonate (MeJA) alters the composition of carbon containing compounds released by roots, which are implicated as key determinants of rhizosphere microbial community structure. In this study, we investigated the influence of the JA defence signalling pathway activation in Arabidopsis thaliana on the structure of associated rhizosphere bacterial communities using 16S rRNA gene amplicon pyrosequencing. Application of MeJA did not directly influence bulk soil microbial communities but significant changes in rhizosphere community composition were observed upon activation of the jasmonate signalling pathway. Our results suggest that JA signalling may mediate plant-bacteria interactions in the soil upon necrotrophic pathogen and herbivorous insect attacks. PMID:23424661

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. Heterotrophic nitrification among denitrifiers.

    PubMed Central

    Castignetti, D; Hollocher, T C

    1984-01-01

    Twelve denitrifying bacteria representing six genera were tested for an ability to nitrify pyruvic oxime heterotrophically. Six of these bacteria exhibited appreciable nitrification activity, yielding as much as 5.8 mM nitrite and little or no nitrate when grown in a mineral salts medium containing 7 mM pyruvic oxime and 0.05% yeast extract. Of the six active bacteria, four (Pseudomonas denitrificans, Pseudomonas aeruginosa, and two strains of Pseudomonas fluorescens) could grow on yeast extract but not pyruvic oxime, one (Pseudomonas aureofaciens) could grow slowly on pyruvic oxime, and one (Alcaligenes faecalis) could apparently grow on pyruvic oxime in the presence of yeast extract but not in its absence. Eight of the twelve bacteria in the resting state could oxidize hydroxylamine to nitrite, and P. aureofaciens was remarkably active in this regard. In general, those denitrifiers active in the nitrification of pyruvic oxime or hydroxylamine or both are abundant in soils. A possible advantage of having nitrification and denitrification capabilities in the same organism is discussed. PMID:6721486

  11. Insights into the effect of soil pH on N(2)O and N(2) emissions and denitrifier community size and activity.

    PubMed

    Cuhel, Jirí; Simek, Miloslav; Laughlin, Ronnie J; Bru, David; Chèneby, Dominique; Watson, Catherine J; Philippot, Laurent

    2010-03-01

    The objective of this study was to investigate how changes in soil pH affect the N(2)O and N(2) 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 H(2)SO(4) solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N(2)O and N(2) emissions using the (15)N 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 N(2)O/(N(2)O + N(2)) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N(2)O production were observed. Denitrification activity and N(2)O 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 N(2)O/(N(2)O + N(2)) 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.

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

    PubMed Central

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

    2013-01-01

    Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96–123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity. PMID

  13. Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments.

    PubMed

    Smith, Jason M; Mosier, Annika C; Francis, Christopher A

    2015-01-01

    The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough--a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.

  14. Structure and activity of bacterial community inhabiting rice roots and the rhizosphere.

    PubMed

    Lu, Yahai; Rosencrantz, Dirk; Liesack, Werner; Conrad, Ralf

    2006-08-01

    Root-derived carbon provides a major source for microbial production and emission of CH4 from rice field soils. Therefore, we characterized the structure and activity of the bacterial community inhabiting rice roots and the rhizosphere. In the first experiment, DNA retrieved from rice roots was analysed for bacterial 16S rRNA genes using cloning, sequencing and in situ hybridization. In the second experiment, rice plants were pulse-labelled with 13CO2 (99% of atom 13C) for 7 days, and the bacterial RNA was isolated from rhizosphere soil and subjected to density gradient centrifugation. RNA samples from density fractions were analysed by terminal restriction fragment length polymorphism fingerprinting, cloning and sequencing. The experiments showed that the dominant bacteria inhabiting rice roots and the rhizosphere particularly belonged to the Alphaproteobacteria, Betaproteobacteria and Firmicutes. The RNA stable isotope probing revealed that the bacteria actively assimilating C derived from the pulse-labelled rice plants were Azospirillum spp. (Alphaproteobacteria) and members of Burkholderiaceae (Betaproteobacteria). Both anaerobic (e.g. Clostridia) and aerobic (e.g. Comamonas) degraders were present at high abundance, indicating that root environments and degradation processes were highly heterogeneous. The relative importance of iron and sulfate reducers suggested that cycling of iron and sulfur is active in the rhizosphere.

  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.

  16. The effects of different disease-resistant cultivars of banana on rhizosphere microbial communities and enzyme activities.

    PubMed

    Sun, Jianbo; Peng, Ming; Wang, Yuguang; Li, Wenbin; Xia, Qiyu

    2013-08-01

    To understand the mechanism of soil microbial ecosystem and biochemical properties in suppressing soilborne plant diseases, the relationship between the soil rhizosphere microbial communities, hydrolase activities, and different disease-resistant cultivars was investigated. There were statistically significant differences in microbial diversity in the rhizosphere soil between the disease-tolerant cultivar Fj01 and susceptible cultivar Baxi. The rhizosphere soil of Fj01 showed a trend of higher microbial diversity than that of Baxi. At the same growth stage, the similar trends of variation in microbial community diversity between the two different cultivars were observed. The bacterial community abundance in rhizosphere soil from the two banana cultivars was quantified by real-time PCR assays. The size of the rhizosphere bacterial population from the Fj01 was significantly larger than that from the Baxi during the growing stage from July to September. The activities of urease and phosphatase were analyzed to study the effects of the two banana cultivars to soil ecosystem functioning. Urease activity was significantly higher in the rhizosphere soil of Fj01 than that of Baxi in the period from July to September. However, phosphatase activity showed no significant difference between the two different rhizosphere soils.

  17. 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

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

    PubMed

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

    2008-04-01

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

  19. 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 niche role according to

  20. 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

  1. 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

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

    PubMed

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

    2013-10-01

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

  3. 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...

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

    PubMed

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

    2008-06-01

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

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

    PubMed

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

    2007-02-01

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

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

    PubMed

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

    2014-08-01

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

  7. Contributions of available substrates and activities of trophic microbial community to methanogenesis in vegetative and reproductive rice rhizospheric soil.

    PubMed

    Chawanakul, Sansanee; Chaiprasert, Pawinee; Towprayoon, Sirintornthep; Tanticharoen, Morakot

    2009-01-01

    Potential of methane production and trophic microbial activities at rhizospheric soil during rice cv. Supanbunri 1 cultivation were determined by laboratory anaerobic diluents vials. The methane production was higher from rhizospheric than non-rhizospheric soil, with the noticeable peaks during reproductive phase (RP) than vegetative phase (VP). Glucose, ethanol and acetate were the dominant available substrates found in rhizospheric soil during methane production at both phases. The predominance activities of trophic microbial consortium in methanogenesis, namely fermentative bacteria (FB), acetogenic bacteria (AGB), acetate utilizing bacteria (AB) and acetoclastic methanogens (AM) were also determined. At RP, these microbial groups were enhanced in the higher of methane production than VP. This correlates with our finding that methane production was greater at the rhizospheric soil with the noticeable peaks during RP (1,150 +/- 60 nmol g dw(-1) d(-1)) compared with VP (510 +/- 30 nmol g dw(-1) d(-1)). The high number of AM showed the abundant (1.1x10(4) cell g dw(-1)) with its high activity at RP, compared to the less activity with AM number at VP (9.8x10(2) cell g dw(-1)). Levels of AM are low in the total microbial population, being less than 1% of AB. These evidences revealed that the microbial consortium of these two phases were different.

  8. 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...

  9. The effect of nitrite on aerobic phosphate uptake and denitrifying activity of phosphate-accumulating organisms.

    PubMed

    Yoshida, Y; Takahashi, K; Saito, T; Tanaka, K

    2006-01-01

    An anaerobic/aerobic/anoxic/aerobic sequencing batch reactor (SBR) was operated with municipal wastewater to investigate the effect of nitrite on biological phosphorus removal (BPR). When nitrite accumulated, aerobic phosphate uptake activity significantly decreased and, in case of hard exposure to nitrite, BPR severely deteriorated. The interesting observation was that the relative anoxic activity of phosphate accumulating organisms (PAOs) increased after nitrite exposure. Moreover batch tests of aerobic phosphate uptake in the presence/absence of nitrite indicated that PAOs with the higher relative anoxic activity are less sensitive to nitrite exposure. From these results, we concluded that BPR is sensitive to nitrite exposure, but BPR containing PAOs with the higher relative anoxic activity is possibly more stable against nitrite than BPR containing PAOs with the lower relative anoxic activity.

  10. 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

  11. 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.

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

    PubMed

    Sahoo, Ranjan Kumar; Tuteja, Narendra

    2013-08-01

    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.

  13. 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

  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.

  15. 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

  16. 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

  17. 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.

  18. 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...

  19. 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

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

    PubMed Central

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

    2012-01-01

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

  1. Violet-Pigmented Pseudomonads With Antifungal Activity From the Rhizosphere of Beans

    PubMed Central

    Ayers, W. A.; Papavizas, G. C.

    1963-01-01

    Bean rhizosphere bacteria antagonistic to four root-infecting fungi and an antibiotic produced by these bacteria were studied. The bacteria were violet-pigmented gram-negative rods, probably belonging to the genus Pseudomonas. The antibiotic, which was localized largely in the bacterial cell mass, was easily extracted with acetone. It was selectively active against a wide variety of plant-pathogenic and saprophytic fungi tested in vitro but was relatively inactive against bacteria. The compound, partially purified by chromatography, was soluble in all organic solvents tried, but nearly insoluble in water. It demonstrated no characteristic ultraviolet- or visible-absorption spectrum and was chemically unidentified. The antagonistic bacteria or crude antibiotic applied to buried buckwheat segments suppressed the colonization of this substrate by Rhizoctonia spp. The data suggested that the bacteria or the antibiotic may play a role in the suppression of root-infecting fungi in soil. PMID:16349643

  2. Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO2

    NASA Astrophysics Data System (ADS)

    Denef, K.; Bubenheim, H.; Lenhart, K.; Vermeulen, J.; van Cleemput, O.; Boeckx, P.; Müller, C.

    2007-05-01

    The aim of this study was to identify the microbial communities that are actively involved in the assimilation of rhizosphere-C and are most sensitive in their activity to elevated atmospheric CO2 in grassland ecosystems. For this, we analyzed 13C signatures in microbial biomarker phospholipid fatty acids (PLFA) from an in situ 13CO2 pulse-labeling experiment in the Gießen Free-Air Carbon dioxide Enrichment grasslands (GiFACE, Germany) exposed to ambient and elevated (i.e. 50% above ambient) CO2 concentrations. Carbon-13 PLFA measurements at 3 h, 10 h and 11 months after the pulse-labeling indicated a much faster transfer of newly produced rhizosphere-C to fungal compared to bacterial PLFA. After 11 months, the proportion of 13C had decreased in fungal PLFA but had increased in bacterial PLFA compared to a few hours after the pulse-labeling. Nevertheless, a significant proportion of the rapidly assimilated rhizosphere-C was still present in fungal PLFA after 11 months. These results demonstrate the dominant role of fungi in the immediate assimilation of rhizodeposits in grassland ecosystems, while also suggesting a long-term retention of rhizosphere-C in the fungal mycelium as well as a possible translocation of the rhizosphere-C from the fungal to bacterial biomass. Elevated CO2 caused an increase in the relative abundance of root-derived PLFA-C in the saprotrophic fungal PLFA 18:2ω6,9 as well as arbuscular mycorrhizal fungal PLFA 16:1ω5, but a decrease in the saprotrophic fungal biomarker PLFA 18:1ω9. This suggests enhanced rhizodeposit-C assimilation only by selected fungal communities under elevated CO2.

  3. 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)

  4. 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

  5. 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

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

    PubMed

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

    2015-02-01

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

  7. 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(-).

  8. 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

  9. 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.

  10. Natural attenuation of perchlorate in denitrified groundwater.

    PubMed

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

    2014-01-01

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

  11. 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

  12. Role of Respiratory Nitrate Reductase in Ability of Pseudomonas fluorescens YT101 To Colonize the Rhizosphere of Maize

    PubMed Central

    Ghiglione, Jean-François; Gourbiere, François; Potier, Patrick; Philippot, Laurent; Lensi, Robert

    2000-01-01

    Selection of the denitrifying community by plant roots (i.e., increase in the denitrifier/total heterotroph ratio in the rhizosphere) has been reported by several authors. However, very few studies to evaluate the role of the denitrifying function itself in the selection of microorganisms in the rhizosphere have been performed. In the present study, we compared the rhizosphere survival of the denitrifying Pseudomonas fluorescens YT101 strain with that of its isogenic mutant deficient in the ability to synthesize the respiratory nitrate reductase, coinoculated in nonplanted or planted soil. We demonstrated that under nonlimiting nitrate conditions, the denitrifying wild-type strain had an advantage in the ability to colonize the rhizosphere of maize. Investigations of the effect of the inoculum characteristics (density of the total inoculum and relative proportions of mutant and wild-type strains) on the outcome of the selection demonstrated that the selective effect of the plant was expressed only during the phase of bacterial multiplication and that the intensity of selection was dependent on the magnitude of this phase. Moreover, application of the de Wit replacement series technique to our results suggests that the advantage of the wild-type strain was maximal when the ratio between the two strains in the inoculum was close to 1:1. This work constitutes the first direct demonstration that the presence of a functional structural gene encoding the respiratory nitrate reductase confers higher rhizosphere competence to a microorganism. PMID:10966422

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

    PubMed

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

    2011-04-01

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

  14. 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.

  15. [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.

  16. Effects of inorganic salts on denitrifying granular sludge: The acute toxicity and working mechanisms.

    PubMed

    Wang, Ru; Zheng, Ping; Ding, A-qiang; Zhang, Meng; Ghulam, Abbas; Yang, Cheng; Zhao, He-Ping

    2016-03-01

    It is highly significant to investigate the toxicity of inorganic salts to denitrifying granular sludge (DGS) and its mechanism since the application of high-rate denitrification is seriously limited in the treatment of saline nitrogen-rich wastewaters. The batch experiments showed that the IC50 (half inhibition concentration) and LC50 (half lethal concentration) of NaCl, Na2SO4 and Na3PO4 on DGS were 11.46, 21.72, 7.46 g/L and 77.35, 100.58, 67.92 g/L respectively. Based on the analysis of specific denitrifying activity, the live cell percentage, the cell structure, and the DNA leakage, the toxicity of low salinity was ascribed to the inhibition of denitrifying activity and the toxicity of high salinity was ascribed to both the inhibition of denitrifying activity and the lethality of denitrifying cell.

  17. 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.

  18. Screening and identification of aerobic denitrifiers

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  19. 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.

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

    PubMed

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

    2014-04-01

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

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

    PubMed

    Sharma, Sapna; Kaur, Mohinder

    2010-06-01

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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. Isolation and molecular characterization of a novel strain of Bacillus with antifungal activity from the sorghum rhizosphere.

    PubMed

    Martinez-Absalon, S C; del C Orozco-Mosqueda, Ma; Martinez-Pacheco, M M; Farias-Rodriguez, R; Govindappa, M; Santoyo, G

    2012-08-16

    We looked for bacterial strains with antifungal activity in the sorghum rhizosphere. A prescreening procedure to search for hemolytic activity among the isolated strains allowed us to detect good fungitoxic activity in a bacterial isolate that we named UM96. This bacterial isolate showed strong growth inhibition in bioassays against the pathogens Diaporthe phaseolorum, Colletotrichum acutatum, Rhizoctonia solani, and Fusarium oxysporum. The supernatant of isolate UM96 also showed strong hemolytic activity, which was not observed in the protease-treated supernatant. However, the supernatant that was treated with protease had similar antagonistic effects to those exhibited by the supernatant that was not treated with this enzyme. These results suggest that a bacteriocin-like compound is responsible for the hemolytic activity; whereas, as far as antifungal effect is concerned, an antibiotic of nonribosomal origin, such as a lipopeptide, might be acting. Further molecular characterization by partial 16S rDNA sequencing placed isolate UM96 in a cluster with Bacillus amyloliquefaciens; however, the highest identity match found in databases of Bacillus species was 91% identity. This suggests that Bacillus sp UM96 might be a novel species.

  7. Regulation of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity in the Model Rhizosphere-Dwelling Bacterium Pseudomonas putida KT2440

    PubMed Central

    An, Ran

    2016-01-01

    ABSTRACT Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqq operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts from the pqq operon to more accurately map the operon structure. GDH specific activity and PQQ levels vary according to growth condition, with the highest levels of both occurring when glucose is used as the sole carbon source and under conditions of low soluble phosphate. Under these conditions, however, PQQ levels limit in vitro phosphate solubilization. GDH specific activity data correlate well with gcd gene expression data, and the levels of expression of the pqqF and pqqB genes mirror the levels of PQQ synthesized, suggesting that one or both of these genes may serve to modulate PQQ levels according to the growth conditions. The pqq gene cluster (pqqFABCDEG) encodes at least two independent transcripts, and expression of the pqqF gene appears to be under the control of an independent promoter and terminator. IMPORTANCE Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a number of different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain through soil, but in many cases it is locked up in forms that are not available for plant uptake. Bacteria such as the model bacterium Pseudomonas putida KT2440 can solubilize insoluble soil phosphates by secreting

  8. 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

  9. 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

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

    USGS Publications Warehouse

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

    2001-01-01

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

  11. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields.

    PubMed

    Tago, Kanako; Ishii, Satoshi; Nishizawa, Tomoyasu; Otsuka, Shigeto; Senoo, Keishi

    2011-01-01

    Denitrifiers can produce and consume nitrous oxide (N(2)O). While little N(2)O is emitted from rice paddy soil, the same soil produces N(2)O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N(2) in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N(2)-producing denitrifiers.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  13. Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian and agricultural zones.

    PubMed

    Dandie, Catherine E; Wertz, Sophie; Leclair, Caissie L; Goyer, Claudia; Burton, David L; Patten, Cheryl L; Zebarth, Bernie J; Trevors, Jack T

    2011-07-01

    Lands under riparian and agricultural management differ in soil properties, water content, plant species and nutrient content and are therefore expected to influence denitrifier communities, denitrification and nitrous oxide (N(2) O) emissions. Denitrifier community abundance, denitrifier community structure, denitrification gene expression and activity were quantified on three dates in a maize field and adjacent riparian zone. N(2) O emissions were greater in the agricultural zone, whereas complete denitrification to N(2) was greater in the riparian zone. In general, the targeted denitrifier community abundance did not change between agricultural and riparian zones. However, nosZ gene expression was greater in the riparian zone than the agricultural zone. The community structure of nirS-gene-bearing denitrifiers differed in June only, whereas the nirK-gene-bearing community structure differed significantly between the riparian and the agricultural zones at all dates. The nirK-gene-bearing community structure was correlated with soil pH, while no significant correlations were found between nirS-gene-bearing community structure and soil environmental variables or N(2) O emissions, denitrification or denitrifier enzyme activity. The results suggested for the nirK and nirS-gene-bearing communities different factors control abundance vs. community structure. The nirK-gene-bearing community structure was also more responsive than the nirS-gene-bearing community structure to change between the two ecosystems.

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

    PubMed

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

    2016-10-01

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

  15. Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter.

    PubMed

    Park, Joo Hwang; Kim, Rumi; Aslam, Zubair; Jeon, Che Ok; Chung, Young Ryun

    2008-02-01

    The taxonomic position of a novel bacterial strain, YC5194(T), with antimicrobial activity, isolated from the rhizosphere of pepper in Jinju, South Korea, was studied using a polyphasic approach. Cells of the strain were Gram-negative, rod-shaped, facultative anaerobes. It grew at a temperature of 15-37 degrees C (optimum 28 degrees C). Growth of the strain occurred between pH 5.5 and 8.5, with an optimum of pH 7.0-7.5. The strain inhibited mycelial growth of Pythium ultimum, Colletotrichum gloeosporioides, Fusarium oxysporum, Botrytis cinerea, Rhizoctonia solani and Botryosphaeria dothidea and growth of Bacillus subtilis. The G+C content of the total DNA was 65.4 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genus Lysobacter (<94.0 to >99.0 % sequence similarity). Chemotaxonomic data (major quinone, Q-8; major polar lipids, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine; major fatty acids, iso-C(15 : 0), summed feature 3, C(16 : 0), iso-C(17 : 1)omega9c and C(18 : 1)omega7c) supported the affiliation of strain YC5194(T) to the genus Lysobacter. Phylogenetic analysis based on 16S rRNA gene sequences, DNA-DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC5194(T) from species of Lysobacter with validly published names. Strain YC5194(T) therefore represents a novel species, for which the name Lysobacter capsici sp. nov. is proposed. The type strain is YC5194(T) (=KCTC 22007(T) =DSM 19286(T)).

  16. 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...

  17. 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.

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

    PubMed

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

    2015-11-01

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

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

    PubMed Central

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

    2016-01-01

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

  20. Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure.

    PubMed

    Rasche, Frank; Hödl, Verania; Poll, Christian; Kandeler, Ellen; Gerzabek, Martin H; van Elsas, Jan D; Sessitsch, Angela

    2006-05-01

    A greenhouse experiment was performed to analyze a potential effect of genetically modified potatoes expressing antibacterial compounds (attacin/cecropin, T4 lysozyme) and their nearly isogenic, nontransformed parental wild types on rhizosphere bacterial communities. To compare plant transformation-related variations with commonly accepted impacts caused by altered environmental conditions, potatoes were cultivated under different environmental conditions, for example using contrasting soil types. Further, plants were challenged with the blackleg pathogen Erwinia carotovora ssp. atroseptica. Rhizosphere soil samples were obtained at the stem elongation and early flowering stages. The activities of various extracellular rhizosphere enzymes involved in the C-, P- and N-nutrient cycles were determined as the rates of fluorescence of enzymatically hydrolyzed substrates containing the highly fluorescent compounds 4-methylumbelliferone or 7-amino-4-methyl coumarin. The structural diversity of the bacterial communities was assessed by 16S rRNA-based terminal restriction fragment length polymorphism analysis, and 16S rRNA gene clone libraries were established for the flowering conventional and T4 lysozyme-expressing Desirée lines grown on the chernozem soil, each line treated with and without E. carotovora ssp. atroseptica. Both genetic transformation events induced a differentiation in the activity rates and structures of associated bacterial communities. In general, T4 lysozyme had a stronger effect than attacin/cecropin. In comparison with the other factors, the impact of the genetic modification was only transient and minor, or comparable to the dominant variations caused by soil type, plant genotype, vegetation stage and pathogen exposure.

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

    PubMed Central

    Wang, Da-qing; Yu, Song

    2016-01-01

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

  2. Comparison of the catabolic activity and catabolic profiles of rhizospheric, gravel-associated and interstitial microbial communities in treatment wetlands.

    PubMed

    Weber, Kela P; Legge, Raymond L

    2013-01-01

    Microbial communities play a critical role in degrading organic contaminants in treatment wetlands; however, an understanding of the different roles played by rhizospheric, gravel-associated and interstitial microbial communities is deficient due to a lack of data directly comparing these microbial communities. Community level physiological profiling (CLPP) was used to compare the catabolic capabilities of rhizospheric, gravel-associated and interstitial microbial communities in vertical-flow planted and unplanted wetland mesocosms. Wetland mesocosms were decommissioned to gather microbial community samples associated with the roots and gravel bed media taken from the top (10 cm depth), middle (30 cm depth) and bottom (60 cm depth). The catabolic capabilities of the rhizospheric microbial communities were seen to be much greater than those of the gravel-associated communities. A decrease in catabolic capability was seen with increasing depth, suggesting that communities near the surface play a larger role in the degradation of carbon-based compounds. A general difference in catabolic profiles based on plant presence/absence was observed for the interstitial water and all gravel-associated samples at all depths, suggesting that the presence of roots within part of the mesocosm not only has a localized effect on the attached microbial population, but also on gravel-associated microbial communities throughout the mesocosms.

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

    PubMed Central

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

    2009-01-01

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

  4. Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine.

    PubMed

    Mingma, Ratchanee; Pathom-aree, Wasu; Trakulnaleamsai, Savitr; Thamchaipenet, Arinthip; Duangmal, Kannika

    2014-01-01

    In this study, actinomycetes from roots and rhizospheric soils of leguminous plants were isolated using starch casein agar supplemented with antifungal and antibacterial antibiotics. Three hundred and seventeen actinomycetes were isolated with 77 isolates obtained from plant roots and 240 isolates from rhizospheric soils. Analysis of whole-organism hydrolysates showed that 289 strains were rich in the LL-isomer of diaminopimelic acid, a result consistent with their assignment to the streptomycetes. The remaining 28 strains were assigned to non-streptomycetes based on the presence of meso-isomer of diaminopimelic acid in cell wall. Sixty-four isolates (20.2%) showed antagonistic activity against soybean pathogen Xanthomonas campestris pv. glycine by agar overlay method. Isolate RM 365 showed the highest activity with an inhibition ratio of 3.79, with no inhibitory activity on the growth of Rhizobium japonicum TISTR 079, Rhizobium sp. TISTR 061 and Rhizobium sp. TISTR 063. The 16S rRNA gene sequence analysis revealed that isolate RM 365 shared 99.28% similarity to Streptomyces caeruleatus GIMN4(T) (GQ329712). In addition, isolates which contained meso-DAP were also identified by 16S rRNA gene sequence analysis. The results showed that they were members of the genus Amycolatopsis, Isoptericola, Micromonospora, Microbispora, Nocardia, Nonomuraea, Promicromonospora and Pseudonocardia.

  5. 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

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

    PubMed

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

    2014-03-01

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

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

    PubMed

    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.

  8. 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

  9. 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.

  10. 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 (N(2)O) occurs in soil environments by the action of denitrifying bacteria possessing nitrous oxide reductase (N(2)OR), a dimeric copper (Cu)-dependent enzyme producing environmentally benign dinitrogen (N(2)). 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 N(2)OR respectively. Results revealed that 0.05 mM Cu caused maximum conversion of N(2)O to N(2) via bacterial reduction of N(2)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 N(2)O reduced to N(2). 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 N(2)O emissions.

  11. The Effects of Cadmium Exposure on Cadmium Fractionation and Enzyme Activities in the Rhizosphere of Two Radish Cultivars (Raphanus sativus L.).

    PubMed

    Xin, Juan; Zhao, Xiaohu; Tan, Qiling; Sun, Xuecheng; Wen, Xin; Qin, Shiyu; Hu, Chengxiao

    2017-02-01

    The effects of increasing Cd additions on plant growth and Cd fractionation and enzyme activities in rhizosphere soil of two radish cultivars were investigated. The results showed that Cd concentrations in shoot and root of cultivar 4 were both higher than for cultivar 19 under different Cd levels. Compared with cultivar 19, the total, shoot and root biomasses of cultivar 4 were significantly reduced with increasing Cd levels. A decrease in soil pH was observed for cultivar 4. The exchangeable Cd concentration of soil from cultivar 4 was significantly higher than for soil from cultivar 19, while the carbonate-bound Cd concentration of soil from cultivar 4 was significantly lower than for cultivar 19. Enzyme activities, especially acid phosphatase activity, were more susceptible to Cd in soil from cultivar 4. These results indicated that cultivar 19 exhibits a stronger ability to adapt to Cd stress than cultivar 4.

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

    PubMed

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

    2014-07-04

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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary.

    PubMed

    Abell, Guy C J; Revill, Andrew T; Smith, Craig; Bissett, Andrew P; Volkman, John K; Robert, Stanley S

    2010-02-01

    Nitrification and denitrification are key steps in nitrogen (N) cycling. The coupling of these processes, which affects the flow of N in ecosystems, requires close interaction of nitrifying and denitrifying microorganisms, both spatially and temporally. The diversity, temporal and spatial variations in the microbial communities affecting these processes was examined, in relation to N cycling, across 12 sites in the Fitzroy river estuary, which is a turbid subtropical estuary in central Queensland. The estuary is a major source of nutrients discharged to the Great Barrier Reef near-shore zone. Measurement of nitrogen fluxes showed an active denitrifying community during all sampling months. Archaeal ammonia monooxygenase (amoA of AOA, functional marker for nitrification) was significantly more abundant than Betaproteobacterial (beta-AOB) amoA. Nitrite reductase genes, functional markers for denitrification, were dominated by nirS and not nirK types at all sites during the year. AOA communities were dominated by the soil/sediment cluster of Crenarchaeota, with sequences found in estuarine sediment, marine and terrestrial environments, whereas nirS sequences were significantly more diverse (where operational taxonomic units were defined at both the threshold of 5% and 15% sequence similarity) and were closely related to sequences originating from estuarine sediments. Terminal-restriction fragment length polymorphism (T-RFLP) analysis revealed that AOA population compositions varied spatially along the estuary, whereas nirS populations changed temporally. Statistical analysis of individual T-RF dominance suggested that salinity and C:N were associated with the community succession of AOA, whereas the nirS-type denitrifier communities were related to salinity and chlorophyll-alpha in the Fitzroy river estuary.

  18. 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 ...

  19. 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.

  20. Optimization, kinetics and antioxidant activity of exopolysaccharide produced from rhizosphere isolate, Pseudomonas fluorescens CrN6.

    PubMed

    Sirajunnisa, Abdul Razack; Vijayagopal, Velayutham; Sivaprakash, Bhaskar; Viruthagiri, Thangavelu; Surendhiran, Duraiarasan

    2016-01-01

    Pseudomonas fluorescens, isolated from rhizosphere soil, was exploited for the production of exopolysaccharide (EPS). A medium was constituted to enhance the yield of EPS. This study involved an agro waste as carbon substrate, rice bran, a replacement of glucose. Plackett-Burman statistical design was applied to evaluate the selected sixteen components from which, rice bran, peptone, NaCl and MnCl2 were found to be effective and significant on the fermentation process. To study the concentration of each component, central composite design was carried out and response surface plots indicated that the following concentrations significantly enhanced the production - rice bran 5.02%, peptone 0.35%, NaCl 0.51%, MnCl2 0.074%. Kinetic modeling was also performed to simulate the process parameters. Logistic model for microbial growth and Luedeking-Piret equation for product formation and substrate utilization were found to fit the experiment. The present investigation resulted in a maximum yield of 4.62g of EPS/L at 48h. High DPPH scavenging ability was a positive indication to use EPS as an antioxidant. The extracted polysaccharide could thus be ecofriendly due to its biodegradability and nontoxicity, and subjected to various industrial and pharmaceutical applications.

  1. Expression of Bradyrhizobium japonicum cbb(3) terminal oxidase under denitrifying conditions is subjected to redox control.

    PubMed

    Bueno, Emilio; Richardson, David J; Bedmar, Eulogio J; Delgado, María J

    2009-09-01

    Bradyrhizobium japonicum utilizes cytochrome cbb(3) oxidase encoded by the fixNOQP operon to support microaerobic respiration under free-living and symbiotic conditions. It has been previously shown that, under denitrifying conditions, inactivation of the cycA gene encoding cytochrome c(550), the electron donor to the Cu-containing nitrite reductase, reduces cbb(3) expression. In order to establish the role of c(550) in electron transport to the cbb(3) oxidase, in this work, we have analyzed cbb(3) expression and activity in the cycA mutant grown under microaerobic or denitrifying conditions. Under denitrifying conditions, mutation of cycA had a negative effect on cytochrome c oxidase activity, heme c (FixP and FixO) and heme b cytochromes as well as expression of a fixP'-'lacZ fusion. Similarly, cbb(3) oxidase was expressed very weakly in a napC mutant lacking the c-type cytochrome, which transfers electrons to the NapAB structural subunit of the periplasmic nitrate reductase. These results suggest that a change in the electron flow through the denitrification pathway may affect the cellular redox state, leading to alterations in cbb(3) expression. In fact, levels of fixP'-'lacZ expression were largely dependent on the oxidized or reduced nature of the carbon source in the medium. Maximal expression observed in cells grown under denitrifying conditions with an oxidized carbon source required the regulatory protein RegR.

  2. 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

  3. Anaerobic and aerobic degradation of pyridine by a newly isolated denitrifying bacterium.

    PubMed Central

    Rhee, S K; Lee, G M; Yoon, J H; Park, Y H; Bae, H S; Lee, S T

    1997-01-01

    New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions were isolated from industrial wastewater. The successful enrichment and isolation of these strains required selenite as a trace element. These isolates appeared to be closely related to Azoarcus species according to the results of 16S rRNA sequence analysis. An isolated strain, pF6, metabolized pyridine through the same pathway under both aerobic and anaerobic conditions. Since pyridine induced NAD-linked glutarate-dialdehyde dehydrogenase and isocitratase activities, it is likely that the mechanism of pyridine degradation in strain pF6 involves N-C-2 ring cleavage. Strain pF6 could degrade pyridine in the presence of nitrate, nitrite, and nitrous oxide as electron acceptors. In a batch culture with 6 mM nitrate, degradation of pyridine and denitrification were not sensitively affected by the redox potential, which gradually decreased from 150 to -200 mV. In a batch culture with the nitrate concentration higher than 6 mM, nitrite transiently accumulated during denitrification significantly inhibited cell growth and pyridine degradation. Growth yield on pyridine decreased slightly under denitrifying conditions from that under aerobic conditions. Furthermore, when the pyridine concentration used was above 12 mM, the specific growth rate under denitrifying conditions was higher than that under aerobic conditions. Considering these characteristics, a newly isolated denitrifying bacterium, strain pF6, has advantages over strictly aerobic bacteria in field applications. PMID:9212408

  4. 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

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

    PubMed

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

    2014-02-01

    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.

  6. Occurrence and potential activity of denitrifiers and methanogens in groundwater at 140 m depth in Pliocene diatomaceous mudstone of northern Japan.

    PubMed

    Katsuyama, Chie; Nashimoto, Hiroaki; Nagaosa, Kazuyo; Ishibashi, Tomotaka; Furuta, Kazuki; Kinoshita, Takeshi; Yoshikawa, Hideki; Aoki, Kazuhiro; Asano, Takahiro; Sasaki, Yoshito; Sohrin, Rumi; Komatsu, Daisuke D; Tsunogai, Urumu; Kimura, Hiroyuki; Suwa, Yuichi; Kato, Kenji

    2013-12-01

    Anaerobic microbial activity has a major influence on the subsurface environment. We investigated the denitrification and methanogenesis in anoxic groundwater at a depth of 140 m in two boreholes drilled in a sedimentary geological setting, where the redox potential fluctuated. The average maximum potential denitrification rates, measured under anaerobic conditions in the two boreholes using an (15) N tracer, were 0.060 and 0.085 nmol (30) N2  mL(-1)  h(-1) . The deduced NirS amino acid sequences obtained from in situ samples were similar to those of isolates belonging to the α-, β-, and γ-Proteobacteria, and the Firmicutes (72-100% similarity). Based on the nirS gene, the same operational taxonomic unit dominated incubated samples from each borehole. Methanogenesis candidates were detected by 16S rRNA gene analysis, but no sequence was detected using primers for the functional methanogenesis gene mcrA. Although the stable isotope signatures suggested that some of the dissolved methane was of biogenic origin, no potential for methane production was evident during the incubations. The groundwater at 140 m depth did not contain oxygen, had an Eh ranging from -144 to 6.8 mV, and was found to be a potential field for denitrification.

  7. 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.

  8. 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.

  9. 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

  10. 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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  13. Fertilization stimulates anaerobic fuel degradation of antarctic soils by denitrifying microorganisms.

    PubMed

    Powell, Shane M; Ferguson, Susan H; Snape, Ian; Siciliano, Steven D

    2006-03-15

    Human activities in the Antarctic have resulted in hydrocarbon contamination of these fragile polar soils. Bioremediation is one of the options for remediation of these sites. However, little is known about anaerobic hydrocarbon degradation in polar soils and the influence of bioremediation practices on these processes. Using a field trial at Old Casey Station, Antarctica, we assessed the influence of fertilization on the anaerobic degradation of a 20-year old fuel spill. Fertilization increased hydrocarbon degradation in both anaerobic and aerobic soils when compared to controls, but was of most benefit for anaerobic soils where evaporation was negligible. This increased biodegradation in the anaerobic soils corresponded with a shift in the denitrifier community composition and an increased abundance of denitrifiers and benzoyl-CoA reductase. A microcosm study using toluene and hexadecane confirmed the degradative capacity within these soils under anaerobic conditions. It was observed that fertilized anaerobic soil degraded more of this hydrocarbon spike when incubated anaerobically than when incubated aerobically. We conclude that denitrifiers are actively involved in hydrocarbon degradation in Antarctic soils and that fertilization is an effective means of stimulating their activity. Further, when communities stimulated to degrade hydrocarbons under anaerobic conditions are exposed to oxygen, hydrocarbon degradation is suppressed. The commonly accepted belief that remediation of polar soils requires aeration needs to be reevaluated in light of this new data.

  14. Nitrogen Redox Metabolism of a Heterotrophic, Nitrifying-Denitrifying Alcaligenes sp. from Soil

    PubMed Central

    Castignetti, Domenic; Hollocher, Thomas C.

    1982-01-01

    Metabolic characteristics of a heterotrophic, nitrifier-denitrifier Alcaligenes sp. isolated from soil were further characterized. Pyruvic oxime and hydroxylamine were oxidized to nitrite aerobically by nitrification-adapted cells with specific activities (Vmax) of 0.066 and 0.003 μmol of N × min−1 × mg of protein−1, respectively, at 22°C. Km values were 15 and 42 μM for pyruvic oxime and hydroxylamine, respectively. The greater pyruvic oxime oxidation activity relative to hydroxylamine oxidation activity indicates that pyruvic oxime was a specific substrate and was not oxidized appreciably via its hydrolysis product, hydroxylamine. When grown as a denitrifier on nitrate, the bacterium could not aerobically oxidize pyruvic oxime or hydroxylamine to nitrite. However, hydroxylamine was converted to nearly equimolar amounts of ammonium ion and nitrous oxide, and the nature of this reaction is discussed. Cells grown as heterotrophic nitrifiers on pyruvic oxime contained two enzymes of denitrification, nitrate reductase and nitric oxide reductase. The nitrate reductase was the dissimilatory type, as evidenced by its extreme sensitivity to inhibition by azide and by its ability to be reversibly inhibited by oxygen. Cells grown aerobically on organic carbon sources other than pyruvic oxime contained none of the denitrifying enzymes surveyed but were able to oxidize pyruvic oxime to nitrite and reduce hydroxylamine to ammonium ion. PMID:16346117

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

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

    PubMed Central

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

    2007-01-01

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

  1. 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.

  2. 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.

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

    SciTech Connect

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

    1998-09-01

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

  4. Bulk soil and rhizosphere bacterial community PCR-DGGE profiles and beta-galactosidase activity as indicators of biological quality in soils contaminated by heavy metals and cultivated with Silene vulgaris (Moench) Garcke.

    PubMed

    Martínez-Iñigo, M J; Pérez-Sanz, A; Ortiz, I; Alonso, J; Alarcón, R; García, P; Lobo, M C

    2009-06-01

    The biological quality of two heavy metal contaminated soils (soil C: Typic Calcixerept, pH 8.3 and soil H: Typic Haploxeraf, pH 7.3) was investigated after growing the metal-tolerant plant Silene vulgaris (Moench) Garcke for two vegetative periods. The activity of the enzyme beta-galactosidase, which is sensitive to the presence of contaminants in soil, and the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of 16S rRNA gene fragments of culturable bacteria from bulk soil and rhizosphere were determined. The microbial enzymatic activity was higher in planted soils than in bare soils at the contamination level of 600 mg of total heavy metals kg(-1) soil. After growing S. vulgaris, beta-galactosidase activity was almost recovered in the calcareous soil. In this soil new bands appeared in the PCR-DGGE profiles of the rhizosphere bacterial community as a response to the exposure to heavy metals.

  5. 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

  6. Alleviated toxicity of cadmium by the rhizosphere of Kandelia obovata (S., L.) Yong.

    PubMed

    Weng, Bosen; Huang, Yong; Liu, Jingchun; Lu, Haoliang; Yan, Chongling

    2014-11-01

    A pot experiment was conducted to investigate the Cadmium (Cd) toxicity alleviated by the rhizosphere of Kandelia obovata (S., L.) Yong (K. obovata), using a rhizobox with Cd concentrations of 0, 12.5, 25, 50 and 100 mg kg(-1) soil. The rhizobox used to plant K. obovata was divided into five sections by nylon cloth (S2-S5). Our results showed that pH was lower in rhizosphere than in non-rhizosphere soil. Microbial biomass C (Cmic) and N (Nmic) was stimulated in rhizosphere zone, but inhibited by Cd additions. Soil enzyme activities were significantly higher in rhizosphere (S2) than in non-rhizosphere soil (S5) (p < 0.05). In addition, DTPA-extractable Cd in different rhizosphere zone soil (S2-S5) was influenced directly under different rates of Cd supply. Moreover, Cd treatments could induce the enhancement of DTPA-extractable Cd. This study suggests that Cd toxicity can be alleviated in the rhizosphere even under high Cd supply.

  7. Isolation and characterization of bacteria from the rhizosphere and bulk soil of Stellera chamaejasme L.

    PubMed

    Cui, Haiyan; Yang, Xiaoyan; Lu, Dengxue; Jin, Hui; Yan, Zhiqiang; Chen, Jixiang; Li, Xiuzhuang; Qin, Bo

    2015-03-01

    This study is the first to describe the composition and characteristics of culturable bacterial isolates from the rhizosphere and bulk soil of the medicinal plant Stellera chamaejasme L. at different growth stages. Using a cultivation-dependent approach, a total of 148 isolates showing different phenotypic properties were obtained from the rhizosphere and bulk soil. Firmicutes and Actinobacteria were the major bacterial groups in both the rhizosphere and bulk soil at all 4 growth stages of S. chamaejasme. The diversity of the bacterial community in the rhizosphere was higher than that in bulk soil in flowering and fruiting stages. The abundance of bacterial communities in the rhizosphere changed with the growth stages and had a major shift at the fruiting stage. Dynamic changes of bacterial abundance and many bacterial groups in the rhizosphere were similar to those in bulk soil. Furthermore, most bacterial isolates exhibited single or multiple biochemical activities associated with S. chamaejasme growth, which revealed that bacteria with multiple physiological functions were abundant and widespread in the rhizosphere and bulk soil. These results are essential (i) for understanding the ecological roles of bacteria in the rhizosphere and bulk soil and (ii) as a foundation for further evaluating their efficacy as effective S. chamaejasme growth-promoting rhizobacteria.

  8. Linking carbon and nitrogen cycles in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Baggs, E.; Morley, N.; Paterson, E.; Villada, A.; Gougoulias, C.; Shaw, L.

    2013-12-01

    Consideration of links between C and N biogeochemical cycles is essential for advancing knowledge of ecosystem functioning. Plant-derived C is a key driver of rhizosphere processes, but the role of this C in driving components of the N cycle is poorly characterised. Here we demonstrate the role of plant-derived C in regulating nitrous oxide (N2O) production and reduction in the rhizosphere. We use isotope (13C, 14C and 15N) techniques and a new isotope-FISH-FACS approach to verify (i) the link between plant-C and activity of microbial nitrate reducers, (ii) uptake of C compounds into pseudomonads, (iii) the role of both composite rhizodeposits and individual compounds in regulating the magnitude of N2O emission, and (iv) their influence on the N2O:N2 product ratio. We examine the potential these relationships offer to use plants to manipulate the rhizosphere for reduction of N2O emissions.

  9. Biodegradation of aromatic hydrocarbons by aquifer microorganisms under denitrifying conditions

    SciTech Connect

    Hutchins, S.R.; Sewell, G.W.; Kovacs, D.A.; Smith, G.A.

    1991-01-01

    Laboratory tests were conducted to evaluate whether denitrification would be a suitable alternative for biorestoration of an aquifer contaminated with JP-4 jet fuel. Microcosms were prepared from uncontaminated and contaminated aquifer material, amended with nitrate, nutrients, and aromatic hydrocarbons, and incubated under a nitrogen atmosphere at 12 C. With uncontaminated core material, there was no observable lag period prior to removal of toluene whereas 30 days was required before biodegradation commenced for xylenes, ethylbenzene, and 1,2,4-trimethylbenzene. An identical test with contaminated aquifer material exhibited not only much longer lag periods but decreased rates of biodegradation; benzene, ethylbenzene, and o-xylene were not significantly degraded within the 6-month time period even though active denitrification occurred at this time. First-order biodegradation rate constants ranged from 0.016 to 0.38/day for uncontaminated core material and from 0.022 to 0.067/day for contaminated core material. Tests with individual compounds in uncontaminated core indicated that benzene and m-xylene inhibited the basal rate of denitrification. These data demonstrate that several aromatic compounds are degraded under denitrifying conditions, but rates of biodegradation may be lower in material contaminated with JP-4 jet fuel.

  10. 13C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline.

    PubMed

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

    2012-05-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2007-07-01

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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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...

  18. 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 ...

  19. Association of earthworm-denitrifier interactions with increased emission of nitrous oxide from soil mesocosms amended with crop residue.

    PubMed

    Nebert, Lucas D; Bloem, Jaap; Lubbers, Ingrid M; van Groenigen, Jan Willem

    2011-06-01

    Earthworm activity is known to increase emissions of nitrous oxide (N(2)O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N(2)O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N(2)O emissions from the soil. We set up a 90-day mesocosm experiment in which (15)N-labeled maize (Zea mays L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm Lumbricus rubellus and/or the endogeic earthworm Aporrectodea caliginosa. We measured N(2)O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes nirS and nosZ through real-time quantitative PCR. Compared to the control, L. rubellus increased denitrification enzyme activity and N(2)O emissions on days 21 and 90 (day 21, P = 0.034 and P = 0.002, respectively; day 90, P = 0.001 and P = 0.007, respectively), as well as cumulative N(2)O emissions (76%; P = 0.014). A. caliginosa activity led to a transient increase of N(2)O emissions on days 8 to 18 of the experiment. Abundance of nosZ was significantly increased (100%) on day 90 in the treatment mixture containing L. rubellus alone. We conclude that L. rubellus increased cumulative N(2)O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source.

  20. Trace Gas Emission from in-Situ Denitrifying Bioreactors

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  1. 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

  2. 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

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

    PubMed

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

    2014-01-21

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

  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.

  5. Responses of soil microbial communities in the rhizosphere of cucumber (Cucumis sativus L.) to exogenously applied p-hydroxybenzoic acid.

    PubMed

    Zhou, Xingang; Yu, Gaobo; Wu, Fengzhi

    2012-08-01

    Changes in soil biological properties have been implicated as one of the causes of soil sickness, a phenomenon that occurs in continuous monocropping systems. However, the causes for these changes are not yet clear. The aim of this work was to elucidate the role of p-hydroxybenzoic acid (PHBA), an autotoxin of cucumber (Cucumis sativus L.), in changing soil microbial communities. p-Hydroxybenzoic acid was applied to soil every other day for 10 days in cucumber pot assays. Then, the structures and sizes of bacterial and fungal communities, dehydrogenase activity, and microbial carbon biomass (MCB) were assessed in the rhizosphere soil. Structures and sizes of rhizosphere bacterial and fungal communities were analyzed by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time PCR, respectively. p-Hydroxybenzoic acid inhibited cucumber seedling growth and stimulated rhizosphere dehydrogenase activity, MBC content, and bacterial and fungal community sizes. Rhizosphere bacterial and fungal communities responded differently to exogenously applied PHBA. The PHBA decreased the Shannon-Wiener index for the rhizosphere bacterial community but increased that for the rhizosphere fungal community. In addition, the response of the rhizosphere fungal community structure to PHBA acid was concentration dependent, but was not for the rhizosphere bacterial community structure. Our results indicate that PHBA plays a significant role in the chemical interactions between cucumber and soil microorganisms and could account for the changes in soil microbial communities in the continuously monocropped cucumber system.

  6. Rhizosphere stoichiometry: are C : N : P ratios of plants, soils, and enzymes conserved at the plant species-level?

    PubMed

    Bell, Colin; Carrillo, Yolima; Boot, Claudia M; Rocca, Jennifer D; Pendall, Elise; Wallenstein, Matthew D

    2014-01-01

    As a consequence of the tight linkages among soils, plants and microbes inhabiting the rhizosphere, we hypothesized that soil nutrient and microbial stoichiometry would differ among plant species and be correlated within plant rhizospheres. We assessed plant tissue carbon (C) : nitrogen (N) : phosphorus (P) ratios for eight species representing four different plant functional groups in a semiarid grassland during near-peak biomass. Using intact plant species-specific rhizospheres, we examined soil C : N : P, microbial biomass C : N, and soil enzyme C : N : P nutrient acquisition activities. We found that few of the plant species' rhizospheres demonstrated distinct stoichiometric properties from other plant species and unvegetated soil. Plant tissue nutrient ratios and components of below-ground rhizosphere stoichiometry predominantly differed between the C4 plant species Buchloe dactyloides and the legume Astragalus laxmannii. The rhizospheres under the C4 grass B. dactyloides exhibited relatively higher microbial C and lower soil N, indicative of distinct soil organic matter (SOM) decomposition and nutrient mineralization activities. Assessing the ecological stoichiometry among plant species' rhizospheres is a high-resolution tool useful for linking plant community composition to below-ground soil microbial and nutrient characteristics. By identifying how rhizospheres differ among plant species, we can better assess how plant-microbial interactions associated with ecosystem-level processes may be influenced by plant community shifts.

  7. Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems ▿

    PubMed Central

    Hai, Brigitte; Diallo, Ndeye Hélène; Sall, Saidou; Haesler, Felix; Schauss, Kristina; Bonzi, Moussa; Assigbetse, Komi; Chotte, Jean-Luc; Munch, Jean Charles; Schloter, Michael

    2009-01-01

    The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited. PMID:19502431

  8. 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

  9. 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.

  10. Autotrophic, Hydrogen-Oxidizing, Denitrifying Bacteria in Groundwater, Potential Agents for Bioremediation of Nitrate Contamination

    PubMed Central

    Smith, Richard L.; Ceazan, Marnie L.; Brooks, Myron 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 Km of 0.45 to 0.60 μM and a Vmax 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 Kms ranged from 0.30 to 3.32 μM, with Vmaxs 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. PMID:16349284

  11. Competition between Two Isolates of Denitrifying Bacteria Added to Soil

    PubMed Central

    Murray, Robert E.; Parsons, Laura L.; Smith, M. Scott

    1992-01-01

    We examined the competitive relationship between two isolates of denitrifying bacteria, both of which grow well under aerobic conditions but differ in their ability to grow under denitrifying conditions. The growth and persistence of the two isolates, added to sterile soil or added to soil previously colonized by the other isolate, were monitored under aerobic and denitrifying (anaerobic) conditions. When isolates were added together to sterile soil, the isolate added at the higher density reduced the growth of the isolate added at the lower density. The magnitude of the growth reduction varied depending on the competitive abilities of the individual isolates and the aeration state of the soil. Prior colonization of soil with one of the isolates conferred a competitive advantage on the colonized isolate but did not lead to the disappearance of the challenging isolate. Fluctuations in aeration state caused large changes in the population density of one isolate and altered the competitive relationship between the two isolates. The competitive effectiveness of each isolate varied with cell density, the degree of prior colonization of the soil by the other isolate, and the aeration state of the soil. PMID:16348820

  12. 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.

  13. Enhanced performance of denitrifying sulfide removal process at high carbon to nitrogen ratios under micro-aerobic condition.

    PubMed

    Chen, Chuan; Zhang, Ruo-Chen; Xu, Xi-Jun; Fang, Ning; Wang, Ai-Jie; Ren, Nan-Qi; Lee, Duu-Jong

    2017-02-11

    The success of denitrifying sulfide removal (DSR) processes, which simultaneously degrade sulfide, nitrate and organic carbon in the same reactor, counts on synergetic growths of autotrophic and heterotrophic denitrifiers. Feeding wastewaters at high C/N ratio would stimulate overgrowth of heterotrophic bacteria in the DSR reactor so deteriorating the growth of autotrophic denitrifiers. The DSR tests at C/N=1.26:1, 2:1 or 3:1 and S/N =5:6 or 5:8 under anaerobic (control) or micro-aerobic conditions were conducted. Anaerobic DSR process has <50% sulfide removal with no elemental sulfur transformation. Under micro-aerobic condition to remove <5% sulfide by chemical oxidation pathway, 100% sulfide removal is achieved by the DSR consortia. Continuous-flow tests under micro-aerobic condition have 70% sulfide removal and 55% elemental sulfur recovery. Trace oxygen enhances activity of sulfide-oxidizing, nitrate-reducing bacteria to accommodate properly the wastewater with high C/N ratios.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2012-06-01

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

  16. Aerobic and anoxic growth and nitrate removal capacity of a marine denitrifying bacterium isolated from a recirculation aquaculture system.

    PubMed

    Borges, Maria-Teresa; Sousa, André; De Marco, Paolo; Matos, Ana; Hönigová, Petra; Castro, Paula M L

    2008-01-01

    Bacterial biofilters used in marine recirculation aquaculture systems need improvements to enhance nitrogen removal efficiency. Relatively little is known about biofilter autochthonous population structure and function. The present study was aimed at isolating and characterizing an autochthonous denitrifying bacterium from a marine biofilter installed at a recirculation aquaculture system. Colonization of four different media in a marine fish farm was followed by isolation of various denitrifying strains and molecular classification of the most promising one, strain T2, as a novel member of the Pseudomonas fluorescens cluster. This strain exhibits high metabolic versatility regarding N and C source utilization and environmental conditions for growth. It removed nitrate through aerobic assimilatory metabolism at a specific rate of 116.2 mg NO(3)-N g dw(-1) h(-1). Dissimilatory NO(3)-N removal was observed under oxic conditions at a limited rate, where transient NO(2)-N formed represented 22% (0.17 mg L(-1)) of the maximum transient NO(2)-N observed under anoxic conditions. Dissimilatory NO(3)-N removal under anoxic conditions occurred at a specific rate of 53.5 mg NO(3)-N g dw(-1) h(-1). The isolated denitrifying strain was able to colonize different materials, such as granular activated carbon (GAC), Filtralite and Bioflow plastic rings, which allow the development of a prototype bioreactor for strain characterization under dynamic conditions and mimicking fish-farm operating conditions.

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

    PubMed

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

    2012-02-01

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

  18. 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.

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

    PubMed

    Yu, Hongting; Li, Min

    2015-03-04

    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.

  20. 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.

  1. Rhizosphere Bacterial Degradation of RDX, Understanding and Enhancement

    DTIC Science & Technology

    2014-02-01

    diazabutanal (NDAB)(Figure 1) (Fournier, Halasz et al. 2002, Seth-Smith, Rosser et al. 2002). NDAB degrades cometabolically by action of white rot fungi ...soil (Miller and Wood 1996). As root exudates are known to stimulate bacterial activity in the rhizosphere, they could in turn enhance the degradation...1504 51 Western blot analysis was also performed using antibodies raised against XplA; however, no clear signal was seen (results not shown

  2. 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

  3. 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.

  4. Performance of agricultural residue media in laboratory denitrifying bioreactors at low temperatures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Woodchip denitrifying bioreactors can remove a substantial fraction of nitrate from agricultural tile drainage; however, questions about cold springtime performance persist. The objectives of this study were to improve the nitrate removal rate of denitrifying bioreactors at warm and cold temperature...

  5. Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR.

    PubMed

    Qiu, X-Y; Hurt, R A; Wu, L-Y; Chen, C-H; Tiedje, J M; Zhou, J-Z

    2004-11-01

    We developed a quantitative competitive PCR (QC-PCR) system to detect and quantify copper-denitrifying bacteria in environmental samples. The primers were specific to copper-dependent nitrite reductase gene (nirK). We were able to detect about 200 copeis of nirK in the presence of abundant non-specific target DNA and about 1.2 x 10(3)Pseudomonas sp. G-179 cells from one gram of sterilized soil by PCR amplification. A 312-bp nirK internal standard (IS) was constructed, which showed very similar amplification efficiency with the target nirKfragment (349 bp) over 4 orders of magnitude (10(3)-10(6)). The accuracy of this system was evaluated by quantifying various known amount of nirK DNA. The linear regressions were obtained with a R(2) of 0.9867 for 10(3)copies of nirK, 0.9917 for 10(4) copies of nirK, 0.9899 for 10(5) copies of nirK and 0.9846 for 10(6) copies of nirK. A high correlation between measured nirK and calculated nirK (slope of 1.0398, R(2)=0.9992) demonstrated that an accurate measurement could be achieved with this system. Using this method, we quantified nirK in several A-horizon and stream sediment samples from eastern Tennessee. In general, the abundance of nirK was in the range of 10(8)-10(9) copies g soil(-1) dry weight. The nirK content in the soil samples appeared correlated with NH(4)(N) content in the soil. The activities of copper-denitrifying bacteria were evaluated by quantifying cDNA of nirK. In most of sample examined, the content of nirK cDNA was less than 10(5) copies g soil(-1) dry weight. Higher nirK cDNA content (>10(6) copies g soil(-1) dry weight) was detected from both sediment samples at Rattlebox Creek and the Walker Branch West Ridge. Although the stream sediment samples at the Walker Branch West Ridge contained less half of the nirK gene content as compared to A-horizon sample, the activities of copper-denitrifying bacteria were almost 600 times higher than in the A-horizon sample.

  6. 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.

  7. 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.

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

    PubMed Central

    Wu, Jing; Wang, Yiming; Lin, Xiangui

    2013-01-01

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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. Denitratisoma oestradiolicum gen. nov., sp. nov., a 17beta-oestradiol-degrading, denitrifying betaproteobacterium.

    PubMed

    Fahrbach, Michael; Kuever, Jan; Meinke, Ruth; Kämpfer, Peter; Hollender, Juliane

    2006-07-01

    A Gram-negative, motile, denitrifying bacterium (strain AcBE2-1(T)) was isolated from activated sludge of a municipal wastewater treatment plant using 17beta-oestradiol (E2) as sole source of carbon and energy. Cells were curved rods, 0.4-0.8 x 0.8-2.0 microm in size, non-fermentative, non-spore-forming, oxidase-positive and catalase-negative. E2 was oxidized completely to carbon dioxide and water by reduction of nitrate to a mixture of dinitrogen monoxide and dinitrogen, with the intermediate accumulation of nitrite. Electron recoveries were between 90 and 100 %, taking assimilated E2 into account. With nitrate as the electron acceptor, the bacterium also grew on fatty acids (C(2) to C(6)), isobutyrate, crotonate, dl-lactate, pyruvate, fumarate and succinate. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain AcBE2-1(T) represents a separate line of descent within the family Rhodocyclaceae (Betaproteobacteria). The closest relatives are the cholesterol-degrading, denitrifying bacteria Sterolibacterium denitrificans DSM 13999(T) and strain 72Chol (=DSM 12783), with <93.9 % sequence similarity. The G+C content of the DNA was 61.4 mol%. Detection of a quinone system with ubiquinone Q-8 as the predominant compound and a fatty acid profile that included high concentrations of C(16 : 1)omega7c/iso-C(15 : 0) 2-OH and C(16 : 0), in addition to C(18 : 1)omega7c and small amounts of C(8 : 0) 3-OH, supported the results of the phylogenetic analysis. On the basis of 16S rRNA gene sequence data in combination with chemotaxonomic and physiological data, strain AcBE2-1(T) (=DSM 16959(T)=JCM 12830(T)) is placed in a new genus Denitratisoma gen. nov. as the type strain of the type species Denitratisoma oestradiolicum gen. nov., sp. nov.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. N2 fixation in the rhizosphere of Thalassia testudinum.

    PubMed

    Capone, D G; Taylor, B F

    1980-08-01

    N2 fixation (C2H2 reduction) associated with the roots, rhizomes, and sediments (rhizosphere cores) of the seagrass Thalassia testudinum was measured at sites in South Florida (Soldier Key, Biscayne Bay) and the Bahamas (Bimini Harbor). Rates of C2H2 reduction were higher in anaerobic than in aerobic assays and were linear for several hours after an initial lag period of 1-2h. Nitrogenase activity was proportional to the weight of rhizomes plus roots but showed no correlation with the total weight of the rhizosphere cores. C2H2 reduction occurred to depths of at least 30 cm but the majority (<85%) of the activity was in the 0- to 20-cm fraction; also the ratio of activities for the 0- to 10- and 10- to 20-cm depths was about 2:1. Most investigations were carried out using anaerobic assays of the 0- to 10-cm fractions and rates calculated for the period of 3-6 h after adding C2H2. These rates were not stimulated by organic compounds (glucose, lactate, succinate) but were approximately halved by a decrease in temperature of 10 degrees C. In a seasonal study at Soldier Key the rates of N2 fixation varied about 20-fold with maximal rates in late summer and minimal rates in winter (January). On a diurnal basis, C2H2 reduction increased in the morning but was depressed in midafternoon, probably due to O2 buildup in the rhizosphere. Daily rates of N2 fixation, during the summer months of 1975-1978, varied between 5 and 24 mg N (-2)m and the estimated annual rates of N2 fixation were 10-50 kg N (-1)ha, taking into account seasonal variations and activities to a depth of 20 cm.

  20. 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

  1. Evidence of antagonistic interactions between rhizosphere microorganisms and mycorrhizal fungi associated with birch ( Betula pubescens)

    NASA Astrophysics Data System (ADS)

    Stark, Sari; Kytöviita, Minna-Maarit

    2005-09-01

    We studied the role of carbon availability in the relationship between soil rhizosphere microorganisms and mycorrhizal fungi (Basidiomycetes) associated with birch ( Betula pubescens L.) seedlings in a greenhouse experiment through artificial herbivory (clipping), glucose addition and microbial toxin treatments. Artificial herbivory significantly decreased the amount of ergosterol, a fungus-specific sterol, in the birch roots and microbial respiration in the soil. Reduction in plant's photosynthetic ability thus reduced availability of carbon for both mycorrhizal fungi and rhizosphere microorganisms. Adding glucose, a carbon source easily assimilable by soil microorganisms, significantly enhanced microbial respiration, and counteracted the negative effects of clipping on microbial respiration. At the same time, the amount of ergosterol in the birch roots was decreased, indicating that enhanced activity of rhizosphere microorganisms had a negative impact on the mycorrhizal fungi. The outcome of glucose addition on mycorrhizal fungi did not interact with the clipping treatment. A fungal and bacterial toxin treatment did not affect microbial respiration, but significantly increased the birch root growth and amount of ergosterol in the treatment without the glucose addition. Our results show that rhizosphere microorganisms may have antagonistic effects on mycorrhizal fungi associated with the birch. We suggest that the antagonistic interactions between rhizosphere microorganisms and mycorrhizal fungi may have an important role in the functions of mycorrhizal systems and its significance in natural systems should be further investigated.

  2. 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

  3. Optical sorting and cultivation of denitrifying anaerobic methane oxidation archaea

    PubMed Central

    Qi, Xiaoqiong; Carberry, David M.; Cai, Chen; Hu, Shihu; Yuan, Zhiguo; Dunlop, Halin Rubinsztein; Guo, Jianhua

    2017-01-01

    Denitrifying anaerobic methane oxidizing (DAMO) microorganisms play an important role in the global carbon and nitrogen cycles as they are able to mediate methane oxidation using nitrite/nitrate under anoxic conditions. However, the physiological properties of DAMO microorganisms remain poorly understood, partially since the organisms are difficult to isolate or cultivate in pure culture and partially because of their long cultivation time. In this study, DAMO cell sorting has been conducted by integrating optical tweezers within enclosed microfluidic chips. This integrated cell sorting method has high purity, low infection rates, and causes no discernable harm to cell viability. The purity of the sorted cells was controlled by the microfluidic chip structure design and operation, while the cell viability was verified by imaging the cultured DAMO archaea after 420 days. PMID:28270994

  4. Kinetics of Denitrifying Growth by Fast-Growing Cowpea Rhizobia

    PubMed Central

    El Hassan, G. A.; Zablotowicz, R. M.; Focht, D. D.

    1985-01-01

    Two fast-growing strains of cowpea rhizobia (A26 and A28) were found to grow anaerobically at the expense of NO3−, NO2−, and N2O as terminal electron acceptors. The two major differences between aerobic and denitrifying growth were lower yield coefficients (Y) and higher saturation constants (Ks) with nitrogenous oxides as electron acceptors. When grown aerobically, A26 and A28 adhered to Monod kinetics, respectively, as follows: Ks, 3.4 and 3.8 μM; Y, 16.0 and 14.0 g · cells eq−1; μmax, 0.41 and 0.33 h−1. Yield coefficients for denitrifying growth ranged from 40 to 70% of those for aerobic growth. Only A26 adhered to Monod kinetics with respect to growth on all three nitrogenous oxides. The apparent Ks values were 41, 270, and 460 μM for nitrous oxide, nitrate, and nitrite, respectively; the Ks for A28 grown on nitrate was 250 μM. The results are kinetically and thermodynamically consistent in explaining why O2 is the preferred electron acceptor. Although no definitive conclusions could be drawn regarding preferential utilization of nitrogenous oxides, nitrite was inhibitory to both strains and effected slower growth. However, growth rates were identical (μmax, 0.41 h−1) when A26 was grown with either O2 or NO3− as an electron acceptor and were only slightly reduced when A28 was grown with NO3− (0.25 h−1) as opposed to O2 (0.33 h−1). PMID:16346745

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

    PubMed

    Houlton, Benjamin Z; Bai, Edith

    2009-12-22

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

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

    PubMed

    Rekosz-Burlaga, Hanna; Garbolińska, Magdalena

    2006-01-01

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

  7. 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.

  8. 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

  9. 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...

  10. INHIBITION OF ALKYLBENZENE BIODEGRADATION UNDER DENITRIFYING CONDITIONS BY USING THE ACETYLENE BLOCK TECHNIQUE

    EPA Science Inventory

    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 degr...

  11. 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.

  12. Identification of the autotrophic denitrifying community in nitrate removal reactors by DNA-stable isotope probing.

    PubMed

    Xing, Wei; Li, Jinlong; Cong, Yuan; Gao, Wei; Jia, Zhongjun; Li, Desheng

    2017-04-01

    Autotrophic denitrification has attracted increasing attention for wastewater with insufficient organic carbon sources. Nevertheless, in situ identification of autotrophic denitrifying communities in reactors remains challenging. Here, a process combining micro-electrolysis and autotrophic denitrification with high nitrate removal efficiency was presented. Two batch reactors were fed organic-free nitrate influent, with H(13)CO3(-) and H(12)CO3(-) as inorganic carbon sources. DNA-based stable-isotope probing (DNA-SIP) was used to obtain molecular evidence for autotrophic denitrifying communities. The results showed that the nirS gene was strongly labeled by H(13)CO3(-), demonstrating that the inorganic carbon source was assimilated by autotrophic denitrifiers. High-throughput sequencing and clone library analysis identified Thiobacillus-like bacteria as the most dominant autotrophic denitrifiers. However, 88% of nirS genes cloned from the (13)C-labeled "heavy" DNA fraction showed low similarity with all culturable denitrifiers. These findings provided functional and taxonomical identification of autotrophic denitrifying communities, facilitating application of autotrophic denitrification process for wastewater treatment.

  13. Buffet hypothesis for microbial nutrition at the rhizosphere

    PubMed Central

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

    2013-01-01

    An emphasis is made on the diversity of nutrients that rhizosphere bacteria may encounter derived from roots, soil, decaying organic matter, seeds, or the microbial community. This nutrient diversity may be considered analogous to a buffet and is contrasting to the hypothesis of oligotrophy at the rhizosphere. Different rhizosphere bacteria may have preferences for some substrates and this would allow a complex community to be established at the rhizosphere. To profit from diverse nutrients, root-associated bacteria should have large degrading capabilities and many transporters (seemingly inducible) that may be encoded in a significant proportion of the large genomes that root-associated bacteria have. Rhizosphere microbes may have a tendency to evolve toward generalists. We propose that many genes with unknown function may encode enzymes that participate in degrading diverse rhizosphere substrates. Knowledge of bacterial genes required for nutrition at the rhizosphere will help to make better use of bacteria as plant-growth promoters in agriculture. PMID:23785373

  14. 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

  15. 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

  16. 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…

  17. Enhanced degradation of Herbicide Isoproturon in wheat rhizosphere by salicylic acid.

    PubMed

    Lu, Yi Chen; Zhang, Shuang; Miao, Shan Shan; Jiang, Chen; Huang, Meng Tian; Liu, Ying; Yang, Hong

    2015-01-14

    This study investigated the herbicide isoproturon (IPU) residues in soil, where wheat was cultivated and sprayed with salicylic acid (SA). Provision of SA led to a lower level of IPU residues in rhizosphere soil compared to IPU treatment alone. Root exudation of tartaric acid, malic acid, and oxalic acids was enhanced in rhizosphere soil with SA-treated wheat. We examined the microbial population (e.g., biomass and phospholipid fatty acid), microbial structure, and soil enzyme (catalase, phenol oxidase, and dehydrogenase) activities, all of which are associated with soil activity and were activated in rhizosphere soil of SA-treated wheat roots. We further assessed the correlation matrix and principal component to figure out the association between the IPU degradation and soil activity. Finally, six IPU degraded products (derivatives) in rhizosphere soil were characterized using ultraperformance liquid chromatography with a quadrupole-time-of-flight tandem mass spectrometer (UPLC/Q-TOF-MS/MS). A relatively higher level of IPU derivatives was identified in soil with SA-treated wheat than in soil without SA-treated wheat plants.

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

    PubMed

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

    2014-07-01

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

  19. [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.

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

    PubMed

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

    2016-10-24

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

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

    PubMed Central

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

    2016-01-01

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

  2. 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.

  3. Effect of carbon dioxide and bicarbonate as inorganic carbon sources on growth and adaptation of autohydrogenotrophic denitrifying bacteria.

    PubMed

    Ghafari, Shahin; Hasan, Masitah; Aroua, Mohamed Kheireddine

    2009-03-15

    Acclimation of autohydrogenotrophic denitrifying bacteria using inorganic carbon source (CO(2) and bicarbonate) and hydrogen gas as electron donor was performed in this study. In this regard, activated sludge was used as the seed source and sequencing batch reactor (SBR) technique was applied for accomplishing the acclimatization. Three distinct strategies in feeding of carbon sources were applied: (I) continuous sparging of CO(2), (II) bicarbonate plus continuous sparging of CO(2), and (III) only bicarbonate. The pH-reducing nature of CO(2) showed an unfavorable impact on denitrification rate; however bicarbonate resulted in a buffered environment in the mixed liquor and provided a suitable mean to maintain the pH in the desirable range of 7-8.2. As a result, bicarbonate as the only carbon source showed a faster adaptation, while carbon dioxide as the only carbon source as well as a complementary carbon source added to bicarbonate resulted in longer acclimation period. Adapted hydrogenotrophic denitrifying bacteria, using bicarbonate and hydrogen gas in the aforementioned pH range, caused denitrification at a rate of 13.33 mg NO(3)(-)-N/g MLVSS/h for degrading 20 and 30 mg NO(3)(-)-N/L and 9.09 mg NO(3)(-)-N/g MLVSS/h for degrading 50mg NO(3)(-)-N/L.

  4. 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.

  5. Emission of nitrous oxide and dinitrogen by diverse earthworm families from Brazil and resolution of associated denitrifying and nitrate-dissimilating taxa.

    PubMed

    Depkat-Jakob, Peter S; Brown, George G; Tsai, Siu M; Horn, Marcus A; Drake, Harold L

    2013-02-01

    The anoxic earthworm gut augments the activity of ingested microorganisms capable of anaerobiosis. Small earthworms (Lumbricidae) emit denitrification-derived N(2)O, whereas the large Octochaetus multiporus (Megascolecidae) does not. To examine this paradox, differently sized species of the families Glossoscolecidae (Rhinodrilus, Glossoscolex, Pontoscolex), Megascolecidae (Amynthas, Perionyx), Acanthodrilidae (Dichogaster), and Eudrilidae (Eudrilus) from Brazil were analyzed. Small species and the large Rhinodrilus alatus emitted N(2)O, whereas the large Glossoscolex paulistus did not, even though its gut could denitrify. N(2) and N(2)O were emitted concomitantly, and R. alatus emitted the highest amount of N(2). Denitrifiers and dissimilatory nitrate reducers were analyzed by barcoded amplicon pyrosequencing of narG, nirK, and nosZ. Gene sequences in gut and soil of the large G. paulistus were similar, whereas sequences in gut and soil of the small Amynthas gracilis were different and were also different compared with those of the gut and soil of G. paulistus. However, the denitrifying gut microbiota for both earthworms appeared to be soil-derived and dominated by Rhizobiales. The results demonstrated that (1) the emission of denitrification-derived N(2)O is widespread in different earthworm families, (2) large earthworms can also emit nitrogenous gases, and (3) ingested members of Rhizobiales are associated with this emission.

  6. [Effects of root-knot nematodes on cucumber leaf N and P contents, soil pH, and soil enzyme activities].

    PubMed

    Xu, Hua; Ruan, Wei-Bin; Gao, Yu-Bao; Song, Xiao-Yan; Wei, Yu-Kun

    2010-08-01

    A pot experiment was conducted to study the effects of inoculation with root-knot nematodes on the cucumber leaf N and P contents, and the rhizospheric and non-rhizospheric soil pH and enzyme activities. The rhizospheric soil pH didn't have a significant decrease until the inoculation rate reached 6000 eggs per plant. With the increase of inoculation rate, the leaf N and P contents, rhizospheric soil peroxidase activity, and rhizospheric and non-rhizospheric soil polyphenol oxidase activity all decreased gradually, rhizospheric soil catalase activity was in adverse, non-rhizospheric soil pH decreased after an initial increase, and non-rhizospheric soil catalase activity had no regular change. After inoculation, rhizospheric soil urease activity decreased significantly, but rhizospheric and non-rhizospheric soil phosphatase activity and non-rhizospheric soil peroxidase activity only had a significant decrease under high inoculation rate. In most cases, there existed significant correlations between rhizospheric soil pH, enzyme activities, and leaf N and P contents; and in some cases, there existed significant correlations between non-rhizospheric soil pH, enzyme activities, and leaf N and P contents.

  7. Adaptation of a phenol-degrading denitrifying bacteria to high concentration of phenol in the medium.

    PubMed

    Son, T T; Błaszczyk, M; Mycielski, R

    1998-01-01

    The growth and uptake of phenol by 8 strains isolated from wastewater sediments in stationary cultures in medium with increasing concentrations of phenol (from 100 to 600 mg/L) under denitrifying conditions were studied. All the strains grew in media containing 250 mg phenol/L and only strains 101/1, 83/2 and 21/1/ in consecutive passages visibly increased both specific growth rate (mu day-1) as well as phenol-degrading activity (mg/L x day). Consecutive passages of the culture in medium containing 400 mg phenol/L resulted in the elimination of 3 out of the 5 strains growing in the medium in the first passage. Only strain 101/1 demonstrated high specific growth rate and phenol-degrading activity in medium containing 600 mg phenol/L. In consecutive passages in medium containing 250, 400 and 600 mg phenol/L the specific growth (mu day-1) and phenol-degrading activity (mg/L x day) of P. aeruginosa 101/1 were 0.38 and 36; 0.12 and 19; 0.09 and 20, respectively.

  8. 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.

  9. Effect of Genetically Modified Pseudomonas putida WCS358r on the Fungal Rhizosphere Microflora of Field-Grown Wheat

    PubMed Central

    Glandorf, Debora C. M.; Verheggen, Patrick; Jansen, Timo; Jorritsma, Jan-Willem; Smit, Eric; Leeflang, Paula; Wernars, Karel; Thomashow, Linda S.; Laureijs, Eric; Thomas-Oates, Jane E.; Bakker, Peter A. H. M.; van Loon, Leendert C.

    2001-01-01

    We released genetically modified Pseudomonas putida WCS358r into the rhizospheres of wheat plants. The two genetically modified derivatives, genetically modified microorganism (GMM) 2 and GMM 8, carried the phz biosynthetic gene locus of strain P. fluorescens 2-79 and constitutively produced the antifungal compound phenazine-1-carboxylic acid (PCA). In the springs of 1997 and 1998 we sowed wheat seeds treated with either GMM 2, GMM 8, or WCS358r (approximately 107 CFU per seed), and measured the numbers, composition, and activities of the rhizosphere microbial populations. During both growing seasons, all three bacterial strains decreased from 107 CFU per g of rhizosphere sample to below the limit of detection (102 CFU per g) 1 month after harvest of the wheat plants. The phz genes were stably maintained, and PCA was detected in rhizosphere extracts of GMM-treated plants. In 1997, but not in 1998, fungal numbers in the rhizosphere, quantified on 2% malt extract agar (total filamentous fungi) and on Komada's medium (mainly Fusarium spp.), were transiently suppressed in GMM 8-treated plants. We also analyzed the effects of the GMMs on the rhizosphere fungi by using amplified ribosomal DNA restriction analysis. Introduction of any of the three bacterial strains transiently changed the composition of the rhizosphere fungal microflora. However, in both 1997 and 1998, GMM-induced effects were distinct from those of WCS358r and lasted for 40 days in 1997 and for 89 days after sowing in 1998, whereas effects induced by WCS358r were detectable for 12 (1997) or 40 (1998) days. None of the strains affected the metabolic activity of the soil microbial population (substrate-induced respiration), soil nitrification potential, cellulose decomposition, plant height, or plant yield. The results indicate that application of GMMs engineered to have improved antifungal activity can exert nontarget effects on the natural fungal microflora. PMID:11472906

  10. Effect of genetically modified Pseudomonas putida WCS358r on the fungal rhizosphere microflora of field-grown wheat.

    PubMed

    Glandorf, D C; Verheggen, P; Jansen, T; Jorritsma, J W; Smit, E; Leeflang, P; Wernars, K; Thomashow, L S; Laureijs, E; Thomas-Oates, J E; Bakker, P A; van Loon, L C

    2001-08-01

    We released genetically modified Pseudomonas putida WCS358r into the rhizospheres of wheat plants. The two genetically modified derivatives, genetically modified microorganism (GMM) 2 and GMM 8, carried the phz biosynthetic gene locus of strain P. fluorescens 2-79 and constitutively produced the antifungal compound phenazine-1-carboxylic acid (PCA). In the springs of 1997 and 1998 we sowed wheat seeds treated with either GMM 2, GMM 8, or WCS358r (approximately 10(7) CFU per seed), and measured the numbers, composition, and activities of the rhizosphere microbial populations. During both growing seasons, all three bacterial strains decreased from 10(7) CFU per g of rhizosphere sample to below the limit of detection (10(2) CFU per g) 1 month after harvest of the wheat plants. The phz genes were stably maintained, and PCA was detected in rhizosphere extracts of GMM-treated plants. In 1997, but not in 1998, fungal numbers in the rhizosphere, quantified on 2% malt extract agar (total filamentous fungi) and on Komada's medium (mainly Fusarium spp.), were transiently suppressed in GMM 8-treated plants. We also analyzed the effects of the GMMs on the rhizosphere fungi by using amplified ribosomal DNA restriction analysis. Introduction of any of the three bacterial strains transiently changed the composition of the rhizosphere fungal microflora. However, in both 1997 and 1998, GMM-induced effects were distinct from those of WCS358r and lasted for 40 days in 1997 and for 89 days after sowing in 1998, whereas effects induced by WCS358r were detectable for 12 (1997) or 40 (1998) days. None of the strains affected the metabolic activity of the soil microbial population (substrate-induced respiration), soil nitrification potential, cellulose decomposition, plant height, or plant yield. The results indicate that application of GMMs engineered to have improved antifungal activity can exert nontarget effects on the natural fungal microflora.

  11. 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.

  12. 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

  13. Host legume-exuded antimetabolites optimize the symbiotic rhizosphere.

    PubMed

    Cai, Tao; Cai, Wentong; Zhang, Jiang; Zheng, Huiming; Tsou, Amy M; Xiao, Lin; Zhong, Zengtao; Zhu, Jun

    2009-08-01

    Rhizobia form symbiotic nodules on host legumes and fix nitrogen for their hosts in exchange for nutrients. In order to establish this mutually beneficial relationship, rhizobia must compete with other soil bacteria in the host legume rhizosphere to colonize plant roots efficiently. A promoter-trap transposon screen in Mesorhizobium tianshanense, a Rhizobium that forms nodules on licorice (Glycyrrhiza uralensis) plants revealed that the expression of msiA, which encodes a putative exporter protein belonging to the LysE family of translocators, is activated by both legume exudates and MsiR, a LysR family transcriptional regulator. Chemical analysis suggests that the msiA-inducing signal in exudates is canavanine, an anti-metabolite present in the seeds and exudates of a variety of legume plants. We show that MsiA serves as a canavanine exporter that is indispensable for canavanine resistance in M. tianshanense. We also show that the expression of MsiA homologues in other rhizobial species is induced by canavanine and is critical for canavanine resistance. Furthermore, rhizobial canavanine resistance is important for root hair adherence as well as for survival in a canavanine-producing legume rhizosphere. Together, these data suggest that host legumes may exude specific antimetabolites into their surroundings to optimize the bacterial population in order to have successful symbiotic events with rhizobia.

  14. Rhizosphere dynamics during phytoremediation of olive mill wastewater.

    PubMed

    Bodini, S F; Cicalini, A R; Santori, F

    2011-03-01

    The potential of phytoremediation as a treatment option for olive mill wastewater (OMW) was tested on five perennial tree species. Cupressus sempervirens and Quercus ilex proved tolerant to six-month OMW treatment followed by six-month water irrigation, whereas Salix sp. and Laurus nobilis and, later, Pinus mugo suffered from phytotoxic effects. Test plants were compared to controls after treatment and irrigation, by monitoring biochemical and microbiological variations in the rhizosphere soil. OMW-treated soils were exposed to 50-fold higher phenols concentrations, which, irrespective of whether the respective plants were OMW-resistant or susceptible, were reduced by more than 90% by the end of the irrigation cycle, owing to significantly increased laccase, peroxidase and β-glucosidase activities, recovery/acquisition of bacterial culturability and transitory development of specialized fungal communities sharing the presence of Geotrichum candidum. Of all results, the identification of Penicillium chrysogenum and Penicillium aurantiogriseum as dominant rhizosphere fungi was distinctive of OMW-tolerant species.

  15. 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.

  16. 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.

  17. 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.

  18. Differential composition of bacterial communities as influenced by phenanthrene and dibenzo[a,h]anthracene in the rhizosphere of ryegrass (Lolium perenne L.).

    PubMed

    Corgié, S C; Beguiristain, T; Leyval, C

    2006-12-01

    Bioremediation technologies of Polycyclic Aromatic Hydrocarbons (PAH) are often limited by the recalcitrance to biodegradation of high molecular weight (HMW) PAH. Rhizosphere is known to increase the biodegradation of PAH but little is known about the biodegradability of these HMW compounds by rhizosphere bacteria. This study compared the effects of a 3 and a 5-ring PAH, phenanthrene (PHE) and dibenzo[a,h]anthracene (dBA) respectively, on the composition of bacterial community, the bacterial density and the biodegradation activity. Compartmentalized devices were designed to harvest three consecutive sections of the rhizosphere. Rhizosphere and non-rhizosphere compartments were filled with PHE or dBA spiked or unspiked sand and inoculated with a soil bacterial inoculum. Different bacterial communities and degradation values were found 5 weeks after spiking with PHE (41-76% biodegradation) and dBA (12-51% biodegradation). In sections closer to the root surface, bacterial populations differed as a function of the distance to roots and the PAH added, whereas in further rhizosphere sections, communities were closer to those of the non-planted treatments. Biodegradation of PHE was also a function of the distance to roots, and decreased from 76 to 42% within 9 mm from the roots. However, biodegradation of dBA was significantly higher in the middle section (3-6 mm from roots) than the others. Rhizosphere degradation of PAH varies with the nature of the PAH, and C fluxes from roots could limit the degradation of dBA.

  19. Dissipation gradients of phenanthrene and pyrene in the Rice rhizosphere.

    PubMed

    Gao, Y; Wu, S C; Yu, X Z; Wong, M H

    2010-08-01

    An experiment was conducted to reveal the effects of rice cultivation as well as polycyclic aromatic carbohydrates (PAHs) degrading bacterium (Acinetobacter sp.) on the dissipation gradients of two PAHs (PHE and PYR) in the rhizosphere. The results showed that the presence of rice root and bacteria significantly accelerated the dissipation rate of PHE and PYR. The root exudates contributed to the formation of dissipation gradients of PHE and PYR along the vertical direction of roots, with a higher dissipation rate in the rhizosphere and near rhizosphere zone than the soil far away the rhizosphere.

  20. Elevated CO2 benefits the soil microenvironment in the rhizosphere of Robinia pseudoacacia L. seedlings in Cd- and Pb-contaminated soils.

    PubMed

    Huang, Shuping; Jia, Xia; Zhao, Yonghua; Bai, Bo; Chang, Yafei

    2017-02-01

    Soil contamination by heavy metals in combination with elevated atmospheric CO2 has important effects on the rhizosphere microenvironment by influencing plant growth. Here, we investigated the response of the R. pseudoacacia rhizosphere microenvironment to elevated CO2 in combination with cadmium (Cd)- and lead (Pb)-contamination. Organic compounds (total soluble sugars, soluble phenolic acids, free amino acids, and organic acids), microbial abundance and activity, and enzyme activity (urease, dehydrogenase, invertase, and β-glucosidase) in rhizosphere soils increased significantly (p < 0.05) under elevated CO2 relative to ambient CO2; however, l-asparaginase activity decreased. Addionally, elevated CO2 alone affected soil microbial community in the rhizosphere. Heavy metals alone resulted in an increase in total soluble sugars, free amino acids, and organic acids, a decrease in phenolic acids, microbial populations and biomass, and enzyme activity, and a change in microbial community in rhizosphere soils. Elevated CO2 led to an increase in organic compounds, microbial populations, biomass, and activity, and enzyme activity (except for l-asparaginase), and changes in microbial community under Cd, Pb, or Cd + Pb treatments relative to ambient CO2. In addition, elevated CO2 significantly (p < 0.05) enhanced the removal ratio of Cd and Pb in rhizosphere soils. Overall, elevated CO2 benefited the rhizosphere microenvironment of R. pseudoacacia seedlings under heavy metal stress, which suggests that increased atmospheric CO2 concentrations could have positive effects on soil fertility and rhizosphere microenvironment under heavy metals.

  1. 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).

  2. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community.

    PubMed

    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 NO(3)(-)-N mg of mixed-liquor volatile suspended solids (MLVSS)(-1) h(-1) to a steady-state value of 0.06 mg of NO(3)(-)-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 [(13)C]methanol to biomark the DNA of the denitrifiers. The extracted [(13)C]DNA and [(12)C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [(13)C]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 [(12)C]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

  3. 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

  4. 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

  5. Environmental controls on denitrifying communities and denitrification rates--Insights from molecular methods

    USGS Publications Warehouse

    Wallenstein, Matthew D.; Myrold, David D.; Firestone, Mary; Voytek, Mary

    2006-01-01

    The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3− pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

  6. 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.

  7. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils.

    PubMed

    Barrett, M; Khalil, M I; Jahangir, M M R; Lee, C; Cardenas, L M; Collins, G; Richards, K G; O'Flaherty, V

    2016-04-01

    The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P < 0.03). Denitrifier gene copy concentrations per gram of soil (GCC) varied in response to carbon type amendment (P < 0.01). Denitrifier GCCs were high (ca. 10(7)) and the bac:nirK, bac:nirS, bac:nir (T) , and bac:nosZ ratios were low (ca. 10(-1)/10) in horizon A in all three respective treatments. Glucose-C amendment favored partial denitrification, resulting in higher nir abundance and higher N2O fluxes compared to the control. DOC amendment, by contrast, resulted in relatively higher nosZ abundance and N2 emissions, thus favoring complete denitrification. We also noted soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.

  8. [Influences of long-term application of organic and inorganic fertilizers on the composition and abundance of nirS-type denitrifiers in black soil].

    PubMed

    Yin, Chang; Fan, Fen-Liang; Li, Zhao-Jun; Song, A-Lin; Zhu, Ping; Peng, Chang; Liang, Yong-Chao

    2012-11-01

    The objectives of this study were to explore the effects of long-term organic and inorganic fertilizations on the composition and abundance of nirS-type denitrifiers in black soil. Soil samples were collected from 4 treatments (i. e. no fertilizer treatment, CK; organic manure treatment, OM; chemical fertilizer treatment (NPK) and combination of organic and chemical fertilizers treatment (MNPK)) in Gongzhuling Long-term Fertilization Experiment Station. Composition and abundance of nirS-type denitrifiers were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR (Q-PCR), respectively. Denitrification enzyme activity (DEA) and soil properties were also measured. Application of organic fertilizers (OM and MNPK) significantly increased the DEAs of black soil, with the DEAs in OM and MNPK being 5.92 and 6.03 times higher than that in CK treatment, respectively, whereas there was no significant difference between NPK and CK. OM and MNPK treatments increased the abundances of nirS-type denitrifiers by 2.73 and 3.83 times relative to that of CK treatment, respectively. The abundance of nirS-type denitrifiers in NPK treatment was not significantly different from that of CK. The T-RFLP analysis of nirS genes showed significant differences in community composition between organic and inorganic treatments, with the emergence of a 79 bp T-RF, a significant decrease in relative abundance of the 84 bp T-RF and a loss of the 99 bp T-RF in all organic treatments. Phylogenetic analysis indicated that the airS-type denitrifiers in the black soil were mainly composed of alpha, beta and gamma-Proteobacteria. The 79 bp-type denitrifiers inhabiting exclusively in organic treatments (OM and MNPK) were affiliated to Pseudomonadaceae in gamma-Proteobacteria and Burkholderiales in beta-Proteobacteria. The 84 bp-types were related to Burkholderiales and Rhodocyclales. Correlation analysis indicated that pH, concentrations of total nitrogen

  9. 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

  10. 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

  11. Complete Genome Sequence of Paenibacillus polymyxa YC0136, a Plant Growth–Promoting Rhizobacterium Isolated from Tobacco Rhizosphere

    PubMed Central

    Liu, Hu; Liu, Kai; Li, Yuhuan; Wang, Chengqiang; Hou, Qihui; Xu, Wenfeng; Fan, Lingchao; Zhao, Jian; Gou, Jianyu

    2017-01-01

    ABSTRACT Paenibacillus polymyxa strain YC0136 is a plant growth–promoting rhizobacterium with antimicrobial activity, which was isolated from tobacco rhizosphere. Here, we report the complete genome sequence of P. polymyxa YC0136. Several genes with antifungal and antibacterial activity were discovered. PMID:28183774

  12. Cropping practices modulate the impact of glyphosate on arbuscular mycorrhizal fungi and rhizosphere bacteria in agroecosystems of the semiarid prairie.

    PubMed

    Sheng, Min; Hamel, Chantal; Fernandez, Myriam R

    2012-08-01

    A growing body of evidence obtained from studies performed under controlled conditions suggests that glyphosate use can modify microbial community assemblages. However, few studies have examined the influence of glyphosate in agroecosystems. We examined 4 wheat-based production systems typical of the Canadian prairie over 2 years to answer the following question: Does preseeding of glyphosate impact soil rhizosphere microorganisms? If so, do cropping practices influence this impact? Glyphosate caused a shift in the species dominating the arbuscular mycorrhizal fungal community in the rhizosphere, possibly through the modification of host plant physiology. Glyphosate stimulated rhizobacterial growth while having no influence on saprotrophic fungi, suggesting a greater abundance of glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in bacteria than in fungi. Glyphosate stimulated rhizosphere bacteria in pea but not in urea-fertilized durum wheat, which is consistent with inhibition of EPSPS tolerance to residual glyphosate through high ammonium levels. Mitigation of the effects of glyphosate on rhizosphere bacteria through tillage suggests a reduction in residual glyphosate activity through increased adsorption to soil binding sites upon soil mixing. The influence of glyphosate on Gram-negative bacteria was mitigated under drought conditions in 2007. Our experiment suggests that interactions between soil fertility, tillage, and cropping practices shape the influence of glyphosate use on rhizosphere microorganisms.

  13. Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

    PubMed Central

    Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J.; Fusi, Marco; Bariselli, Paola; Reddy, Muppala; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

    2016-01-01

    Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes. PMID:27597846

  14. Arsenic in the rhizosphere soil solution of ferns.

    PubMed

    Wei, Chaoyang; Zheng, Huan; Yu, Jiangping

    2012-12-01

    The aim of this study was to explore the evidence of arsenic hyperaccumulation in plant rhizosphere solutions. Six common fern plants were selected and grown in three types of substrate: arsenic (As) -tailings, As-spiked soil, and soil-As-tailing composites. A rhizobox was designed with an in-situ collection of soil solutions to analyze changes in the As concentration and valence as well as the pH, dissolved organic carbon (DOC) and total nitrogen (TN). Arsenite composed less than 20% of the total As, and As depletion was consistent with N depletion in the rhizosphere solutions of the various treatments. The As concentrations in the rhizosphere and non-rhizosphere solutions in the presence of plants were lower than in the respective controls without plants, except for in the As-spiked soils. The DOC concentrations were invariably higher in the rhizosphere versus non-rhizosphere solutions from the various plants; however, no significant increase in the DOC content was observed in Pteris vittata, in which only a slight decrease in pH appeared in the rhizosphere compared to non-rhizosphere solutions. The results showed that As reduction by plant roots was limited, acidification-induced solubilization was not the mechanism for As hyperaccumulation.

  15. Enhancement of polycyclic aromatic hydrocarbon biodegradation in the rhizosphere

    SciTech Connect

    Kim, S.C.; Banks, M.K.; Schwab, A.P.

    1994-12-31

    Polycyclic aromatic hydrocarbons (PAHs) are a class of potentially hazardous chemicals that exhibit toxic, mutagenic or carcinogenic properties. Microbial degradation is the major route through which PAHs are removed from contaminated environments although other mechanisms such as volatilization, leaching and photodegradation may also be effective. The rhizosphere contains a diversity of microorganisms that contribute to plant health and soil homeostasis. Recent studies indicate that microorganisms in the rhizosphere can degrade toxicants of concern to human health and the environment. The increased density and diversity of rhizosphere microflora may be an important factor for enhanced microbial degradation of PAHs. The objective of this study is to evaluate degradation of a number of different PAHs in rhizosphere and non-rhizosphere soil. It has been shown that the biodegradation rates of PAHs increase as the number of PAH rings decrease, but there is little information about the biodegradation in rhizosphere soil. The study will provide results from a microcosm experiment designed to evaluate degradation of PAHs in rhizosphere and non-rhizosphere. Also, kinetic models will be developed to represent data collected.

  16. Characterization of the microbial community in the rhizosphere of Phragmites australis (cav.) trin ex. steudel growing in the Sun Island Wetland.

    PubMed

    Ma, Fang; Wu, Jieting; Wang, Li; Yang, Jixian; Li, Shiyang; Li, Zhe; Zhag, Xue

    2014-03-01

    Rhizospheric microorganisms are important for environmental conservancy. The constancy and variability of the microorganisms in the rhizosphere of Phragmites australis in relation to the spatiotemporal variations in wetland ecosystems were studied. During the peak and trough of the vegetative period of the Phragmites australis growing across the hydrologic gradients of the Sun Island Wetland, Biolog and denaturing gradient gel electrophoresis (DGGE) were used to investigate the rhizospheric microbial characteristics. Both methods demonstrated that the microbial activity, richness, and diversity decreased from summer to autumn. However, these properties did not show significant correlation with hydrologic gradient, except that the genetic richness and diversity of the fungi decreased with it. Cluster analysis also demonstrated that the rhizospheric microbial community seemed to be largely affected by a vegetative period. In addition, this research was extended to a broader range of determining the universal microorganisms, which showed notable adaptability.

  17. 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

  18. 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

  19. 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.

  20. Rhizosphere effects of PAH-contaminated soil phytoremediation using a special plant named Fire Phoenix.

    PubMed

    Liu, Rui; Xiao, Nan; Wei, Shuhe; Zhao, Lixing; An, Jing

    2014-03-01

    The rhizosphere effect of a special phytoremediating species known as Fire Phoenix on the degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated, including changes of the enzymatic activity and microbial communities in rhizosphere soil. The study showed that the degradation rate of Σ8PAHs by Fire Phoenix was up to 99.40% after a 150-day culture. The activity of dehydrogenase (DHO), peroxidase (POD) and catalase (CAT) increased greatly, especially after a 60-day culture, followed by a gradual reduction with an increase in the planting time. The activity of these enzymes was strongly correlated to the higher degradation performance of Fire Phoenix growing in PAH-contaminated soils, although it was also affected by the basic characteristics of the plant species itself, such as the excessive, fibrous root systems, strong disease resistance, drought resistance, heat resistance, and resistance to barren soil. The activity of polyphenoloxidase (PPO) decreased during the whole growing period in this study, and the degradation rate of Σ8PAHs in the rhizosphere soil after having planted Fire Phoenix plants had a significant (R(2)=0.947) negative correlation with the change in the activity of PPO. Using an analysis of the microbial communities, the results indicated that the structure of microorganisms in the rhizosphere soil could be changed by planting Fire Phoenix plants, namely, there was an increase in microbial diversity compared with the unplanted soil. In addition, the primary advantage of Fire Phoenix was to promote the growth of flora genus Gordonia sp. as the major bacteria that can effectively degrade PAHs.

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography.

    PubMed

    Ginige, Maneesha P; Keller, Jürg; Blackall, Linda L

    2005-12-01

    The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [13C]acetate was used in SIP to label the DNA of the denitrifiers. The [13C]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C library were closely related to the bacterial families Comamonadaceae and Rhodocyclaceae in the class Betaproteobacteria. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking up [14C]acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the wastewater industry to enhance denitrification.

  6. Flavonoids: their structure, biosynthesis and role in the rhizosphere, including allelopathy.

    PubMed

    Weston, Leslie A; Mathesius, Ulrike

    2013-02-01

    Flavonoids are biologically active low molecular weight secondary metabolites that are produced by plants, with over 10,000 structural variants now reported. Due to their physical and biochemical properties, they interact with many diverse targets in subcellular locations to elicit various activities in microbes, plants, and animals. In plants, flavonoids play important roles in transport of auxin, root and shoot development, pollination, modulation of reactive oxygen species, and signalling of symbiotic bacteria in the legume Rhizobium symbiosis. In addition, they possess antibacterial, antifungal, antiviral, and anticancer activities. In the plant, flavonoids are transported within and between plant tissues and cells, and are specifically released into the rhizosphere by roots where they are involved in plant/plant interactions or allelopathy. Released by root exudation or tissue degradation over time, both aglycones and glycosides of flavonoids are found in soil solutions and root exudates. Although the relative role of flavonoids in allelopathic interference has been less well-characterized than that of some secondary metabolites, we present classic examples of their involvement in autotoxicity and allelopathy. We also describe their activity and fate in the soil rhizosphere in selected examples involving pasture legumes, cereal crops, and ferns. Potential research directions for further elucidation of the specific role of flavonoids in soil rhizosphere interactions are considered.

  7. 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.

  8. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    DOE PAGES

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; ...

    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

  9. 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

  10. Soil denitrifier community size changes with land use change to perennial bioenergy cropping systems

    NASA Astrophysics Data System (ADS)

    Thompson, Karen A.; Deen, Bill; Dunfield, Kari E.

    2016-10-01

    Dedicated biomass crops are required for future bioenergy production. However, the effects of large-scale land use change (LUC) from traditional annual crops, such as corn-soybean rotations to the perennial grasses (PGs) switchgrass and miscanthus, on soil microbial community functioning is largely unknown. Specifically, ecologically significant denitrifying communities, which regulate N2O production and consumption in soils, may respond differently to LUC due to differences in carbon (C) and nitrogen (N) inputs between crop types and management systems. Our objective was to quantify bacterial denitrifying gene abundances as influenced by corn-soybean crop production compared to PG biomass production. A field trial was established in 2008 at the Elora Research Station in Ontario, Canada (n  =  30), with miscanthus and switchgrass grown alongside corn-soybean rotations at different N rates (0 and 160 kg N ha-1) and biomass harvest dates within PG plots. Soil was collected on four dates from 2011 to 2012 and quantitative PCR was used to enumerate the total bacterial community (16S rRNA) and communities of bacterial denitrifiers by targeting nitrite reductase (nirS) and N2O reductase (nosZ) genes. Miscanthus produced significantly larger yields and supported larger nosZ denitrifying communities than corn-soybean rotations regardless of management, indicating large-scale LUC from corn-soybean to miscanthus may be suitable in variable Ontario climatic conditions and under varied management, while potentially mitigating soil N2O emissions. Harvesting switchgrass in the spring decreased yields in N-fertilized plots, but did not affect gene abundances. Standing miscanthus overwinter resulted in higher 16S rRNA and nirS gene copies than in fall-harvested crops. However, the size of the total (16S rRNA) and denitrifying bacterial communities changed differently over time and in response to LUC, indicating varying controls on these communities.

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

    PubMed

    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.

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

    DOE PAGES

    Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; ...

    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

  13. 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

  14. 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.

  15. 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.

  16. miR156 modulates rhizosphere acidification in response to phosphate limitation in Arabidopsis.

    PubMed

    Lei, Kai Jian; Lin, Ya Ming; An, Guo Yong

    2016-03-01

    Rhizosphere acidification is a general response to Pi deficiency, especially in dicotyledonous plants. However, the signaling pathway underlying this process is still unclear. Here, we demonstrate that miR156 is induced in the shoots and roots of wild type Arabidopsis plants during Pi starvation. The rhizosphere acidification capacity was increased in 35S:MIR156 (miR156 overexpression) plants, but was completely inhibited in 35S:MIM156 (target mimicry) plants. Both 35S:MIR156 and 35S:MIM156 plants showed altered proton efflux and H(+)-ATPase activity. In addition, significant up-regulation of H(+)-ATPase activity in 35S:MIR156 roots coupled with increased citric acid and malic acid exudates was observed. qRT-PCR results showed that most H(+)-ATPase and PPCK gene transcript levels were decreased in 35S:MIM156 plants, which may account for the decreased H(+)-ATPase activity in 35S:MIM156 plants. MiR156 also affect the root architecture system. Collectively, our results suggest that miR156 regulates the process of rhizosphere acidification in plants.

  17. 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

  18. Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing.

    PubMed

    Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin; Zhou, Zhi; Wu, Chen; Nagarajan, Sanjay

    2015-01-01

    Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere.

  19. Disentangling the influence of earthworms in sugarcane rhizosphere

    PubMed Central

    Braga, Lucas P. P.; Yoshiura, Caio A.; Borges, Clovis D.; Horn, Marcus A.; Brown, George G.; Drake, Harold L.; Tsai, Siu M.

    2016-01-01

    For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW−, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW− treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW− rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated. PMID:27976685

  20. Colonization of lettuce rhizosphere and roots by tagged Streptomyces

    PubMed Central

    Bonaldi, Maria; Chen, Xiaoyulong; Kunova, Andrea; Pizzatti, Cristina; Saracchi, Marco; Cortesi, Paolo

    2015-01-01

    Beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. We studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified Streptomyces spp. Five Streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, Sclerotinia sclerotiorum, were transformed with pIJ8641 plasmid harboring an enhanced green fluorescent protein marker and resistance to apramycin. The fitness of transformants was compared to the wild-type strains and all of them grew and sporulated at similar rates and retained the production of enzymes and selected secondary metabolites as well as in vitro inhibition of S. sclerotiorum. The tagged ZEA17I strain was selected to study the dynamics of lettuce roots and rhizosphere colonization in non-sterile growth substrate. The transformed strain was able to colonize soil, developing roots, and rhizosphere. When the strain was inoculated directly on the growth substrate, significantly more t-ZEA17I was re-isolated both from the rhizosphere and the roots when compared to the amount obtained after seed coating. The re-isolation from the rhizosphere and the inner tissues of surface-sterilized lettuce roots demonstrated that t-ZEA17I is both rhizospheric and endophytic. PMID:25705206

  1. Nitrogen Removal from Micro-Polluted Reservoir Water by Indigenous Aerobic Denitrifiers

    PubMed Central

    Huang, Ting-Lin; Zhou, Shi-Lei; Zhang, Hai-Han; Zhou, Na; Guo, Lin; Di, Shi-Yu; Zhou, Zi-Zhen

    2015-01-01

    accumulation in either system. Our results show that aerobic denitrifying bacteria remain highly active after domestication and demonstrate the applicability of such organisms in the bioremediation of oligotrophic ecosystems. PMID:25867475

  2. 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

  3. 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.

  4. Role of Arbuscular Mycorrhizal Fungi in Phytoremediation of Soil Rhizosphere Spiked with Poly Aromatic Hydrocarbons

    PubMed Central

    2005-01-01

    Results from an innovative approach to improve remediation in the rhizosphere by encouraging healthy plant growth and thus enhancing microbial activity are reported. The effect of arbuscular mycorrhizal fungi (Am) on remediation efficacy of wheat, mungbean and eggplant grown in soil spiked with polyaromatic hydrocarbons (PAH) was assessed in a pot experiment. The results of this study showed that Am inoculation enhanced dissipation amount of PAHs in planted soil, plant uptake PAHs, dissipation amount of PAHs in planted versus unplanted spiked soil and loss of PAHs by the plant-promoted biodegradation. A number of parameters were monitored including plant shoot and root dry weight, plant tissue water content, plant chlorophyll, root lipid content, oxido-reductase enzyme activities in plant and soil rhizosphere and total microbial count in the rhizospheric soil. The observed physiological data indicate that plant growth and tolerance increased with Am, but reduced by PAH. This was reflected by levels of mycorrhizal root colonization which were higher for mungbean, moderate for wheat and low for eggplant. Levels of Am colonization increased on mungbean > wheat > eggplant. This is consistent with the efficacy of plant in dissipation of PAHs in spiked soil. Highly significant positive correlations were shown between of arbuscular formation in root segments (A)) and plant water content, root lipids, peroxidase, catalase polyphenol oxidase and total microbial count in soil rhizosphere as well as PAH dissipation in spiked soil. As consequence of the treatment with Am, the plants provide a greater sink for the contaminants since they are better able to survive and grow. PMID:24049473

  5. Novel P450nor Gene Detection Assay Used To Characterize the Prevalence and Diversity of Soil Fungal Denitrifiers

    PubMed Central

    Novinscak, Amy; Goyer, Claudia; Zebarth, Bernie J.; Burton, David L.; Chantigny, Martin H.

    2016-01-01

    ABSTRACT Denitrifying fungi produce nitrous oxide (N2O), a potent greenhouse gas, as they generally lack the ability to convert N2O to dinitrogen. Contrary to the case for bacterial denitrifiers, the prevalence and diversity of denitrifying fungi found in the environment are not well characterized. In this study, denitrifying fungi were isolated from various soil ecosystems, and novel PCR primers targeting the P450nor gene, encoding the enzyme responsible for the conversion of nitric oxide to N2O, were developed, validated, and used to study the diversity of cultivable fungal denitrifiers. This PCR assay was also used to detect P450nor genes directly from environmental soil samples. Fungal denitrification capabilities were further validated using an N2O gas detection assay and a PCR assay targeting the nirK gene. A collection of 492 facultative anaerobic fungi was isolated from 15 soil ecosystems and taxonomically identified by sequencing the internal transcribed spacer sequence. Twenty-seven fungal denitrifiers belonging to 10 genera had the P450nor and the nirK genes and produced N2O from nitrite. N2O production is reported in strains not commonly known as denitrifiers, such as Byssochlamys nivea, Volutella ciliata, Chloridium spp., and Trichocladium spp. The prevalence of fungal denitrifiers did not follow a soil ecosystem distribution; however, a higher diversity was observed in compost and agricultural soils. The phylogenetic trees constructed using partial P450nor and nirK gene sequences revealed that both genes clustered taxonomically closely related strains together. IMPORTANCE A PCR assay targeting the P450nor gene involved in fungal denitrification was developed and validated. The newly developed P450nor primers were used on fungal DNA extracted from a collection of fungi isolated from various soil environments and on DNA directly extracted from soil. The results indicated that approximatively 25% of all isolated fungi possessed this gene and were able to

  6. 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

  7. Rhizosphere Organic Anions Play a Minor Role in Improving Crop Species' Ability to Take Up Residual Phosphorus (P) in Agricultural Soils Low in P Availability.

    PubMed

    Wang, Yanliang; Krogstad, Tore; Clarke, Jihong L; Hallama, Moritz; Øgaard, Anne F; Eich-Greatorex, Susanne; Kandeler, Ellen; Clarke, Nicholas

    2016-01-01

    Many arable lands have accumulated large reserves of residual phosphorus (P) and a relatively large proportion of soil P is less available for uptake by plants. Root released organic anions are widely documented as a key physiological strategy to enhance P availability, while limited information has been generated on the contribution of rhizosphere organic anions to P utilization by crops grown in agricultural soils that are low in available P and high in extractable Ca, Al, and Fe. We studied the role of rhizosphere organic anions in P uptake from residual P in four common crops Triticum aestivum, Avena sativa, Solanum tuberosum, and Brassica napus in low- and high-P availability agricultural soils from long-term fertilization field trials in a mini-rhizotron experiment with four replications. Malate was generally the dominant organic anion. More rhizosphere citrate was detected in low P soils than in high P soil. B. napus showed 74-103% increase of malate in low P loam, compared with clay loam. A. sativa had the greatest rhizosphere citrate concentration in all soils (5.3-15.2 μmol g(-1) root DW). A. sativa also showed the highest level of root colonization by arbuscular mycorrhizal fungi (AMF; 36 and 40%), the greatest root mass ratio (0.51 and 0.66) in the low-P clay loam and loam respectively, and the greatest total P uptake (5.92 mg P/mini-rhizotron) in the low-P loam. B. napus had 15-44% more rhizosphere acid phosphatase (APase) activity, ~0.1-0.4 units lower rhizosphere pH than other species, the greatest increase in rhizosphere water-soluble P in the low-P soils, and the greatest total P uptake in the low-P clay loam. Shoot P content was mainly explained by rhizosphere APase activity, water-soluble P and pH within low P soils across species. Within species, P uptake was mainly linked to rhizosphere water soluble P, APase, and pH in low P soils. The effects of rhizosphere organic anions varied among species and they appeared to play minor roles in

  8. Rhizosphere Organic Anions Play a Minor Role in Improving Crop Species' Ability to Take Up Residual Phosphorus (P) in Agricultural Soils Low in P Availability

    PubMed Central

    Wang, Yanliang; Krogstad, Tore; Clarke, Jihong L.; Hallama, Moritz; Øgaard, Anne F.; Eich-Greatorex, Susanne; Kandeler, Ellen; Clarke, Nicholas

    2016-01-01

    Many arable lands have accumulated large reserves of residual phosphorus (P) and a relatively large proportion of soil P is less available for uptake by plants. Root released organic anions are widely documented as a key physiological strategy to enhance P availability, while limited information has been generated on the contribution of rhizosphere organic anions to P utilization by crops grown in agricultural soils that are low in available P and high in extractable Ca, Al, and Fe. We studied the role of rhizosphere organic anions in P uptake from residual P in four common crops Triticum aestivum, Avena sativa, Solanum tuberosum, and Brassica napus in low- and high-P availability agricultural soils from long-term fertilization field trials in a mini-rhizotron experiment with four replications. Malate was generally the dominant organic anion. More rhizosphere citrate was detected in low P soils than in high P soil. B. napus showed 74–103% increase of malate in low P loam, compared with clay loam. A. sativa had the greatest rhizosphere citrate concentration in all soils (5.3–15.2 μmol g−1 root DW). A. sativa also showed the highest level of root colonization by arbuscular mycorrhizal fungi (AMF; 36 and 40%), the greatest root mass ratio (0.51 and 0.66) in the low-P clay loam and loam respectively, and the greatest total P uptake (5.92 mg P/mini-rhizotron) in the low-P loam. B. napus had 15–44% more rhizosphere acid phosphatase (APase) activity, ~0.1–0.4 units lower rhizosphere pH than other species, the greatest increase in rhizosphere water-soluble P in the low-P soils, and the greatest total P uptake in the low-P clay loam. Shoot P content was mainly explained by rhizosphere APase activity, water-soluble P and pH within low P soils across species. Within species, P uptake was mainly linked to rhizosphere water soluble P, APase, and pH in low P soils. The effects of rhizosphere organic anions varied among species and they appeared to play minor roles in

  9. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria.

    PubMed Central

    Smith, G B; Tiedje, J M

    1992-01-01

    The dissimilatory nitrite reductase gene (nir) from denitrifying bacterium Pseudomonas stutzeri JM300 was isolated and sequenced. In agreement with recent sequence information from another strain of P. stutzeri (strain ZoBell), strain JM300 nir is the first gene in an operon and is followed immediately by a gene which codes for a tetraheme protein; 2.5 kb downstream from the nitrite reductase carboxyl terminus is the cytochrome c551 gene. P. stutzeri JM300 nir is 67% homologous to P. aeruginosa nir and 88% homologous to P. stutzeri ZoBell nir. Within the nitrite reductase promoter region is an fnr-like operator very similar to an operator upstream of a separate anaerobic pathway, that for arginine catabolism in P. aeruginosa. The denitrification genes in P. stutzeri thus may be under the same regulatory control as that found for other anaerobic pathways of pseudomonads. We have generated gene probes from restriction fragments within the nitrite reductase operon to evaluate their usefulness in ecology studies of denitrification. Probes generated from the carboxyl terminus region hybridized to denitrifying bacteria from five separate genera and did not cross-hybridize to any nondenitrifying bacteria among six genera tested. The denitrifier probes were successful in detecting denitrifying bacteria from samples such as a bioreactor consortium, aquifer microcosms, and denitrifying toluene-degrading enrichments. The probes also were used to reveal restriction fragment length polymorphism patterns indicating the diversity of denitrifiers present in these mixed communities. Images PMID:1539983

  10. Actinomycetes in the rhizosphere of semidesert soils of Mongolia

    NASA Astrophysics Data System (ADS)

    Norovsuren, Zh.; Zenova, G. M.; Mosina, L. V.

    2007-04-01

    The population density of actinomycetes in the desert-steppe soil, rhizosphere, and the above-ground parts of plants varies from tens to hundreds of thousands of colony-forming units (CFU) per gram of substrate. The actinomycetal complexes of the brown desert-steppe soil without plant roots are more diverse in their taxonomic composition than the actinomycetal complexes in the rhizosphere and the aboveground parts of plants. Additionally to representatives of the Streptomyces and Micromonospora genera, actinomycetes from the Nocardia, Saccharopolyspora, Thermomonospora, and Actinomadura genera were identified in the soil. The population density of actinomycetes in the rhizosphere and in the soil reached hundreds of thousand CFU/g; it considerably exceeded the population density of actinomycetes in the aboveground parts of plants. The maximum population density of actinomycetes was determined in the rhizosphere of Asparagus gobicus, Salsola pestifera, and Cleistogenes songorica.

  11. 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...

  12. Emergence of plant and rhizospheric microbiota as stable interactomes.

    PubMed

    Bandyopadhyay, Prasun; Bhuyan, Soubhagya Kumar; Yadava, Pramod Kumar; Varma, Ajit; Tuteja, Narendra

    2017-03-01

    The growing human population and depletion of resources have necessitated development of sustainable agriculture. Beneficial plant-microbe associations have been known for quite some time now. To maintain sustainability, one could show better reliance upon beneficial attributes of the rhizosphere microbiome. To harness the best agronomic traits, understanding the entire process of recruitment, establishment, and maintenance of microbiota as stable interactome within the rhizosphere is important. In this article, we highlight the process of recruitment and establishment of microbiota within rhizosphere. Further, we have discussed the interlinkages and the ability of multiple (microbial and plant) partners to interact with one another forming a stable plant holobiont system. Lastly, we address the possibility of exploring the knowledge gained from the holobiont system to tailor the rhizosphere microbiome for better productivity and maintenance of agroecosystems. The article provide new insights into the broad principles of stable plant-microbe interactions which could be useful for sustaining agriculture and food security.

  13. Cold-adapted and rhizosphere-competent strain of Rahnella sp. with broad-spectrum plant growth-promotion potential.

    PubMed

    Vyas, Pratibha; Joshi, Robin; Sharma, K C; Rahi, Praveen; Gulati, Ashu; Gulati, Arvind

    2010-12-01

    A phosphate-solubilizing bacterial strain isolated from Hippophae rhamnoides rhizosphere was identified as Rahnella sp. based on its phenotypic features and 16S rRNA gene sequence. The bacterial strain showed the growth characteristics of a cold-adapted psychrotroph, with the multiple plant growth-promoting traits of inorganic and organic phosphate solubilization, 1-aminocyclopropane-1- carboxylate-deaminase activity, ammonia generation, and siderophore production. The strain also produced indole- 3-acetic acid, indole-3-acetaldehyde, indole-3-acetamide, indole-3-acetonitrile, indole-3-lactic acid, and indole-3- pyruvic acid in tryptophan-supplemented nutrient broth. Gluconic, citric and isocitric acids were the major organic acids detected during tricalcium phosphate solubilization. A rifampicin-resistant mutant of the strain exhibited high rhizosphere competence without disturbance to the resident microbial populations in pea rhizosphere. Seed bacterization with a charcoal-based inoculum significantly increased growth in barley, chickpea, pea, and maize under the controlled environment. Microplot testing of the inoculum at two different locations in pea also showed significant increase in growth and yield. The attributes of coldtolerance, high rhizosphere competence, and broad-spectrum plant growth-promoting activity exhibited the potential of Rahnella sp. BIHB 783 for increasing agriculture productivity.

  14. Characterization of Bacillus isolates of potato rhizosphere from andean soils of Peru and their potential PGPR characteristics.

    PubMed

    Calvo, Pamela; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza; Zúñiga, Doris

    2010-10-01

    Bacillus spp. are well known rhizosphere residents of many crops and usually show plant growth promoting (PGP) activities that include biocontrol capacity against some phytopatogenic fungi. Potato crops in the Andean Highlands of Peru face many nutritional and phytophatogenic problems that have a significant impact on production. In this context is important to investigate the natural presence of these microorganisms in the potato rhizosphere and propose a selective screening to find promising PGP strains. In this study, sixty three Bacillus strains isolated from the rhizosphere of native potato varieties growing in the Andean highlands of Peru were screened for in vitro antagonism against Rhizoctonia solani and Fusarium solani. A high prevalence (68%) of antagonists against R. solani was found. Ninety one percent of those strains also inhibited the growth of F. solani. The antagonistic strains were also tested for other plant growth promotion activities. Eighty one percent produced some level of the auxin indole-3-acetic acid, and 58% solubilized tricalcium phosphate. Phylogenetic analysis revealed that the majority of the strains belonged to the B. amyloliquefaciens species, while strains Bac17M11, Bac20M1 and Bac20M2 may correspond to a putative new Bacillus species. The results suggested that the rhizosphere of native potatoes growing in their natural habitat in the Andes is a rich source of Bacillus fungal antagonists, which have a potential to be used in the future as PGP inoculants to improve potato crop.

  15. Characterization of Bacillus isolates of potato rhizosphere from andean soils of Peru and their potential PGPR characteristics

    PubMed Central

    Calvo, Pamela; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza; Zúñiga, Doris

    2010-01-01

    Bacillus spp. are well known rhizosphere residents of many crops and usually show plant growth promoting (PGP) activities that include biocontrol capacity against some phytopatogenic fungi. Potato crops in the Andean Highlands of Peru face many nutritional and phytophatogenic problems that have a significant impact on production. In this context is important to investigate the natural presence of these microorganisms in the potato rhizosphere and propose a selective screening to find promising PGP strains. In this study, sixty three Bacillus strains isolated from the rhizosphere of native potato varieties growing in the Andean highlands of Peru were screened for in vitro antagonism against Rhizoctonia solani and Fusarium solani. A high prevalence (68%) of antagonists against R. solani was found. Ninety one percent of those strains also inhibited the growth of F. solani. The antagonistic strains were also tested for other plant growth promotion activities. Eighty one percent produced some level of the auxin indole-3-acetic acid, and 58% solubilized tricalcium phosphate. Phylogenetic analysis revealed that the majority of the strains belonged to the B. amyloliquefaciens species, while strains Bac17M11, Bac20M1 and Bac20M2 may correspond to a putative new Bacillus species. The results suggested that the rhizosphere of native potatoes growing in their natural habitat in the Andes is a rich source of Bacillus fungal antagonists, which have a potential to be used in the future as PGP inoculants to improve potato crop. PMID:24031569

  16. 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

  17. Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community.

    PubMed

    Shi, Lu; Du, Nanshan; Shu, Sheng; Sun, Jin; Li, Shuzhan; Guo, Shirong

    2017-02-13

    Paenibacillus polymyxa (P. polymyxa) NSY50, isolated from vinegar residue substrate, suppresses the growth of Fusarium oxysporum in the cucumber rhizosphere and protects the host plant from pathogen invasion. The aim of the present study was to evaluate the effects of NSY50 application on cucumber growth, soil properties and composition of the rhizospheric soil microbial community after exposure to Fusarium oxysporum. Bacterial and fungal communities were investigated by Illumina sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) regions (ITS1 and ITS2). The results showed that NSY50 effectively reduced the incidence of Fusarium wilt (56.4%) by altering the soil physico-chemical properties (e.g., pH, Cmic, Rmic, total N and Corg) and enzyme activities, especially of urease and β-glucosidase, which were significantly increased by 2.25- and 2.64-fold, respectively, relative to the pathogen treatment condition. More specifically, NSY50 application reduced the abundance of Fusarium and promoted potentially beneficial groups, including the Bacillus, Actinobacteria, Streptomyces, Actinospica, Catenulispora and Pseudomonas genera. Thus, our results suggest that NSY50 application can improve soil properties, shift the microbial community by increasing beneficial strains and decreasing pathogen colonization in the cucumber rhizosphere, and reduce the occurrence of cucumber Fusarium wilt, thereby promoting cucumber growth.

  18. Genetic and functional diversity among fluorescent pseudomonads isolated from the rhizosphere of banana.

    PubMed

    Naik, Popavath Ravindra; Sahoo, Nirakar; Goswami, Devrishi; Ayyadurai, Niraikulam; Sakthivel, Natarajan

    2008-10-01

    Fluorescent pseudomonads from banana rhizospheric soil were isolated and screened for the production of enzymes and hormones such as phosphatase, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, protease, and antifungal metabolites. Of 95 isolates, 50 (52%) isolates solubilized tri-calcium phosphate (TCP), 63 (66%) isolates produced plant growth hormone IAA, 10 (11%) isolates exhibited ACC deaminase, and 23 (24%) isolates produced protease. Isolates were screened for antifungal activity toward phytopathogenic fungi. Gene-specific primers have identified the putative antibiotic producing isolates. These putative isolates were grown in the production media and production of antibiotics was confirmed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). Genotypic analysis by BOX (bacterial repetitive BOX element)-polymerase chain reaction (PCR) resulted into three distinct genomic clusters at a 50% similarity level and 62 distinct BOX profiles. Based on the sequence similarity of 16S rRNA and construction of subsequent phylogenetic tree analysis, isolates were designated as Pseudomonas monteilii, P. plecoglossicida, P. fluorescens, P. fulva, P. mosselii, P. aeruginosa, P. alcaligenes, and P. pseudoalcaligenes. Present study revealed the genetic and functional diversity among isolates of fluorescent pseudomonads associated with rhizospheric soil of banana and also identified P. monteilii as dominant species. The knowledge on genetic and functional diversity of fluorescent pseudomonads associated with banana rhizosphere is useful to understand their ecological role and for their utilization in sustainable agriculture.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Synergistic effect of beneficial rhizosphere microflora in biocontrol and plant growth promotion.

    PubMed

    Kannan, Vijayaragahavan; Sureendar, Raman

    2009-04-01

    Biological systems are getting more relevance than chemical control of plant pathogens as they are not only eco-friendly and economic in approach but are also involved in improving the soil consistency and maintenance of natural soil flora. Plant growth promoting rhizosphere microorganisms were isolated from three different tree rhizospheres using selective culture media. Five microorganisms were selected from each rhizosphere soil based on their efficiency and screened for their ability to promote plant growth as a consortium. Each of the developed consortium has a phosphate solubilizer, nitrogen fixer, growth hormone producer, heterotrophic member and an antagonist. The plant growth promoting ability of the microbial members present in the consortium was observed by estimating the IAA production level and also by the nitrogenase activity of the nitrogen fixers. The biocontrol potentiality of the consortium and the antagonist present in the consortium were checked by both dual plate assay and cross-streaking technique. Consortial treatments effected very good growth promotion in Lycopersicon esculentum Mill and the treated plants also developed resistance against wilt pathogen, Fusarium oxysporum f. sp. lycopersici though the effect was well pronounced with consortium developed from Santalum album.

  4. 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.

  5. 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

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

    DOE PAGES

    Timm, Collin M.; Campbell, Alicia G.; Utturkar, Sagar M.; ...

    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

  7. Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community

    PubMed Central

    Shi, Lu; Du, Nanshan; Shu, Sheng; Sun, Jin; Li, Shuzhan; Guo, Shirong

    2017-01-01

    Paenibacillus polymyxa (P. polymyxa) NSY50, isolated from vinegar residue substrate, suppresses the growth of Fusarium oxysporum in the cucumber rhizosphere and protects the host plant from pathogen invasion. The aim of the present study was to evaluate the effects of NSY50 application on cucumber growth, soil properties and composition of the rhizospheric soil microbial community after exposure to Fusarium oxysporum. Bacterial and fungal communities were investigated by Illumina sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) regions (ITS1 and ITS2). The results showed that NSY50 effectively reduced the incidence of Fusarium wilt (56.4%) by altering the soil physico-chemical properties (e.g., pH, Cmic, Rmic, total N and Corg) and enzyme activities, especially of urease and β-glucosidase, which were significantly increased by 2.25- and 2.64-fold, respectively, relative to the pathogen treatment condition. More specifically, NSY50 application reduced the abundance of Fusarium and promoted potentially beneficial groups, including the Bacillus, Actinobacteria, Streptomyces, Actinospica, Catenulispora and Pseudomonas genera. Thus, our results suggest that NSY50 application can improve soil properties, shift the microbial community by increasing beneficial strains and decreasing pathogen colonization in the cucumber rhizosphere, and reduce the occurrence of cucumber Fusarium wilt, thereby promoting cucumber growth. PMID:28198807

  8. 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

  9. 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.

  10. 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

  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. [Transformation and mobility of arsenic in the rhizosphere and non-rhizosphere soils at different growth stages of rice].

    PubMed

    Yang, Wen-Tao; Wang, Ying-Jie; Zhou, Hang; Yi, Kai-Xin; Zeng, Min; Peng, Pei-Qin; Liao, Bo-Han

    2015-02-01

    Speciation and bioavailability of arsenic in the rhizosphere and non-rhizosphere soils at different growth stages (tillering stage, jointing stage, booting stage, filling stage and maturing stage) of rice (Oryza sativa L.) were studied using toxicity characteristic leaching procedure (TCLP) and arsenic speciation analysis. Pot experiments were conducted and the soil samples were taken from a certain paddy soil in Hunan Province contaminated by mining industry. The results showed that: (1) With the extension of rice growth period, pH values and TCLP extractable arsenic levels in the rhizosphere and non-rhizosphere soils increased gradually. Soil pH and TCLP extractable arsenic levels in non-rhizosphere soils were higher than those in the rhizosphere soils at the same growth stage. (2) At the different growth stages of rice, contents of exchangeable arsenic (AE-As) in rhizosphere and non-rhizosphere soils were lower than those before the rice planting, and increased gradually with the extension of the rice growing period. Contents of Al-bound arsenic (Al-As), Fe-bound arsenic (Fe-As) and Ca-bound arsenic (Ca-As) increased gradually after rice planting, but not significantly. Residual arsenic (O-As) and total arsenic (T-As) decreased gradually after rice planting, by 37.30% and 14.69% in the rhizosphere soils and by 31.38% and 8.67% in the non-rhizosphere soils, respectively. (3) At the different growth stages of rice, contents of various forms of arsenic in the soils were in the following order: residual arsenic (O-As) > Fe-bound arsenic ( Fe-As) > Al-bound arsenic (Al-As) > Ca-bound arsenic (Ca-As) > exchangeable arsenic (AE-As). In the pH range of 5.0- 5.8, significant positive linear correlations were found between most forms of arsenic or TCLP extractable arsenic levels and pH values, while the Ca-bound arsenic was poorly correlated with pH values in the rhizosphere soils.

  13. Isolation and physiological characterization of psychrophilic denitrifying bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway).

    PubMed

    Canion, Andy; Prakash, Om; Green, Stefan J; Jahnke, Linda; Kuypers, Marcel M M; Kostka, Joel E

    2013-05-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(3) -10(6) cells of psychrophilic nitrate-respiring bacteria g(-1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40°C demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15°C, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  14. Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

    NASA Technical Reports Server (NTRS)

    Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

    2013-01-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  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.

  16. An Apple Fruit Fermentation (AFF) Treatment Improves the Composition of the Rhizosphere Microbial Community and Growth of Strawberry (Fragaria × ananassa Duch 'Benihoppe') Seedlings.

    PubMed

    Zhang, Jie; Pang, Hui; Ma, Mengxia; Bu, Yufen; Shao, Wei; Huang, Weijing; Ji, Qianlong; Yao, Yuncong

    2016-01-01

    Plant growth can be promoted by the application of apple fruit fermentation (AFF), despite unclear of the underlying mechanisms, the effects involved in AFF on rhizosphere microorganisms have been hypothesized. We investigated the consequences of applying AFF alone or in combination with Bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA were performed to determine AFF effects on rhizosphere. Moreover, the growth index and antioxidant enzyme activities were determined 30 days after treatments. We identified five dominant bacteria in AFF: Coprinus atramentarius, Bacillus megaterium, Bacillus licheniformis, Weissella and B. subtilis. The greatest number of bacterial species were observed in the rhizosphere of control matrix (water treated), and the lowest diversity appeared in the rhizosphere soil treated with 108 cfu/mL B. licheniformis alone. Combining AFF plus B. licheniformis in one treatment resulted in the largest leaf area, plant height, root length, plant weight, and the markedly higher activities of antioxidant enzymes. We conclude that a combination of AFF plus B. licheniformis treatment to matrix can increase antioxidant enzymes activities in strawberry seedlings, optimize the status of rhizosphere microbial, and promote plant growth.

  17. An Apple Fruit Fermentation (AFF) Treatment Improves the Composition of the Rhizosphere Microbial Community and Growth of Strawberry (Fragaria × ananassa Duch ‘Benihoppe’) Seedlings

    PubMed Central

    Bu, Yufen; Shao, Wei; Huang, Weijing; Ji, Qianlong; Yao, Yuncong

    2016-01-01

    Plant growth can be promoted by the application of apple fruit fermentation (AFF), despite unclear of the underlying mechanisms, the effects involved in AFF on rhizosphere microorganisms have been hypothesized. We investigated the consequences of applying AFF alone or in combination with Bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA were performed to determine AFF effects on rhizosphere. Moreover, the growth index and antioxidant enzyme activities were determined 30 days after treatments. We identified five dominant bacteria in AFF: Coprinus atramentarius, Bacillus megaterium, Bacillus licheniformis, Weissella and B. subtilis. The greatest number of bacterial species were observed in the rhizosphere of control matrix (water treated), and the lowest diversity appeared in the rhizosphere soil treated with 108 cfu/mL B. licheniformis alone. Combining AFF plus B. licheniformis in one treatment resulted in the largest leaf area, plant height, root length, plant weight, and the markedly higher activities of antioxidant enzymes. We conclude that a combination of AFF plus B. licheniformis treatment to matrix can increase antioxidant enzymes activities in strawberry seedlings, optimize the status of rhizosphere microbial, and promote plant growth. PMID:27755580

  18. 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.

  19. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar.

    PubMed

    Frey, Beat; Pesaro, Manuel; Rüdt, Andreas; Widmer, Franco

    2008-06-01

    We assessed the effects of phytoextraction on the dynamics of Pseudomonas spp. and ammonia-oxidizing bacterial populations in a heavy metal (HM) polluted soil. Hybrid poplars were grown in two-compartment root containers with a medium history (> 4 years) of HM pollution for 13 weeks. Bulk and poplar rhizosphere soils were analysed by denaturing gradient gel electrophoresis (DGGE) of Pseudomonas (sensu stricto) 16S rRNA and amoA gene fragments. DGGE patterns revealed that Pseudomonas and amoA-containing populations in the contaminated soils were markedly different from those in the uncontaminated soils. Pseudomonas and amoA profiles appeared to be stable over time in the bulk soils. In contrast, contaminated rhizosphere soils revealed a clear shift of populations with removal of HM becoming similar or at least shifted to the populations of the uncontaminated soils. The effect of phytoextraction was, however, not evident in the bulk samples, which still contained large amounts of HM. Cloning and sequencing of dominant DGGE bands revealed that Pseudomonas were phylogenetically related to the Pseudomonas fluorescens cluster and the amoA sequences to Nitrosospira spp. At the last sampling, major prominent band sequences from contaminated rhizosphere soils were identical to sequences obtained from uncontaminated rhizosphere soils, indicating that the populations were dominated by the same phylotypes. This study suggests that two taxonomically different populations are able to recover after the relief of HM stress by phytoextraction practices, whereas bulk microbial activities still remained depressed.

  20. Allelochemicals in the rhizosphere soil of Euphorbia himalayensis.

    PubMed

    Liu, Quan; Lu, Dengxue; Jin, Hui; Yan, Zhiqiang; Li, Xiuzhuang; Yang, Xiaoyan; Guo, Hongru; Qin, Bo

    2014-08-27

    Weed infestation has been known to cause considerable reductions in crop yields, thereby hindering sustainable agriculture. Many plants in genus Euphorbia affect neighboring plants and other organisms by releasing chemicals into the environment. In view of the serious threat of weeds to agriculture, the allelochemicals of Euphorbia himalayensis and their allelopathic effects were investigated. The extract of root exudates from rhizosphere soil exhibited allelopathic activities against crops (wheat, rape, and lettuce) and grasses (Poa annua, Festuca rubra, and red clover). Bioassay-guided fractionation and isolation from the root extract of E. himalayensis led to the characterization of two ellagic acid derivatives and a jatrophane diterpene, which observably showed phytotoxic activities against lettuce, Festuca arundinacea, and F. rubra. They were further confirmed by ultra-performance liquid chromatography-tandem mass spectrometry to have concentrations of 3.6, 3.8, and 8.99 nmol/g in the rhizospere soil, respectively. Bioassay indicated that the combination of the allelochemicals could be selective plant growth regulator in agriculture.

  1. 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

  2. Bacterial community composition in the rhizosphere of a transgenic, herbicide-resistant maize (Zea mays) and comparison to its non-transgenic cultivar Bosphore.

    PubMed

    Schmalenberger, Achim; Tebbe, Christoph C

    2002-04-01

    Bacterial communities in rhizospheres of transgenic maize (Zea mays, with the pat-gene conferring resistance to the herbicide glufosinate; syn. l-phosphinothricin) were compared to its isogenic, non-transgenic cultivar. Total DNA was extracted from bacterial cell consortia collected from rhizospheres of plants grown in an agricultural field. With the use of three different primer pairs binding to evolutionarily conserved regions of the bacterial 16S rRNA gene, partial sequences were amplified by polymerase chain reaction (PCR). The PCR products were subjected to single-strand conformation polymorphism (SSCP) to generate genetic profiles which corresponded to the diversity of the amplified sequences. Genetic profiles of rhizospheres consisted of 40-60 distinguishable bands depending on the chosen primer pairs, and the variability between independent replicates was very low. Neither the genetic modification nor the use of the herbicide Liberty (syn. Basta; active ingredient: glufosinate) affected the SSCP profiles as investigated with digital image analysis. In contrast, PCR-SSCP profiles of bacterial communities from rhizospheres of sugar beet, grown in the same field as a control crop, were clearly different. A less pronounced but significant difference was also observed with rhizosphere samples from fine roots of maize plants collected 35 and 70 days after sowing. Sequencing of the dominant 30 products from one typical SSCP profile generated from transgenic maize rhizospheres indicated the presence of typical soil and rhizosphere bacteria: half of the bands could be attributed to Proteobacteria, mainly of the alpha- and beta-subgroups. Other SSCP bands could be assigned to members of the following phylogenetic groups: Cytophaga-Flavobacterium-Bacteroides, Chlamydiales-Verrucomicrobium, Planctomyces, Holophaga and to Gram-positive bacteria with a high G+C DNA content.

  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.

  4. Effects of Clonal Integration on Microbial Community Composition and Processes in the Rhizosphere of the Stoloniferous Herb Glechoma longituba (Nakai) Kuprian

    PubMed Central

    Lei, Ningfei; Li, Jun; Ni, Shijun; Chen, Jinsong

    2014-01-01

    The effects of rhizodeposition on soil C and N availabilities lead to substantial changes of microbial community composition and processes in the rhizosphere of plants. Under heterogeneous light, photosynthates can be translocated or shared between exposed and shaded ramets by clonal integration. Clonal integration may enhance the rhizodeposition of the shaded ramets, which further influences nutrient recycling in their rhizosphere. To test the hypothesis, we conducted a pot experiment by the stoloniferous herb Glechoma longituba subjected to heterogeneous light. Microbial biomass and community composition in the rhizosphere of shaded offspring ramets, assessed by phospholipid fatty acids (PLFAs) analysis, were markedly altered by clonal integration. Clonal integration positively affected C, N availabilities, invertase and urease activities, N mineralization (Nmin) and nitrification rates (Nnitri) in the rhizosphere of shaded offspring ramets. However, an opposite pattern was also observed in phenoloxidase (POXase) and peroxidase (PODase) activities. Our results demonstrated that clonal integration facilitated N assimilation and uptake in the rhizosphere of shaded offspring ramets. The experiment provides insights into the mechanism of nutrient recycling mediated by clonal integration. PMID:25243590

  5. 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

  6. Simultaneous enrichment of denitrifying anaerobic methane-oxidizing microorganisms and anammox bacteria in a hollow-fiber membrane biofilm reactor.

    PubMed

    Ding, Zhao-Wei; Lu, Yong-Ze; Fu, Liang; Ding, Jing; Zeng, Raymond J

    2017-01-01

    In this study, the coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes and anaerobic ammonium oxidation (anammox) bacteria was successfully enriched in a hollow-fiber membrane biofilm reactor (HfMBR) using freshwater sediment as the inoculum. The maximal removal rates of nitrate and ammonium were 78 mg N/L/day (131 mg N/m(2)/day) and 26 mg N/L/day (43 mg N/m(2)/day), respectively. Due to the high rate of methane mass transfer in HfMBR, the activity of DAMO archaea continued to increase during the enrichment period, indicating that HfMBR could be a powerful tool to enrich DAMO microorganisms. Effects of partial methane pressure, temperature, and pH on the cocultures were obvious. However, the microbial activity in HfMBR could be recovered quickly after the shock change of environmental factors. Furthermore, the result also found that DAMO bacteria likely had a stronger competitive advantage than anammox bacteria under the operating conditions in this study. High-throughput sequencing 16S rRNA genes illustrated that the dominant microbes were NC10, Euryarchaeota, Proteobacteria, Planctomycetes, and Chlorobi with relative abundance of 38.8, 26.2, 13.78, 6.2, and 3.6 %, respectively.

  7. Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology.

    PubMed

    Bisht, Sandeep; Pandey, Piyush; Bhargava, Bhavya; Sharma, Shivesh; Kumar, Vivek; Sharma, Krishan D

    2015-03-01

    The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective.

  8. 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

  9. Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere.

    PubMed

    Shrestha, Minita; Shrestha, Pravin Malla; Frenzel, Peter; Conrad, Ralf

    2010-12-01

    Nitrogen, one of the limiting factors for the yield of rice, can also have an important function in methane oxidation, thus affecting its global budget. Rice microcosms, planted in the greenhouse, were treated with the N-fertilizers urea (UPK) and ammonium sulfate (APK) or were only treated with phosphorous and potassium (PK). Methane oxidation rates in PK and UPK treatments were similar during most of the rice-growing season, revealing no effect of urea. However, ammonium sulfate strongly suppressed methanogenesis providing an unfavorable environment for methanotrophs in APK treatment. Roots and rhizospheric soil samples, collected from six different growth stages of the rice plant, were analyzed by terminal restriction fragment length polymorphism (T-RFLP) of the pmoA gene. Assignment of abundant T-RFs to cloned pmoA sequences indicated that the populations on roots were dominated by type-I methanotrophs, whereas the populations in rhizospheric soil were dominated by type-II methanotrophs irrespectively of growth stages and fertilizer treatments. Non-metric multidimensional scaling ordination analysis of T-RFLP profiles revealed that the methanotrophic community was significantly (P<0.001) affected by the different fertilizer treatments; however, the effect was stronger on the roots than in the rhizospheric soil. Contrary to pmoA gene-based analysis, pmoA transcript-based T-RFLP/cloning/sequencing analysis in rhizospheric soil showed type I as the predominant methanotrophs in both PK and UPK treatments. Collectively, our study showed that type-I methanotrophs were dominant and probably active in rhizospheric soil throughout the season irrespective of nitrogen fertilizer used, whereas type-II methanotrophs were relatively more dominant under unfavorable conditions, such as in APK treatment.

  10. Cyanogenic Pseudomonads Influence Multitrophic Interactions in the Rhizosphere

    PubMed Central

    Rudrappa, Thimmaraju; Splaine, Robert E.; Biedrzycki, Meredith L.; Bais, Harsh P.

    2008-01-01

    In the rhizosphere, plant roots cope with both pathogenic and beneficial bacterial interactions. The exometabolite production in certain bacterial species may regulate root growth and other root-microbe interactions in the rhizosphere. Here, we elucidated the role of cyanide production in pseudomonad virulence affecting plant root growth and other rhizospheric processes. Exposure of Arabidopsis thaliana Col-0 seedlings to both direct (with KCN) and indirect forms of cyanide from different pseudomonad strains caused significant inhibition of primary root growth. Further, we report that this growth inhibition was caused by the suppression of an auxin responsive gene, specifically at the root tip region by pseudomonad cyanogenesis. Additionally, pseudomonad cyanogenesis also affected other beneficial rhizospheric processes such as Bacillus subtilis colonization by biofilm formation on A. thaliana Col-0 roots. The effect of cyanogenesis on B. subtilis biofilm formation was further established by the down regulation of important B. subtilis biofilm operons epsA and yqxM. Our results show, the functional significance of pseudomonad cyanogenesis in regulating multitrophic rhizospheric interactions. PMID:18446201

  11. 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.

  12. 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.

  13. Significance of rhizosphere microorganisms in reclaiming water in a CELSS.

    PubMed

    Greene, C; Bubenheim, D L; Wignarajah, K

    1997-01-01

    Plant-microbe interactions, such as those of the rhizosphere, may be ideally suited for recycling water in a Controlled Ecological Life Support System (CELSS). The primary contaminant of waste hygiene water will be surfactants or soaps. We identified changes in the microbial ecology in the rhizosphere of hydroponical1y grown lettuce during exposure to surfactant. Six week old lettuce plants were transferred into a chamber with a recirculating hydroponic system. Microbial density and population composition were determined for the nutrient solution prior to introduction of plants and then again with plants prior to surfactant addition. The surfactant Igepon was added to the recirculating nutrient solution to a final concentration of 1.0 g L-1. Bacteria density and species diversity of the solution were monitored over a 72-h period following introduction of Igepon. Nine distinct bacterial types were identified in the rhisosphere; three species accounted for 87% of the normal rhizosphere population. Microbial cell number increased in the presence of Igepon, however species diversity declined. At the point when Igepon was degraded from solution, diversity was reduced to only two species. Igepon was found to be degraded directly by only one species found in the rhizosphere. Since surfactants are degraded from the waste hygiene water within 24 h, the potential for using rhizosphere bacteria as a waste processor in a CELSS is promising.

  14. 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.

  15. 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.

  16. Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor.

    PubMed

    Hwang, C; Wu, W-M; Gentry, T J; Carley, J; Carroll, S L; Schadt, C; Watson, D; Jardine, P M; Zhou, J; Hickey, R F; Criddle, C S; Fields, M W

    2006-08-01

    High levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the Y-12 National Security Complex in Oak Ridge, TN. A field-scale denitrifying fluidized bed reactor (FBR) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. After inoculation, biofilms developed on the granular activated carbon particles. Changes in the bacterial community of the FBR were evaluated with clone libraries (n = 500 partial sequences) of the small-subunit rRNA gene for samples taken over a 4-month start-up period. Early phases of start-up operation were characterized by a period of selection, followed by low diversity and predominance by Azoarcus-like sequences. Possible explanations were high pH and nutrient limitations. After amelioration of these conditions, diversification increased rapidly, with the appearance of Dechloromonas, Pseudomonas, and Hydrogenophaga sequences. Changes in NO3, SO4, and pH also likely contributed to shifts in community composition. The detection of sulfate-reducing-bacteria-like sequences closely related to Desulfovibrio and Desulfuromonas in the FBR have important implications for downstream applications at the field site.

  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. The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa.

    PubMed

    Muratova, Anna; Dubrovskaya, Ekaterina; Golubev, Sergey; Grinev, Vyacheslav; Chernyshova, Marina; Turkovskaya, Olga

    2015-09-01

    We studied the catabolism of the polycyclic aromatic hydrocarbon phenanthrene by four rhizobacterial strains and the possibility of enzymatic oxidation of this compound and its microbial metabolites by the root exudates of alfalfa (Medicago sativa L.) in order to detect the possible coupling of the plant and microbial metabolisms under the rhizospheric degradation of the organic pollutant. A comparative study of phenanthrene degradation pathways in the PAH-degrading rhizobacteria Ensifer meliloti, Pseudomonas kunmingensis, Rhizobium petrolearium, and Stenotrophomonas sp. allowed us to identify the key metabolites from the microbial transformation of phenanthrene, including 9,10-phenanthrenequinone, 2-carboxybenzaldehyde, and 1-hydroxy-2-naphthoic, salicylic, and o-phthalic acids. Sterile alfalfa plants were grown in the presence and absence of phenanthrene (0.03 g kg(-1)) in quartz sand under controlled environmental conditions to obtain plant root exudates. The root exudates were collected, concentrated by ultrafiltration, and the activity of oxidoreductases was detected spectrophotometrically by the oxidation rate for various substrates. The most marked activity was that of peroxidase, whereas the presence of oxidase and tyrosinase was detected on the verge of the assay sensitivity. Using alfalfa root exudates as a crude enzyme preparation, we found that in the presence of the synthetic mediator, the plant peroxidase could oxidize phenanthrene and its microbial metabolites. The results indicate the possibility of active participation of plants in the rhizospheric degradation of polycyclic aromatic hydrocarbons and their microbial metabolites, which makes it possible to speak about the coupling of the plant and microbial catabolisms of these contaminants in the rhizosphere.

  19. 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.

  20. 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

  1. Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

    PubMed Central

    Hu, Jie; Friman, Ville-Petri; Gu, Shao-hua; Wang, Xiao-fang; Eisenhauer, Nico; Yang, Tian-jie; Ma, Jing; Shen, Qi-rong; Jousset, Alexandre

    2016-01-01

    ABSTRACT Bacterial communities associated with plant roots play an important role in the suppression of soil-borne pathogens, and multispecies probiotic consortia may enhance disease suppression efficacy. Here we introduced defined Pseudomonas species consortia into naturally complex microbial communities and measured the importance of Pseudomonas community diversity for their survival and the suppression of the bacterial plant pathogen Ralstonia solanacearum in the tomato rhizosphere microbiome. The survival of introduced Pseudomonas consortia increased with increasing diversity. Further, high Pseudomonas diversity reduced pathogen density in the rhizosphere and decreased the disease incidence due to both intensified resource competition and interference with the pathogen. These results provide novel mechanistic insights into elevated pathogen suppression by diverse probiotic consortia in naturally diverse plant rhizospheres. Ecologically based community assembly rules could thus play a key role in engineering functionally reliable microbiome applications. PMID:27965449

  2. Response characteristics of Scirpus trioueter and its rhizosphere to pyrene contaminated soils at different growth stages.

    PubMed

    Zhang, X Y; Liu, X Y; Liu, S S; Liu, F H; Chen, L S; Xu, G; Zhong, C L; Su, P C; Cao, Z N

    2012-08-01

    Scirpus triqueter (Triangular club-rush), a typical wetland species, is used to study the response characteristics to pyrene. A pot experiment was conducted to investigate the growth parameters (height, diameter, shoot number, total volume, underground biomass, above-ground biomass and total biomass), and enzymes (catalase and superoxide dismutase) of S. triqueter. The characteristics of soil enzymes (catalase and polyphenol oxidase) and microorganisms (bacteria and fungi) were also assessed after pyrene treatment. Elevated pyrene concentration (80 mgkg(-1)) in the soil reduced the shoot number and biomass significantly, especially at the early growth stage. In root tissue, the enzyme catalase was activated at 80 mgkg(-1) of pyrene. Compared to roots, shoots had higher enzyme activities. Catalase activities in the rhizosphere increased throughout the growth period of S. triqueter. Polyphenol oxidase activities in the rhizosphere were higher than those in the bulk soil and unplanted soil. The populations of bacteria (total bacteria, pyrene-tolerant bacteria, and actinomyces) and fungi decreased under the stress of high pyrene concentration, while that of pyrene-tolerant bacteria increased with the increasing pyrene concentration. The presence of pyrene did not benefit the growth of S. triqueter. S. triqueter and soil enzymes varied within the growth stages. The presence of S. triqueter could improve the activity of soil enzymes and facilitate the propagation of microorganisms which could help eliminate pyrene contamination.

  3. 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.

  4. Characteristics of self-alkalization in high-rate denitrifying automatic circulation (DAC) reactor fed with methanol and sodium acetate.

    PubMed

    Li, Wei; Zheng, Ping; Guo, Jun; Ji, Junyuan; Zhang, Meng; Zhang, Zonghe; Zhan, Enchao; Abbas, Ghulam

    2014-02-01

    Denitrification is a self-alkalization process. In this experiment, the characteristics of self-alkalization in high-rate heterotrophic denitrifying automatic circulation (DAC) reactor fed with methanol and sodium acetate were investigated, respectively. The results showed that, (1) The self-alkalization of high-rate denitrifying reactors was remarkably strong both with methanol and sodium acetate as carbon sources, while the effluent pH was much lower than the stoichiometric values and the malfunction from self-alkalization of denitrification was far less serious than expected. (2) The self-adaptation of the reactors was attributed to the neutralization of carbon dioxide (oxidization product of organic matter) and the self-adaptation of denitrifying sludge. The formation and discharge of calcium carbonate precipitates gave rise to lower effluent pH and alkalinity than the stoichiometric values.

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

    PubMed

    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 N(2)O 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 N(2)O 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 N(2)O 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 N(2)O accumulation (ρ = 0.62), whereas nirK amino acid residues were unrelated to N(2)O 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 N(2)O 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

  6. Genetic Diversity of Benzoyl Coenzyme A Reductase Genes Detected in Denitrifying Isolates and Estuarine Sediment Communities

    PubMed Central

    Song, Bongkeun; Ward, Bess B.

    2005-01-01

    Benzoyl coenzyme A (benzoyl-CoA) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-CoA) in the metabolism of many aromatic compounds. The diversity of benzoyl-CoA reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the Arthur Kill in New Jersey and the Chesapeake Bay in Maryland was investigated. Degenerate primers were developed from the known benzoyl-CoA reductase genes from Thauera aromatica, Rhodopseudomonas palustris, and Azoarcus evansii. PCR amplification detected benzoyl-CoA reductase genes in the denitrifying isolates belonging to α-, β-, or γ-Proteobacteria as well as in the sediment samples. Phylogenetic analysis, sequence similarity comparison, and conserved indel determination grouped the new sequences into either the bcr type (found in T. aromatica and R. palustris) or the bzd type (found in A. evansii). All the Thauera strains and the isolates from the genera Acidovorax, Bradyrhizobium, Paracoccus, Ensifer, and Pseudomonas had bcr-type benzoyl-CoA reductases with amino acid sequence similarities of more than 97%. The genes detected from Azarocus strains were assigned to the bzd type. A total of 50 environmental clones were detected from denitrifying consortium and sediment samples, and 28 clones were assigned to either the bcr or the bzd type of benzoyl-CoA reductase genes. Thus, we could determine the genetic capabilities for anaerobic degradation of aromatic compounds in sediment communities of the Chesapeake Bay and the Arthur Kill on the basis of the detection of two types of benzoyl-CoA reductase genes. The detected genes have future applications as genetic markers to monitor aromatic compound degradation in natural and engineered ecosystems. PMID:15812036

  7. 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."

  8. Pseudomonas yangmingensis sp. nov., an alkaliphilic denitrifying species isolated from a hot spring.

    PubMed

    Wong, Biing-Teo; Lee, Duu-Jong

    2014-01-01

    This study isolated and identified a facultative, alkaliphilic, denitrifying Pseudomonas strain designed as CRS1 from a hot spring, Yang-Ming Mountain, Taiwan. The biochemical characterization, phenotypic characteristics and phylogenetic relationship of strain CRS1 were studied. On the basis of the 16S rRNA sequence similarity, phenotypic and genotypic characteristics and chemotaxonomic data, the strain CRS1 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas yangmingensis sp. nov., is proposed. The strain CRS1 is a facultative autotrophic bacterium that has capability of mixotrophic and heterotrophic denitrification.

  9. 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

  10. Changes in Bacterial Denitrifier Community Abundance over Time in an Agricultural Field and Their Relationship with Denitrification Activity▿

    PubMed Central

    Dandie, Catherine E.; Burton, David L.; Zebarth, Bernie J.; Henderson, Sherri L.; Trevors, Jack T.; Goyer, Claudia

    2008-01-01

    This study measured total bacterial and denitrifier community abundances over time in an agricultural soil cropped to potatoes (Solanum tuberosum L.) by using quantitative PCR. Samples were collected on 10 dates from spring to autumn and from three spatial locations: in the potato “hill” between plants (H), close to the plant (Hp), and in the “furrow” (F). The denitrification rates, N2O emissions, and environmental parameters were also measured. Changes in denitrifier abundance over time and spatial location were small (1.7- to 2.7-fold for the nirK, nosZ, and cnorBB guilds), whereas the cnorBP community (Pseudomonas mandelii and closely related spp.) showed an ∼4.6-fold change. The seasonal patterns of denitrifier gene numbers varied with the specific community: lower nosZ gene numbers in April and May than in June and July, higher cnorBP gene numbers in May and June than in March and April and September and November, higher nirK gene numbers in early spring than in late autumn, and no change in cnorBB gene numbers. Gene numbers were higher for the Hp than the H location for the nosZ and nirK communities and for the cnorBP community on individual dates, presumably indicating an effect of the plant on denitrifier abundance. Higher cnorBP gene numbers for the H location than the F location and for nosZ and cnorBB on individual dates reflect the effect of spatial location on abundance. Denitrifier abundance changes were not related to any environmental parameter, although a weak relationship exists between cnorBP gene numbers, extractable organic carbon values, and temperature. Denitrification and N2O emissions were mostly regulated by inorganic nitrogen availability and water-filled pore space but were uncoupled from denitrifier community abundances measured in this system. PMID:18689522

  11. Distribution of nitrogenous nutrients and denitrifiers strains in estuarine sediment profiles of the Tanshui River, northern Taiwan

    NASA Astrophysics Data System (ADS)

    Fan, L. F.; Shieh, W. Y.; Wu, W. F.; Chen, C.-P.

    2006-09-01

    Chemical profiles of both oxidized (nitrate and sulfate) and reduced (ammonium, sulfide, acid-volatile sulfide [AVS], and pyrite) materials and the corresponding distribution of denitrifier microbial communities were measured at low tide in sediments at Guandu in the estuary of the Tanshui River, northern Taiwan in August 2002. Denitrifier strains were isolated for physiological and phylogenic analyses. Based on the distribution of nitrogenous compounds and denitrifier abundances, the vertical profile of Guandu sediments could be separated into four layers: a mixed layer (the top 1 cm of depth, respectively containing 0.82-2.37 and 535.9-475.0 μM of nitrate and ammonium), a nitrate-concentrated layer (1-5 cm in depth, 2.37-0.53 and 475.0-1192.1 μM, respectively), a denitrifier-aggregation layer (5-7 cm in depth, 0.53-0.72 and 1192.1-1430.1 μM, respectively), and an ammonium-enriched layer (7-12 cm in depth, 0.72-0.78 and 1430.1-2196.6 μM, respectively). Denitrifier strains were detected in all layers except for the mixed layer. A variety of metabolic processes by these strains may occur in different layers. Bacillus jeotgali-, Bacillus sphaericus-, and Bacillus firmus-related strains isolated from the nitrate-concentrated layer may be involved in the nitrification-denitrification coupling process due to the relatively low nitrate concentrations (maximum = 2.37 μM), and may contribute to denitrification not nitrification. Bacillus bataviensis- and B. jeotgali-related strains isolated from the denitrifier-aggregation layer comprised the predominant denitrifier population (3.64 × 10 4 cells/g of denitrifier abundance). They possess the ability of dissimilatory nitrate reduction to ammonium (DNRA). Bacillus jeotgali-related strains and two newly identified strains of GD0705 and GD0706 isolated from the ammonium-enriched layer possibly use fermentative processes as the main metabolic pathway instead of denitrification when nitrate is scarce, and this further

  12. [Responses of rhizosphere nitrogen and phosphorus transformations to different acid rain intensities in a hilly red soil tea plantation].

    PubMed

    Chen, Xi; Chen, Fu-sheng; Ye, Su-qiong; Yu, Su-qin; Fang, Xiang-min; Hu, Xiao-fei

    2015-01-01

    Tea (Camellia sinensis) plantation in hilly red soil region has been long impacted by acid deposition, however its effects on nitrogen (N) and phosphorus (P) transformations in rhizosphere soils remain unclear. A 25-year old tea plantation in a typical hilly red soil region was selected for an in situ simulation experiment treated by pH 4.5, pH 3.5, pH 2.5 and control. Rhizosihere and bulk soils were collected in the third year from the simulated acid deposition experiment. Soil mineral N, available P contents and major enzyme activities were analyzed using the chemical extraction and biochemical methods, and N and P mineralization rates were estimated using the indoor aerobic incubation methods. Our results showed that compared to the control, the treatments of pH 4.5, pH 3.5 and pH 2.5, respectively decreased 7.1%, 42.1% and 49.9% NO3(-)-N, 6.4%, 35.9% and 40.3% mineral N, 10.5%, 41.1% and 46.9% available P, 18.7%, 30.1% and 44.7% ammonification rate, 3.6%, 12.7% and 38.8% net N-mineralization rate, and 31.5%, 41.8% and 63.0% P mineralization rate in rhizosphere soils; however, among the 4 treatments, rhizosphere soil nitrification rate was not significantly different, the rhizosphere soil urease and acid phosphatase activities generally increased with the increasing intensity of acid rain (P<0.05). In bulk soil, compared with the control, the treatments of pH 4.5, pH 3.5 and pH 2.5 did not cause significant changes in NO3(-)-N, mineral N, available P as well as in the rates of nitrification, ammonification, net N-mineralization and P mineralization. With increasing the acid intensity, the rhizosphere effects of NH4+-N, NO3(-)-N, mineral N, ammonification and net N-mineralization rates were altered from positive to negative effects, those of urease and acid phosphatease showed the opposite trends, those of available P and P mineralization were negative and that of nitrification was positive. In sum, prolonged elevated acid rain could reduce N and P transformation

  13. Long-term impact of anaerobic reaction time on the performance and granular characteristics of granular denitrifying biological phosphorus removal systems.

    PubMed

    Wang, Yayi; Guo, Gang; Wang, Hong; Stephenson, Tom; Guo, Jianhua; Ye, Liu

    2013-09-15

    Removal of nitrogen and phosphorus (P) from wastewater is successfully and widely practiced in systems employing both granular sludge technology and enhanced biological P removal (EBPR) processes; however, the key parameter, anaerobic reaction time (AnRT), has not been thoroughly investigated. Successful EBPR is highly dependent on an appropriate AnRT, which induces carbon and polyphosphate metabolism by phosphorus accumulating organisms (PAOs). Therefore, the long-term impact of AnRT on denitrifying P removal performance and granular characteristics was investigated in three identical granular sludge sequencing batch reactors with AnRTs of 90 (R1), 120 (R2) and 150 min (R3). The microbial community structures and anaerobic stoichiometric parameters related to various AnRTs were monitored over time. Free nitrite acid (FNA) accumulation (e.g., 0.0008-0.0016 mg HNO2-N/L) occurred frequently owing to incomplete denitrification in the adaptation period, especially in R3, which influenced the anaerobic/anoxic intracellular intermediate metabolites and activities of intracellular enzymes negatively, resulting in lower levels of poly-P and reduced activity of polyphosphate kinase. As a result, the Accumulibacter-PAOs population decreased from 51 ± 2.5% to 43 ± 2.1% when AnRT was extended from 90 to 150 min, leading to decreased denitrifying P removal performance. Additionally, frequent exposure of microorganisms to the FNA accumulation and anaerobic endogenous conditions in excess AnRT cases (e.g., 150 min) stimulated increased extracellular polymeric substances (EPS) production by microorganisms, resulting in enhanced granular formation and larger granules (size of 0.6-1.2 mm), but decreasing anaerobic PHA synthesis and glycogen hydrolysis. Phosphorus removal capacity was mediated to some extent by EPS adsorption in granular sludge systems that possessed more EPS, longer AnRT and relatively higher GAOs.

  14. 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.

  15. 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

  16. 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.

  17. Predicting N2O emissions from nitrifying and denitrifying biofilms: a modeling study.

    PubMed

    Sabba, Fabrizio; Picioreanu, Cristian; Boltz, Joshua P; Nerenberg, Robert

    2017-02-01

    Wastewater treatment plants can be significant sources of nitrous oxide (N2O), a potent greenhouse gas. While our understanding of N2O emissions from suspended-growth processes has advanced significantly, less is known about emissions from biofilm processes. Biofilms may behave differently due to their substrate gradients and microbial stratification. In this study, we used mathematical modeling to explore the mechanisms of N2O emissions from nitrifying and denitrifying biofilms. Our ammonia-oxidizing bacteria biofilm model suggests that N2O emissions from biofilm can be significantly greater than from suspended-growth systems. The driving factor is the diffusion of hydroxylamine, a nitrification intermediate, from the aerobic to the anoxic regions of the biofilm. The presence of nitrite-oxidizing bacteria further increased emissions. For denitrifying biofilms, our results suggest that emissions are generally greater than for suspended-growth systems. However, the magnitude of the difference depends on the bulk dissolved oxygen, chemical oxygen demand, and nitrate concentrations, as well as the biofilm thickness. Overall, the accumulation and diffusion of key intermediates, i.e. hydroxylamine and nitrite, distinguish biofilms from suspended-growth systems. Our research suggests that the mechanisms of N2O emissions from biofilms are much more complex than suspended-growth systems, and that emissions may be higher in many cases.

  18. Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

    PubMed Central

    Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

    2016-01-01

    Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3–64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7–25.4%), Firmicutes (3.0–20.1%), Acidobacteria (2.7–15.7%), Actinobacteria (2.2–8.7%), Bacteroidetes (0.5–9.7%), and Verrucomicrobia (2.4–5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen. PMID:27782192

  19. Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

    NASA Astrophysics Data System (ADS)

    Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

    2016-10-01

    Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3–64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7–25.4%), Firmicutes (3.0–20.1%), Acidobacteria (2.7–15.7%), Actinobacteria (2.2–8.7%), Bacteroidetes (0.5–9.7%), and Verrucomicrobia (2.4–5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

  20. Simultaneous domestic wastewater and nitrate sewage treatment by DEnitrifying AMmonium OXidation (DEAMOX) in sequencing batch reactor.

    PubMed

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

    2017-05-01

    A novel DEAMOX system was developed for nitrogen removal from domestic wastewater and nitrate (NO3(-)-N) sewage in sequencing batch reactor (SBR). High nitrite (NO2(-)-N) was produced from NO3(-)-N reduction in partial-denitrification process, which served as electron acceptor for anammox and was removed with ammonia (NH4(+)-N) in domestic wastewater simultaneously. A 500-days operation demonstrated that the efficient and stable nitrogen removal performance could be achieved by DEAMOX. The total nitrogen (TN) removal efficiency was as high as 95.8% with influent NH4(+)-N of 63.58 mg L(-1) and NO3(-)-N of 69.24 mg L(-1). The maximum NH4(+)-N removal efficiency reached up to 94.7%, corresponding to the NO3(-)-N removal efficiency of 97.8%. The biomass of partial-denitrification and anammox bacteria was observed to be wall-growth. The deteriorated nitrogen removal performance occurred due to excess denitrifying microbial growth in the outer layer of sludge consortium, which prevented the substrate transfer for anammox inside. However, an excellent nitrogen removal could be guaranteed by scrapping the superficial denitrifying biomass at regular intervals. Furthermore, the high-throughput sequencing analysis revealed that the Thauera genera (26.33%) was possibly responsible for the high NO2(-)-N accumulation in partial-denitrification and Candidatus Brocadia (1.7%) was the major anammox species.

  1. Selenite Reduction by a Denitrifying Culture: Batch- and Packed-Bed- Reactor Studies

    SciTech Connect

    William A. Apel; Sridhar Viamajala; Yared Bereded-Samuel; James N. Petersen

    2006-08-01

    Selenite reduction by a bacterial consortium enriched from an oil refinery waste sludge was studied under denitrifying conditions using acetate as the electron donor. Fed-batch studies with nitrate as the primary electron acceptor showed that accumulation of nitrite led to a decrease in the extent of selenite reduction. Also, when nitrite was added as the primary electron acceptor, rapid selenite reduction was observed only after nitrite was significantly depleted from the medium. These results indicate that selenite reduction was inhibited at high nitrite concentrations. In addition to batch experiments, continuous flow selenite reduction experiments were performed in packed-bed columns using immobilized enrichment cultures. These experiments were carried out in three phases: In phase-I, a continuous nitrate feed with different inlet selenite concentration was applied; in phase-II, nitrate was fed in a pulsed fashion; and in phase-III, nitrate was fed in a continuous mode but at much lower concentrations than the other two phases. During the phase-I experiments, little selenite was removed from the influent. However, when the column was operated in the pulse feed strategy (phase II), or in the continuous mode with low nitrate levels (phase-III), significant quantities of selenium was removed from solution and retained in the immobilization matrix in the column. Thus, immobilized denitrifying cultures can be effective in removing selenium from waste streams, but nitrate-limited operating conditions might be required.

  2. Dynamic changes of rhizosphere properties and antioxidant enzyme responses of wheat plants (Triticum aestivum L.) grown in mercury-contaminated soils.

    PubMed

    Li, Yonghua; Sun, Hongfei; Li, Hairong; Yang, Linsheng; Ye, Bixiong; Wang, Wuyi

    2013-10-01

    A pot experiment was conducted to investigate the dynamic changes in the rhizosphere properties and antioxidant enzyme responses of wheat plants (Triticum aestivum L.) grown in three levels of Hg-contaminated soils. The concentrations of soluble Hg and dissolved organic carbon (DOC) in the rhizosphere soil solutions of the wheat plants were characterised by the sequence before sowing>trefoil stage>stooling stage, whereas the soil solution pH was found to follow an opposite distribution pattern. The activities of antioxidant enzymes in wheat plants under Hg stress were substantially altered. Greater superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities were observed in the wheat plants grown in a highly polluted soil than in a slightly polluted soil (with increases of 11-27% at the trefoil stage and 26-70% at the stooling stage); however, increasing concentrations of Hg up to seriously polluted level led to reduced enzyme activities. The present results suggest that wheat plants could positively adapt to environmental Hg stress, with rhizosphere acidification, the enhancement of DOC production and greater antioxidant enzyme activities perhaps being three important mechanisms involved in the metal uptake/tolerance in the rhizospheres of wheat plants grown in Hg-contaminated soils.

  3. 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

  4. [Effects of growth years of Paeonia lactiflora on bacterial community in rhizosphere soil and paeoniflorin content].

    PubMed

    Yuan, Xiao-Feng; Peng, San-Mei; Wang, Bo-Lin; Ding, Zhi-Shan

    2014-08-01

    To explore the relationship between microecological environment and Paeonia lactiflora the effects of growth years of P. lactillora on rhizosphere bacterial communities were studied by PCR-DGGE and the paeoniflorin content determined by HPLC. Results showed that the soil pH increased with growing years of P. lactillora. In the fourth year, soil pH and enzyme activity reached the highest level, while organic matter content was the lowest. The bacterial diversity had a positive correlation with growing years varied from 3.38 to 3.61. Sequencing results demonstrated that Gammaproteobacteria, llphaproteobacteria, Actinobacteria, Acidobacte- ria and Firmicutes were predominant bacteria kinds in the soil of P. lactillora. Gammaproteobacteria was only detected in the bulk soil, while llphaproteobacteria, Acidobacteria G1l, Actinobacteria were only in the rhizosphere soil and the bacterial community among different growing years were similar except few species. HLPC results showed that paeoniflorin content was 3.26%, 3.30%, 3.36%, 3.41% separately from one to four-year-old P. lactiflora with an upward trend. The correlation analysis indicated that the paeoniflorin content had a positive correlation with soil pH and bacterial diversity, conversely, had a negative correlation with organic matter con- tent. During the growth years the rhizosphere bacterial diversity increased without changes of predominant bacteria and the paeoniflorin content increased without significant differences while its production increased significantly, which was different from the plants showing replanting diseases. This is in line with the farming practice choosing 4-year-old P. lactllora, but not the 1-3 year old one. In addition, the accumulation of paeoniflorin is closely related to soil pH, organic matter content and bacteria diversity, confirming that the geoherblism of P. lactiflora is closely related with microbial environment in the soil.

  5. 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

  6. [Phosphorus rhizosphere depletion effect of four aquatic plants].

    PubMed

    Wang, Zhen-yu; Wen, Sheng-fang; Xing, Bao-shan; Gao, Dong-mei; Li, Feng-min; Hu, Hong-ying; Sakoda, Akiyoshi; Sagehashi, Masaki

    2008-09-01

    Four aquatic plants (Alternanthera philoxeroides, Typha latifolia, Sagittaria sagittifolia, Phragmites communis ) were cultured on P-enriched soil in a pot experiment to assess the phosphorus rhizosphere depletion effect and analysis the ratio of root to shoot, root morphology, phosphorus uptake efficiency and phosphorus use efficiency. An obvious variation in P concentration of the soil in the rhizophere and non- rhizophere was observed. Compared with the non-rhizosphere (available P: 167.53 microg x g(-1)), the available P in the rhizosphere soil of Alternanthera philoxeroides, Typha latifolia, Sagittaria sagittifolia and Phragmites communis was reduced to 80.17, 124.37, 155.38 and 161.75 microg x g(-1) respectively, with 81%, 42%, 18% and 16% reduction ratio of water-soluble phosphorus. More effective phosphorus depletion was achieved in Alternanthera philoxeroides by higher phosphorus uptake efficiency (1.32 mg x m(-1)), while rooting system was small and phosphorus use efficiency was low (0.34 g x mg(-1)). Phosphorus uptake efficiency of Typha latjfolia is much lower (0.52 mg x m(-1)) than that of Alternanthera philoxeroides, however, its strong rooting system enhanced soil exploration, with higher phosphorus use efficiency (0.64 g x mg(-1)) and the ratio of root to shoot (0.35). Alternantshera philoxeroides and Typha latfolia were more effective in phosphorus depletion of the rhizosphere soil than that in Sagittaria sagittifolia and Phragmites communis.

  7. 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

  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. 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.

  10. Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves

    PubMed Central

    Pinto, Fernando N.; Egas, Conceição; Almeida, Adelaide; Cunha, Angela; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

    2010-01-01

    Background Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants. Methodology/Principal Findings A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment. Conclusions/Significance In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments. PMID:21124923

  11. Denitrifying alphaproteobacteria from the Arabian Sea that express nosZ, the gene encoding nitrous oxide reductase, in oxic and suboxic waters.

    PubMed

    Wyman, Michael; Hodgson, Sylvia; Bird, Clare

    2013-04-01

    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.

  12. 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

  13. Degradation of toluene by a mixed population of archetypal aerobes, microaerophiles, and denitrifiers: laboratory sand column experiment and multispecies biofilm model formulation.

    PubMed

    Kim, Hyun-Su; Jaffé, Peter R

    2008-02-01

    An experiment was conducted in a saturated sand column with three bacterial strains that have different growth characteristics on toluene, Pseudomonas putida F1 which degrades toluene only under aerobic conditions, Thauera aromatica T1 which degrades toluene only under denitrifying conditions, and Ralstonia pickettii PKO1 has a facultative nature and can perform nitrate-enhanced biodegradation of toluene under hypoxic conditions (DO <2 mg/L). Steady-state concentration profiles showed that oxygen and nitrate appeared to be utilized simultaneously, regardless of the dissolved oxygen concentration and the results from fluorescent in-situ hybridization (FISH) indicated that PKO1 maintained stable cells numbers throughout the column, even when the pore water oxygen concentration was high. Since PKO1's growth rate under aerobic condition is much lower than that of F1, except under hypoxic conditions, these observations were not anticipated. Therefore these observations require a mechanistic explanation that can account for localized low oxygen concentrations under aerobic conditions. To simulate the observed dynamics, a multispecies biofilm model was implemented. This model formulation assumes the formation of a thin biofilm that is composed of the three bacterial strains. The individual strains grow in response to the substrate and electron acceptor flux from bulk fluid into the biofilm. The model was implemented such that internal changes in bacterial composition and substrate concentration can be simulated over time and space. The model simulations from oxic to denitrifying conditions compared well to the experimental profiles of the chemical species and the bacterial strains, indicating the importance of accounting for the biological activity of individual strains in biofilms that span different redox conditions.

  14. 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.

  15. 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

  16. Effects of elevated CO(2) and Pb on the microbial community in the rhizosphere of Pinus densiflora.

    PubMed

    Kim, Sunghyun; Hong, Sun Hwa; Cho, Kyungsook; Lee, Insook; Yoo, Gayoung; Kang, Hojeong

    2012-12-01

    Rising levels of atmospheric CO(2) may stimulate forest productivity in the future, resulting in increased carbon storage in terrestrial ecosystems. However, heavy metal contamination may interfere with this, though the response is not yet known. In this study, we investigated the effect of elevated CO(2) and Pb contamination on microorganisms and decomposition in pine tree forest soil. Three-year old pine trees (Pinus densiflora) were planted in Pb contaminated soils (500 mg/kg-soil) and uncontaminated soils and cultivated for three months in a growth chamber where the CO(2) concentration was controlled at 380 or 760 mg/kg. Structures of the microbial community were comparatively analyzed in bulk and in rhizosphere soil samples using community-level physiological profiling (CLPP) and 16S rRNA gene PCR-DGGE (denaturing gradient gel electrophoresis). Additionally, microbial activity in rhizospheric soil, growth and the C/N ratio of the pine trees were measured. Elevated CO(2) significantly increased microbial activities and diversity in Pb contaminated soils due to the increase in carbon sources, and this increase was more distinctive in rhizospheric soil than in bulk soils. In addition, increased plant growth and C/N ratios of pine needles at elevated CO(2) resulted in an increase in cation exchange capacity (CEC) and dissolved organic carbon (DOC) of the rhizosphere in Pb contaminated soil. Taken together, these findings indicate that elevated CO(2) levels and heavy metals can affect the soil carbon cycle by changing the microbial community and plant metabolism.

  17. Responses of salt marsh plant rhizosphere diazotroph assemblages to changes in marsh elevation, edaphic conditions and plant host species.

    PubMed

    Davis, Debra A; Gamble, Megan D; Bagwell, Christopher E; Bergholz, Peter W; Lovell, Charles R

    2011-02-01

    An important source of new nitrogen in salt marsh ecosystems is microbial diazotrophy (nitrogen fixation). The diazotroph assemblages associated with the rhizospheres (sediment directly affected by the roots) of salt marsh plants are highly diverse, somewhat stable, and consist mainly of novel organisms. In Crab Haul Creek Basin, North Inlet, SC, the distribution of plant types into discrete zones is dictated by relatively minor differences in marsh elevation and it was hypothesized that the biotic and abiotic properties of the plant zones would also dictate the composition of the rhizosphere diazotroph assemblages. Over a period of 1 year, rhizosphere sediments were collected from monotypic stands of the black needlerush, Juncus roemerianus, the common pickleweed, Salicornia virginica, the short and tall growth forms of the smooth cordgrass Spartina alterniflora, and a mixed zone of co-occurring S. virginica and short form, S. alterniflora. DNA was extracted, purified and nifH sequences PCR amplified for denaturing gradient gel electrophoresis (DGGE) analysis to determine the composition of the diazotroph assemblages. The diazotroph assemblages were strongly influenced by season, abiotic environmental parameters and plant host. Sediment chemistry and nitrogen fixation activity were also significantly influenced by seasonal changes. DGGE bands that significantly affected seasonal and zone specific clustering were identified and most of these sequences were from novel diazotrophs, unaffiliated with any previously described organisms. At least one third of the recovered nifH sequences were from a diverse assemblage of Chlorobia, and γ-, α-, β- and δ-Proteobacteria. Diazotrophs that occurred throughout the growing season and among all zones (frequently detected) were also mostly novel. These significant sequences indicated that diazotrophs driving the structure of the assemblages were diverse, versatile, and some were ubiquitous while others were seasonally

  18. Genome Sequence of the Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench.

    PubMed

    Fujinami, Shun; Oikawa, Yuji; Araki, Takuma; Shinmura, Yui; Midorikawa, Ryota; Ishizaka, Hikari; Kato, Chiaki; Horikoshi, Koki; Ito, Masahiro; Tamegai, Hideyuki

    2014-12-18

    Pseudomonas sp. strain MT-1 was the first deep-sea denitrifier isolated and characterized from mud recovered from a depth of 11,000 m in the Mariana Trench. We report here the genome sequence of this bacterium, which contributes to our understanding of denitrification and bioenergetics in the deep sea.

  19. 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.

  20. 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

  1. Impact of plant functional group, plant species, and sampling time on the composition of nirK-type denitrifier communities in soil.

    PubMed

    Bremer, Christina; Braker, Gesche; Matthies, Diethart; Reuter, Andreas; Engels, Christof; Conrad, Ralf

    2007-11-01

    We studied the influence of eight nonleguminous grassland plant species belonging to two functional groups (grasses and forbs) on the composition of soil denitrifier communities in experimental microcosms over two consecutive years. Denitrifier community composition was analyzed by terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. The impact of experimental factors (plant functional group, plant species, sampling time, and interactions between them) on the structure of soil denitrifier communities (i.e., T-RFLP patterns) was analyzed by canonical correspondence analysis. While the functional group of a plant did not affect nirK-type denitrifier communities, plant species identity did influence their composition. This effect changed with sampling time, indicating community changes due to seasonal conditions and a development of the plants in the microcosms. Differences in total soil nitrogen and carbon, soil pH, and root biomass were observed at the end of the experiment. However, statistical analysis revealed that the plants affected the nirK-type denitrifier community composition directly, e.g., through root exudates. Assignment of abundant T-RFs to cloned nirK sequences from the soil and subsequent phylogenetic analysis indicated a dominance of yet-unknown nirK genotypes and of genes related to nirK from denitrifiers of the order Rhizobiales. In conclusion, individual species of nonleguminous plants directly influenced the composition of denitrifier communities in soil, but environmental conditions had additional significant effects.

  2. 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

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

    PubMed

    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.

  4. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

    PubMed Central

    Kong, Angela Y. Y.; Hristova, Krassimira; Scow, Kate M.; Six, Johan

    2011-01-01

    Real-time quantitative PCR assays, targeting part of the ammonia-monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with 15N pool dilution techniques to investigate the effects of long-term agricultural management practices on potential gross N mineralization and nitrification rates, as well as ammonia-oxidizing bacteria (AOB), denitrifier, and total bacterial community sizes within different soil microenvironments. Three soil microenvironments [coarse particulate organic matter (cPOM; >250 μm), microaggregate (53–250 μm), and silt-and-clay fraction (<53 μm)] were physically isolated from soil samples collected across the cropping season from conventional, low-input, and organic maize-tomato systems (Zea mays L.- Lycopersicum esculentum L.). We hypothesized that (i) the higher N inputs and soil N content of the organic system foster larger AOB and denitrifier communities than in the conventional and low-input systems, (ii) differences in potential gross N mineralization and nitrification rates across the systems correspond with AOB and denitrifier abundances, and (iii) amoA, nosZ, and 16S rRNA gene abundances are higher in the microaggregates than in the cPOM and silt-and-clay microenvironments. Despite 13 years of different soil management and greater soil C and N content in the organic compared to the conventional and low-input systems, total bacterial communities within the whole soil were similar in size across the three systems (~5.15×108 copies g−1 soil). However, amoA gene densities were ~2 times higher in the organic (1.75×108 copies g−1 soil) than the other systems at the start of the season and nosZ gene abundances were ~2 times greater in the conventional (7.65×107 copies g−1 soil) than in the other systems by the end of the season. Because organic management did not consistently lead to larger AOB and denitrifier communities than the other two systems, our first hypothesis was not corroborated. Our second

  5. [Effects of different peony cultivars on community structure of arbuscular mycorrhizal fungi in rhizosphere soil].

    PubMed

    Guo, Shao-Xia; Liu, Run-Jin

    2010-08-01

    This paper studied the community structure of arbuscular mycorrhizal (AM) fungi in the rhizosphere soil of different peony (Paeonia suffruticosa) cultivars grown in Zhaolou Peony Garden of Heze in Shandong Province. A number of parameters describing this community structure, e. g., spore density, species- and genera composition, species richness, distribution frequency, species diversity indices, and Sorenson's similarity coefficient, were examined. The species- and genera composition, species richness, and distribution frequency of AM fungi in rhizosphere soil varied with planted peony cultivars. A total of 10 AM fungal species were isolated from the rhizosphere soil of cultivars 'Fengdan' and 'Zhaofen', 9 species from the rhizosphere soil of 'Wulong pengsheng' and 'Luoyang red', and 8 species from the rhizosphere soil of 'Hu red'. The spore density was the highest (59 per 50 g soil) in the rhizosphere soil of 'Fengdan', but the lowest (47 per 50 g soil) in the rhizosphere soil of 'Hu red'; the species diversity index was the highest (1.89) in the rhizosphere soil of 'Zhaofen', but the lowest (1.71) in the rhizosphere soil of 'Hu red'; and the mycorrhizal colonization rate was the highest (63.6%) in rhizosphere soil of 'Fengdan' and 'Hu red', but the lowest (52.7%) in the rhizosphere soil of 'Wulong pengsheng'. The Sorenson's similarity coefficient of AM fungal species composition in the rhizosphere soil among the test cultivars ranged from 0.71 to 0.95, being the highest between 'Wulong pengsheng' and 'Fengdan', and the lowest between 'Luoyang red' and 'Hu red'. It was concluded that the gene type of peony could change the community structure of AM fungi in rhizosphere soil.

  6. Community composition of nirS-type denitrifier in a shallow eutrophic lake.

    PubMed

    Yang, Jiang-Ke; Cheng, Zhan-Bing; Li, Jia; Miao, Li-Hong

    2013-11-01

    Denitrification is a major biological process to reduce nitrate to molecular nitrogen (N2). In shallow eutrophic lakes, this process can remove the largest portion of fixed nitrogen and plays an important role in self-purification of this ecosystem. To understand the structure of denitrifying communities in a shallow eutrophic lake, denitrifier communities in four sub-lakes of East Lake in Wuhan, China, were explored by restriction fragment length polymorphisms (RFLP) analysis and sequencing of nirS gene clone libraries. nirS is a functional marker gene for denitrification encoding cytochrome cd 1-containing nitrite reductase, which catalyzes the reduction of nitrite to nitric oxide. Both RFLP fingerprints clustering analysis and phylogeny analysis based on the amino acid sequences of NirS revealed that NirS-type communities in East Lake sediment could be roughly divided into three clusters. Cluster I accounted for 74-82 % of clones from the moderately eutrophic sub-lakes Tuan, Tang Ling, and Guo Zheng. Cluster II accounted for 76 % of the communities in hypertrophic sub-lake Miao Lake and cluster III as a minor group (7 % of the total), mainly presented in Miao Lake. Phylogenetic analysis revealed that cluster I was related to the reference clones from a broad range of ecological environments, and clusters II and III were more phylogenetically related to the reference clones from entrophic environments. Canonical correspondence analysis indicated that total nitrogen, total phosphate, total organic carbon, and NH4-N and NO2-N were important environmental factors affecting the dispersion of NirS-type denitrifier in the sediments. Cluster I showed a weak relationship with the nutrient content, while cluster II and III were positively related with the nutrient content. Principal coordinates analysis indicated that NirS-type communities from Tuan Lake, Tang Ling Lake, and Guo Zheng Lake sediments were divergent from those found in river, estuary sediment, and forest

  7. 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.

  8. Purification, Characterization, and Genetic Analysis of Cu-Containing Dissimilatory Nitrite Reductase from a Denitrifying Halophilic Archaeon, Haloarcula marismortui

    PubMed Central

    Ichiki, Hirotaka; Tanaka, Yoko; Mochizuki, Kiyotaka; Yoshimatsu, Katsuhiko; Sakurai, Takeshi; Fujiwara, Taketomo

    2001-01-01

    Cu-containing dissimilatory nitrite reductase (CuNiR) was purified from denitrifying cells of a halophilic archaeon, Haloarcula marismortui. The purified CuNiR appeared blue in the oxidized state, possessing absorption peaks at 600 and 465 nm in the visible region. Electron paramagnetic resonance spectroscopy suggested the presence of type 1 Cu (gII = 2.232; AII = 4.4 mT) and type 2 Cu centers (gII = 2.304; AII = 13.3 mT) in the enzyme. The enzyme contained two subunits, whose apparent molecular masses were 46 and 42 kDa, according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. N-terminal amino acid sequence analysis indicated that the two subunits were identical, except that the 46-kDa subunit was 16 amino acid residues longer than the 42-kDa subunit in the N-terminal region. A nirK gene encoding the CuNiR was cloned and sequenced, and the deduced amino acid sequence with a residual length of 361 amino acids was homologous (30 to 41%) with bacterial counterparts. Cu-liganding residues His-133, Cys-174, His-182, and Met-187 (for type 1 Cu) and His-138, His-173, and His-332 (for type 2 Cu) were conserved in the enzyme. As generally observed in the halobacterial enzymes, the enzymatic activity of the purified CuNiR was enhanced during increasing salt concentration and reached its maximum in the presence of 2 M NaCl with the value of 960 μM NO2− · min−1 · mg−1. PMID:11418554

  9. Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics.

    PubMed

    Drigo, Barbara; Kowalchuk, George A; Knapp, Brigitte A; Pijl, Agata S; Boschker, Henricus T S; van Veen, Johannes A

    2013-02-01

    Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and diversity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by (13) C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the (13) C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.

  10. 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

  11. 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.

  12. Endophytic and rhizosphere bacteria associated with the roots of the halophyte Salicornia europaea L. - community structure and metabolic potential.

    PubMed

    Szymańska, Sonia; Płociniczak, Tomasz; Piotrowska-Seget, Zofia; Hrynkiewicz, Katarzyna

    2016-11-01

    The main objective of our study was to assess density and diversity of rhizosphere (R) and endophytic (E) microorganisms associated with the halophyte S. europaea. Microorganisms were isolated from two saline sites (S1: 55dSm(-1), anthropogenic origin; S2: 112dSm(-1), natural salinity) located in central Poland and compared with microbial populations in the soil (S) using culture-independent (phospholipid fatty acids analysis, PLFA) and culture-dependent techniques. The endophytic and rhizosphere bacteria were identified and screened for nifH and acdS genes, and their metabolic properties were assessed. Strains with the potential to promote plant growth were selected for further study. PLFA analysis revealed that Gram-negative bacteria were dominant at both saline test sites; the total microbial biomass depended on the site (S1E>S). In contrast, culture-dependent techniques revealed that Gram-positive bacteria (Actinobacteria and Firmicutes) were dominant (S1: E-77.3%, R-86.3% and S2: E-59.1%, R-87.5%). Proteobacteria were observed in the rhizosphere at the lowest frequency (S1: 13.7% and S2: 12.5%). Greater salinity decreased the range and specificity of metabolic activity among the endophytes. These conditions also resulted in a broader spectrum of metabolic abilities in rhizobacteria; however, these metabolic processes were present at lower levels.

  13. Rhizosphere colonization and arsenic translocation in sunflower (Helianthus annuus L.) by arsenate reducing Alcaligenes sp. strain Dhal-L.

    PubMed

    Cavalca, Lucia; Corsini, Anna; Bachate, Sachin Prabhakar; Andreoni, Vincenza

    2013-10-01

    In the present study, six arsenic-resistant strains previously isolated were tested for their plant growth promoting characteristics and heavy metal resistance, in order to choose one model strain as an inoculum for sunflower plants in pot experiments. The aim was to investigate the effect of arsenic-resistant strain on sunflower growth and on arsenic uptake from arsenic contaminated soil. Based on plant growth promoting characteristics and heavy metal resistance, Alcaligenes sp. strain Dhal-L was chosen as an inoculum. Beside the ability to reduce arsenate to arsenite via an Ars operon, the strain exhibited 1-amino-cyclopropane-1-carboxylic acid deaminase activity and it was also able to produce siderophore and indole acetic acid. Pot experiments were conducted with an agricultural soil contaminated with arsenic (214 mg kg⁻¹). A real time PCR method was set up based on the quantification of ACR3(2) type of arsenite efflux pump carried by Alcaligenes sp. strain Dhal-L, in order to monitor presence and colonisation of the strain in the bulk and rhizospheric soil. As a result of strain inoculation, arsenic uptake by plants was increased by 53 %, whereas ACR3(2) gene copy number in rhizospheric soil was 100 times higher in inoculated than in control pots, indicating the colonisation of strain. The results indicated that the presence of arsenate reducing strains in the rhizosphere of sunflower influences arsenic mobilization and promotes arsenic uptake by plant.

  14. Changes in rice allelopathy and rhizosphere microflora by inhibiting rice phenylalanine ammonia-lyase gene expression.

    PubMed

    Fang, Changxun; Zhuang, Yuee; Xu, Tiecheng; Li, Yingzhe; Li, Yue; Lin, Wenxiong

    2013-02-01

    Gene expression of phenylalanine ammonia-lyase (PAL) in allelopathic rice PI312777 was inhibited by RNA interference (RNAi). Transgenic rice showed lower levels of PAL gene expression and PAL activity than wild type rice (WT). The concentrations of phenolic compounds were lower in the root tissues and root exudates of transgenic rice than in those of wild type plants. When barndyardgrass (BYG) was used as the receiver plant, the allelopathic potential of transgenic rice was reduced. The sizes of the bacterial and fungal populations in rice rhizospheric soil at the 3-, 5-, and 7-leaf stages were estimated by using quantitative PCR (qPCR), which showed a decrease in both populations at all stages of leaf development analyzed. However, PI312777 had a larger microbial population than transgenic rice. In addition, in T-RFLP studies, 14 different groups of bacteria were detected in WT and only 6 were detected in transgenic rice. This indicates that there was less rhizospheric bacterial diversity associated with transgenic rice than with WT. These findings collectively suggest that PAL functions as a positive regulator of rice allelopathic potential.

  15. 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.

  16. [Bacillus isolates from rhizosphere of cacti improve germination and bloom in Mammillaria spp. (Cactaceae)].

    PubMed

    Chávez-Ambriz, Lluvia A; Hernández-Morales, Alejandro; Cabrera-Luna, José A; Luna-Martínez, Laura; Pacheco-Aguilar, Juan R

    Cacti are the most representative vegetation of arid zones in Mexico where rainfall is scarce, evapotranspiration is high and soil fertility is low. Plants have developed physiological strategies such as the association with microorganisms in the rhizosphere zone to increase nutrient uptake. In the present work, four bacterial isolates from the rhizosphere of Mammillaria magnimamma and Coryphantha radians were obtained and named as QAP3, QAP19, QAP22 and QAP24, and were genetically identified as belonging to the genus Bacillus, exhibiting in vitro biochemical properties such as phosphate solubilization, indoleacetic acid production and ACC deaminase activity related to plant growth promotion, which was tested by inoculating M. magnimamma seeds. It was found that all isolates increased germination from 17 to 34.3% with respect to the uninoculated control seeds, being QAP24 the one having the greatest effect, accomplishing the germination of viable seeds (84.7%) three days before the control seeds. Subsequently, the inoculation of Mammillari zeilmanniana plants with this isolate showed a positive effect on bloom, registering during two months from a one year period, an increase of up to 31.0% in the number of flowering plants compared to control plants. The characterized Bacillus spp. isolates have potential to be used in conservation programs of plant species from arid zones.

  17. 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

  18. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Rhee, Moon-Soo; Kwon, O-Yu; Shin, Kee-Sun

    2009-10-01

    A novel cellulolytic bacterium, strain S23(T), was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, alpha-galactosidase, and beta-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C(15:0) (51.9%), iso-C(16:0) (14.7%), and iso-C(15:0) (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23(T) and other Paenibacillus species were between 89.9% and 95.9%, and S23(T) was most closely related to Paenibacillus tarimensis SA-7-6(T). On the basis of phylogenetic and phenotypic properties of strain S23(T), the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23(T) (=KCTC 13695(T) =KACC 14199(T) =JCM 16419(T)).

  19. The antimicrobial volatile power of the rhizospheric isolate Pseudomonas donghuensis P482

    PubMed Central

    Ossowicki, Adam; Jafra, Sylwia

    2017-01-01

    Soil and rhizosphere bacteria produce an array of secondary metabolites including a wide range of volatile organic compounds (VOCs). These compounds play an important role in the long-distance interactions and communication between (micro)organisms. Furthermore, bacterial VOCs are involved in plant pathogens inhibition and induction of soil fungistasis and suppressivenes. In the present study, we analysed the volatile blend emitted by the rhizospheric isolate Pseudomonas donghuensis P482 and evaluated the volatile effect on the plant pathogenic fungi and bacteria as well as one oomycete. Moreover, we investigated the role of the GacS/GacA system on VOCs production in P. donghuensis P482. The results obtained demonstrated that VOCs emitted by P. donghuensis P482 have strong antifungal and antioomycete, but not antibacterial activity. The production of certain volatiles such as dimethyl sulfide, S-methyl thioacetate, methyl thiocyanate, dimethyl trisulfide, 1-undecan and HCN is depended on the GacS/GacA two-component regulatory system. Apparently, these compounds play an important role in the pathogens suppression as the gacA mutant entirely lost the ability to inhibit via volatiles the growth of tested plant pathogens. PMID:28358818

  20. 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.

  1. Nitrate removal by nitrate-dependent Fe(II) oxidation in an upflow denitrifying biofilm reactor.

    PubMed

    Zhou, Jun; Wang, Hongyu; Yang, Kai; Sun, Yuchong; Tian, Jun

    2015-01-01

    A continuous upflow biofilm reactor packed with ceramsite was constructed for nitrate removal under an anaerobic atmosphere without an organic carbon source. Denitrifying bacteria, Pseudomonas sp. W1, Pseudomonas sp. W2 and Microbacterium sp. W5, were added to the bioreactor as inocula. Nitrate concentration, nitrite accumulation and nitrogen removal efficiency in the effluent were investigated under various conditions set by several parameters including pH, hydraulic retention time (HRT), ratios of carbon to nitrogen (C/N) and temperature. The results illustrated that the maximum removal efficiency of nitrogen was 85.39%, under optimum reaction parameters, approximately pH 6.5-7, HRT = 48 hours and C/N = 13.1:1 at temperature of 30 °C, which were determined by experiment.

  2. Ultrastructure of the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera," a novel polygon-shaped bacterium.

    PubMed

    Wu, Ming L; van Teeseling, Muriel C F; Willems, Marieke J R; van Donselaar, Elly G; Klingl, Andreas; Rachel, Reinhard; Geerts, Willie J C; Jetten, Mike S M; Strous, Marc; van Niftrik, Laura

    2012-01-01

    "Candidatus Methylomirabilis oxyfera" is a newly discovered denitrifying methanotroph that is unrelated to previously known methanotrophs. This bacterium is a member of the NC10 phylum and couples methane oxidation to denitrification through a newly discovered intra-aerobic pathway. In the present study, we report the first ultrastructural study of "Ca. Methylomirabilis oxyfera" using scanning electron microscopy, transmission electron microscopy, and electron tomography in combination with different sample preparation methods. We observed that "Ca. Methylomirabilis oxyfera" cells possess an atypical polygonal shape that is distinct from other bacterial shapes described so far. Also, an additional layer was observed as the outermost sheath, which might represent a (glyco)protein surface layer. Further, intracytoplasmic membranes, which are a common feature among proteobacterial methanotrophs, were never observed under the current growth conditions. Our results indicate that "Ca. Methylomirabilis oxyfera" is ultrastructurally distinct from other bacteria by its atypical cell shape and from the classical proteobacterial methanotrophs by its apparent lack of intracytoplasmic membranes.

  3. Carbon availability and the distribution of denitrifying organisms influence N2O production in the hyporheic zone

    NASA Astrophysics Data System (ADS)

    Farrell, T. B.; Quick, A. M.; Reeder, W. J.; Tonina, D.; Benner, S. G.; Feris, K. P.

    2013-12-01

    It has been estimated that 10% of greenhouse gas N2O emissions take place within river networks, with the majority of these processes occurring in the hyporheic zone (HZ). These emissions are the result of microbially-mediated nitrogen transformations (i.e. nitrification and denitrification) and yet the role of microbial distribution and function in this complex system is not well understood. We hypothesized that the concentration and availability of organic carbon influences the production of redox gradients, DIN (via mineralization, nitrification, and loss of DIN via denitrification), and ultimately N2O production in the HZ by controlling the distribution and activity of denitrifying microbial communities. Further, we hypothesized that by linking the distribution of denitrifying microbial communities and their associated functional genes (i.e. the relative abundance of N2O vs. N2 producing genetic elements) to flow dynamics and biogeochemical processes, we can begin to better understand what controls N2O production in hyporheic networks. To address these hypotheses we performed a series of column experiments designed to determine the influence of carbon concentration on redox gradient development and N2O flux along a one-dimensional flow path. Intact sediment cores were amended with 0.01%, 0.05%, 0.15%, and 0.5% dry mass riparian vegetation (>90% Populus sp.) to serve as an endogenous particulate organic matter (POM) source. During quasi-steady state conditions dissolved oxygen (DO), NH4+, NO3-, and N2O levels were measured. As predicted, a positive relationship between the level of POM amendment and development of a gradient of oxic and anoxic conditions was observed. There was negligible N2O production within columns inoculated with 0.01% and 0.05% DOC likely because these POC treatments were too low to create anoxic conditions necessary to stimulate denitrification. Maximum N2O flux was observed with the 0.15% POC treatment. Both oxic and anoxic conditions

  4. Measurement of the oxygen isotopic composition of nitrate in seawater and freshwater using the denitrifier method

    USGS Publications Warehouse

    Casciotti, K.L.; Sigman, D.M.; Hastings, M. Galanter; Böhlke, J.K.; Hilkert, A.

    2002-01-01

    We report a novel method for measurement of the oxygen isotopic composition (18O/16O) of nitrate (NO3-) from both seawater and freshwater. The denitrifier method, based on the isotope ratio analysis of nitrous oxide generated from sample nitrate by cultured denitrifying bacteria, has been described elsewhere for its use in nitrogen isotope ratio (15N/14N) analysis of nitrate.1Here, we address the additional issues associated with 18O/16O analysis of nitrate by this approach, which include (1) the oxygen isotopic difference between the nitrate sample and the N2O analyte due to isotopic fractionation associated with the loss of oxygen atoms from nitrate and (2) the exchange of oxygen atoms with water during the conversion of nitrate to N2O. Experiments with 18O-labeled water indicate that water exchange contributes less than 10%, and frequently less than 3%, of the oxygen atoms in the N2O product for Pseudomonas aureofaciens. In addition, both oxygen isotope fractionation and oxygen atom exchange are consistent within a given batch of analyses. The analysis of appropriate isotopic reference materials can thus be used to correct the measured 18O/16O ratios of samples for both effects. This is the first method tested for 18O/16O analysis of nitrate in seawater. Benefits of this method, relative to published freshwater methods, include higher sensitivity (tested down to 10 nmol and 1 μM NO3-), lack of interference by other solutes, and ease of sample preparation.

  5. Modeling of Cr(VI) Bioreduction Under Fermentative and Denitrifying Conditions

    NASA Astrophysics Data System (ADS)

    Molins, S.; Steefel, C.; Yang, L.; Beller, H. R.

    2011-12-01

    The mechanisms of bioreductive immobilization of Cr(VI) were investigated by reactive transport modeling of a set of flow-through column experiments performed using natural Hanford 100H aquifer sediment. The columns were continuously eluted with 5 μM Cr(VI), 5 mM lactate as the electron donor, and selected electron acceptors (tested individually). Here we focus on the two separate experimental conditions that showed the most removal of Cr(VI) from solution: fermentation and denitrification. In each case, a network of enzymatic and abiotic reaction pathways was considered to interpret the rate of chromate reduction. The model included biomass growth and decay, and thermodynamic limitations on reaction rates, and was constrained by effluent concentrations measured by IC and ICP-MS and additional information from bacterial isolates from column effluent. Under denitrifying conditions, Cr(VI) reduction was modeled as co-metabolic with nitrate reduction based on experimental observations and previous studies on a denitrifying bacterium derived from the Hanford 100H aquifer. The reactive transport model results supported this interpretation of the reaction mechanism and were used to quantify the efficiency of the process. The models results also suggest that biomass growth likely relied on a nitrogen source other than ammonium (e.g. nitrate). Under fermentative conditions and based on cell suspension studies performed on a bacterial isolate from the columns, the model assumes that Cr(VI) reduction is carried out directly by fermentative bacteria that convert lactate into acetate and propionate. The evolution to complete lactate fermentation and Cr(VI) reduction took place over a week's time and simulations were used to determine an estimate for a lower limit of the rate of chromate reduction by calibration with the flow-through column experimental results. In spite of sulfate being added to these columns, sulfate reduction proceeded at a slow rate and was not well

  6. Biotransformation of explosive-grade nitrocellulose under denitrifying and sulfidogenic conditions.

    PubMed

    Freedman, David L; Cashwell, James M; Kim, Byung J

    2002-01-01

    Waste nitrocellulose (NC) is regulated as a hazardous material. The objective of this study was to determine if NC exposed to denitrifying and sulfidogenic conditions would undergo sufficient removal of the nitro groups to yield a material that is no longer explosive. Enrichment cultures were established with methanol as the electron donor for nitrate-reducing conditions and lactate for sulfate-reducing conditions. NC was added to the cultures at 10 g/l. A statistically significant decrease in the nitrogen (N) content of NC occurred in both enrichment cultures, from approximately 13.1-13.2% in virgin NC to 12.2-12.4%. This was accompanied by an increase in nitrogen gas formation. The presence of a primary substrate (methanol and lactate) was necessary to affect this change; NC itself did not serve as an electron donor. In cultures that were carrying out denitrification but were then depleted of nitrate, with methanol still present, a slightly greater removal of nitro groups from NC occurred along with additional formation of nitrogen gas. NC did not have an inhibitory affect on the denitrification process but it did significantly slow the rate of lactate consumption and sulfate reduction. Fourier Transform Infrared Spectroscopy (FTIR) results indicated that NC exposed to denitrifying conditions was enriched in hydroxyl groups, consistent with removal of some of the nitro groups by hydrolysis of the nitrate esters. NC exposed to nitrate- and sulfate-reducing conditions and virgin NC were also compared based on their explosive properties using a small-scale burning test. The biologically treated NC exhibited somewhat less reactivity, but was still rated as explosive. The decrease in%N, increase in N2, and FTIR results demonstrated that NC does undergo biotransformation in the presence of nitrate- and sulfate-reducing enrichment cultures, but the extent of denitration does not appear to be adequate to yield a nonhazardous product.

  7. Granulation in high-load denitrifying upflow sludge bed (USB) pulsed reactors.

    PubMed

    Franco, A; Roca, E; Lema, J M

    2006-03-01

    In this work, the effect of the application of a pulse system to anoxic upflow sludge bed (USB) denitrifying reactors for enhancing sludge granulation was studied. In all, three 0.8 L reactors (two operated with flow pulsation, P1 with effluent recycling and P2 without recycling, and one without pulsation and effluent recycling, no pulsation (NP)) were fed with a mixture of NaNO3 and glucose and inoculated with methanogenic granular sludge. The organic loading rate (OLR) and the nitrogen loading rate (NLR) were progressively increased and, at the end of the experiment, extremely high values were obtained (67.5 kgCOD/m3d and 11.25 kgN-NO3-/m3 d). Ammonia and nitrite accumulation in reactor NP were important in the maturation stage, decreasing the denitrification efficiency to 90%, while in reactor P1 only low nitrite values were obtained in the last few days of the experiment. In reactor P2, nitrogen removal was 100% most of the time. Several operational problems (flotation and the subsequent wash out of biomass) appeared in the NP reactor when working at high denitrifying loading rates, while in reactors P1 and P2 there were no notable problems, mainly due to the good characteristics of the sludge developed and the efficient degasification produced by the pulsing flow. The sludge formed in the NP reactor presented a flocculent structure and a total disintegration of the initial methanogenic granules occurred, while a small-sized granular biomass with a high specific density was developed in the pulsed reactors due to the shear stress produced.

  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. 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.

  10. 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.

  11. 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

  12. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    PubMed

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  13. Uncultured bacterial diversity in tropical maize (Zea mays L.) rhizosphere.

    PubMed

    Chauhan, Puneet Singh; Chaudhry, Vasvi; Mishra, Sandhya; Nautiyal, Chandra Shekhar

    2011-02-01

    Structure of maize (Zea mays L.) rhizosphere bacteria was evaluated to explore the feasibility of identifying novel rhizosphere bacteria using culture-independent method based on direct amplification and analysis of 16S rRNA gene (rRNA) sequences and especially to obtain a better understanding of bacterial community structure and diversity from maize. A total of 274 sequences were analyzed and assigned 48.00% Proteobacteria, 10.30% Actinobacteria, 9.90% Bacteroidetes, 6.60% Verrucomicrobia, 4.80% Acidobacteria, 1.80% Firmicutes, 1.50% Chloroflexi, 1.50% TM7, 1.10% Deinococcus-Thermus, 0.70% Planctomycetes, 0.70% Gemmatimonadetes and 0.40% Cyanobacteria. Economically important phyla Actinobacteria was second most dominant group after Proteobacteria, in our clone library. It would be interesting to hypothesize that root exudates from maize rhizosphere favors growth of Actinobacteria like microbes to eliminate pathogenic bacteria and decompose plant matter, for enhanced plant and soil health. An additional 12.8% of clone library (35 operational taxonomical units (OTUs) from 43 clones) with less than 94% similarity to any GenBank sequence could not be assigned to any known phylum and may represent unidentified bacterial lineages and suggests that a large amount of the rhizobacterial diversity remains to be characterized by culturing.

  14. 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.

  15. Differences in soil properties and bacterial communities between the rhizosphere and bulk soil and among different production areas of the medicinal plant Fritillaria thunbergii.

    PubMed

    Shi, Ji-Yan; Yuan, Xiao-Feng; Lin, Hui-Rong; Yang, Yuan-Qiang; Li, Zong-Yuan

    2011-01-01

    To explore rhizosphere effects, geographical differences and their effects on the bacterial community associated with the geoherb Fritillaria thunbergii, some physicochemical properties of soil samples (3 sampling sites × 2 habitats (rhizosphere and bulk soil)) were measured and the soil bacterial community detected by PCR-denaturing gradient gel electrophoresis (DGGE). Among the three regions, soil pH varied between 4.48 and 7.73 indicating that F. thunbergii could grow both in acid and slightly alkaline soil. As the authentic Dao-di producing area, Ningbo showed the highest soil quality with the highest content of organic matter (OM) (2.46%), phosphatase (268 mg kg(-1) 24 h(-1)) and urease activity (1481 mg kg(-1) 24 h(-1)). In comparison with the bulk soil, pH, organic carbon content, and phosphatase and urease activities were all lower in the rhizosphere, suggesting that the roots may secrete some unique metabolites in root exudates. Statistical analyses showed that soil properties of Ningbo and Panan in Zhejiang province were more similar to each other than those in Nantong in Jiangsu province. In addition, PCR-DGGE analysis showed that main bacterial population identified in F. thunbergii was proteobacteria (18 bands, 55%), acidobacteria (4, 12%), actinobacteria (4, 12%) and bacterioidetes (6, 18%). Overall, soil properties and microbial communities varied not only between the rhizosphere and bulk soil but also among the three regions. We suggest that the plant, together with the soil properties, cooperatively shape the structure of the rhizosphere bacteria, and that the soil properties have a close relationship with the geoherbalism of F. thunbergii.

  16. 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.

  17. Different Selective Effects on Rhizosphere Bacteria Exerted by Genetically Modified versus Conventional Potato Lines

    PubMed Central

    Hannula, Silja Emilia; Andreote, Fernando Dini; Pereira e Silva, Michele de Cássia; Salles, Joana Falcão; de Boer, Wietse; van Veen, Johannes; van Elsas, Jan Dirk

    2013-01-01

    Background In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with 13C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released 13C labelled carbonaceous compounds. Methodology/Principal findings The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released 13C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the 13C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types. Conclusions/Significance Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by

  18. Repression of oxalic acid-mediated mineral phosphate solubilization in rhizospheric isolates of Klebsiella pneumoniae by succinate.

    PubMed

    Rajput, Mahendrapal Singh; Naresh Kumar, G; Rajkumar, Shalini

    2013-02-01

    Two strains of Klebsiella (SM6 and SM11) were isolated from rhizospheric soil that solubilized mineral phosphate by secretion of oxalic acid from glucose. Activities of enzymes for periplasmic glucose oxidation (glucose dehydrogenase) and glyoxylate shunt (isocitrate lyase and glyoxylate oxidase) responsible for oxalic acid production were estimated. In presence of succinate, phosphate solubilization was completely inhibited, and the enzymes glucose dehydrogenase and glyoxylate oxidase were repressed. Significant activity of isocitrate lyase, the key enzyme for carbon flux through glyoxylate shunt and oxalic acid production during growth on glucose suggested that it could be inducible in nature, and its inhibition by succinate appeared to be similar to catabolite repression.

  19. [Effects of inoculating plant growth-promoting rhizobacteria on the biological characteristics of walnut (Juglans regia) rhizosphere soil under drought condition].

    PubMed

    Liu, Fang-Chun; Xing, Shang-Jun; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao

    2014-05-01

    Effects of four plant growth-promoting rhizobacteria (PGPR) , namely Pseudomonas sp. YT3, Bacillus subtilis DZ1, B. cereus L90 and B. fusiformis L13 on the biological characteristics of walnut (Juglans regia) rhizosphere soil under drought stress were investigated. Results showed that drought stress had little effect on available nutrients of walnut rhizosphere soil, but significantly decreased the activity of organic carbon by 18.4% and increased the pH from 7.34 to 7.79. Under drought stress condition, the inoculation of Bacillus cereus L90 significantly increased high-labile organic carbon in walnut rhizosphere by 14.5% relative to the un-inoculated control, and decreased the pH to 7.41. Compared with the irrigated control, the total microbial populations, root exudates, microbial biomass carbon, and microbial biomass nitrogen in walnut rhizosphere soil were significantly decreased by 36.0%, 20.7%, 33.5% and 30.7%, respectively, because of drought stress. However, L90 inoculation decreased these deficits to 14.1%, 10.3%, 12.1% and 12.7%, respectively. Some terminal restriction fragments (T-RFs) disappeared under the drought condition and PGPR inoculation had great influence on T-RFs according to Terminal Restriction Fragment Length Polymorphism profiles. The Margalef index and the Shannon index of walnut rhizosphere soil significantly decreased, but the Simpson index increased relative to the irrigated control. Compared with the un-inoculated control, the Margalef index significantly increased from 0.42 to 0.99, as well as the Shannon index increased from 0.52 to 0.98. However, the Simpson index de- creased from 0.60 to 0.39. Inoculating YT3, DZ1 and L13 had weaker effects on the biological characteristics of walnut rhizosphere soil compared to inoculating L90, suggesting L90 inoculation could interfere with the suppression of drought stress to the biological characteristics of walnut rhizosphere soil.

  20. 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

  1. 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

  2. Effect of earthworm feeding guilds on ingested dissimilatory nitrate reducers and denitrifiers in the alimentary canal of the earthworm.

    PubMed

    Depkat-Jakob, Peter S; Hilgarth, Maik; Horn, Marcus A; Drake, Harold L

    2010-09-01

    The earthworm gut is an anoxic nitrous oxide (N(2)O)-emitting microzone in aerated soils. In situ conditions of the gut might stimulate ingested nitrate-reducing soil bacteria linked to this emission. The objective of this study was to determine if dissimilatory nitrate reducers and denitrifiers in the alimentary canal were affected by feeding guilds (epigeic [Lumbricus rubellus], anecic [Lumbricus terrestris], and endogeic [Aporrectodea caliginosa]). Genes and gene transcripts of narG (encodes a subunit of nitrate reductase and targets both dissimilatory nitrate reducers and denitrifiers) and nosZ (encodes a subunit of N(2)O reductase and targets denitrifiers) were detected in guts and soils. Gut-derived sequences were similar to those of cultured and uncultured soil bacteria and to soil-derived sequences obtained in this study. Gut-derived narG sequences and narG terminal restriction fragments (TRFs) were affiliated mainly with Gram-positive organisms (Actinobacteria). The majority of gut- and uppermost-soil-derived narG transcripts were affiliated with Mycobacterium (Actinobacteria). In contrast, narG sequences indicative of Gram-negative organisms (Proteobacteria) were dominant in mineral soil. Most nosZ sequences and nosZ TRFs were affiliated with Bradyrhizobium (Alphaproteobacteria) and uncultured soil bacteria. TRF profiles indicated that nosZ transcripts were more affected by earthworm feeding guilds than were nosZ genes, whereas narG transcripts were less affected by earthworm feeding guilds than were narG genes. narG and nosZ transcripts were different and less diverse in the earthworm gut than in mineral soil. The collective results indicate that dissimilatory nitrate reducers and denitrifiers in the earthworm gut are soil derived and that ingested narG- and nosZ-containing taxa were not uniformly stimulated in the guts of worms from different feeding guilds.

  3. Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

    PubMed Central

    Lünsmann, Vanessa; Kappelmeyer, Uwe; Taubert, Anja; Nijenhuis, Ivonne; von Bergen, Martin; Müller, Jochen A.; Jehmlich, Nico

    2016-01-01

    ABSTRACT Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCE Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results

  4. [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.

  5. Simultaneous pollutant removal and electricity generation in denitrifying microbial fuel cell with boric acid-borate buffer solution.

    PubMed

    Chen, Gang; Zhang, Shaohui; Li, Meng; Wei, Yan

    2015-01-01

    A double-chamber denitrifying microbial fuel cell (MFC), using boric acid-borate buffer solution as an alternative to phosphate buffer solution, was set up to investigate the influence of buffer solution concentration, temperature and external resistance on electricity generation and pollutant removal efficiency. The result revealed that the denitrifying MFC with boric acid-borate buffer solution was successfully started up in 51 days, with a stable cell voltage of 205.1 ± 1.96 mV at an external resistance of 50 Ω. Higher concentration of buffer solution favored nitrogen removal and electricity generation. The maximum power density of 8.27 W/m(3) net cathodic chamber was obtained at a buffer solution concentration of 100 mmol/L. An increase in temperature benefitted electricity generation and nitrogen removal. A suitable temperature for this denitrifying MFC was suggested to be 25 °C. Decreasing the external resistance favored nitrogen removal and organic matter consumption by exoelectrogens.

  6. Population Densities of Rhizobium japonicum Strain 123 Estimated Directly in Soil and Rhizospheres

    PubMed Central

    Reyes, V. G.; Schmidt, E. L.

    1979-01-01

    Rhizobium japonicum serotype 123 was enumerated in soil and rhizospheres by fluorescent antibody techniques. Counting efficiency was estimated to be about 30%. Indigenous populations of strain 123 ranged from a few hundred to a few thousand per gram of field soil before planting. Rhizosphere effects from field-grown soybean plants were modest, reaching a maximum of about 2 × 104 cells of strain 123 per g of inner rhizosphere soil in young (16-day-old) plants. Comparably slight rhizosphere stimulation was observed with field corn. High populations of strain 123 (2 × 106 to 3 × 106 cells per g) were found only in the disintegrating taproot rhizospheres of mature soybeans at harvest, and these populations declined rapidly after harvest. Pot experiments with the same soil provided data similar to those derived from the field experiments. Populations of strain 123 reached a maximum of about 105 cells per g of soybean rhizosphere soil, but most values were lower and were only slightly higher than values in wheat rhizosphere soil. Nitrogen treatments had little effect on strain 123 densities in legume and nonlegume rhizospheres or on the nodulation success of strain 123. No evidence was obtained for the widely accepted theory of specific stimulation, which has been proposed to account for the initiation of the Rhizobium-legume symbiosis. PMID:16345383

  7. Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3

    PubMed Central

    Uzelac, Gordana; Bertani, Iris; Kojic, Milan; Paszkiewicz, Konrad H.; Studholme, David J.; Passos da Silva, Daniel

    2014-01-01

    Pseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3. PMID:24994800

  8. Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.

    PubMed

    Uzelac, Gordana; Bertani, Iris; Kojic, Milan; Paszkiewicz, Konrad H; Studholme, David J; Passos da Silva, Daniel; Venturi, Vittorio

    2014-07-03

    Pseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3.

  9. 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...

  10. 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...

  11. Draft Genome Sequence of Arthrobacter chlorophenolicus Strain Mor30.16, Isolated from the Bean Rhizosphere.

    PubMed

    Miranda-Ríos, José Antonio; Ramírez-Trujillo, José Augusto; Nova-Franco, Bárbara; Lozano-Aguirre Beltrán, Luis Fernando; Iturriaga, Gabriel; Suárez-Rodríguez, Ramón

    2015-05-07

    Bacteria of the genus Arthrobacter are commonly found in the soil and plant rhizosphere. In this study we report the draft genome of Arthrobacter chlorophenolicus strain Mor30.16 that was isolated from rhizosphere of beans grown in Cuernavaca Morelos, Mexico. This strain promotes growth and ameliorates drought stress in bean plants.

  12. Draft Genome Sequence of Arthrobacter chlorophenolicus Strain Mor30.16, Isolated from the Bean Rhizosphere

    PubMed Central

    Miranda-Ríos, José Antonio; Ramírez-Trujillo, José Augusto; Nova-Franco, Bárbara; Lozano-Aguirre Beltrán, Luis Fernando; Iturriaga, Gabriel

    2015-01-01

    Bacteria of the genus Arthrobacter are commonly found in the soil and plant rhizosphere. In this study we report the draft genome of Arthrobacter chlorophenolicus strain Mor30.16 that was isolated from rhizosphere of beans grown in Cuernavaca Morelos, Mexico. This strain promotes growth and ameliorates drought stress in bean plants. PMID:25953176

  13. 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...

  14. Isolation of Acanthamoeba from the rhizosphere of maize and lucerne plants

    NASA Astrophysics Data System (ADS)

    Orosz, Erika; Farkas, Ágnes; Ködöböcz, László; Becsak, Péter; Danka, József; Kucsera, István; Füleky, György

    2013-04-01

    Acanthamoeba species are free-living amoebae that can be found in almost every range of environments. Within this genus, a number of species are recognized as human pathogens, potentially causing Acanthamoeba keratitis, granulomatous amoebic encephalitis, and chronic granulomatous lesions. Soil and water samples were taken from experimental station at Julianna Major of Plant Protection Institute of Centre for Agricultural Research, Hungarian Academy of Sciences. We detected living Acanthamoeba spp. based on culture- confirmed detection combined with the molecular taxonomic identification method. Living Acanthamoeba spp. were detected in thirteen (65%) samples. The presence of Acanthamoeba spp. in the samples depends significantly on the rhizosphere plants. The most frequently identified living Acanthamoeba genotype was T4 followed by T11, T2/T6 and T17. Genotypes T4 and T11 of Acanthamoeba, are responsible for Acanthamoeba keratitis as well as granulomatous amoebic encephalitis, and should therefore be considered as a potential health risk associated with human activities in the environment.

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

    PubMed

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

    2015-10-27

    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.

  16. 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