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Sample records for rhizosphere

  1. 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)

  2. 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...

  3. 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 ...

  4. 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

  5. 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.

  6. 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

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  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. 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

  17. 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

  18. Relevance of extracellular DNA in rhizosphere

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  19. 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. 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.

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    PubMed

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

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

  9. [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.

  10. 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

  11. 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.

  12. 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

  13. 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

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

    NASA Astrophysics Data System (ADS)

    1997-01-01

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

  15. 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.

  16. 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.

  17. [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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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

  4. [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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. [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.

  11. 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

    The aquatic rhizosphere is a region around the roots of aquatic plants. Many studies focusing on terrestrial rhizosphere have led to a good understanding of the interactions between the roots, its exudates and its associated rhizobacteria. The rhizosphere of free-floating roots, however, is a different habitat that poses several additional challenges, including rapid diffusion rates of signals and nutrient molecules, which are further influenced by the hydrodynamic forces. These can lead to rapid diffusion and complicates the studying of diffusible factors from both plant and/or rhizobacterial origins. These plant systems are being increasingly used for self purification of water bodies to provide sustainable solution. A better understanding of these processes will help in improving their performance for ecological engineering of freshwater systems. The same principles can also be used to improve the yield of hydroponic cultures. Novel toolsets and approaches are needed to investigate the processes occurring in the aquatic rhizosphere. We are interested in understanding the interaction between root exudates and the complex microbial communities that are associated with the roots, using a systems biology approach involving metabolomics and metagenomics. With this aim, we have developed a RhizoFlowCell (RFC) system that provides a controlled study of aquatic plants, observed the root biofilms, collect root exudates and subject the rhizosphere system to changes in various chemical or physical perturbations. As proof of concept, we have used RFC to test the response of root exudation patterns of Pandanus amaryllifolius after exposure to the pollutant naphthalene. Complexity of root exudates in the aquatic rhizosphere was captured using this device and analysed using LC-qTOF-MS. The highly complex metabolomic profile allowed us to study the dynamics of the response of roots to varying levels of naphthalene. The metabolic profile changed within 5mins after spiking with

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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...

  7. 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...

  8. 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.

  9. 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

  10. 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...

  11. 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.

  12. 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.

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

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

    2014-01-01

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

  15. Is rhizosphere remediation sufficient for sustainable revegetation of mine tailings?

    PubMed Central

    Huang, Longbin; Baumgartl, Thomas; Mulligan, David

    2012-01-01

    Background Revegetation of mine tailings (fine-grained waste material) starts with the reconstruction of root zones, consisting of a rhizosphere horizon (mostly topsoil and/or amended tailings) and the support horizon beneath (i.e. equivalent to subsoil – mostly tailings), which must be physically and hydro-geochemically stable. This review aims to discuss key processes involved in the development of functional root zones within the context of direct revegetation of tailings and introduces a conceptual process of rehabilitating structure and function in the root zones based on a state transition model. Scope Field studies on the revegetation of tailings (from processing base metal ore and bauxite residues) are reviewed. Particular focus is given to tailings' properties that limit remediation effectiveness. Aspects of root zone reconstruction and vegetation responses are also discussed. Conclusions When reconstructing a root zone system, it is critical to restore physical structure and hydraulic functions across the whole root zone system. Only effective and holistically restored systems can control hydro-geochemical mobility of acutely and chronically toxic factors from the underlying horizon and maintain hydro-geochemical stability in the rhizosphere. Thereafter, soil biological capacity and ecological linkages (i.e. carbon and nutrient cycling) may be rehabilitated to integrate the root zones with revegetated plant communities into sustainable plant ecosystems. A conceptual framework of system transitions between the critical states of root zone development has been proposed. This will illustrate the rehabilitation process in root zone reconstruction and development for direct revegetation with sustainable plant communities. Sustainable phytostabilization of tailings requires the systematic consideration of hydro-geochemical interactions between the rhizosphere and the underlying supporting horizon. It further requires effective remediation strategies to

  16. 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.

  17. 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

  18. Diversity of free-living nitrogen-fixing microorganisms in the rhizosphere and non-rhizosphere of pioneer plants growing on wastelands of copper mine tailings.

    PubMed

    Zhan, Jing; Sun, Qingye

    2012-03-20

    The composition of free-living nitrogen-fixing microbial communities in rhizosphere and non-rhizosphere of pioneer plants growing on wastelands of copper mine tailings was studied by the presence of nifH genes using Polymerase Chain Reaction-Denatured Gradient Gel Electrophoresis (PCR-DGGE) approach. Eleven rhizosphere tailing samples and nine non-rhizosphere tailing samples from six plant communities were collected from two wastelands with different discarded periods. The nested PCR method was used to amplify the nifH genes from environmental DNA extracted from tailing samples. Twenty-two of 37 nifH gene sequences retrieved from DGGE gels clustered in Proteobacteria (α-Proteobacteria and β-Proteobacteria) and 15 nifH gene sequences in Cyanobacteria. Most nifH gene fragments sequenced were closely related to uncultured bacteria and cyanobacteria and exhibited less than 90% nucleotide acid identity with bacteria in the database, suggesting that the nifH gene fragments detected in copper mine tailings may represent novel sequences of nitrogen-fixers. Our results indicated that the non-rhizosphere tailings generally presented higher diversity of nitrogen-fixers than rhizosphere tailings and the diversity of free-living nitrogen-fixers in tailing samples was mainly affected by the physico-chemical properties of the wastelands and plant species, especially the changes of nutrient and heavy metal contents caused by the colonization of plant community.

  19. Plasticity of rhizosphere hydraulic properties as a key for efficient utilization of scarce resources

    PubMed Central

    Carminati, Andrea; Vetterlein, Doris

    2013-01-01

    Background It is known that the soil near roots, the so-called rhizosphere, has physical and chemical properties different from those of the bulk soil. Rhizosphere properties are the result of several processes: root and soil shrinking/swelling during drying/wetting cycles, soil compaction by root growth, mucilage exuded by root caps, interaction of mucilage with soil particles, mucilage shrinking/swelling and mucilage biodegradation. These processes may lead to variable rhizosphere properties, i.e. the presence of air-filled gaps between soil and roots; water repellence in the rhizosphere caused by drying of mucilage around the soil particles; or water accumulation in the rhizosphere due to the high water-holding capacity of mucilage. The resulting properties are not constant in time but they change as a function of soil condition, root growth rate and mucilage age. Scope We consider such a variability as an expression of rhizosphere plasticity, which may be a strategy for plants to control which part of the root system will have a facilitated access to water and which roots will be disconnected from the soil, for instance by air-filled gaps or by rhizosphere hydrophobicity. To describe such a dualism, we suggest classifying rhizosphere into two categories: class A refers to a rhizosphere covered with hydrated mucilage that optimally connects roots to soil and facilitates water uptake from dry soils. Class B refers to the case of air-filled gaps and/or hydrophobic rhizosphere, which isolate roots from the soil and may limit water uptake from the soil as well water loss to the soil. The main function of roots covered by class B will be long-distance transport of water. Outlook This concept has implications for soil and plant water relations at the plant scale. Root water uptake in dry conditions is expected to shift to regions covered with rhizosphere class A. On the other hand, hydraulic lift may be limited in regions covered with rhizosphere class B. New

  20. Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection

    PubMed Central

    De Tender, Caroline; Haegeman, Annelies; Vandecasteele, Bart; Clement, Lieven; Cremelie, Pieter; Dawyndt, Peter; Maes, Martine; Debode, Jane

    2016-01-01

    Adding biochar, the solid coproduct of biofuel production, to peat can enhance strawberry growth, and disease resistance against the airborne fungal pathogen Botrytis cinerea. Additionally, biochar can induce shifts in the strawberry rhizosphere microbiome. However, the moment that this biochar-mediated shift occurs in the rhizosphere is not known. Further, the effect of an above-ground infection on the strawberry rhizosphere microbiome is unknown. In the present study we established two experiments in which strawberry transplants (cv. Elsanta) were planted either in peat or in peat amended with 3% biochar. First, we established a time course experiment to measure the effect of biochar on the rhizosphere bacterial and fungal communities over time. In a second experiment, we inoculated the strawberry leaves with B. cinerea, and studied the impact of the infection on the rhizosphere bacterial community. The fungal rhizosphere community was stabilized after 1 week, except for the upcoming Auriculariales, whereas the bacterial community shifted till 6 weeks. An effect of the addition of biochar to the peat on the rhizosphere microbiome was solely measured for the bacterial community from week 6 of plant growth onwards. When scoring the plant development, biochar addition was associated with enhanced root formation, fruit production, and postharvest resistance of the fruits against B. cinerea. We hypothesize that the bacterial rhizosphere microbiome, but also biochar-mediated changes in chemical substrate composition could be involved in these events. Infection of the strawberry leaves with B. cinerea induced shifts in the bacterial rhizosphere community, with an increased bacterial richness. This disease-induced effect was not observed in the rhizospheres of the B. cinerea-infected plants grown in the biochar-amended peat. The results show that an above-ground infection has its effect on the strawberry rhizosphere microbiome, changing the bacterial interactions in the

  1. Ecological effects of crude oil residues on the functional diversity of soil microorganisms in three weed rhizospheres.

    PubMed

    Zhang, Qian-ru; Zhou, Qi-xing; Ren, Li-ping; Zhu, Yong-guan; Sun, Shu-lan

    2006-01-01

    Ecological effects of crude oil residues on weed rhizospheres are still vague. The quantitative and diversity changes and metabolic responses of soil-bacterial communities in common dandelion (Taraxacum officinale), jerusalem artichoke (Silphium perfoliatum L.) and evening primrose (Acalypha australis L.) rhizospheric soils were thus examined using the method of carbon source utilization. The results indicated that there were various toxic effects of crude oil residues on the growth and reproduction of soil bacteria, but the weed rhizospheres could mitigate the toxic effects. Total heterotrophic counting colony-forming units (CFUs) in the rhizospheric soils were significantly higher than those in the non-rhizospheric soils. The culturable soil-bacterial CFUs in the jerusalem artichoke (S. perfoliatum) rhizosphere polluted with 0.50 kg/pot of crude oil residues were almost twice as much as those with 0.25 kg/pot and without the addition of crude oil residues. The addition of crude oil residues increased the difference in substrate evenness, substrate richness, and substrate diversity between non-rhizospheric and rhizospheric soils of T. officinale and A. australis, but there was no significant (p>0.05) difference in the Shannon's diversity index between non-rhizospheric and rhizospheric soils of S. perfoliatum. The rhizospheric response of weed species to crude oil residues suggested that S. perfoliatum may be a potential weed species for the effective plant-microorganism bioremediation of contaminated soils by crude oil residues.

  2. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere.

    PubMed

    Berg, Gabriele; Smalla, Kornelia

    2009-04-01

    The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.

  3. 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.

  4. 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.

  5. 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.

  6. Impact of a Recombinant Biocontrol Bacterium, Pseudomonas fluorescens pc78, on Microbial Community in Tomato Rhizosphere

    PubMed Central

    Kong, Hyun Gi; Kim, Nam Hee; Lee, Seung Yeup; Lee, Seon-Woo

    2016-01-01

    Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer. PMID:27147933

  7. Peptidoglycan from Bacillus cereus mediates commensalism with rhizosphere bacteria from the Cytophaga-Flavobacterium group.

    PubMed

    Peterson, Snow Brook; Dunn, Anne K; Klimowicz, Amy K; Handelsman, Jo

    2006-08-01

    Previous research in our laboratory revealed that the introduction of Bacillus cereus UW85 can increase the populations of bacteria from the Cytophaga-Flavobacterium (CF) group of the Bacteroidetes phylum in the soybean rhizosphere, suggesting that these rhizosphere microorganisms have a beneficial relationship (G. S. Gilbert, J. L. Parke, M. K. Clayton, and J. Handelsman, Ecology 74:840-854, 1993). In the present study, we determined the frequency at which CF bacteria coisolated with B. cereus strains from the soybean rhizosphere and the mechanism by which B. cereus stimulates the growth of CF rhizosphere strains in root exudate media. In three consecutive years of sampling, CF strains predominated among coisolates obtained with B. cereus isolates from field-grown soybean roots. In root exudate media, the presence of B. cereus was required for CF coisolate strains to reach high population density. However, rhizosphere isolates from the phylum Proteobacteria grew equally well in the presence and absence of B. cereus, and the presence of CF coisolates did not affect the growth of B. cereus. Peptidoglycan isolated from B. cereus cultures stimulated growth of the CF rhizosphere bacterium Flavobacterium johnsoniae, although culture supernatant from B. cereus grown in root exudate media did not. These results suggest B. cereus and CF rhizosphere bacteria have a commensal relationship in which peptidoglycan produced by B. cereus stimulates the growth of CF bacteria.

  8. Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field

    PubMed Central

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

    2014-01-01

    Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field. PMID:24955843

  9. 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.

  10. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.

    SciTech Connect

    Gottel, Neil R; Castro Gonzalez, Hector F; Kerley, Marilyn K; Yang, Zamin; Pelletier, Dale A; Podar, Mircea; Karpinets, Tatiana V; Uberbacher, Edward C; Tuskan, Gerald A; Vilgalys, Rytas; Doktycz, Mitchel John; Schadt, Christopher Warren

    2011-01-01

    The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.

  11. Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

    PubMed Central

    Schreiter, Susanne; Ding, Guo-Chun; Heuer, Holger; Neumann, Günter; Sandmann, Martin; Grosch, Rita; Kropf, Siegfried; Smalla, Kornelia

    2014-01-01

    The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce. PMID:24782839

  12. Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce.

    PubMed

    Schreiter, Susanne; Ding, Guo-Chun; Heuer, Holger; Neumann, Günter; Sandmann, Martin; Grosch, Rita; Kropf, Siegfried; Smalla, Kornelia

    2014-01-01

    The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.

  13. Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

    SciTech Connect

    Nuccio, Erin E.; Anderson-Furgeson, James; Estera, Katerina Y.; Pett-Ridge, Jennifer; de Valpine, Perry; Brodie, Eoin L.; Firestone, Mary K.

    2016-05-09

    The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacent to the roots of wild oat (Avena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. In conclusion, these results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have

  14. Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

    DOE PAGES

    Nuccio, Erin E.; Anderson-Furgeson, James; Estera, Katerina Y.; ...

    2016-05-09

    The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacentmore » to the roots of wild oat (Avena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. In conclusion, these results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that

  15. Rhizosphere competent Pantoea agglomerans enhances maize (Zea mays) and chickpea (Cicer arietinum L.) growth, without altering the rhizosphere functional diversity.

    PubMed

    Mishra, Aradhana; Chauhan, Puneet Singh; Chaudhry, Vasvi; Tripathi, Manisha; Nautiyal, Chandra Shekhar

    2011-10-01

    Plant growth promoting Pantoea agglomerans NBRISRM (NBRISRM) was able to produce 60.4 μg/ml indole acetic acid and solubilize 77.5 μg/ml tri-calcium phosphate under in vitro conditions. Addition of 2% NaCl (w/v) in the media induced the IAA production and phosphate solubilization by 11% and 7%, respectively. For evaluating the plant growth promotory effect of NBRISRM inoculation a micro plot trial was conducted using maize and chickpea as host plants. The results revealed significant increase in all growth parameters tested in NBRISRM inoculated maize and chickpea plants, which were further confirmed by higher macronutrients (N, P and K) accumulation as compared to un-inoculated controls. Throughout the growing season of maize and chickpea, rhizosphere population of NBRISRM were in the range 10(7)-10(8) CFU/g soil and competing with 10(7)-10(9) CFU/g soil with heterogeneous bacterial population. Functional richness, diversity, and evenness were found significantly higher in maize rhizosphere as compared to chickpea, whereas NBRISRM inoculation were not able to change it, in both crops as compared to their un-inoculated control. To the best of our knowledge this is first report where we demonstrated the effect of P. agglomerans strain for improving maize and chickpea growth without altering the functional diversity.

  16. [Influence of elevated atmospheric CO2 on rhizosphere microbes and arbuscular mycorrhizae].

    PubMed

    Chen, Jing; Chen, Xin; Tang, Jianjun

    2004-12-01

    The changes of microbial communities in rhizosphere and the formation of mycorrhizae play an important role in affecting the dynamics of plant communities and terrestrial ecosystems. This paper summarized and discussed the effects of elevated atmospheric CO2 on them. Under elevated atmospheric CO2, the carbohydrates accumulated in root systems increased, and the rhizospheric environment and its microbial communities as well as the formation of mycorrhizae changed. It is suggested that the researches in the future should be focused on the effects of rhizosphere microbes and arbuscular mycorrhizae on regulating the carbon dynamics of plant communities and terrestrial ecosystems under elevated atmospheric CO2.

  17. [Characteristics of soil microelements contents in the rhizospheres of different vegetation in hilly-gully region of Loess Plateau].

    PubMed

    Zhang, Chao; Liu, Guo-Bin; Xue, Sha; Zhang, Chang-Sheng

    2012-03-01

    To explore the rhizosphere effect of the microelements in the soils under different vegetation types in Loess Plateau, this paper analyzed the organic C, total N, Mn, Cu, Fe, and Zn contents in the rhizosphere soil and bulk soil of six vegetation types in hilly-gully region of Loess Plateau. Among the six vegetation types, Caragana korshinskii, Heteropappus altaicus, and Artemisia capillaries had higher organic C and total N contents in rhizosphere soil than in bulk soil. With the exception of C. korshinskii and H. rhamnoides, all the six vegetation types had a significantly lower pH in rhizosphere soil than in bulk soil. The six vegetation types had a lower available Mn content in rhizosphere soil than in bulk soil, and the C. korshinskii, Astragalus adsurgen, and Panicum virgatum had a significantly higher available Cu content in rhizosphere soil than in bulk soil. The six vegetation types except A. adsurgens had a slightly higher available Fe content in rhizosphere soil than in bulk soil, and A. adsurgens, P. virgatum, H. altaicus, and A. capillaries had a significant accumulation of available Zn in rhizosphere soil. There existed significant positive correlations between the rhizosphere soil and bulk soil of the six vegetation types in the relationships between the organic C and total N contents and the available Mn and Zn contents and between the contents of available Mn and Zn. In rhizosphere soil, available Mn and Zn contents were significantly negative- ly correlated with pH value. Due to the differences in root growth characteristics, rhizosphere pH value, and microbial structure composition, the microelements contents in the rhizosphere soil of the six vegetation types differed, with the contents of Mn, Cu, Fe, and Zn being higher in the rhizosphere soil of H. altaicus than in that of the other vegetation types.

  18. 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

  19. Plant Rhizosphere Effects on Metal Mobilization and Transport

    SciTech Connect

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

    1999-06-01

    A mechanistic understanding of mobilization or immobilization of nutrient and pollutant metal ions by plants is largely lacking. It begins with a lack of knowledge on the chemical nature of rhizosphere components that are reactive with metal ions. This fundamental knowledge is critical to the design and implementation of phytoremediation for metal-contaminated DOE sites. Therefore, the objectives of this project include (1) To obtain a comprehensive composition of major organic components in plant root exudates as a function of different metal ions and plant species; (2) To examine plant metabolic response(s) to these metal ion treatments, with emphasis on production of metal reactive compounds; (3) To investigate the effect(s) of soil microbial (e.g. mycorrhizae) association on (1) and (2).

  20. MOLECULAR PHYLOGENETIC AND BIOGEOCHEMICAL STUDIES OF SULFATE-REDUCING BACTERIA IN THE RHIZOSPHERE OF SPARTINA ALTERNIFLORA

    EPA Science Inventory

    The population composition and biogeochemistry of sulfate-reducing bacteria (SRB) in the rhizosphere of the marsh grass Spartina alterniflora was investigated over two growing seasons using molecular probing, enumerations of culturable SRB, and measurements of SO42- reduction rat...

  1. Going back to the roots: the microbial ecology of the rhizosphere.

    PubMed

    Philippot, Laurent; Raaijmakers, Jos M; Lemanceau, Philippe; van der Putten, Wim H

    2013-11-01

    The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.

  2. [Status and changes of soil nutrients in rhizosphere of Abelmoschus manihot different planting age].

    PubMed

    Tang, Li-Xia; Tan, Xian-He; Zhang, Yu; Liu, Xiao-Ning

    2013-11-01

    Using soil chemical analysis method and combining with ICP-AES determination of mineral nutrition element content in rhizosphere soil of different planting age Abelmoschus Corolla Results show that along with the increase of planting age, the nitrogen (total N), available P and organic matter in rhizosphere soil of Abelmoschus Corolla content declined year by year and the soil got acidification. Heavy metal element content in agricultural land does not exceed national standards, but the content of element mercury (Hg) in rhizosphere soil of different planting age Abelmoschus Corolla declined. Request of microelement such as manganese (Mn) and zinc (Zn) had a increase tendency, but the content of magnesium (Mg) and sodium (Na) increased, and other nutrient elements had no changed rules or unchanged apparently. Consequently, exploring the change rules of different planting age Abelmoschus Corolla soil in rhizosphere as theoretical guidance of rational fertilization and subducting continuous cropping obstscles.

  3. Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil

    PubMed Central

    De Maayer, Pieter; Oberholster, Tanzelle; Henschel, Joh; Louw, Michele K.; Cowan, Don

    2016-01-01

    Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth. PMID:27064484

  4. Molecular responses in root-associative rhizospheric bacteria to variations in plant exudates

    NASA Astrophysics Data System (ADS)

    Abdoun, Hamid; McMillan, Mary; Pereg, Lily

    2015-04-01

    Plant exudates are a major factor in the interface of plant-soil-microbe interactions and it is well documented that the microbial community structure in the rhizosphere is largely influenced by the particular exudates excreted by various plants. Azospirillum brasilense is a plant growth promoting rhizobacterium that is known to interact with a large number of plants, including important food crops. The regulatory gene flcA has an important role in this interaction as it controls morphological differentiation of the bacterium that is essential for attachment to root surfaces. Being a response regulatory gene, flcA mediates the response of the bacterial cell to signals from the surrounding rhizosphere. This makes this regulatory gene a good candidate for analysis of the response of bacteria to rhizospheric alterations, in this case, variations in root exudates. We will report on our studies on the response of Azospirillum, an ecologically, scientifically and agriculturally important bacterial genus, to variations in the rhizosphere.

  5. 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.

  6. PRODUCTION OF PLANT GROWTH PROMOTING SUBSTANCES IN BACTERIAL ISOLATES FROM THE SEAGRASS RHIZOSPHERE

    EPA Science Inventory

    Plants and rhizosphere bacteria have evolved chemical signals that enable their mutual growth. These relationships have been well investigated with agriculturally important plants, but not in seagrasses, which are important to the stability of estuaries. Seagrasses are rooted in ...

  7. Phosphate Solubilization Potentials of Rhizosphere Isolates from Central Anatolia (Turkey)

    NASA Astrophysics Data System (ADS)

    Ogut, M.; Er, F.

    2009-04-01

    Plant available-phosphorus (P) is usually low in Anatolian soils due mainly to the precipitation as calcium (Ca) and magnesium (Mg) phosphates in alkaline conditions. Phosphate solubilizing microorganisms (PSM) can enhance plant P-availability by dissolving the hardly soluble-P within the rhizosphere, which is the zone that surrounds the plant roots. PSM's can be used as seed- or soil-inocula to increase plant P-uptake and the overall growth. A total of 162 PSM's were isolated from the rhizosphere of wheat plants excavated from different fields located along a 75 km part of a highway in Turkey. The mean, the standart deviation, and the median for solubilized-P (ppm) in a 24 h culture in a tricalcium phosphate broth were 681, 427, and 400 for glucose; 358, 266, and 236 for sucrose; and 102, 117, and 50 for starch, respectively. There was not a linear relationship between the phosphate solubilized in the liquid cultures and the solubilization index obtained in the Pikovskaya's agar. Nine isolates representing both weak and strong solubilizers [Bacillus megaterium (5), Bacillus pumilis (1), Pseudomonas syringae pv. phaseolica (1), Pseudomonas fluorescens (1), Arthrobacter aurescens (1) as determined by the 16S rRNA gene sequence analysis] were further studied in a five day incubation. Pseudomonas syringae pv. phaseolica solubilized statistically (P<0.05) higher phosphate (409 ppm) than all the other strains did. There was not a statistically significant (P<0.05) difference in solubilized-P among the Bacillus strains. The pH of the medium fell to the levels between 4 and 5 from the initial neutrality. The phosphate solubilizing strains variably produced gluconic, 2-keto-D-gluconic, glycolic, acetic and butyric acids. The organic acids produced by these microorganisms seem to be the major source of phosphate solubilization in vitro.

  8. [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.

  9. Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi

    PubMed Central

    de Boer, Wietse; Hundscheid, Maria P. J.; Klein Gunnewiek, Paulien J. A.; de Ridder-Duine, Annelies S.; Thion, Cecile; van Veen, Johannes A.; van der Wal, Annemieke

    2015-01-01

    Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria. PMID:26393509

  10. Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi.

    PubMed

    de Boer, Wietse; Hundscheid, Maria P J; Klein Gunnewiek, Paulien J A; de Ridder-Duine, Annelies S; Thion, Cecile; van Veen, Johannes A; van der Wal, Annemieke

    2015-01-01

    Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria.

  11. [Chemical characteristics of the rhizosphere soil of water spinach cultivars differing in Cd accumulation].

    PubMed

    Gong, Yu-Lian; Yang, Zhong-Yi

    2014-08-01

    A rhizobox experiment was conducted to investigate the chemical characteristics of the rhizosphere soils of two water spinach cultivars differing in Cd accumulation, QLQ (a low-Cd cultivar) and T308 (a high-Cd cultivar). The results showed that the diethylenetriamine pentacetate acid extractable Cd (DTPA-Cd) concentration in the rhizos-phere soil of QLQ was significantly higher than that of T308 (P < 0.05). pH and Eh in the rhizosphere soil of QLQ were significantly higher than those of T308 (P < 0.05), while EC was opposite. Contents of organic matter and dissolved organic matter (DOM) in the rhizosphere soil of QLQ were both higher than those of T308. In contaminated soil, the composition and concentration of low molecular weight organic acids in the rhizosphere between the two cultivars were both different. Acetic, propionic, citric and fumaric acids were detected in the rhizosphere soil of T308, and only citric and fumaric acids were detected in that of QLQ. The total concentration of low molecular weight organic acids in the rhizosphere soil of QLQ (1.93 nmol x g(-1) DM) was lower than that of T308 (15.11 nmol x g(-1) DM) (P < 0.01). Compared with the high-Cd cultivar (T308), the chemical characteristics of the rhizosphere soil of the low-Cd cultivar (QLQ) were obviously distinct, i. e., the relatively higher content of organic matter, the lower content of low molecular weight organic acids with a specific composition, less acidification of soil, and a lower ability in reduction, correspondingly lowering the mobility of Cd in soil and reducing Cd accumulation by plant.

  12. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

    PubMed Central

    Trivedi, Pankaj; He, Zhili; Van Nostrand, Joy D; Albrigo, Gene; Zhou, Jizhong; Wang, Nian

    2012-01-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in ‘Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of ‘Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the ‘Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the ‘Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by ‘Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and

  13. 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

  14. Unique Organic Matter and Microbial Properties in the Rhizosphere of a Wetland Soil

    SciTech Connect

    Kaplan, Daniel I.; Xu, Chen; Huang, Shan; Lin, Youmin; Tolic, Nikola; Roscioli, Kristyn M.; Santschi, Peter H.; Jaffe, Peter R.

    2016-04-19

    Wetlands attenuate the migration of many contaminants through a wide range of biogeochemical reactions. Recent research has shown that the rhizosphere, the zone near plant roots, in wetlands is especially effective at promoting contaminant attenuation. The objective of this study was to compare the soil organic matter (OM) composition and microbial communities of a rhizosphere soil (primarily an oxidized environment) to that of the bulk wetland soil (primarily a reduced environment). The rhizosphere had elevated C, N, Mn, and Fe concentrations and total bacteria, including Anaeromyxobacter, counts (as identified by qPCR). Furthermore, the rhizosphere contained several organic molecules that were not identified in the nonrhizosphere soil (54% of the >2200 ESI-FTICR-MS identified compounds). The rhizosphere OM molecules generally had (1) greater overall molecular weights, (2) less aromaticity, (3) more carboxylate and N-containing COO functional groups, and (4) a greater hydrophilic character. These latter two OM properties typically promote metal binding. This study showed for the first time that not only the amount but also the molecular characteristics of OM in the rhizosphere may in part be responsible for the enhanced immobilization of contaminants in wetlands. These finding have implications on the stewardship and long-term management of contaminated wetlands

  15. 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.

  16. Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea.

    PubMed

    Alzubaidy, Hanin; Essack, Magbubah; Malas, Tareq B; Bokhari, Ameerah; Motwalli, Olaa; Kamanu, Frederick Kinyua; Jamhor, Suhaiza Ahmad; Mokhtar, Noor Azlin; Antunes, André; Simões, Marta Filipa; Alam, Intikhab; Bougouffa, Salim; Lafi, Feras F; Bajic, Vladimir B; Archer, John A C

    2016-02-01

    Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.

  17. Unique Organic Matter and Microbial Properties in the Rhizosphere of a Wetland Soil.

    PubMed

    Kaplan, Daniel I; Xu, Chen; Huang, Shan; Lin, Youmin; Tolić, Nikola; Roscioli-Johnson, Kristyn M; Santschi, Peter H; Jaffé, Peter R

    2016-04-19

    Wetlands attenuate the migration of many contaminants through a wide range of biogeochemical reactions. Recent research has shown that the rhizosphere, the zone near plant roots, in wetlands is especially effective at promoting contaminant attenuation. The objective of this study was to compare the soil organic matter (OM) composition and microbial communities of a rhizosphere soil (primarily an oxidized environment) to that of the bulk wetland soil (primarily a reduced environment). The rhizosphere had elevated C, N, Mn, and Fe concentrations and total bacteria, including Anaeromyxobacter, counts (as identified by qPCR). Furthermore, the rhizosphere contained several organic molecules that were not identified in the nonrhizosphere soil (54% of the >2200 ESI-FTICR-MS identified compounds). The rhizosphere OM molecules generally had (1) greater overall molecular weights, (2) less aromaticity, (3) more carboxylate and N-containing COO functional groups, and (4) a greater hydrophilic character. These latter two OM properties typically promote metal binding. This study showed for the first time that not only the amount but also the molecular characteristics of OM in the rhizosphere may in part be responsible for the enhanced immobilization of contaminants in wetlands. These finding have implications on the stewardship and long-term management of contaminated wetlands.

  18. Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

    PubMed Central

    Kawasaki, Akitomo; Donn, Suzanne; Ryan, Peter R.; Mathesius, Ulrike; Devilla, Rosangela; Jones, Amanda

    2016-01-01

    The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that host root microbial communities that increase productivity. The eudicot model species Arabidopsis has been used to investigate these processes, however a model for monocotyledons is also required. We characterized the rhizosphere microbiome and root exudates of Brachypodium distachyon, to develop it as a rhizosphere model for cereal species like wheat. The Brachypodium rhizosphere microbial community was dominated by Burkholderiales. However, these communities were also dependent on how tightly they were bound to roots, the root type they were associated with (nodal or seminal roots), and their location along the roots. Moreover, the functional gene categories detected in microorganisms isolated from around root tips differed from those isolated from bases of roots. The Brachypodium rhizosphere microbiota and root exudate profiles were similar to those reported for wheat rhizospheres, and different to Arabidopsis. The differences in root system development and cell wall chemistry between monocotyledons and eudicots may also influence the microorganism composition of these major plant types. Brachypodium is a promising model for investigating the microbiome of wheat. PMID:27727301

  19. Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

    PubMed

    Mark Ibekwe, A; Ors, Selda; Ferreira, Jorge F S; Liu, Xuan; Suarez, Donald L

    2017-02-01

    Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in

  20. 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

  1. Arsenic dynamics in the rhizosphere and its sequestration on rice roots as affected by root oxidation.

    PubMed

    Pan, Weisong; Wu, Chuan; Xue, Shengguo; Hartley, William

    2014-04-01

    A pot experiment was conducted to investigate the effects of root oxidation on arsenic (As) dynamics in the rhizosphere and As sequestration on rice roots. There were significant differences (P < 0.05) in pH values between rhizosphere and non-rhizosphere soils, with pH 5.68-6.16 in the rhizosphere and 6.30-6.37 in non-rhizosphere soils as well as differences in redox potentials (P < 0.05). Percentage arsenite was lower (4%-16%) in rhizosphere soil solutions from rice genotypes with higher radial oxygen loss (ROL) compared with genotypes with lower ROL (P < 0.05). Arsenic concentrations in iron plaque and rice straw were significantly negatively correlated (R = -0.60, P < 0.05). Genotypes with higher ROL (TD71 and Yinjingruanzhan) had significantly (P < 0.001) lower total As in rice grains (1.35 and 0.96 mg/kg, respectively) compared with genotypes with lower ROL (IAPAR9, 1.68 mg/kg; Nanyangzhan 2.24 mg/kg) in the As treatment, as well as lower inorganic As (P < 0.05). The present study showed that genotypes with higher ROL could oxidize more arsenite in rhizosphere soils, and induce more Fe plaque formation, which subsequently sequestered more As. This reduced As uptake in aboveground plant tissues and also reduced inorganic As accumulation in rice grains. The study has contributed to further understanding the mechanisms whereby ROL influences As uptake and accumulation in rice.

  2. Spatio-Temporal Patterns in Rhizosphere Oxygen Profiles in the Emergent Plant Species Acorus calamus

    PubMed Central

    Wenlin, Wang; Ruiming, Han; Yinjing, Wan; Bo, Liu; Xiaoyan, Tang; Bin, Liang; Guoxiang, Wang

    2014-01-01

    Rhizosphere oxygen profiles are the key to understanding the role of wetland plants in ecological remediation. Though in situ determination of the rhizosphere oxygen profiles has been performed occasionally at certain growing stages within days, comprehensive study on individual roots during weeks is still missing. Seedlings of Acorus calamus, a wetland monocot, were cultivated in silty sediment and the rhizosphere oxygen profiles were characterized at regular intervals, using micro-optodes to examine the same root at four positions along the root axis. The rhizosphere oxygen saturation culminated at 42.9% around the middle part of the root and was at its lowest level, 3.3%, at the basal part of the root near the aboveground portion. As the plant grew, the oxygen saturation at the four positions remained nearly constant until shoot height reached 15 cm. When shoot height reached 60 cm, oxygen saturation was greatest at the point halfway along the root, followed by the point three-quarters of the way down the root, the tip of the root, and the point one-quarter of the way down. Both the internal and rhizosphere oxygen saturation steadily increased, as did the thickness of stably oxidized microzones, which ranged from 20 µm in younger seedlings to a maximum of 320 µm in older seedlings. The spatial patterns of rhizosphere oxygen profiles in sediment contrast with those from previous studies on radial oxygen loss in A. calamus that used conventional approaches. Rhizosphere oxygen saturation peaked around the middle part of roots and the thickness of stably oxidized zones increased as the roots grew. PMID:24866504

  3. Microbial carbon turnover in the plant-rhizosphere-soil continuum

    NASA Astrophysics Data System (ADS)

    Malik, Ashish; Dannert, Helena; Griffiths, Robert; Thomson, Bruce; Gleixner, Gerd

    2014-05-01

    Soil microbial biomass contributes significantly to maintenance of soil organic matter (SOM). It is well known that biochemical fractions of soil microorganisms have varying turnover and therefore contribute differentially to soil C storage. Here we compare the turnover rates of different microbial biochemical fractions using a pulse chase 13CO2 plant labelling experiment. The isotope signal was temporally traced into rhizosphere soil microorganisms using the following biomarkers: DNA, RNA, fatty acids and chloroform fumigation extraction derived microbial biomass size classes. C flow into soil microbial functional groups was assessed through phospholipid and neutral lipid fatty acid (PLFA/NLFA) analyses. Highest 13C enrichment was seen in the low molecular weight (LMW) size class of microbial biomass (Δδ13C =151) and in nucleic acids (DNA: 38o RNA: 66) immediately after the pulse followed by a sharp drop. The amount of 13C in the high molecular weight (HMW) microbial biomass (17-81) and total fatty acids (32-54) was lower initially and stayed relatively steady over the 4 weeks experimental period. We found significant differences in turnover rates of different microbial biochemical and size fractions. We infer that LMW cytosolic soluble compounds are rapidly metabolized and linked to respiratory C fluxes, whereas mid-sized products of microbial degradation and HMW polymeric compounds have lower renewal rate in that order. The turnover of cell wall fatty acids was also very slow. DNA and RNA showed faster turnover rate; and as expected RNA renewal was the fastest due to its rapid production by active microorganisms independent of cell replication. 13C incorporation into different functional groups confirmed that mutualistic arbuscular mycorrhizal fungi rely on root C and are important in the initial plant C flux. We substantiated through measurements of isotope incorporation into bacterial RNA that rhizosphere bacteria are also important in the initial C conduit

  4. Preliminary investigations of the rhizosphere nature of hydroponically grown lettuces

    NASA Astrophysics Data System (ADS)

    Antunes, Inês; Paille, Christel; Lasseur, Christophe

    Due to capabilities of current launchers, future manned exploration beyond the Earth orbit will imply long journeys and extended stays on planet surfaces. For this reason, it is of a great importance to develop a Regenerative Life Support System that enables the crew to be, to a very large extent, metabolic consumables self-sufficient. In this context, the European Space Agency, associated with a scientific and engineering con-sortium, initiated in 1989 the Micro-Ecological Life Support System Alternative (MELiSSA) project. This concept, inspired on a terrestrial ecosystem (i.e. a lake), comprises five intercon-nected compartments inhabited by micro-organisms and higher-plants aiming to produce food, fresh water, and oxygen from organic waste, carbon dioxide, and minerals. Given the important role of the higher-plant compartment for the consumption of carbon dioxide and the production of oxygen, potable water, and food, it was decided to study the microbial communities present in the root zone of the plants (i.e. the rhizosphere), and their synergistic and antagonistic influences in the plant growth. This understanding is important for later investigations concerning the technology involved in the higher plant compartment, since the final goal is to integrate this compartment inside the MELiSSA loop and to guarantee a healthy and controlled environment for the plants to grow under reduced-gravity conditions. To perform a preliminary assessment of the microbial populations of the root zone, lettuces were grown in a hydroponic system and their growth was characterized in terms of nutrient uptake, plant diameter, and plant wet and dry weights. In parallel, the microbial population, bacteria and fungi, present in the hydroponic medium and also inside and outside the roots were analyzed in terms of quantity and nature. The goal of this presentation is to give a preliminary review in the plant root zone of the micro-organisms communities and as well their proportions

  5. Distributions and compositions of old and emerging flame retardants in the rhizosphere and non-rhizosphere soil in an e-waste contaminated area of South China.

    PubMed

    Wang, Shaorui; Wang, Yan; Song, Mengke; Luo, Chunling; Li, Jun; Zhang, Gan

    2016-01-01

    We investigated rhizosphere effects on the distributions and compositions of polybrominated diphenyl ethers (PBDEs), novel brominated flame retardants (NBFRs), and dechlorane plus (DPs) in rhizosphere soils (RS) and non-rhizosphere soils (NRS) in an e-waste recycling area in South China. The concentrations of PBDEs, NBFRs, and DPs ranged from 13.9 to 351, 11.6 to 70.8, and 0.64 to 8.74 ng g(-1) in RS and 7.56 to 127, 8.98 to 144, and 0.38 to 8.45 ng g(-1) in NRS, respectively. BDE-209 and DBDPE were the dominant congeners of PBDEs and NBFRs, respectively. PBDEs, NBFRs, and DPs were more enriched in RS than NRS in most vegetables species. Further analysis suggested that the differentiation of the rhizosphere effect on halogenated flame retardants (HFRs) was not solely controlled by the octanol-water coefficients. This difference was also reflected by the correlations between total organic carbon (TOC) and PBDEs, NBFRs, or DPs, which indicated that organic carbon was a more pivotal controlling factor for PBDEs and DPs than for NBFRs in soil. We also found significant positive correlations between PBDEs and their replacement products, which indicated a similar emission pattern and environmental behaviour.

  6. Response of N₂O emissions to elevated water depth regulation: comparison of rhizosphere versus non-rhizosphere of Phragmites australis in a field-scale study.

    PubMed

    Gu, Xiao-Zhi; Chen, Kai-Ning; Wang, Zhao-de

    2016-03-01

    Emissions of nitrous oxide (N2O) from wetland ecosystems are globally significant and have recently received increased attention. However, relatively few direct studies of these emissions in response to water depth-related changes in sediment ecosystems have been conducted, despite the likely role they play as hotspots of N2O production. We investigated depth-related differential responses of the dissolved inorganic nitrogen distribution in Phragmites australis (Cav.) Trin. ex Steud. rhizosphere versus non-rhizosphere sediments to determine if they accelerated N2O emissions and the release of inorganic nitrogen. Changes in static water depth and P. australis growth both had the potential to disrupt the distribution of porewater dissolved NH4 (+), NO3 (-), and NO2 (-) in profiles, and NO3 (-) had strong surface aggregation tendency and decreased significantly with depth. Conversely, the highest NO2 (-) contents were observed in deep water and the lowest in shallow water in the P. australis rhizosphere. When compared with NO3 (-), NH4 (+), and NO2 (-), fluxes from the rhizosphere were more sensitive to the effects of water depth, and both fluxes increased significantly at a depth of more than 1 m. Similarly, N2O emissions were obviously accelerated with increasing depth, although those from the rhizosphere were more readily controlled by P. australis. Pearson's correlation analysis showed that water depth was significantly related to N2O emission and NO2 (-) fluxes, and N2O emissions were also strongly dependent on NO2 (-) fluxes (r = 0.491, p < 0.05). The results presented herein provide new insights into inorganic nitrogen biogeochemical cycles in freshwater sediment ecosystems.

  7. Ecosystem-level controls on root-rhizosphere respiration.

    PubMed

    Hopkins, Francesca; Gonzalez-Meler, Miquel A; Flower, Charles E; Lynch, Douglas J; Czimczik, Claudia; Tang, Jianwu; Subke, Jens-Arne

    2013-07-01

    Recent advances in the partitioning of autotrophic from heterotrophic respiration processes in soils in conjunction with new high temporal resolution soil respiration data sets offer insights into biotic and environmental controls of respiration. Besides temperature, many emerging controlling factors have not yet been incorporated into ecosystem-scale models. We synthesize recent research that has partitioned soil respiration into its process components to evaluate effects of nitrogen, temperature and photosynthesis on autotrophic flux from soils at the ecosystem level. Despite the widely used temperature dependence of root respiration, gross primary productivity (GPP) can explain most patterns of ecosystem root respiration (and to some extent heterotrophic respiration) at within-season time-scales. Specifically, heterotrophi crespiration is influenced by a seasonally variable supply of recent photosynthetic products in the rhizosphere. The contribution of stored root carbon (C) to root respiratory fluxes also varied seasonally, partially decoupling the proportion of photosynthetic C driving root respiration. In order to reflect recent insights, new hierarchical models, which incorporate root respiration as a primary function of GPP and which respond to environmental variables by modifying Callocation belowground, are needed for better prediction of future ecosystem C sequestration.

  8. 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.

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

    PubMed Central

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

    2015-01-01

    The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective. PMID:26221084

  10. Comparative bioremediation potential of four rhizospheric microbial species against lindane.

    PubMed

    Abhilash, P C; Srivastava, Shubhi; Singh, Nandita

    2011-01-01

    Four microbial species (Kocuria rhizophila, Microbacterium resistens, Staphylococcus equorum and Staphylococcus cohnii subspecies urealyticus) were isolated from the rhizospheric zone of selected plants growing in a lindane contaminated environment and acclimatized in lindane spiked media (5-100 μg mL⁻¹). The isolated species were inoculated with soil containing 5, 50 and 100 mg kg⁻¹ of lindane and incubated at room temperature. Soil samples were collected periodically to evaluate the microbial dissipation kinetics, dissipation rate, residual lindane concentration and microbial biomass carbon (MBC). There was a marked difference (p < 0.05) in the MBC content and lindane dissipation rate of microbial isolates cultured in three different lindane concentrations. Further, the dissipation rate tended to decrease with increasing lindane concentrations. After 45 d, the residual lindane concentrations in three different spiked soils were reduced to 0%, 41% and 33%, respectively. Among the four species, S. cohnii subspecies urealyticus exhibited maximum dissipation (41.65 mg kg⁻¹) and can be exploited for the in situ remediation of low to medium level lindane contaminated soils.

  11. 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.

  12. 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

  13. Peudomonas fluorescens diversity and abundance in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Amina, Melinai; Ahmed, Bensoltane; Khaladi, Mederbel

    2010-05-01

    It is now over 30 years since that a several plant associated strains of fluorescent Pseudomonas spp. are known to produce antimicrobial metabolites, playing a significant role in the biological control of a lot of plant diseases. For that, the interest in the use of these bacteria for biocontrol of plant pathogenic agents has increased. However, few comprehensive studies have described the abundance of this soil borne bacteria in the region of Mascara (Northern-Algerian West). In the connection of this problem, this work was done by monitoring the number of indigenous Pseudomonas fluorescens organisms in three stations characterizing different ecosystems, to document their abundance, diversity and investigate the relationship between P. fluorescens abundance and soil properties. Our quantitative plate counting results hence the conception of their ecology in the rhizosphere. Thus, quantitative results has confirmed that P. fluorescens are successful root colonizers with strong predominance and competed for many ecological niche, where their distribution were correlated significantly (P<0.05) with the majority of soil properties. Keywords: P. Fluorescens, Ecosystems, Abundance, Diversity, Correlated, Soil Properties.

  14. 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

  15. 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

  16. Phenanthrene-degrader community dynamics in rhizosphere soil from a common annual grass

    SciTech Connect

    Miya, R.K.; Firestone, M.K.

    2000-04-01

    Enhanced rates of phenanthrene biodegradation were observed in rhizosphere soils planted with slender oat (Avena barbata Pott ex Link) compared with unplanted bulk soil controls. Soil microbial populations were characterized using a modified most probable number (MPN) method to determine quantitative shifts in heterotrophic and phenanthrene degrader communities while principal component analysis (PCA) of fatty acid methyl ester (FAME) data from isolated phenanthrene degraders was used to identify qualitative differences and degrader community diversity. The average heterotrophic bacterial population over time was about three times larger in rhizosphere soil than in bulk soil while phenanthrene degrading populations increased by as much as an order of magnitude between 24 and 28 days after planting (DAP). Thus, phenanthrene degraders were selectively enriched in rhizosphere soil compared with bulk soil. The greatest selection for degraders occurred during the later stages of plant development from 24 to 32 DAP. A PCA plot of the FAME data from phenanthrene degrader isolates indicated that the rhizosphere degraders were less diverse than bulk soil degraders. These results give some insight into the mechanisms responsible for enhanced biodegradation and selective degrader enrichment in Rhizosphere soils.

  17. [Effects of different organic fertilizers on the microbes in rhizospheric soil of flue-cured tobacco].

    PubMed

    Zhang, Yun-Wei; Xu, Zhi; Tang, Li; Li, Yan-Hong; Song, Jian-Qun; Xu, Jian-Qin

    2013-09-01

    A field experiment was conducted to study the effects of applying different organic fertilizers (refined organic fertilizer and bio-organic fertilizer) and their combination with 20% reduced chemical fertilizers on the microbes in rhizospheric soil of flue-cured tobacco, the resistance of the tobacco against bacterial wilt, and the tobacco yield and quality. As compared with conventional chemical fertilization (CK), applying refined organic fertilizer (ROF) or bio-organic fertilizer (BIO) in combining with 20% reduced chemical fertilization increased the bacterial number and the total microbial number in the rhizospheric soil significantly. Applying BIO in combining with 20% reduced chemical fertilization also increased the actinomyces number in the rhizospheric soil significantly, with an increment of 44.3% as compared with that under the application of ROF in combining with 20% reduced chemical fertilization, but decreased the fungal number. As compared with CK, the ROF and BIO increased the carbon use capacity of rhizospheric microbes significantly, and the BIO also increased the capacity of rhizospheric microbes in using phenols significantly. Under the application of ROF and BIO, the disease incidence and the disease index of bacterial wilt were decreased by 4% and 8%, and 23% and 15.9%, and the proportions of high grade tobacco leaves increased significantly by 10.5% and 9.7%, respectively, as compared with those in CK. BIO increased the tobacco yield and its output value by 17.1% and 18.9% , respectively, as compared with ROF.

  18. [Effects of Chinese onion' s root exudates on cucumber seedlings growth and rhizosphere soil microorganisms].

    PubMed

    Yang, Yang; Liu, Shou-wei; Pan, Kai; Wu, Feng-zhi

    2013-04-01

    Taking the Chinese onion cultivars with different allelopathy potentials as the donor and cucumber as the accepter, this paper studied the effects of Chinese onion' s root exudates on the seedlings growth of cucumber and the culturable microbial number and bacterial community structure in the seedlings rhizosphere soil. The root exudates of the Chinese onion cultivars could promote the growth of cucumber seedlings, and the stimulatory effect increased with the increasing concentration of the root exudates. However, at the same concentrations of root exudates, the stimulatory effect had no significant differences between the Chinese onion cultivars with strong and weak allelopathy potential. The root exudates of the Chinese onion cultivars increased the individual numbers of bacteria and actinomyces but decreased those of fungi and Fusarium in rhizosphere soil, being more significant for the Chinese onion cultivar with high allelopathy potential (L-06). The root exudates of the Chinese onion cultivars also increased the bacterial community diversity in rhizosphere soil. The cloning and sequencing results indicated that the differential bacteria bands were affiliated with Actinobacteria, Proteobacteria, and Anaerolineaceae, and Anaerolineaceae only occurred in the rhizosphere soil in the treatment of high allelopathy potential Chinese onion (L-06). It was suggested that high concentration (10 mL per plant) of root exudates from high allelopathy potential Chinese onion (L-06) could benefit the increase of bacterial community diversity in cucumber seedlings rhizosphere soil.

  19. Rhizosphere bacteriome of the medicinal plant Sapindus saponaria L. revealed by pyrosequencing.

    PubMed

    Garcia, A; Polonio, J C; Polli, A D; Santos, C M; Rhoden, S A; Quecine, M C; Azevedo, J L; Pamphile, J A

    2016-11-03

    Sapindus saponaria L. of Sapindaceae family is popularly known as soldier soap and is found in Central and South America. A study of such medicinal plants might reveal a more complex diversity of microorganisms as compared to non-medicinal plants, considering their metabolic potential and the chemical communication between their natural microbiota. Rhizosphere is a highly diverse microbial habitat with respect to both the diversity of species and the size of the community. Rhizosphere bacteriome associated with medicinal plant S. saponaria is still poorly known. The objective of this study was to assess the rhizosphere microbiome of the medicinal plant S. saponaria using pyrosequencing, a culture-independent approach that is increasingly being used to estimate the number of bacterial species present in different environments. In their rhizosphere microbiome, 26 phyla were identified from 5089 sequences of 16S rRNA gene, with a predominance of Actinobacteria (33.54%), Acidobacteria (22.62%), and Proteobacteria (24.72%). The rarefaction curve showed a linear increase, with 2660 operational taxonomic units at 3% distance sequence dissimilarity, indicating that the rhizosphere microbiome associated with S. saponaria was highly diverse with groups of bacteria important for soil management, which could be further exploited for agricultural and biotechnological purposes.

  20. A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

    PubMed

    Shang, Shuanghua; Yi, Yanli

    2015-12-01

    The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

  1. Impact of the lavender rhizosphere on the mercury uptake in field conditions.

    PubMed

    Sierra, M J; Rodríguez-Alonso, J; Millán, R

    2012-11-01

    Lavender plants as well as their rhizosphere and bulk soil were sampled on a wide range of soils with different land use within the Almadén mercury mining district. The aim of this work is to evaluate the role of the rhizosphere on mercury behavior in soil-lavender plant system including chemometric analysis. The edaphic parameters that significantly differed between lavender rhizosphere and bulk soil were: total Hg; easily available Hg; electrical conductivity; organic matter; cation exchange capacity; soluble ions (Cl(-); SO(4)(2-); PO(4)(3-); NO(3)(-); Al(+); Mn(2+); Ca(2+) and Mg(2+)). The most important variable in the differentiation is electrical conductivity. Furthermore, both organic matter and Mn(2+) in rhizosphere soil seem to block Hg availability to plant. However, the presence of sulfates seems to favor it. Regarding other relationships, Hg seems to block Pb uptake by lavender plants and, on the other hand, the presence of Mn(2+) seems to favor it. Furthermore, Hg root uptake by lavender and its distribution throughout the plant have been studied. The more available Hg in rhizosphere soil, the more Hg is translocated to aerial part and less Hg is retained by root. In all cases, the Hg concentration in the root was higher than in the aerial part.

  2. 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.

  3. Rhizosphere Bacteria Enhance Selenium Accumulation and Volatilization by Indian Mustard1

    PubMed Central

    de Souza, Mark P.; Chu, Dara; Zhao, May; Zayed, Adel M.; Ruzin, Steven E.; Schichnes, Denise; Terry, Norman

    1999-01-01

    Indian mustard (Brassica juncea L.) accumulates high tissue Se concentrations and volatilizes Se in relatively nontoxic forms, such as dimethylselenide. This study showed that the presence of bacteria in the rhizosphere of Indian mustard was necessary to achieve the best rates of plant Se accumulation and volatilization of selenate. Experiments with the antibiotic ampicillin showed that bacteria facilitated 35% of plant Se volatilization and 70% of plant tissue accumulation. These results were confirmed by inoculating axenic plants with rhizosphere bacteria. Compared with axenic controls, plants inoculated with rhizosphere bacteria had 5-fold higher Se concentrations in roots (the site of volatilization) and 4-fold higher rates of Se volatilization. Plants with bacteria contained a heat-labile compound in their root exudate; when this compound was added to the rhizosphere of axenic plants, Se accumulation in plant tissues increased. Plants with bacteria had an increased root surface area compared with axenic plants; the increased area was unlikely to have caused their increased tissue Se accumulation because they did not accumulate more Se when supplied with selenite or selenomethionine. Rhizosphere bacteria also possibly increased plant Se volatilization because they enabled plants to overcome a rate-limiting step in the Se volatilization pathway, i.e. Se accumulation in plant tissues. PMID:9952452

  4. Rhizosphere effect of Scirpus triqueter on soil microbial structure during phytoremediation of diesel-contaminated wetland.

    PubMed

    Wei, Jing; Liu, Xiaoyan; Zhang, Xinying; Chen, Xueping; Liu, Shanshan; Chen, Lisha

    2014-01-01

    Though phytoremediation has been widely used to restore various contaminated sites, it is still unclear how soil microbial communities respond microecologically to plants and pollutants during the process. In this paper, batch microcosms imitating in situ phytoremediation of petroleum-contaminated wetland by Scirpus triqueter were set up to monitor the influence of plant rhizosphere effect on soil microbes. Palmitic acid, one of the main root exudates of S. triqueter, was added to strengthen rhizosphere effect. Abundances of certain microbial subgroups were quantified by phospholipid fatty acid profiles. Results showed that diesel removal extents were significantly higher in the rhizosphere (57.6 +/-4.2-65.5 +/- 6.9%) than those in bulk soil (27.8 +/-6.5-36.3 +/- 3.2%). In addition, abundances of saturated, monounsaturated, and polyunsaturated fatty acids were significantly higher (P < 0.05) in planted soil than those in the bulk soil. When it was less than 15,000 mg diesel kg soil-1, increasing diesel concentration led to higher abundances of fungi, Gram-positive and Gram-negative bacteria. The addition of palmitic acid amplified the rhizosphere effect on soil microbial populations and diesel removal. Principal component analysis revealed that plant rhizosphere effect was the dominant factor affecting microbial structure. These results provided new insights into plant-microbe-pollutant coactions responsible for diesel degradation, and they were valuable to facilitate phytoremediation of diesel contamination in wetland habitats.

  5. Root growth and exudate production define the frequency of horizontal plasmid transfer in the Rhizosphere.

    PubMed

    Mølbak, Lars; Molin, Søren; Kroer, Niels

    2007-01-01

    To identify the main drivers of plasmid transfer in the rhizosphere, conjugal transfer was studied in the rhizospheres of pea and barley. The donor Pseudomonas putida KT2442, containing plasmid pKJK5::gfp, was coated onto the seeds, while the recipient P. putida LM24, having a chromosomal insertion of dsRed, was inoculated into the growth medium. Mean transconjugant-to-donor ratios in vermiculite were 4.0+/-0.8 x 10(-2) in the pea and 5.9+/-1.4 x 10(-3) in the barley rhizospheres. In soil, transfer ratios were about 10 times lower. As a result of a 2-times higher root exudation rate in pea, donor densities in pea (1 x 10(6)-2 x 10(9) CFU g(-1) root) were about 10 times higher than in barley. No difference in recipient densities was observed. In situ visualization of single cells on the rhizoplane and macroscopic visualization of the colonization pattern showed that donors and transconjugants were ubiquitously distributed in the pea rhizosphere, while they were only located on the upper parts of the barley roots. Because the barley root elongated about 10 times faster than the pea root, donors were probably outgrown by the elongating barley root. Thus by affecting the cell density and distribution, exudation and root growth appear to be key parameters controlling plasmid transfer in the rhizosphere.

  6. Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice.

    PubMed

    Chen, Si; Li, Xingxing; Lavoie, Michel; Jin, Yujian; Xu, Jiahui; Fu, Zhengwei; Qian, Haifeng

    2017-01-01

    Diclofop-methyl (DM), a widely used herbicide in food crops, may partly contaminate the soil surface of natural ecosystems in agricultural area and exert toxic effects at low dose to nontarget plants. Even though rhizosphere microorganisms strongly interact with root cells, little is known regarding their potential modulating effect on herbicide toxicity in plants. Here we exposed rice seedlings (Xiushui 63) to 100μg/L DM for 2 to 8days and studied the effects of DM on rice rhizosphere microorganisms, rice systemic acquired resistance (SAR) and rice-microorganisms interactions. The results of metagenomic 16S rDNA Illumina tags show that DM increases bacterial biomass and affects their community structure in the rice rhizosphere. After DM treatment, the relative abundance of the bacterium genera Massilia and Anderseniella increased the most relative to the control. In parallel, malate and oxalate exudation by rice roots increased, potentially acting as a carbon source for several rhizosphere bacteria. Transcriptomic analyses suggest that DM induced SAR in rice seedlings through the salicylic acid (but not the jasmonic acid) signal pathway. This response to DM stress conferred resistance to infection by a pathogenic bacterium, but was not influenced by the presence of bacteria in the rhizosphere since SAR transcripts did not change significantly in xenic and axenic plant roots exposed to DM. The present study provides new insights on the response of rice and its associated microorganisms to DM stress.

  7. Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico.

    PubMed

    Aguirre-Garrido, J Félix; Montiel-Lugo, Daniel; Hernández-Rodríguez, César; Torres-Cortes, Gloria; Millán, Vicenta; Toro, Nicolás; Martínez-Abarca, Francisco; Ramírez-Saad, Hugo C

    2012-05-01

    The nature reserve of Tehuacan-Cuicatlan in central Mexico is known for its diversity and endemism mainly in cactus plants. Although the xerophytic flora is reasonably documented, the bacterial communities associated with these species have been largely neglected. We assessed the diversity and composition of bacterial communities in bulk (non-rhizospheric) soil and the rhizosphere of three cactus plant species: Mammillaria carnea, Opuntia pilifera and Stenocereus stellatus, approached using cultivation and molecular techniques, considering the possible effect of dry and rainy seasons. Cultivation-dependent methods were focused on putative N(2)-fixers and heterotrophic aerobic bacteria, in the two media tested the values obtained for dry season samples grouped together regardless of the sample type (rhizospheric or non-rhizospheric), these groups also included the non-rhizospheric sample for rainy season, on each medium. These CFU values were smaller and significantly different from those obtained on rhizospheric samples from rainy season. Genera composition among isolates of the rhizospheric samples was very similar for each season, the most abundant taxa being α-Proteobacteria, Actinobacteria and Firmicutes. Interestingly, the genus Ochrobactrum was highly represented among rhizospheric samples, when cultured in N-free medium. The structure of the bacterial communities was approached with molecular techniques targeting partial 16S rRNA sequences such as denaturing gradient gel electrophoresis and serial analysis of ribosomal sequence tags. Under these approaches, the most represented bacterial phyla were Actinobacteria, Proteobacteria and Acidobacteria. The first two were also highly represented when using isolation techniques.

  8. 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.

  9. 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.

  10. 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

  11. RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere.

    PubMed

    Mynampati, Kalyan Chakravarthy; Lee, Yong Jian; Wijdeveld, Arjan; Reuben, Sheela; Samavedham, Lakshminarayanan; Kjelleberg, Staffan; Swarup, Sanjay

    2015-12-01

    In aquatic systems, one of the non-destructive ways to quantify toxicity of contaminants to plants is to monitor changes in root exudation patterns. In aquatic conditions, monitoring and quantifying such changes are currently challenging because of dilution of root exudates in water phase and lack of suitable instrumentation to measure them. Exposure to pollutants would not only change the plant exudation, but also affect the microbial communities that surround the root zone, thereby changing the metabolic profiles of the rhizosphere. This study aims at developing a device, the RhizoFlowCell, which can quantify metabolic response of plants, as well as changes in the microbial communities, to give an estimate of the stress to which the rhizosphere is exposed. The usefulness of RhizoFlowCell is demonstrated using naphthalene as a test pollutant. Results show that RhizoFlowCell system is useful in quantifying the dynamic metabolic response of aquatic rhizosphere to determine ecosystem health.

  12. 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.

  13. 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.

  14. 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

  15. Use of Bioluminescence Markers To Detect Pseudomonas spp. in the Rhizosphere

    PubMed Central

    de Weger, Letty A.; Dunbar, Paul; Mahafee, Walter F.; Lugtenberg, Ben J. J.; Sayler, Gary S.

    1991-01-01

    The use of bioluminescence as a sensitive marker for detection of Pseudomonas spp. in the rhizosphere was investigated. Continuous expression of the luxCDABE genes, required for bioluminescence, was not detectable in the rhizosphere. However, when either a naphthalene-inducible luxCDABE construct or a constitutive luxAB construct (coding only for the luciferase) was introduced into the Pseudomonas cells, light emission could be initiated just prior to measurement by the addition of naphthalene or the substrate for luciferase, n-decyl aldehyde, respectively. These Pseudomonas cells could successfully be detected in the rhizosphere by using autophotography or optical fiber light measurement techniques. Detection required the presence of 103 to 104 CFU/cm of root, showing that the bioluminescence technique is at least 1,000-fold more sensitive than β-galactosidase-based systems. Images PMID:16348610

  16. Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere

    PubMed Central

    Paungfoo-Lonhienne, Chanyarat; Yeoh, Yun Kit; Kasinadhuni, Naga Rup Pinaki; Lonhienne, Thierry G. A.; Robinson, Nicole; Hugenholtz, Philip; Ragan, Mark A.; Schmidt, Susanne

    2015-01-01

    Fungi play important roles as decomposers, plant symbionts and pathogens in soils. The structure of fungal communities in the rhizosphere is the result of complex interactions among selection factors that may favour beneficial or detrimental relationships. Using culture-independent fungal community profiling, we have investigated the effects of nitrogen fertilizer dosage on fungal communities in soil and rhizosphere of field-grown sugarcane. The results show that the concentration of nitrogen fertilizer strongly modifies the composition but not the taxon richness of fungal communities in soil and rhizosphere. Increased nitrogen fertilizer dosage has a potential negative impact on carbon cycling in soil and promotes fungal genera with known pathogenic traits, uncovering a negative effect of intensive fertilization. PMID:25728892

  17. Use of bioluminescence markers to detect Pseudomonas spp. in the Rhizosphere

    SciTech Connect

    De Weger, L.A.; Lugtenberg, B.J.J. ); Dunbar, P.; Sayler, G.S. ); Mahafee, W.F. )

    1991-12-01

    The use of bioluminescence as a sensitive marker for detection of Pseudomonas spp. in the rhizosphere was investigated. Continuous expression of the luxCDABE genes, required for bioluminescence, was not detectable in the rhizosphere. However, when either a naphthalene-inducible luxCDABE construct or a constitutive luxAB construct (coding only for the luciferase) was introduced into the Pseudomonas cells, light emission could be initiated just prior to measurement by the addition of naphthalene or the substrate for luciferase, n-decyl aldehyde, respectively. These Pseudomonas cells could successfully be detected in rhizosphere by using autophotography or optical fiber light measurement techniques. Detection required the presence of 10{sup 3} to 10{sup 4} CFU/cm of root, showing that the bioluminescence technique is at least 1,000-fold more sensitive than {beta}-galactosidase-based systems.

  18. 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.

  19. [Fungal population structure and its biological effect in rhizosphere soil of continuously cropped potato].

    PubMed

    Meng, Pin-Pin; Liu, Xing; Qiu, Hui-Zhen; Zhang, Wen-Ming; Zhang, Chun-Hong; Wang, Di; Zhang, Jun-Lian; Shen, Qi-Rong

    2012-11-01

    Continuous cropping obstacle is one of the main restriction factors in potato industry. In order to explore the mechanisms of potato's continuous cropping obstacle and to reduce the impact on potato's tuber yield, a field experiment combined with PCR-DGGE molecular fingerprinting was conducted to investigate the fungal population structure and its biological effect in rhizosphere soil of continuously cropped potato. With the increasing year of potato' s continuous cropping, the numbers of visible bands in rhizosphere fungal DGGE profiles increased obviously. As compared with that of CK (rotation cropping), the operational taxonomic unit (OTU) in treatments of one to five years continuous cropping was increased by 38.5%, 38.5%, 30.8%, 46.2%, and 76.9% respectively, indicating that potato's continuous cropping caused an obvious increase in the individual numbers of dominant fungal populations in rhizosphere soil. Also with the increasing year of potato's continuous cropping, the similarity of the fungal population structure among the treatments had a gradual decrease. The sequencing of the fungal DGGE bands showed that with the increasing year of continuous cropping, the numbers of the potato's rhizosphere soil-borne pathogens Fusarium oxysporum and F. solani increased obviously, while the number of Chaetomium globosum, as a biocontrol species, had a marked decrease in the fifth year of continuous cropping. It was suggested that potato' s continuous cropping caused the pathogen fungal populations become the dominant microbial populations in rhizosphere soil, and the rhizosphere micro-ecological environment deteriorated, which in turn affected the root system, making the root vigor and its absorption area reduced, and ultimately, the tuber yield decreased markedly.

  20. Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics.

    PubMed

    Gomes, Newton C Marcial; Fagbola, Olajire; Costa, Rodrigo; Rumjanek, Norma Gouvea; Buchner, Arno; Mendona-Hagler, Leda; Smalla, Kornelia

    2003-07-01

    The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.

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

    PubMed

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

    2015-07-01

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

  2. 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

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

    PubMed

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

    2016-09-01

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

  4. Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower.

    PubMed

    Wei, Xuexin; Yan, Shouwei; Li, Dai; Pang, Huancheng; Li, Yuyi; Zhang, Jianli

    2015-12-01

    A Gram-stain-negative, non-spore-forming, rod-shaped and aerobic bacterium, designated Xi19T, was isolated from a soil sample collected from the rhizosphere of sunflower (Helianthus annuus) in Wuyuan county of Inner Mongolia, China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate was related to species of the genus Rhizobium, sharing the greatest 16S rRNA gene sequence similarity with Rhizobium rhizoryzae J3-AN59T (98.4 %), followed by Rhizobium pseudoryzae J3-A127T (97.4 %). There were low similarities ( < 91 %) between the atpD, recA and glnII gene sequences of the novel strain and those of members of the genus Rhizobium. DNA-DNA hybridization values between strain Xi19T and the most related strain Rhizobium rhizoryzae J3-AN59T were low. The major cellular fatty acids of strain Xi19T were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. Q-10 was identified as the predominant ubiquinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain Xi19T was 60.2 mol%. On the basis of physiological and biochemical characteristics, coupled with genotypic data obtained in this work, strain Xi19T represents a novel species of the genus Rhizobium, for which the name Rhizobium helianthi is proposed. The type strain is Xi19T ( = CGMCC 1.12192T = KCTC 23879T).

  5. Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere

    PubMed Central

    Tian, Fang; Ding, Yanqin; Zhu, Hui; Yao, Liangtong; Du, Binghai

    2009-01-01

    The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging to six bacterial divisions, namely β-, γ-, α-Proteobacteria, Sphingobacteria, Bacilli, and Actinobacteria. Especially, γ-Proteobacteria consisting of Pseudomonas, Enterobacter, Serratia, Pantoea, Erwinia and Stenotrophomonas genus encountered 18 different ARDRA groups. Results also showed a greater siderophore-producing bacterial diversity than previous researches. For example, Sphingobacterium (isolates G-2-21-1 and G-2-27-2), Pseudomonas poae (isolate G-2-1-1), Enterobacter endosymbiont (isolates G-2-10-2 and N-5-10), Delftia acidovorans (isolate G-1-15), and Achromobacter xylosoxidans (isolates N-46-11HH and N-5-20) were reported to be able to produce siderophores under low-iron conditions for the first time. Gram-negative isolates were more frequently encountered, with more than 95% total frequency. For Gram-positive bacteria, the Bacillus and Rhodococcus were the only two genera, with 1.7% total frequency. Furthermore, the Pseudomonas and Enterobacter were dominant in this environment, with 44.5% and 24.7% total frequency, respectively. It was also found that 75 percent of the isolates that had the high percentages of siderophore units (% between 40 and 60) belonged to Pseudomonas. Pseudomonas sp. G-229-21 screened out in this study may have potential to apply to low-iron soil to prevent plant soil-borne fungal pathogen diseases. PMID:24031358

  6. Biological control of potato black scurf by rhizosphere associated bacteria

    PubMed Central

    Tariq, Mohsin; Yasmin, Sumera; Hafeez, Fauzia Y.

    2010-01-01

    The present work was carried out to study the potential of plant rhizosphere associated bacteria for the biocontrol of potato black scurf disease caused by Rhizoctonia solani Khun AG-3. A total of twenty-eight bacteria isolated from diseased and healthy potato plants grown in the soil of Naran and Faisalabad, Pakistan were evaluated for their antagonistic potential. Nine bacterial strains were found to be antagonistic in vitro, reduced the fungal growth and caused the lysis of sclerotia of R. solani in dual culture assay as well as in extracellular metabolite efficacy test. The selected antagonistic strains were further tested for the production and efficacy of volatile and diffusible antibiotics, lytic enzymes and siderophores against R. solani. Selected antagonistic bacteria were also characterized for growth promoting attributes i.e., phosphate solubilization, nitrogen fixation and indole acetic acid production. Biocontrol efficacy and percent yield increase by these antagonists was estimated in greenhouse experiment. Statistical analysis showed that two Pseudomonas spp. StT2 and StS3 were the most effective with 65.1 and 73.9 percent biocontrol efficacy, as well as 87.3 and 98.3 percent yield increase, respectively. Potential antagonistic bacterial strain StS3 showed maximum homology to Pseudomonas sp. as determined by 16S rRNA gene sequencing. These results suggest that bacterial isolates StS3 and StT2 have excellent potential to be used as effective biocontrol agents promoting plant growth with reduced disease incidence. PMID:24031515

  7. Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.

    PubMed

    Zhang, Xiao-Xia; Gao, Ju-Sheng; Zhang, Lei; Zhang, Cai-Wen; Ma, Xiao-Tong; Zhang, Jun

    2016-09-01

    The taxonomy of strain 1DS3-10T, a Gram-staining-positive, endospore-forming bacterium isolated from rice rhizosphere, was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel strain was grouped with established members of the genus Bacillus and appeared to be closely related to the type strains Bacillus benzoevorans DSM 5391T (97.9 %), Bacillus circulans DSM 11T (97.7 %), Bacillus novalis JCM 21709T (97.3 %), Bacillus soli JCM 21710T (97.3 %), Bacillus oceanisediminis CGMCC 1.10115T (97.3 %) and BacillusnealsoniiFO-92T (97.1 %). The fatty acid profile of strain 1DS3-10T, which showed a predominance of iso-C15 : 0 and anteiso-C15 : 0, supported the allocation of the strain to the genus Bacillus. The predominant menaquinone was MK-7 (100 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminolipids. Cell-wall peptidoglycan contained meso-diaminopimelic acid. DNA-DNA hybridization values between strain 1DS3-10T and the type strains of closely related species were 25-33 %, which supported that 1DS3-10T represented a novel species in the genus Bacillus. The results of some physiological and biochemical tests also allowed the phenotypic differentiation of strain 1DS3-10T from the most closely related recognized species. On the basis of the phylogenetic and phenotypic evidence, strain 1DS3-10T represents a novel species of the genus Bacillus, for which the name Bacillus oryzisoli sp. nov. is proposed. The type strain of the novel species is 1DS3-10T (=ACCC 19781T=DSM 29761T).

  8. Aquatic Plant Control Research Program: The Rhizosphere Microbiology of Rooted Aquatic Plants.

    DTIC Science & Technology

    1988-04-01

    AD-A94 93 *T: I ZSH~z:UI inI UNCASIFI H4.5fo’AOC) I’l W4,F/G 8/1 HL IWE. ,.n~SP1.4 AQUATIC PLANT CONTROLFILE C ~~RESEARCH PROGRAM US~ ~ AryCop of...Egns MISCELLANEOUS PAPER A-88-4 THE RHIZOSPHERE MICROBIOLOGY OF ROOTED AQUATIC PLANTS A 4 &L-Aby MA) Douglas Gunnison, John W. Barko o ~ ’.Environmental...Washington, DC 20314-1000 ELEMENT NO NO NO ACCESSION NO 11 TITLE (Include Security Classification) The Rhizosphere Microbiology of Rooted Aquatic Plants

  9. Rewetting Rate of Dry Rhizosphere Limited by Mucilage Viscosity and Mucilage Hydrophobicity

    NASA Astrophysics Data System (ADS)

    Reeder, S.; Zarebanadkouki, M.; Kroener, E.; Ahmed, M. A.; Carminati, A.; Kostka, S.

    2014-12-01

    During root water uptake from dry soils, the highly nonlinear relation between hydraulic conductivity and water content as well as the radial root geometry result in steep water potential gradients close to the root surface. The hydraulic properties of the rhizosphere - the interface between root and soil - are one of the most important and least understood components in controlling root water uptake. Previous research using young lupine plants revealed that after irrigation it took 1-2 days for the water content of the dry rhizosphere to increase. How can this delay be explained? Our hypotheses: a) mucilage - a polymeric plant exudate - alters rhizosphere hydraulic properties, b) its hydrophobic moieties make the rhizosphere water repellent when dry, c) mucilage is a highly viscous, gelatinous material, the dryer it gets the more viscous it becomes, d) mucilage viscosity reduces rhizosphere hydraulic conductivity. To test our hypotheses we used mucilage extracted from chia seed as an analogue for root mucilage. We measured: 1) the contact angle between water and pure dry and wet mucilage, dry soil treated with various concentrations of mucilage, 2) mucilage viscosity as function of concentration and shear rate, 3) saturated hydraulic conductivity as function of mucilage concentration, 4) swelling of dry mucilage in water. Finally, to mimic flow of water across the rhizosphere, we measured the capillary rise in soils treated with different mucilage concentrations. The results showed that: 1) dry mucilage has a contact angle >90° while it loses its water repellency when it gets wet, 2) viscosity and saturated hydraulic conductivity can change several orders of magnitude with a small change in mucilage concentration, 3) 1g of dry mucilage absorbs 300g water in its fully swollen state, 4) the swelling rate of mucilage showed an exponential behavior with half time of 5 hours. Capillary rise became slower in soils with higher mucilage concentration, while the final

  10. Rewetting Rate of Dry Rhizosphere Limited by Mucilage Viscosity and Mucilage Hydrophobicity

    NASA Astrophysics Data System (ADS)

    Reeder, Stacey; Zarebanadkouki, Mohsen; Kroener, Eva; Ahmed, Mutez Ali; Carminati, Andrea; Kostka, Stanley

    2015-04-01

    During root water uptake from dry soils, the highly nonlinear relation between hydraulic conductivity and water content as well as the radial root geometry result in steep water potential gradients close to the root surface. The hydraulic properties of the rhizosphere - the interface between root and soil - are one of the most important and least understood components in controlling root water uptake. Previous research using young lupine plants revealed that after irrigation it took 1-2 days for the water content of the dry rhizosphere to increase. How can this delay be explained? Our hypotheses are that: a) mucilage - a polymeric plant exudate - alters rhizosphere hydraulic properties, b) its hydrophobic moieties make the rhizosphere water repellent when dry, c) mucilage is a highly viscous, gelatinous material, the dryer it gets the more viscous it becomes, d) mucilage viscosity reduces rhizosphere hydraulic conductivity. To test our hypotheses we used mucilage extracted from chia seed as an analogue for root mucilage. We measured: 1) the contact angle between water and pure dry and wet mucilage, dry soil treated with various concentrations of mucilage, 2) mucilage viscosity as function of concentration and shear rate, 3) saturated hydraulic conductivity as function of mucilage concentration, 4) swelling of dry mucilage in water. Finally, to mimic flow of water across the rhizosphere, we measured the capillary rise in soils treated with different mucilage concentrations. The results showed that: 1) dry mucilage has a contact angle > 90° while it loses its water repellency when it gets wet, 2) viscosity and saturated hydraulic conductivity can change several orders of magnitude with a small change in mucilage concentration, 3) 1g of dry mucilage absorbs 300g water in its fully swollen state, 4) the swelling rate of mucilage showed an exponential behavior with half time of 5 hours. Capillary rise became slower in soils with higher mucilage concentration, while the

  11. Legumes increase rhizosphere carbon and nitrogen relative to cereals in California agricultural plots

    NASA Astrophysics Data System (ADS)

    Bergman, R.; Maltais-landry, G.

    2013-12-01

    Nitrogen (N) is an essential nutrient to plant growth, therefore a sufficient supply is needed for high yields. By using N-fixing plants like legumes in crop rotation, we can increase soil N and yields of following crops. Furthermore, legumes also affect soil carbon (C) and C:N ratios, which impacts nutrient cycling in soils. We assessed the effects of two legumes (vetch, fava bean) and a cereal mixture (oats and wheat) on soil N and C by comparing both rhizosphere and bulk soils. We studied the impacts of these plants with different management types (organic, low-input conventional, unfertilized) to see if plant effects on soil C and N changed across management. We used plots from the Long-Term Research on Agricultural Systems (LTRAS) experiment (Davis, CA) to conduct this experiment, where three plots were under each management type. Within each of these plots, we sampled three micro-plots, where we collected rhizosphere soil from fava bean, vetch, and cereals as well as bulk soil, i.e. non-rhizosphere soil. We collected 108 samples, each of which were dried and ball-milled into a fine, uniform powder. Tin capsules with 15-30mg of soil were then analyzed with a Carlo Erba Elemental analyzer to measure how much N and C was present in each of the samples. The different management types didn't affect the relationship among plants, but soil C and N were highest in organic and lowest in unfertilized plots. We found that N was significantly higher in legume rhizosphere than cereal rhizosphere and bulk soils. Soil C was also higher in legumes vs. cereals and bulk soils, but the only significant difference was with the bulk soils. This ultimately resulted in lower C:N ratios in the rhizosphere of legumes, only vetch, however, had significantly lower soil C:N than cereals. Vetch had higher N, and lower C and C:N than fava bean, but the difference between the two legumes was never significant. Similarly, cereals had higher C and N and lower C:N than bulk soils, although

  12. [Effect of reed rhizosphere on nitrogen and COD removal efficiency in subsurface flow constructed wetlands].

    PubMed

    Dai, Yuan-yuan; Yang, Xin-ping; Zhou, Li-xiang

    2008-12-01

    Nitrogen removal efficiency was investigated in three subsurface flow constructed wetlands (CWs) with and without reed. Root bag made of nylon sieve with 300 mesh was used to enwrap the reed root in one of reed CWs to distinguish reed rhizosphere from non-rhizosphere. The CWs with root bag enwrapped reed root (hereinafter called as mesh CWs) and other CWs were fed with artificial ammonium-rich wastewater. The results indicated that the COD and N removal occurred mainly in the front of CWs, and C and nitrogen removal occurred concurrently along the stream way. When C/N ratio of influent was 5, the removal efficiencies of NH4+ -N in control CWs, reed CWs and mesh CWs were 66.2%, 94.2% and 82.2%, respectively. TN removal efficiencies were 67.2%, 90.7% and 76.1% respectively. Simultaneous nitrification and denitrification phenomenon in this study was also observed. The removal efficiency of organic carbon was different from nitrogen removal efficiency, mesh CWs showed the highest COD removal efficiency with 80.9%, while control CWs and reed CWs were 72.2% and 56.2%, respectively. C/N ratio of wastewater throughout the bed was more than 5 in three CWs, which indicated carbon source supply was enough for denitrification. The oxidation-reduction position (ORP) and concentration of total organic carbon in rhizosphere and non-rhizosphere were detected. The ORP in the front of mesh CWs's rhizosphere was much higher than that in control CWs and non-rhizosphere in mesh CWs, which were 11-311 mV and 62-261 mV, respectively. Root exudates also showed the difference between rhizosphere and non-rhizosphere in mesh CWs, the TOC of them were 21.3-54.6 mg x L(-1) and 6.65-12.0 mg x L(-1). Due to the higher ORP and concentration of TOC, the nitrogen removal efficiency in plant CWs was much higher than that in control CWs.

  13. Effect of soil water content on spatial distribution of root exudates and mucilage in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Holz, Maire; Zarebanadkouki, Mohsen; Kuzyakov, Yakov; Carminati, Andrea

    2016-04-01

    Water and nutrients are expected to become the major factors limiting food production. Plant roots employ various mechanisms to increase the access to these limited soil resources. Low molecular root exudates released into the rhizosphere increase nutrient availability, while mucilage improves water availability under low moisture conditions. However, studies on the spatial distribution and quantification of exudates in soil are scarce. Our aim was therefore to quantify and visualize root exudates and mucilage distribution around growing roots using neutron radiography and 14C imaging at different levels of water stress. Maize plants were grown in rhizotrons filled with a silty soil and were exposed to varying soil conditions, from optimal to dry. Mucilage distribution around the roots was estimated from the profiles of water content in the rhizosphere - note that mucilage increases the soil water content. The profiles of water content around different root types and root ages were measured with neutron radiography. Rhizosphere extension was approx. 0.7 mm and did not differ between wet and dry treatments. However, water content (i.e. mucilage concentration) in the rhizosphere of plants grown in dry soils was higher than for plants grown under optimal conditions. This effect was particularly pronounced near the tips of lateral roots. The higher water contents near the root are explained as the water retained by mucilage. 14C imaging of root after 14CO2 labeling of shoots (Pausch and Kuzyakov 2011) was used to estimate the distribution of all rhizodeposits. Two days after labelling, 14C distribution was measured using phosphor-imaging. To quantify 14C in the rhizosphere a calibration was carried out by adding given amounts of 14C-glucose to soil. Plants grown in wet soil transported a higher percentage of 14C to the roots (14Croot/14Cshoot), compared to plants grown under dry conditions (46 vs. 36 %). However, the percentage of 14C allocated from roots to

  14. Rhizosphere selection of Pseudomonas putida KT2440 variants with increased fitness associated to changes in gene expression.

    PubMed

    Quesada, José Miguel; Fernández, Matilde; Soriano, María Isabel; Barrientos-Moreno, Laura; Llamas, María Antonia; Espinosa-Urgel, Manuel

    2016-08-03

    As the interface between plant roots and soil, the rhizosphere is a complex environment where nutrients released by the plant promote microbial growth. Increasing evidences indicate that the plant also exerts a selective pressure on microbial populations in the rhizosphere, favouring colonization by certain groups. In this work, we have designed an experimental setup to begin analysing the evolution of a specific bacterial population in the rhizosphere, using Pseudomonas putida KT2440 as model organism. After several rounds of selection without passage through laboratory growth conditions, derivatives of this strain with increased fitness in the rhizosphere were isolated. Detailed analysis of one of these clones indicated that this effect is specific for rhizosphere conditions and derives from changes in its transcriptional profile in this environment, with 43 genes being differentially expressed with respect to the parental strain. Several of these genes belong to functional categories which could affect stress adaptation and availability of particular nutrients. By inactivating two genes identified as upregulated in the selected clone (coding for a stress-response protein and a rRNA modifying protein), these functions were shown to contribute to rhizosphere fitness. Our data also suggest the existence of different evolutionary pathways leading to increased rhizosphere fitness.

  15. 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.

  16. Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants.

    PubMed

    Marques, Joana M; da Silva, Thais F; Vollu, Renata E; Blank, Arie F; Ding, Guo-Chun; Seldin, Lucy; Smalla, Kornelia

    2014-05-01

    The hypothesis that sweet potato genotypes containing different starch yields in their tuberous roots can affect the bacterial communities present in the rhizosphere (soil adhering to tubers) was tested in this study. Tuberous roots of field-grown sweet potato of genotypes IPB-149 (commercial genotype), IPB-052, and IPB-137 were sampled three and six months after planting and analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analysis of 16S rRNA genes PCR-amplified from total community DNA. The statistical analysis of the DGGE fingerprints showed that both plant age and genotypes influenced the bacterial community structure in the tuber rhizosphere. Pyrosequencing analysis showed that the IPB-149 and IPB-052 (both with high starch content) displayed similar bacterial composition in the tuber rhizosphere, while IPB-137 with the lowest starch content was distinct. In comparison with bulk soil, higher 16S rRNA gene copy numbers (qPCR) and numerous genera with significantly increased abundance in the tuber rhizosphere of IPB-137 (Sphingobium, Pseudomonas, Acinetobacter, Stenotrophomonas, Chryseobacterium) indicated a stronger rhizosphere effect. The genus Bacillus was strongly enriched in the tuber rhizosphere samples of all sweet potato genotypes studied, while other genera showed a plant genotype-dependent abundance. This is the first report on the molecular identification of bacteria being associated with the tuber rhizosphere of different sweet potato genotypes.

  17. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

    NASA Astrophysics Data System (ADS)

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-04-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

  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. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

    PubMed Central

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-01-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere. PMID:27080869

  20. [Responses of microbes in rhizospheric soil of Abies faxoniana to elevated atmospheric CO2 concentration and temperature].

    PubMed

    Xiao, Ling; Wang, Kaiyun; Zhang, Yuanbin; Wu, Fuzhong; Lu, Yejiang

    2006-05-01

    With independent and top-enclosed chamber system, this paper studied the responses of culturable bacteria, fungi, and actinomycetes in rhizospheric soil of Abies faxoniana sapling to elevated atmospheric CO2 concentration (ambient +350( +/- 25) [micromol x mol(-1), EC), temperature (ambient + 2. 2 (+/- 0.5) degrees C; ET), and their combination (ECT) under high-frigid conditions of West Sichuan Province. The results showed that in comparing with the control, treatments EC and ET increased the number of rhizospheric bacteria by 35%, 164% and 312%, and 30%, 115% and 209% in June, August and October, respectively, but had little effects on the numbers of rhizospheric actinomycetes and fungi. In treatment ECT, the numbers of rhizospheric actinomycetes and fungi increased by 49%, 50% and 96% ,and 151%, 57% and 48% in June, August and October, respectively, while that of rhizospheric bacteria had little variation. EC, ET and ECT had significant effects on the total number of rhizospheric microbes, with the R/S being 1.93,1.27 and 1.46, respectively,but had little effects on non-rhizospheric microbes.

  1. 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.

  2. 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.

  3. 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

  4. Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.

    PubMed

    Kim, Dong Hyun; Singh, Priyanka; Farh, Mohamed El-Agamy; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Lee, Hyun A; Yang, Deok-Chun

    2016-09-01

    A novel bacterial strain, designated DCY106(T), was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY106(T) is Gram-negative, yellow-pigmented, non-flagellate, motile, non-spore-forming, rod-shaped, and strictly aerobic. The strain grows optimally at 25-30 °C and pH 6.5-7.5. Phylogenetically, strain DCY106(T) is closely related to Flavobacterium arsenitoxidans KCTC 22507(T) (98.41 %), followed by Flavobacterium cutihirudini LMG 26922(T) (97.67 %), Flavobacterium nitrogenifigens LMG 28694(T) (97.59 %), Flexibacter auranticus LMG 3987(T) (97.38 %), Flavobacterium defluvi KCTC 12612(T) (97.21 %) and Flavobacterium chilense LMG 26360(T) (97.05 %). The 16S rRNA gene sequence similarities to all other Flavobacterium species were below 97 %. The DNA G+C content of strain DCY106(T) is 34.2 mol% and the DNA-DNA relatedness between strain DCY106(T) and F. cutihirudini LMG 26922(T), F. auranticus LMG 3987(T), F. defluvi KCTC 12612(T) and F. chilense LMG 26360(T) were below 40.0 %. The menaquinone of the type MK-6 was found to be the predominant respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids (APL1, APL6) and one unidentified lipid L2. C15:0, iso-C15:0 and summed feature 3 (iso-C15:0 2OH/C16:1 ω7c) were identified as the major fatty acids present in DCY106(T). The results of physiological and biochemical tests allowed strain DCY106(T) to be differentiated phenotypically from other recognized species belonging to the genus Flavobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Flavobacterium panacis sp. nov. is proposed with the type strain designated as DCY106(T) (= JCM 31468(T)= KCTC 42747(T)).

  5. Diversity of rhizospheric halotolerant bacteria associated with chenopod plants Atriplex and Suaeda.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants growing in saline soils are exposed to various levels of moisture and salinity stress during their life cycle. Plant associated microbes may help mediate such stress. We analyzed rhizospheric, soil and leaf litter microbial communities associated with two saline-adapted chenopod plants, Suae...

  6. Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil

    PubMed Central

    Kumar, Madan; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Manish

    2016-01-01

    We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium isolated from rhizospheric soil in the backwaters of Alappuzha, Kerala, India. The strain is alkalotolerant and grows on medium containing lignin as a sole carbon source. Genes and pathways related to lignin degradation were complemented by genomic analysis. PMID:27811115

  7. 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…

  8. Survival of Potentially Pathogenic Human-Associated Bacteria in the Rhizosphere of Hydroponically Grown Wheat

    NASA Technical Reports Server (NTRS)

    Morales, Anabelle; Garland, Jay L.; Lim, Daniel V.

    1996-01-01

    Plants may serve as reservoirs for human-associated bacteria (H-AB) in long-term space missions containing bioregenerative life support systems. The current study examined the abilities of five human-associated potential pathogens, Pseudomonas aeruginosa, Pseudomonas cepacia, Staphylococcus aureus, Streptococcus pyogenes, and Escherichia coli, to colonize and grow in the rhizosphere of hydroponically grown wheat, a candidate crop for life support. All of these bacteria have been recovered from past NASA missions and present potential problems for future missions. The abilities of these organisms to adhere to the roots of axenic five-day-old wheat (Triticum aestivum L. cv. Yecora rojo) were evaluated by enumeration of the attached organisms after a one hour incubation of roots in a suspension (approximately 10(exp 8 cu/ml)) of the H-AB. Results showed that a greater percentage of P. aeruginosa cells adhered to the wheat roots than the other four H-AB. Similarly incubated seedlings were also grown under attempted axenic conditions for seven days to examine the potential of each organism to proliferate in the rhizosphere (root colonization capacity). P. cepacia and P. aeruginosa showed considerable growth. E. coli and S. aureus showed no significant growth, and S. pyogenes died off in the wheat rhizosphere. Studies examining the effects of competition on the survival of these microorganisms indicated that P. aeruginosa was the only organism that survived in the rhizosphere of hydroponically grown wheat in the presence of different levels of microbial competition.

  9. Draft genome sequences of four Streptomyces isolates from the Populus trichocarpa root endosphere and rhizosphere

    DOE PAGES

    Klingeman, Dawn M.; Utturkar, Sagar; Lu, Tse -Yuan S.; ...

    2015-11-12

    Draft genome sequences for four Actinobacteria from the genus Streptomyces are presented. Streptomyces is a metabolically diverse genus that is abundant in soils and has been reported in association with plants. The strains described in this study were isolated from the Populus trichocarpa endosphere and rhizosphere.

  10. Irrigation differentially impacts populations of indigenous antibiotic-producing Pseudomonas spp. in the rhizosphere of wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This work determined the impact of irrigation on the seasonal dynamics of populations of Pseudomonas spp. producing the antibiotics phenazine-1-carboxylic acid (Phz+) and 2,4-diacetylphloroglucinol (Phl+) in the rhizosphere of wheat grown in the low precipitation zone (150 to 300 mm annually) of the...

  11. Draft Genome Sequence of Bacillus Species from the Rhizosphere of the Desert Plant Rhazya stricta

    PubMed Central

    Abo-Aba, S. E. M.; Sabir, Jamal S. M.; Baeshen, Mohammed N.; Sabir, Meshaal J.; Mutwakil, Mohammed H. Z.; Baeshen, Nabih A.; D’Amore, Rosalinda

    2015-01-01

    In order to better understand the ecology and diversity of microbes in the rhizosphere of desert plants, we undertook a survey of Bacillus species isolated from soil around Rhazya stricta plants from the area around Jeddah, in The Kingdom, Saudi Arabia. We have sequenced the genomes of 8 Bacillus isolates representing four different species. PMID:26543104

  12. Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: It has frequently been shown that plants interact with soils to shape rhizosphere microbiomes. However, previous work has not distinguished between effects of soil properties per se, and effects attributable to the resident microbial communities of those soils; different soils also represent d...

  13. Nonequilibrium water dynamics in the rhizosphere: How mucilage affects water flow in soils

    NASA Astrophysics Data System (ADS)

    Kroener, Eva; Zarebanadkouki, Mohsen; Kaestner, Anders; Carminati, Andrea

    2014-08-01

    The flow of water from soil to plant roots is controlled by the properties of the narrow region of soil close to the roots, the rhizosphere. In particular, the hydraulic properties of the rhizosphere are altered by mucilage, a polymeric gel exuded by the roots. In this paper we present experimental results and a conceptual model of water flow in unsaturated soils mixed with mucilage. A central hypothesis of the model is that the different drying/wetting rate of mucilage compared to the bulk soil results in nonequilibrium relations between water content and water potential in the rhizosphere. We coupled this nonequilibrium relation with the Richards equation and obtained a constitutive equation for water flow in soil and mucilage. To test the model assumptions, we measured the water retention curve and the saturated hydraulic conductivity of sandy soil mixed with mucilage from chia seeds. Additionally, we used neutron radiography to image water content in a layer of soil mixed with mucilage during drying and wetting cycles. The radiographs demonstrated the occurrence of nonequilibrium water dynamics in the soil-mucilage mixture. The experiments were simulated by numerically solving the nonequilibrium model. Our study provides conceptual and experimental evidences that mucilage has a strong impact on soil water dynamics. During drying, mucilage maintains a greater soil water content for an extended time, while during irrigation it delays the soil rewetting. We postulate that mucilage exudation by roots attenuates plant water stress by modulating water content dynamics in the rhizosphere.

  14. Predicting ecological roles in the rhizosphere using metabolome and transportome modeling

    SciTech Connect

    Larsen, Peter E.; Collart, Frank R.; Dai, Yang; Blanchard, Jeffrey L.

    2015-09-02

    The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.

  15. Development of Culture Medium for the Isolation of Flavobacterium and Chryseobacterium from Rhizosphere Soil

    PubMed Central

    Nishioka, Tomoki; Elsharkawy, Mohsen Mohamed; Suga, Haruhisa; Kageyama, Koji; Hyakumachi, Mitsuro; Shimizu, Masafumi

    2016-01-01

    An effective medium designated phosphate separately autoclaved Reasoner’s 2A supplemented with cycloheximide and tobramycin (PSR2A-C/T) has been developed for the isolation of Flavobacterium and Chryseobacterium strains from the plant rhizosphere. It consists of Reasoner’s 2A agar (R2A) prepared by autoclaving phosphate and agar separately and supplementing with 50 mg L−1 cycloheximide and 1 mg L−1 tobramycin. A comparison was made among the following nine media: PSR2A-C/T, PSR2A-C/T supplemented with NaCl, R2A agar, R2A agar supplemented with cycloheximide and tobramycin, 1/4-strength tryptic soy agar (TSA), 1/10-strength TSA, soil-extract agar, Schaedler anaerobe agar (SAA), and SAA supplemented with gramicidin, for the recovery of Flavobacterium and Chryseobacterium strains from the Welsh onion rhizosphere. Flavobacterium strains were only isolated on PSR2A-C/T, and the recovery rate of Chryseobacterium strains was higher from PSR2A-C/T than from the eight other media. In order to confirm the effectiveness of PSR2A-C/T, bacteria were isolated from onion rhizosphere soil with this medium. Flavobacterium and Chryseobacterium strains were successfully isolated from this sample at a similar rate to that from the Welsh onion rhizosphere. PMID:27098502

  16. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

    PubMed Central

    Tkacz, Andrzej; Cheema, Jitender; Chandra, Govind; Grant, Alastair; Poole, Philip S

    2015-01-01

    We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant–microbe interactions/rhizosphere microbiota/selection. PMID:25909975

  17. Nutrient depletion from rhizosphere solution by maize grown in soil with long-term compost amendment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improved understanding of rhizosphere chemistry will enhance our ability to model nutrient dynamics and on a broader scale, to develop effective management strategies for applied plant nutrients. With a controlled-climate study, we evaluated in situ changes in macro-nutrient concentrations in the rh...

  18. Bacterial Communities in the Rhizospheres of Three Mangrove Tree Species from Beilun Estuary, China

    PubMed Central

    Wu, Peng; Xiong, Xiaofei; Xu, Zhanzhou; Lu, Chuqian; Cheng, Hao; Lyu, Xiangli; Zhang, Jinghuai; He, Wei; Deng, Wei; Lyu, Yihua; Lou, Quansheng; Hong, Yiguo; Fang, Hongda

    2016-01-01

    The bacterial communities played important roles in the high productivity mangrove ecosystem. In this study, we investigated the vertical distributions of rhizosphere bacteria from three mangrove species (Bruguiera gymnorrhiza, Kandelia candel and Aegiceras corniculatum) in Beilun Estuary, China using high throughput DNA pyrosequencing of the 16S rRNA gene. Phylogenetic analysis showed that bacterial communities from mangrove rhizosphere sediments were dominated by Proteobacteria (mostly Deltaproteobacteria and Gammaproteobacteria), followed by Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. However, the ANOVA analysis on Shannon and Chao1 indices indicated that bacterial communities among sediments of the three mangrove species varied more strongly than the sampling depths. In addition, the PCA result demonstrated that the bacterial communities could be separated into three groups according to the mangrove species. Moreover, the dominated orders Rhodospirillales, GCA004 and envOPS12 were significantly different among sediments of the three mangrove species. The results of this study provided valuable information about the distribution feature of rhizosphere bacteria from Chinese mangrove plants and shed insights into biogeochemical transformations driven by bacteria in rhizosphere sediments. PMID:27695084

  19. Method for RNA extraction and cDNA library construction from microbes in crop rhizosphere soil.

    PubMed

    Fang, Changxun; Xu, Tiecheng; Ye, Changliang; Huang, Likun; Wang, Qingshui; Lin, Wenxiong

    2014-02-01

    Techniques to analyze the transcriptome of the soil rhizosphere are essential to reveal the interactions and communications between plants and microorganisms in the soil ecosystem. In this study, different volumes of Al₂(SO₄)₃ were added to rhizosphere soil samples to precipitate humic substances, which interfere with most procedures of RNA and DNA analyses. After humic substances were precipitated, cells of soil microorganisms were broken by vortexing with glass beads, and then DNA and RNA were recovered using Tris-HCl buffer with LiCl, SDS, and EDTA. The crude extract was precipitated and dissolved in RNAse-free water, and then separated by agarose gel electrophoresis. We determined the optimum volume of Al₂(SO₄)₃ for treating rhizosphere soil of rice, tobacco, sugarcane, Rehmannia glutinosa, and Pseudostellaria heterophylla. The crude nucleic acids extract from rice soil was treated with DNase I and then RNA was purified using a gel filtration column. The purified RNA was reverse-transcribed into single-strand cDNA and then ligated with an adaptor at each end before amplifying ds cDNA. The ds cDNA was sub-cloned for subsequent gene sequence analysis. We conducted qPCR to amplify 16S ribosomal DNA and observed highly efficient amplification. These results show that the extraction method can be optimized to isolate and obtain high-quality nucleic acids from microbes in different rhizosphere soils, suitable for genomic and post-genomic analyses.

  20. Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields.

    PubMed

    Bai, Li; Cui, Jiaqi; Jie, Weiguang; Cai, Baiyan

    2015-11-01

    We used rhizosphere soil sampled from one field during zero year and two years of continuous cropping of high-protein soybean to analyze the taxonomic community compositions of fungi during periods of high-incidence of root rot. Our objectives were to identify the dominant pathogens in order to provide a theoretical basis for the study of pathogenesis as well as control tactics for soybean root rot induced by continuous cropping. A total of 17,801 modified internal transcribed spacer (ITS) sequences were obtained from three different soybean rhizosphere soil samples after zero year and 1 or 2 years of continuous cropping using 454 high-throughput sequencing. The dominant eumycote fungal were identified to be Ascomycota and Basidiomycota in the three soil samples. Continuous cropping of soybean affected the diversity of fungi in rhizosphere soils and increased the abundance of Thelebolus and Mortierellales significantly. Thanatephorus, Fusarium, and Alternaria were identified to be the dominant pathogenic fungal genera in rhizosphere soil from continuously cropped soybean fields.

  1. Soil Microbial Communities associated to Plant Rhizospheres in an Organic Farming System in Alabama

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The microbial communities under different organic crop rhizospheres (0-10 and 10-20 cm) were characterized using fatty acid methyl ester (FAME) and pyrosequencing techniques. The soil was a silt loam (12.8% clay, 71.8% silt and15.4% sand). Soils at this site are characterized as having pH of ~6.53,...

  2. Soil microbial communities associated to plant rhizospheres in an organic farming system in Alabama

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The microbial communities under different organic crop rhizospheres (0-10 and 10-20 cm) were characterized using fatty acid methyl ester (FAME) and pyrosequencing techniques. The soil was a silt loam (12.8% clay, 71.8% silt and15.4% sand). Soils at this site are characterized as having pH of ~6.53, ...

  3. Microbial electricity generation in rice paddy fields: recent advances and perspectives in rhizosphere microbial fuel cells.

    PubMed

    Kouzuma, Atsushi; Kaku, Nobuo; Watanabe, Kazuya

    2014-12-01

    Microbial fuel cells (MFCs) are devices that use living microbes for the conversion of organic matter into electricity. MFC systems can be applied to the generation of electricity at water/sediment interfaces in the environment, such as bay areas, wetlands, and rice paddy fields. Using these systems, electricity generation in paddy fields as high as ∼80 mW m(-2) (based on the projected anode area) has been demonstrated, and evidence suggests that rhizosphere microbes preferentially utilize organic exudates from rice roots for generating electricity. Phylogenetic and metagenomic analyses have been conducted to identify the microbial species and catabolic pathways that are involved in the conversion of root exudates into electricity, suggesting the importance of syntrophic interactions. In parallel, pot cultures of rice and other aquatic plants have been used for rhizosphere MFC experiments under controlled laboratory conditions. The findings from these studies have demonstrated the potential of electricity generation for mitigating methane emission from the rhizosphere. Notably, however, the presence of large amounts of organics in the rhizosphere drastically reduces the effect of electricity generation on methane production. Further studies are necessary to evaluate the potential of these systems for mitigating methane emission from rice paddy fields. We suggest that paddy-field MFCs represent a promising approach for harvesting latent energy of the natural world.

  4. Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere?

    PubMed Central

    Bouffaud, Marie-Lara; Renoud, Sébastien; Moënne-Loccoz, Yvan; Muller, Daniel

    2016-01-01

    Plant evolutionary history influences the taxonomic composition of the root-associated bacterial community, but whether it can also modulate its functioning is unknown. Here, we tested the hypothesis that crop diversification is a significant factor determining the ecology of the functional group of nitrogen-fixing bacteria the rhizosphere of Poaceae. A greenhouse experiment was carried out using a range of Poaceae, i.e. four Zea mays varieties (from two genetic groups) and teosinte (representing maize’s ancestor), sorghum (from the same Panicoideae subfamily), and wheat (from neighboring Pooideae subfamily), as well as the dicot tomato as external reference. Diazotroph rhizosphere community was characterized at 21 days in terms of size (quantitative PCR of nifH genes), composition (T-RFLP and partial sequencing of nifH alleles) and functioning (quantitative RT-PCR, T-RFLP and partial sequencing of nifH transcripts). Plant species and varieties had a significant effect on diazotroph community size and the number of nifH transcripts per root system. Contrarily to expectations, however, there was no relation between Poaceae evolutionary history and the size, diversity or expression of the rhizosphere diazotroph community. These results suggest a constant selection of this functional group through evolution for optimization of nitrogen fixation in the rhizosphere. PMID:26902960

  5. Iron mineralogy and uranium-binding environment in the rhizosphere of a wetland soil

    SciTech Connect

    Kaplan, Daniel I.; Kukkadapu, Ravi; Seaman, John C.; Arey, Bruce W.; Dohnalkova, Alice C.; Buettner, Shea; Li, Dien; Varga, Tamas; Scheckel, Kirk G.; Jaffé, Peter R.

    2016-11-01

    Wetlands mitigate the migration of groundwater contaminants through the creation of biogeochemical gradients that enhance multiple contaminant-binding processes. Our hypothesis was that wetland plants not only contribute organic carbon, produce strong redox gradients, and elevate microbial populations to soils, but together these conditions also promote the formation of Fe (oxyhydr)oxides within the plant rhizosphere that may also contribute to contaminant immobilization. Mineralogy and U binding environments of the rhizosphere (plant-impacted soil zone) were evaluated in samples collected from contaminated and non-contaminated areas of a wetland on the Savannah River Site in South Carolina. Based on Mossbauer spectroscopy, rhizosphere soil collected from the field study site was greatly enriched with poorly crystalline nanoparticulate Fe-oxide/ferrihydrite-like materials and nano-goethite (<15-nm). X-ray computed tomography or various microscopy techniques showed that root plaques, tens-of microns thick, were consisted of highly oriented nanoparticles in an orientation suggestive that the roots were involved in the Fe-nanoparticle formation. Because of detection limits, SEM/EDS could not confirm whether U was enriched in the rhizosphere but did demonstrate that U was enriched on root plaques. Uranium in the plaques was always found in association with P and frequently with Fe. Together these findings suggest that plants may not only alter soil microbial and chemical conditions, but also mineralogical conditions that may be conducive to aqueous contaminant immobilization in wetlands.

  6. Rhizosphere Competitiveness of Trichloroethylene-Degrading, Poplar-Colonizing Recombinant Bacteria

    PubMed Central

    Shim, Hojae; Chauhan, Sadhana; Ryoo, Doohyun; Bowers, Kally; Thomas, Stuart M.; Canada, Keith A.; Burken, Joel G.; Wood, Thomas K.

    2000-01-01

    Indigenous bacteria from poplar tree (Populus canadensis var. eugenei ‘Imperial Carolina’) and southern California shrub rhizospheres, as well as two tree-colonizing Rhizobium strains (ATCC 10320 and ATCC 35645), were engineered to express constitutively and stably toluene o-monooxygenase (TOM) from Burkholderia cepacia G4 by integrating the tom locus into the chromosome. The poplar and Rhizobium recombinant bacteria degraded trichloroethylene at a rate of 0.8 to 2.1 nmol/min/mg of protein and were competitive against the unengineered hosts in wheat and barley rhizospheres for 1 month (colonization occurred at a level of 1.0 × 105 to 23 × 105 CFU/cm of root). In addition, six of these recombinants colonized poplar roots stably and competitively with populations as large as 79% ± 12% of all rhizosphere bacteria after 28 days (0.2 × 105 to 31 × 105 CFU/cm of root). Furthermore, five of the most competitive poplar recombinants (e.g., Pb3-1 and Pb5-1, which were identified as Pseudomonas sp. strain PsK recombinants) retained the ability to express TOM for 29 days as 100% ± 0% of the recombinants detected in the poplar rhizosphere expressed TOM constitutively. PMID:11055909

  7. 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.

  8. 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

  9. 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.

  10. RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS OF PCR-AMPLIFIED NIFH SEQUENCES FROM WETLAND PLANT RHIZOSPHERE COMMUNITIES

    EPA Science Inventory

    We describe a method to assess the community structure of N2-fixing bacteria in the rhizosphere. Total DNA was extracted from Spartina alterniflora and Sesbania macrocarpa root zones by bead-beating and purified by CsCl-EtBr gradient centrifugation. The average DNA yield was 5.5 ...

  11. Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization.

    PubMed

    Unno, Yusuke; Shinano, Takuro

    2013-01-01

    While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil.

  12. Bacterial Communities in the Rhizospheres of Three Mangrove Tree Species from Beilun Estuary, China.

    PubMed

    Wu, Peng; Xiong, Xiaofei; Xu, Zhanzhou; Lu, Chuqian; Cheng, Hao; Lyu, Xiangli; Zhang, Jinghuai; He, Wei; Deng, Wei; Lyu, Yihua; Lou, Quansheng; Hong, Yiguo; Fang, Hongda

    2016-01-01

    The bacterial communities played important roles in the high productivity mangrove ecosystem. In this study, we investigated the vertical distributions of rhizosphere bacteria from three mangrove species (Bruguiera gymnorrhiza, Kandelia candel and Aegiceras corniculatum) in Beilun Estuary, China using high throughput DNA pyrosequencing of the 16S rRNA gene. Phylogenetic analysis showed that bacterial communities from mangrove rhizosphere sediments were dominated by Proteobacteria (mostly Deltaproteobacteria and Gammaproteobacteria), followed by Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. However, the ANOVA analysis on Shannon and Chao1 indices indicated that bacterial communities among sediments of the three mangrove species varied more strongly than the sampling depths. In addition, the PCA result demonstrated that the bacterial communities could be separated into three groups according to the mangrove species. Moreover, the dominated orders Rhodospirillales, GCA004 and envOPS12 were significantly different among sediments of the three mangrove species. The results of this study provided valuable information about the distribution feature of rhizosphere bacteria from Chinese mangrove plants and shed insights into biogeochemical transformations driven by bacteria in rhizosphere sediments.

  13. Desulfurization of aromatic sulfonates by rhizosphere bacteria: high diversity of the asfA gene.

    PubMed

    Schmalenberger, Achim; Kertesz, Michael A

    2007-02-01

    The plant growth-promoting effect of Pseudomonas putida S-313 is associated with its ability to desulfurize arylsulfonates. To understand this further, other plant-associated bacteria able to desulfurize a range of arylsulfonates were isolated from the rhizospheres of winter and spring barley. The isolates belonged to the beta-proteobacteria, including bacteria from the Variovorax paradoxus group and from the Acidovorax genus. They desulfurized toluenesulfonate to p-cresol, and were found to contain orthologues of the P. putida S-313 asfA gene (> 70% sequence identity to AsfA), which is required for aryldesulfonation in this species. Further putative asfA orthologues were identified in several bacteria and cyanobacteria whose genomes have been sequenced, but of these only Cupriavidus (Ralstonia) metallidurans was able to utilize arylsulfonates as sulfur source. Cultivation of V. paradoxus, C. metallidurans or P. putida S-313 with toluenesulfonate as sulfur source led to a 100-fold increase in expression of the asfA homologues, which was largely repressed when sulfate was added. Polymerase chain reaction with degenerate primers was used to generate asfAB clone libraries from spring- and winter-barley rhizosphere DNA. Cluster analysis of 76 sequenced AsfA fragments revealed a broad diversity, with the majority of the sequences clustered together with AsfA from bacteria that are able to utilize toluenesulfonate as sulfur source. The diversity of asfA in barley rhizosphere underlines the importance of the desulfonation process for bacteria that inhabit the plant rhizosphere.

  14. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types ▿†

    PubMed Central

    Gottel, Neil R.; Castro, Hector F.; Kerley, Marilyn; Yang, Zamin; Pelletier, Dale A.; Podar, Mircea; Karpinets, Tatiana; Uberbacher, Ed; Tuskan, Gerald A.; Vilgalys, Rytas; Doktycz, Mitchel J.; Schadt, Christopher W.

    2011-01-01

    The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere. PMID:21764952

  15. Variable effects of maize mucilage on rhizosphere rewetting - a new method to collect mucilage

    NASA Astrophysics Data System (ADS)

    Ahmed, M. A.

    2015-12-01

    Recent experiments suggested that the mucilaginous fraction of root exudates may cause water repellency of the rhizosphere. Our objectives were to: 1) investigate whether maize rhizosphere turns hydrophobic; 2) measure the contact angle of mucilage collected from plants growing in wet and dry soils; and 3) find a quantitative relation between rhizosphere rewetting, particle size, soil matric potential and mucilage concentration. Maize plants were grown in sandy soil for five weeks. The soil was then allowed to dry and it was irrigated. The soil water content during irrigation was imaged using neutron radiography. In a parallel experiment, mucilage was collected from brace roots. The contact angle was measured for varying mucilage concentration. Additionally, capillary rise experiments were performed in soils of different particle size and mucilage concentration. We then used a pore-network model in which mucilage was randomly distributed in a cubic lattice. The general idea was that the 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 stayed temporarily dry after irrigation; 2) in both plants growing in wet and dry soils, mucilage became hydrophobic after drying. Mucilage contact angle increased with mucilage concentration. Interestingly, the contact angle of mucilage from plants growing in dry soil was higher than the one from plants growing in wet soils; 3) water could easily cross the rhizosphere when the mucilage concentration was below a given threshold. In contrast, above a critical mucilage concentration water could not flow through the rhizosphere

  16. Mycological composition in the rhizosphere of winter wheat in different crop production systems

    NASA Astrophysics Data System (ADS)

    Frac, Magdalena; Lipiec, Jerzy; Usowicz, Boguslaw

    2010-05-01

    Fungi play an important role in the soil ecosystem as decomposers of plant residues, releasing nutrients that sustain and stimulate processes of plant growth. Some fungi possess antagonistic properties towards plant pathogens. The structure of plant and soil communities is influenced by the interactions among its component species and also by anthropogenic pressure. In the study of soil fungi, particular attention is given to the rhizosphere. Knowledge of the structure and diversity of the fungal community in the rhizosphere lead to the better understanding of pathogen-antagonist interactions. The aim of this study was to evaluate the mycological composition of the winter wheat rhizosphere in two different crop production systems. The study was based on a field experiment established in 1994 year at the Experimental Station in South-East Poland. The experiment was conducted on grey-brown podzolic soil. In this experiment winter wheat were grown in two crop production systems: ecological and conventional - monoculture. The research of fungi composition was conducted in 15th year of experiment. Rhizosphere was collected two times during growing season, in different development stage: shooting phase and full ripeness phase. Martin medium and the dilutions 10-3 and 10-4 were used to calculate the total number cfu (colony forming units) of fungi occurring in the rhizosphere of winter wheat. The fungi were identified using Czapeka-Doxa medium for Penicillium, potato dextrose agar for all fungi and agar Nirenberga (SNA) for Fusarium. High number of antagonistic fungi (Penicillium sp., Trichoderma sp.) was recorded in the rhizosphere of wheat in ecological system. The presence of these fungi can testify to considerable biological activity, which contributes to the improvement of the phytosanitary condition of the soil. However, the decrease of the antagonistic microorganism number in the crop wheat in monoculture can be responsible for appearance higher number of the

  17. Effect of volatile substances released from Origanum majorana and Ocimum basilicum on the rhizosphere and phyllosphere fungi of Phaseolus vulgaris.

    PubMed

    Afifi, A F

    1978-01-01

    Differences were found in the counts and occurrence of fungi in the phyllosphere and thizosphere of two representatives of the Lamiacea family, Origanum majorana and Ocimum basilicum, and in the phyllosphere and rhizosphere of Phaseolus vulgaris growing separately or in coenosis with O. majorana or O. basilicum. Both the volatile substances released from ground leaves of the two latter plant species and the root exudates affected considerably spore germination of isolated phylospheric and rhizospheric fungi. The results indicated a possible role of root exudates and volatile substances released from leaves in colonization of rhizosphere and/or phyllosphere by fungi, especially in associations of various plants.

  18. [Contribution of wheat rhizosphere respiration to soil respiration under elevated atmospheric CO2 and nitrogen application].

    PubMed

    Kou, Tai-ji; Xu, Xiao-feng; Zhu, Jian-guo; Xie, Zu-bin; Guo, Da-yong; Miao, Yan-fang

    2011-10-01

    With the support of free-air carbon dioxide enrichment (FACE) system and by using isotope 13C technique, and through planting wheat (Triticum aestivum L., C3 crop) on a soil having been planted with maize (Zea mays L., C4 crop) for many years, this paper studied the effects of elevated atmospheric CO2 and nitrogen application on the delta 13C value of soil emitted CO2 and the wheat rhizosphere respiration. With the growth of wheat, the delta 13C value of soil emitted CO2 had a gradual decrease. Elevated atmospheric CO2 concentration (200 micromol mol(-1)) decreased the delta 13C value of emitted CO2 at booting and heading stages significantly when the nitrogen application rate was 250 kg hm(-2) (HN), and at jointing and booting stages significantly when the nitrogen application rate was 150 kg hm(-2) (LN). Nevertheless, the elevated atmospheric CO2 promoted the proportions of wheat rhizosphere respiration to soil respiration at booting and heading stages significantly. From jointing stage to maturing stage, the proportions of wheat rhizosphere respiration to soil respiration were 24%-48% (HN) and 21%-48% (LN) under elevated atmospheric CO2, and 20%-36% (HN) and 19%-32% (LN) under ambient atmospheric CO2. Under both elevated and ambient atmospheric CO2 concentrations, the delta 13C value of emitted CO2 and the rhizosphere respiration had different responses to the increased nitrogen application rate, and there was a significant interactive effect of atmospheric CO2 concentration and nitrogen application rate on the wheat rhizosphere respiration at jointing stage.

  19. A mechanistic model of microbial competition in the rhizosphere of wetland plants

    NASA Astrophysics Data System (ADS)

    Aslkhodapasand, F.; Mayer, K. U.; Neumann, R. B.

    2014-12-01

    Wetlands are the largest natural source of methane to the atmosphere. Although they cover only 4-6% of earth's surface, wetlands contribute 20-39% of global methane emissions. Hollow aerenchyma tissues inside the roots, stems and leaves of plants represent one of the most important methane emission pathways for wetlands. Up to 90% of the emitted methane can diffuse through these hollow tissues that directly connect the atmosphere to the anoxic soils where methane is generated. Thus, concentrations of methane surrounding plant roots directly impact the amount of methane emitted by wetlands. Methane concentrations are controlled by a variety of microbial processes occurring in the soil around the roots of plants (aka the rhizosphere). The rhizosphere is a microbial hotspot sustained by plant inputs of organic carbon and oxygen; plant roots exude excess organic carbon generated in photosynthesis into the rhizosphere and atmospheric oxygen diffuses down to the rhizosphere through the hollow aerenchyma tissues. This environment supports a variety of microbial communities that compete with each other for available carbon and oxygen, including methanogens, methanotrophs, and heterotrophs. Methanogens ferment organic carbon into methane, a reaction that is inhibited by oxygen; methanotrophs use oxygen to oxidize methane into carbon dioxide; and heterotrophs use oxygen to oxidize organic carbon into carbon dioxide. We are interested in understanding how competition between these communities alters methane concentrations and responds to variations in plant inputs. To this end, we have developed a mechanistic root-scale model that describes microbial competition for organic carbon and oxygen in the rhizosphere of wetland plants. Our results focus on variations in rates of methane production, methane oxidation, heterotrophic respiration, and diffusion of methane into plant roots as a result of changes in carbon and oxygen inputs. The study provides insight into how plant

  20. The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome.

    PubMed

    Pii, Youry; Borruso, Luigimaria; Brusetti, Lorenzo; Crecchio, Carmine; Cesco, Stefano; Mimmo, Tanja

    2016-02-01

    Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar

  1. 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.

  2. 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

  3. Spatial variability of bacteria in the rhizosphere of Elsholtzia splendens under Cu contamination.

    PubMed

    Yuan, Xiaofeng; Luan, Jing; Shi, Jiyan

    2014-01-01

    Elsholtzia splendens is a well-known Cu-tolerant plant; yet, the impact of Cu-contaminated soil on bacterial community in its rhizosphere is not known. We studied the spatial variability of bacteria in the rhizosphere using Cu-contaminated soil with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR. In the uncontaminated soil, the content of the dissolved organic carbon (DOC) and bacterial diversity gradually increased in the rhizosphere soil along the root growth direction (from the interface zone to the meristematic zone), while for the Cu-contaminated soil, the highest DOC content and the strongest potential bioavailability of Cu were found in the interface zone, which also had the lowest bacteria diversity. Bacteria diversity was positively correlated with DOC in the uncontaminated soil (p < 0.01) but not in the contaminated soil. Compared with uncontaminated soil, some species such as Firmicutes only existed in the rhizosphere of contaminated soil, while the very small amount (if any) of some species exists such as Deinococcus-Thermus, indicating that the contaminated environment altered the bacterial composition. Moreover, spatial variation of the bacterial community was found among different soil zones. Real-time PCR confirmed the spatial variation via the gene expression of flagellin (fliC) and chemotaxis gene (cheA). The spatial characteristics of cheA expression were consistent with that of DOC and bacterial diversity. In conclusion, we demonstrated that the spatial variation of the bacterial community in the rhizosphere was present, independent of Cu contamination. DOC and Cu toxicity may affect specific gene expressions such as fliC and cheA, resulting in bacterial spatial variation.

  4. Image-based modelling of nutrient movement in and around the rhizosphere

    PubMed Central

    Daly, Keith R.; Keyes, Samuel D.; Masum, Shakil; Roose, Tiina

    2016-01-01

    In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model. PMID:26739861

  5. Mobilization of cadmium by dissolved organic matter in the rhizosphere of hyperaccumulator Sedum alfredii.

    PubMed

    Li, Tingqiang; Liang, Chengfeng; Han, Xuan; Yang, Xiaoe

    2013-05-01

    Pot experiments were conducted to investigate the role of dissolved organic matter (DOM) in the Cd speciation in the rhizosphere of hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii and its effects on Cd mobility. After growing HE S. alfredii, the rhizosphere soil solution pH of heavily polluted soil (HPS) and slightly polluted soil (SPS) was reduced by 0.49 and 0.40 units, respectively, due to enhanced DOC derived from root exudation. The total Cd concentration in soil solution decreased significantly but the decrease accounted for less than 1% of the total Cd uptake in the shoots of HE S. alfredii. Visual MINTEQ speciation predicted that Cd-DOM complexes were the dominant Cd species in soil solutions after the growth of S. alfredii for both soils, followed by the free metal Cd(2+) species. However, Cd-DOM complexes fraction in the rhizosphere soil solution of HE S. alfredii (89.1% and 74.6% for HPS and SPS, respectively) were much greater than NHE S. alfredii (82.8% and 64.7% for HPS and SPS, respectively). Resin equilibration experiment results indicated that DOM from the rhizosphere (R-DOM) of both ecotypes of S. alfredii had the ability to form complexes with Cd, whereas the degree of complexation was significantly higher for HE-R-DOM (79-89%) than NHE-R-DOM (63-74%) in the undiluted sample. The addition of HE-R-DOM significantly (P<0.05) increased the solubility of four Cd minerals while NHE-R-DOM was not as effective at the same concentration. It was concluded that DOM in the rhizosphere of hyperaccumulating ecotype of S. alfredii could significantly increase Cd mobility through the formation of soluble DOM-metal complexes.

  6. Metarhizium robertsii Produces an Extracellular Invertase (MrINV) That Plays a Pivotal Role in Rhizospheric Interactions and Root Colonization

    PubMed Central

    Liao, Xinggang; Fang, Weiguo; Lin, Liangcai; Lu, Hsiao-Ling; Leger, Raymond J. St.

    2013-01-01

    As well as killing pest insects, the rhizosphere competent insect-pathogenic fungus Metarhizium robertsii also boosts plant growth by providing nitrogenous nutrients and increasing resistance to plant pathogens. Plant roots secrete abundant nutrients but little is known about their utilization by Metarhizium spp. and the mechanistic basis of Metarhizium-plant associations. We report here that M. robertsii produces an extracellular invertase (MrInv) on plant roots. Deletion of MrInv (⊿MrInv) reduced M. robertsii growth on sucrose and rhizospheric exudates but increased colonization of Panicum virgatum and Arabidopsis thaliana roots. This could be accounted for by a reduction in carbon catabolite repression in ⊿MrInv increasing production of plant cell wall-degrading depolymerases. A non-rhizosphere competent scarab beetle specialist Metarhizium majus lacks invertase which suggests that rhizospheric competence may be related to the sugar metabolism of different Metarhizium species. PMID:24205119

  7. Metarhizium robertsii produces an extracellular invertase (MrINV) that plays a pivotal role in rhizospheric interactions and root colonization.

    PubMed

    Liao, Xinggang; Fang, Weiguo; Lin, Liangcai; Lu, Hsiao-Ling; St Leger, Raymond J

    2013-01-01

    As well as killing pest insects, the rhizosphere competent insect-pathogenic fungus Metarhizium robertsii also boosts plant growth by providing nitrogenous nutrients and increasing resistance to plant pathogens. Plant roots secrete abundant nutrients but little is known about their utilization by Metarhizium spp. and the mechanistic basis of Metarhizium-plant associations. We report here that M. robertsii produces an extracellular invertase (MrInv) on plant roots. Deletion of MrInv (ΔMrInv) reduced M. robertsii growth on sucrose and rhizospheric exudates but increased colonization of Panicum virgatum and Arabidopsis thaliana roots. This could be accounted for by a reduction in carbon catabolite repression in ΔMrInv increasing production of plant cell wall-degrading depolymerases. A non-rhizosphere competent scarab beetle specialist Metarhizium majus lacks invertase which suggests that rhizospheric competence may be related to the sugar metabolism of different Metarhizium species.

  8. 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

  9. Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed

    PubMed Central

    Smalla, K.; Wieland, G.; Buchner, A.; Zock, A.; Parzy, J.; Kaiser, S.; Roskot, N.; Heuer, H.; Berg, G.

    2001-01-01

    The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands. PMID:11571180

  10. Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing.

    PubMed

    Correa-Galeote, David; Bedmar, Eulogio J; Fernández-González, Antonio J; Fernández-López, Manuel; Arone, Gregorio J

    2016-01-01

    Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize

  11. Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing

    PubMed Central

    Correa-Galeote, David; Bedmar, Eulogio J.; Fernández-González, Antonio J.; Fernández-López, Manuel; Arone, Gregorio J.

    2016-01-01

    Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize

  12. 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

  13. 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

  14. 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

  15. Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens

    NASA Astrophysics Data System (ADS)

    Jiang, Longfei; Song, Mengke; Yang, Li; Zhang, Dayi; Sun, Yingtao; Shen, Zhenguo; Luo, Chunling; Zhang, Gan

    2016-10-01

    Bacterial communities of rhizospheric soils play an important role in the tolerance and uptake of metal-tolerant/hyperaccumulating plants to metals, e.g. the Cu-tolerant Elsholtzia splendens native to China. In this work, pyrosequencing of the bacterial 16S rRNA gene was firstly applied to investigate the rhizospheric bacterial community of E. splendens grown at Cu contaminated sites. The 47 phyla including 11 dominant phyla (>1%) in E. splendens rhizosphere were presented. The effects of Cu and other environmental factors (total organic carbon, total nitrogen and pH) on the rhizospheric bacterial community were studied comprehensively. The phyla abundances were affected by the environmental factors to different extent, and we found pH, instead of Cu concentration, influenced UniFrac distance significantly and was identified as the most important environmental factor affecting bacterial community. In addition, the influence of environmental factors on gene profiles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). Our study illustrates a view about Cu-tolerant E. splendens rhizospheric bacterial communities (composition, diversity and gene profiles) and their influencing factors, giving a hand for the understanding on bacterial community is formed and affected in rhizosphere.

  16. Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

    PubMed

    Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

    2015-08-01

    Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments.

  17. Assessing the influence of the rhizosphere on soil hydraulic properties using X-ray computed tomography and numerical modelling

    PubMed Central

    Daly, Keith R.; Mooney, Sacha J.; Bennett, Malcolm J.; Crout, Neil M. J.; Roose, Tiina; Tracy, Saoirse R.

    2015-01-01

    Understanding the dynamics of water distribution in soil is crucial for enhancing our knowledge of managing soil and water resources. The application of X-ray computed tomography (CT) to the plant and soil sciences is now well established. However, few studies have utilized the technique for visualizing water in soil pore spaces. Here this method is utilized to visualize the water in soil in situ and in three-dimensions at successive reductive matric potentials in bulk and rhizosphere soil. The measurements are combined with numerical modelling to determine the unsaturated hydraulic conductivity, providing a complete picture of the hydraulic properties of the soil. The technique was performed on soil cores that were sampled adjacent to established roots (rhizosphere soil) and from soil that had not been influenced by roots (bulk soil). A water release curve was obtained for the different soil types using measurements of their pore geometries derived from CT imaging and verified using conventional methods, such as pressure plates. The water, soil, and air phases from the images were segmented and quantified using image analysis. The water release characteristics obtained for the contrasting soils showed clear differences in hydraulic properties between rhizosphere and bulk soil, especially in clay soil. The data suggest that soils influenced by roots (rhizosphere soil) are less porous due to increased aggregation when compared with bulk soil. The information and insights obtained on the hydraulic properties of rhizosphere and bulk soil will enhance our understanding of rhizosphere biophysics and improve current water uptake models. PMID:25740922

  18. Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens

    PubMed Central

    Jiang, Longfei; Song, Mengke; Yang, Li; Zhang, Dayi; Sun, Yingtao; Shen, Zhenguo; Luo, Chunling; Zhang, Gan

    2016-01-01

    Bacterial communities of rhizospheric soils play an important role in the tolerance and uptake of metal-tolerant/hyperaccumulating plants to metals, e.g. the Cu-tolerant Elsholtzia splendens native to China. In this work, pyrosequencing of the bacterial 16S rRNA gene was firstly applied to investigate the rhizospheric bacterial community of E. splendens grown at Cu contaminated sites. The 47 phyla including 11 dominant phyla (>1%) in E. splendens rhizosphere were presented. The effects of Cu and other environmental factors (total organic carbon, total nitrogen and pH) on the rhizospheric bacterial community were studied comprehensively. The phyla abundances were affected by the environmental factors to different extent, and we found pH, instead of Cu concentration, influenced UniFrac distance significantly and was identified as the most important environmental factor affecting bacterial community. In addition, the influence of environmental factors on gene profiles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). Our study illustrates a view about Cu-tolerant E. splendens rhizospheric bacterial communities (composition, diversity and gene profiles) and their influencing factors, giving a hand for the understanding on bacterial community is formed and affected in rhizosphere. PMID:27782202

  19. Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem.

    PubMed

    Rodríguez-Caballero, G; Caravaca, F; Fernández-González, A J; Alguacil, M M; Fernández-López, M; Roldán, A

    2017-04-15

    The main goal of this study was to assess the effect of the inoculation of four autochthonous shrub species with the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices on the rhizosphere bacterial community and to ascertain whether such an effect is dependent on the host plant species. Additionally, analysis of rhizosphere soil chemical and biochemical properties was performed to find relationships between them and the rhizosphere bacterial communities. Non-metric multidimensional scaling analysis and subsequent permutational multivariate analysis of variance revealed differences in bacterial community composition and structure between non-inoculated and inoculated rhizospheres. Moreover, an influence of the plant species was observed. Different bacterial groups were found to be indicator taxonomic groups of non-inoculated and inoculated rhizospheres, Gemmatimonadetes and Anaerolineaceae, respectively, being the most notable indicators. As shown by distance based redundancy analysis, the shifts in bacterial community composition and structure mediated by the inoculation with the AM fungus were mainly related to changes in plant nutrients and growth parameters, such as the shoot phosphorus content. Our findings suggest that the AM fungal inoculum was able to modify the rhizosphere bacterial community assemblage while improving the host plant performance.

  20. 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

  1. Impact of biochar and root-induced changes on metal dynamics in the rhizosphere of Agrostis capillaris and Lupinus albus.

    PubMed

    Houben, David; Sonnet, Philippe

    2015-11-01

    Rhizosphere interactions are deemed to play a key role in the success of phytoremediation technologies. Here, the effects of biochar and root-induced changes in the rhizosphere of Agrostis capillaris L. and Lupinus albus L. on metal (Cd, Pb and Zn) dynamics were investigated using a biotest on a 2mm soil layer and a sequential extraction procedure (Tessier's scheme). In the bulk soil, the application of 5% biochar significantly reduced the exchangeable pool of metals primarily due to a liming effect which subsequently promoted the metal shift into the carbonate-bound pool. However, metals were re-mobilized in the rhizosphere of both A. capillaris and L. albus due to root-induced acidification which counteracted the liming effect of biochar. As a result, the concentrations of metals in roots and shoots of both plants were not significantly reduced by the application of biochar. Although the study should be considered a worst-case scenario because experimental conditions induced the intensification of rhizosphere processes, the results highlight that changes in rhizosphere pH can impact the effectiveness of biochar to immobilize metals in soil. Biochar has thus a potential as amendment for reducing metal uptake by plants, provided the acidification of the rhizosphere is minimized.

  2. Cadmium uptake and speciation changes in the rhizosphere of cadmium accumulator and non-accumulator oilseed rape varieties.

    PubMed

    Su, Dechun; Xing, Jianping; Jiao, Weiping; Wong, Woonchung

    2009-01-01

    Characteristics of cadmium (Cd) uptake kinetics and distribution of Cd speciation in the rhizosphere for Cd accumulator and non-accumulator oilseed rape varieties were investigated under nutrient solution and rhizobox soil culture conditions. The results showed that the maximal influx (V(max)) for Cd2+ and Km were significantly different for the two oilseed rape varieties. The value of V(max) for Cd accumulator oilseed rape Zhucang Huazi was two-fold greater than that for oilseed rape Chuan you II-93. The exchangeable Cd concentration in the rhizosphere was significantly lower than in non-rhizospheric soils supplemented with CdSO4 for both the varieties. Carbonate-bound Cd in the rhizosphere of Cd accumulator oilseed rape was significantly higher than that in the rhizosphere of non-accumulator oilseed rape and non-rhizospheric soil. Cd accumulator oilseed rape had a higher Cd2+ affinity and more ability to uptake insoluble Cd in the soil than the non-accumulator oilseed rape.

  3. ESTCP Technology Demonstration Final Report: Field Demonstration of Rhizosphere-Enhanced Treatment of Organics-Contaminated Soils on Native American Lands With Application to Northern FUD Sites

    DTIC Science & Technology

    2004-06-01

    the rhizosphere, exudation of contaminant analogs by roots and stimulation of specific microbial degradation pathways, and using trees either to...control the hydrology, or to take up and degrade trichloroethylene (TCE), or both. Rhizosphere-enhanced remediation is based on root exudation of excess...Rhizosphere-enhanced remediation (or rhizodegradation in 1A above) is a form of phytoremediation based on root exudation of excess plant-produced

  4. Abiotic/biotic coupling in the rhizosphere: a reactive transport modeling analysis

    USGS Publications Warehouse

    Lawrence, Corey R.; Steefel, Carl; Maher, Kate

    2014-01-01

    A new generation of models is needed to adequately simulate patterns of soil biogeochemical cycling in response changing global environmental drivers. For example, predicting the influence of climate change on soil organic matter storage and stability requires models capable of addressing complex biotic/abiotic interactions of rhizosphere and weathering processes. Reactive transport modeling provides a powerful framework simulating these interactions and the resulting influence on soil physical and chemical characteristics. Incorporation of organic reactions in an existing reactive transport model framework has yielded novel insights into soil weathering and development but much more work is required to adequately capture root and microbial dynamics in the rhizosphere. This endeavor provides many advantages over traditional soil biogeochemical models but also many challenges.

  5. Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere

    PubMed Central

    Kai, Marco; Effmert, Uta; Piechulla, Birgit

    2016-01-01

    Rhizobacteria produce an enormous amount of volatile compounds, however, the function of these metabolites is scarcely understood. Investigations evaluating influences on plants performed in various laboratories using individually developed experimental setups revealed different and often contradictory results, e.g., ranging from a significant plant growth promotion to a dramatic suppression of plant development. In addition to these discrepancies, these test systems neglected properties and complexity of the rhizosphere. Therefore, to pursue further investigations of the role of bacterial volatiles in this underground habitat, the applied methods have to simulate its natural characteristics as much as possible. In this review, we will describe and discuss pros and cons of currently used bioassays, give insights into rhizosphere characteristics, and suggest improvements for test systems that would consider in natura conditions and would allow gaining further knowledge of the potential function and significance of rhizobacterial volatiles in plant life. PMID:26903987

  6. Genotypic Diversity, Antibiotic Resistance and Bacteriocin Production of Enterococci Isolated from Rhizospheres

    PubMed Central

    Klibi, Naouel; Ben Slimen, Naouel; Fhoula, Imen; López, Maria; Ben Slama, Karim; Daffonchio, Daniele; Boudabous, Abdellatif; Torres, Carmen; Ouzari, Hadda

    2012-01-01

    This study aimed to identify and to characterize rhizospheric-derived enterococci. The results showed the prevalence of Enterococcus faecium species (97%) vs. Enterococcus durans (3%). Susceptibility testing for antibiotics showed a low percentage of resistance to erythromycin (3.2%) and tetracycline (11.2%), and intermediate resistance to vancomycin (6.5%). Nevertheless, a high proportion of bacteriocin production was recorded. Furthermore, PCR detection of antibiotic resistance and bacteriocin production-encoding genes was investigated. Pulsed-field gel electrophoresis typing (PFGE) showed a great variability of enterococci in the rhizosphere. Moreover, mutilocus-sequence-typing analysis (MLST) revealed the identification of three new sequence types (STs), which were registered as ST613, ST614 and ST615. PMID:23124764

  7. 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.

  8. 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

  9. Accumulation of the Antibiotic Phenazine-1-Carboxylic Acid in the Rhizosphere of Dryland Cereals

    PubMed Central

    Mavrodi, Dmitri V.; Mavrodi, Olga V.; Parejko, James A.; Bonsall, Robert F.; Kwak, Youn-Sig; Paulitz, Timothy C.; Weller, David M.

    2012-01-01

    Natural antibiotics are thought to function in the defense, fitness, competitiveness, biocontrol activity, communication, and gene regulation of microorganisms. However, the scale and quantitative aspects of antibiotic production in natural settings are poorly understood. We addressed these fundamental questions by assessing the geographic distribution of indigenous phenazine-producing (Phz+) Pseudomonas spp. and the accumulation of the broad-spectrum antibiotic phenazine-1-carboxylic acid (PCA) in the rhizosphere of wheat grown in the low-precipitation zone (<350 mm) of the Columbia Plateau and in adjacent, higher-precipitation areas. Plants were collected from 61 commercial wheat fields located within an area of about 22,000 km2. Phz+ Pseudomonas spp. were detected in all sampled fields, with mean population sizes ranging from log 3.2 to log 7.1 g−1 (fresh weight) of roots. Linear regression analysis demonstrated a significant inverse relationship between annual precipitation and the proportion of plants colonized by Phz+ Pseudomonas spp. (r2 = 0.36, P = 0.0001). PCA was detected at up to nanomolar concentrations in the rhizosphere of plants from 26 of 29 fields that were selected for antibiotic quantitation. There was a direct relationship between the amount of PCA extracted from the rhizosphere and the population density of Phz+ pseudomonads (r2 = 0.46, P = 0.0006). This is the first demonstration of accumulation of significant quantities of a natural antibiotic across a terrestrial ecosystem. Our results strongly suggest that natural antibiotics can transiently accumulate in the plant rhizosphere in amounts sufficient not only for inter- and intraspecies signaling but also for the direct inhibition of sensitive organisms. PMID:22138981

  10. 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

  11. 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.

  12. 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

  13. Biofilm formation and indole-3-acetic acid production by two rhizospheric unicellular cyanobacteria.

    PubMed

    Ahmed, Mehboob; Stal, Lucas J; Hasnain, Shahida

    2014-08-01

    Microorganisms that live in the rhizosphere play a pivotal role in the functioning and maintenance of soil ecosystems. The study of rhizospheric cyanobacteria has been hampered by the difficulty to culture and maintain them in the laboratory. The present work investigated the production of the plant hormone indole-3-acetic acid (IAA) and the potential of biofilm formation on the rhizoplane of pea plants by two cyanobacterial strains, isolated from rice rhizosphere. The unicellular cyanobacteria Chroococcidiopsis sp. MMG-5 and Synechocystis sp. MMG-8 that were isolated from a rice rhizosphere, were investigated. Production of IAA by Chroococcidiopsis sp. MMG-5 and Synechocystis sp. MMG-8 was measured under experimental conditions (pH and light). The bioactivity of the cyanobacterial auxin was demonstrated through the alteration of the rooting pattern of Pisum sativum seedlings. The increase in the concentration of L-tryptophan and the time that this amino acid was present in the medium resulted in a significant enhancement of the synthesis of IAA (r > 0.900 at p = 0.01). There was also a significant correlation between the concentration of IAA in the supernatant of the cyanobacteria cultures and the root length and number of the pea seedlings. Observations made by confocal laser scanning microscopy revealed the presence of cyanobacteria on the surface of the roots and also provided evidence for the penetration of the cyanobacteria in the endorhizosphere. We show that the synthesis of IAA by Chroococcidiopsis sp. MMG-5 and Synechocystis sp. MMG-8 occurs under different environmental conditions and that the auxin is important for the development of the seedling roots and for establishing an intimate symbiosis between cyanobacteria and host plants.

  14. Predicting ecological roles in the rhizosphere using metabolome and transportome modeling

    DOE PAGES

    Larsen, Peter E.; Collart, Frank R.; Dai, Yang; ...

    2015-09-02

    The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. New algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad’s ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter ofmore » plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism’s transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.« less

  15. Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO(2).

    PubMed

    Drigo, Barbara; van Veen, Johannes A; Kowalchuk, George A

    2009-10-01

    Soil community responses to increased atmospheric CO(2) concentrations are expected to occur mostly through interactions with changing vegetation patterns and plant physiology. To gain insight into the effects of elevated atmospheric CO(2) on the composition and functioning of microbial communities in the rhizosphere, Carex arenaria (a non-mycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown under defined atmospheric conditions with either ambient (350 p.p.m.) or elevated (700 p.p.m.) CO(2) concentrations. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) and quantitative-PCR were carried out to analyze, respectively, the structure and abundance of the communities of actinomycetes, Fusarium spp., Trichoderma spp., Pseudomonas spp., Burkholderia spp. and Bacillus spp. Responses of specific functional groups, such as phloroglucinol, phenazine and pyrrolnitrin producers, were also examined by quantitative-PCR, and HPLC (high performance liquid chromatography) was employed to assess changes in exuded sugars in the rhizosphere. Multivariate analysis of group-specific community profiles showed disparate responses to elevated CO(2) for the different bacterial and fungal groups examined, and these responses were dependent on plant type and soil nutrient availability. Within the bacterial community, the genera Burkholderia and Pseudomonas, typically known as successful rhizosphere colonizers, were significantly influenced by elevated CO(2), whereas the genus Bacillus and actinomycetes, typically more dominant in bulk soil, were not. Total sugar concentrations in the rhizosphere also increased in both plants in response to elevated CO(2). The abundances of phloroglucinol-, phenazine- and pyrrolnitrin-producing bacterial communities were also influenced by elevated CO(2), as was the abundance of the fungal genera Fusarium and Trichoderma.

  16. A Hydrophobic Mutant of Rhizobium etli Altered in Nodulation Competitiveness and Growth in the Rhizosphere

    PubMed Central

    Araujo, Ricardo S.; Robleto, Eduardo A.; Handelsman, Jo

    1994-01-01

    We isolated and characterized CE3003, a Tn5-induced mutant with altered colony morphology derived from Rhizobium etli CE3. CE3003 produced domed colonies and was highly hydrophobic as indicated by its ability to partition into hexadecane, whereas its parent produced flat colonies and was hydrophilic. On bean plants, CE3003 induced nodules and reduced acetylene. CE3003 and CE3 grew at similar rates when they were grown separately or together in culture medium or inoculated singly onto bean seeds. However, when they were mixed at a 1:1 ratio and applied to seeds, CE3003 achieved significantly lower populations than CE3 in the rhizosphere. Five days after coinoculation of CE3 and CE3003, the population of the mutant was less than 10% of the population of CE3 in the bean rhizosphere. To determine the nodulation competitiveness of the mutant, it was coinoculated with CE3 at various ratios at planting, and the ratio of the nodules occupied by each strain was determined 21 days later. A 17,000-fold excess of CE3003 in mixed inocula was required to obtain equal nodule occupancy by the two strains. A genomic library of strain CE3 was mobilized into CE3003, and we identified a cosmid, pRA3003, that restored the parental colony morphology and hydrophilicity to the mutant. Restoration of the parental colony morphology was accompanied by recovery of the ability to grow competitively in the rhizosphere and to compete for nodulation of beans. The data show an association between cell surface hydrophobicity, nodulation competitiveness, and competitive growth in the rhizosphere in mutant CE3003. Images PMID:16349248

  17. 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.

  18. 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.

  19. Iron mineralogy and uranium-binding environment in the rhizosphere of a wetland soil.

    PubMed

    Kaplan, Daniel I; Kukkadapu, Ravi; Seaman, John C; Arey, Bruce W; Dohnalkova, Alice C; Buettner, Shea; Li, Dien; Varga, Tamas; Scheckel, Kirk G; Jaffé, Peter R

    2016-11-01

    Wetlands mitigate the migration of groundwater contaminants through a series of biogeochemical gradients that enhance multiple contaminant-binding processes. The hypothesis of this study was that wetland plant roots contribute organic carbon and release O2 within the rhizosphere (plant-impact soil zone) that promote the formation of Fe(III)-(oxyhydr)oxides. In turn, these Fe(III)-(oxyhydr)oxides stabilize organic matter that together contribute to contaminant immobilization. Mineralogy and U binding environments of the rhizosphere were evaluated in samples collected from contaminated and non-contaminated areas of a wetland on the Savannah River Site in South Carolina. Based on Mössbauer spectroscopy, rhizosphere soil was greatly enriched with nanogoethite, ferrihydrite-like nanoparticulates, and hematite, with negligible Fe(II) present. X-ray computed tomography and various microscopy techniques showed that root plaques were tens-of-microns thick and consisted of highly oriented Fe-nanoparticles, suggesting that the roots were involved in creating the biogeochemical conditions conducive to the nanoparticle formation. XAS showed that a majority of the U in the bulk wetland soil was in the +6 oxidation state and was not well correlated spatially to Fe concentrations. SEM/EDS confirm that U was enriched on root plaques, where it was always found in association with P. Together these findings support our hypothesis and suggest that plants can alter mineralogical conditions that may be conducive to contaminant immobilization in wetlands.

  20. Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System.

    PubMed

    Taketani, Rodrigo Gouvêa; Lançoni, Milena Duarte; Kavamura, Vanessa Nessner; Durrer, Ademir; Andreote, Fernando Dini; Melo, Itamar Soares

    2017-01-01

    The rhizosphere is viewed as a deterministic environment led by the interaction between plants and microorganisms. In the case of semi-arid plants, this interaction is strengthened by the harshness of the environment. We tested the hypothesis that dry season represents a constraint on the bacterial diversity of the rhizosphere from semi-arid plants. To accomplish this, we sampled two leguminous species at five locations during the dry and rainy seasons in the Caatinga biome and characterised bacterial community structures using qPCR and 16S rRNA sequencing. We found that the main differences between seasons were due to reduced phylogenetic diversity caused by dryness. Variation partitioning indicated that environmental characteristics significant impacts in β-diversity. Additionally, distance decay relationship and taxa area relationship indicate a higher spatial turnover at the rainy season. During the dry season, decreased bacterial abundance is likely due to the selection of resistant or resilient microorganisms; with the return of the rain, the sensitive populations start to colonise the rhizosphere by a process that is strongly influenced by environmental characteristics. Thus, we propose that the reduction of PD and strong influence of environmental parameters on the assemblage of these communities make them prone to functional losses caused by climatic disturbances.

  1. 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.

  2. Disentangling who is who during rhizosphere acidification in root interactions: combining fluorescence with optode techniques

    PubMed Central

    Faget, Marc; Blossfeld, Stephan; von Gillhaussen, Philipp; Schurr, Ulrich; Temperton, Vicky M.

    2013-01-01

    Plant–soil interactions can strongly influence root growth in plants. There is now increasing evidence that root–root interactions can also influence root growth, affecting architecture and root traits such as lateral root formation. Both when species grow alone or in interaction with others, root systems are in turn affected by as well as affect rhizosphere pH. Changes in soil pH have knock-on effects on nutrient availability. A limitation until recently has been the inability to assign species identity to different roots in soil. Combining the planar optode technique with fluorescent plants enables us to distinguish between plant species grown in natural soil and in parallel study pH dynamics in a non-invasive way at the same region of interest (ROI). We measured pH in the rhizosphere of maize and bean in rhizotrons in a climate chamber, with ROIs on roots in proximity to the roots of the other species as well as not-close to the other species. We found clear dynamic changes of pH over time and differences between the two species in rhizosphere acidification. Interestingly, when roots of the two species were interacting, the degree of acidification or alkalization compared to bulk soil was less strong then when roots were not growing in the vicinity of the other species. This cutting-edge approach can help provide a better understanding of plant–plant and plant–soil interactions. PMID:24137168

  3. 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.

  4. [Effects of elevated rhizosphere CO2 concentration on the photosynthetic characteristics, yield, and quality of muskmelon].

    PubMed

    Liu, Yi-Ling; Sun, Zhou-Ping; Li, Tian-Lai; Gu, Feng-Ying; He, Yu

    2013-10-01

    By using aeroponics culture system, this paper studied the effects of elevated rhizosphere CO2 concentration on the leaf photosynthesis and the fruit yield and quality of muskmelon during its anthesis-fruiting period. In the fruit development period of muskmelon, as compared with those in the control (350 microL CO2 x L (-1)), the leaf chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci), and the maximal photochemical efficiency of PS II (Fv/Fm) in treatments 2500 and 5000 microL CO2 x L(-1) decreased to some extents, but the stomatal limitation value (Ls) increased significantly, and the variation amplitudes were larger in treatment 5000 microL CO2 x L(-1) than in treatment 2500 microL CO2 x L(-1). Under the effects of elevated rhizosphere CO2 concentration, the fruit yield per plant and the Vc and soluble sugar contents in fruits decreased markedly, while the fruit organic acid content was in adverse. It was suggested that when the rhizosphere CO2 concentration of muskmelon during its anthesis-fruiting period reached to 2500 microL x L(-1), the leaf photosynthesis and fruit development of muskmelon would be depressed obviously, which would result in the decrease of fruit yield and quality of muskmelon.

  5. Mechanisms for cellular transport and release of allelochemicals from plant roots into the rhizosphere.

    PubMed

    Weston, Leslie A; Ryan, Peter R; Watt, Michelle

    2012-05-01

    Allelochemicals and other metabolites released by plant roots play important roles in rhizosphere signalling, plant defence and responses to abiotic stresses. Plants use a variety of sequestration and transport mechanisms to move and export bioactive products safely into the rhizosphere. The use of mutants and molecular tools to study gene expression has revealed new information regarding the diverse group of transport proteins and conjugation processes employed by higher plants. Transport systems used for moving secondary products into and out of root cells are similar to those used elsewhere in the plant but are closely linked to soil environmental conditions and local root health. Root cells can rapidly generate and release large quantities of allelochemicals in response to stress or local rhizosphere conditions, so the production and transport of these compounds in cells are often closely linked. Plants need to manage the potentially toxic allelochemicals and metabolites they produce by sequestering them to the vacuole or other membrane-bound vesicles. These compartments provide secure storage areas and systems for safely moving bioactive chemicals throughout the cytosol. Release into the apoplast occurs either by exocytosis or through membrane-bound transport proteins. This review discusses the possible transport mechanisms involved in releasing specific root-produced allelochemicals by combining microscopic observations of the specialized root cells with the physical and chemical properties of the exudates.

  6. Disentangling who is who during rhizosphere acidification in root interactions: combining fluorescence with optode techniques.

    PubMed

    Faget, Marc; Blossfeld, Stephan; von Gillhaussen, Philipp; Schurr, Ulrich; Temperton, Vicky M

    2013-01-01

    Plant-soil interactions can strongly influence root growth in plants. There is now increasing evidence that root-root interactions can also influence root growth, affecting architecture and root traits such as lateral root formation. Both when species grow alone or in interaction with others, root systems are in turn affected by as well as affect rhizosphere pH. Changes in soil pH have knock-on effects on nutrient availability. A limitation until recently has been the inability to assign species identity to different roots in soil. Combining the planar optode technique with fluorescent plants enables us to distinguish between plant species grown in natural soil and in parallel study pH dynamics in a non-invasive way at the same region of interest (ROI). We measured pH in the rhizosphere of maize and bean in rhizotrons in a climate chamber, with ROIs on roots in proximity to the roots of the other species as well as not-close to the other species. We found clear dynamic changes of pH over time and differences between the two species in rhizosphere acidification. Interestingly, when roots of the two species were interacting, the degree of acidification or alkalization compared to bulk soil was less strong then when roots were not growing in the vicinity of the other species. This cutting-edge approach can help provide a better understanding of plant-plant and plant-soil interactions.

  7. 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.

  8. Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage▿ †

    PubMed Central

    Mirete, Salvador; de Figueras, Carolina G.; González-Pastor, Jose E.

    2007-01-01

    Metal resistance determinants have traditionally been found in cultivated bacteria. To search for genes involved in nickel resistance, we analyzed the bacterial community of the rhizosphere of Erica andevalensis, an endemic heather which grows at the banks of the Tinto River, a naturally metal-enriched and extremely acidic environment in southwestern Spain. 16S rRNA gene sequence analysis of rhizosphere DNA revealed the presence of members of five phylogenetic groups of Bacteria and the two main groups of Archaea mostly associated with sites impacted by acid mine drainage (AMD). The diversity observed and the presence of heavy metals in the rhizosphere led us to construct and screen five different metagenomic libraries hosted in Escherichia coli for searching novel nickel resistance determinants. A total of 13 positive clones were detected and analyzed. Insights about their possible mechanisms of resistance were obtained from cellular nickel content and sequence similarities. Two clones encoded putative ABC transporter components, and a novel mechanism of metal efflux is suggested. In addition, a nickel hyperaccumulation mechanism is proposed for a clone encoding a serine O-acetyltransferase. Five clones encoded proteins similar to well-characterized proteins but not previously reported to be related to nickel resistance, and the remaining six clones encoded hypothetical or conserved hypothetical proteins of uncertain functions. This is the first report documenting nickel resistance genes recovered from the metagenome of an AMD environment. PMID:17675438

  9. 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.

  10. 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.

  11. Application of rhizosphere interaction of hyperaccumulator Noccaea caerulescens to remediate cadmium-contaminated agricultural soil.

    PubMed

    Yang, Yong; Jiang, Rong-Feng; Wang, Wei; Li, Hua-Fen

    2011-10-01

    There is an urgent requirement for selecting appropriate technologies to solve food safety problems due to soil contamination. In this study, the hyperaccumulator Noccaea caerulescens and a high Cd accumulator pakchoi cultivar (Brassica rapa L. spp. Chinenesis cv.) were grown in a moderately Cd-contaminated soil with three planting systems (monocrop, inter-crop, and crop-rotation) and three growing durations (25, 50, and 75 days) to study the role of rhizosphere interaction of both species on the uptake of Cd. The Cd accumulations in the shoot of pakchoi were significantly reduced in the inter-crop treatment, also the decreased percentage increased with rhizosphere interaction between the two species. In the inter-crop systems of 75 days, the Cd concentration and amount in the shoot of pakchoi represented 54% and 83% reduction, respectively, while the total depletion of Cd decreased by approximate 19%. Although the Cd concentration and amount in the shoot of pakchoi were significantly reduced by 52% and 44%, respectively, in the crop-rotation treatment, the decreased percentage were markedly lower than in the inter-crop treatment. Therefore, the rhizosphere interaction of hyperaccumulator with non-hyperaccumulator may reduce the risk of vegetable contamination during making full use of or remediating the contaminated soil.

  12. 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

  13. Thallium contamination of soils/vegetation as affected by sphalerite weathering: a model rhizospheric experiment.

    PubMed

    Vaněk, Aleš; Grösslová, Zuzana; Mihaljevič, Martin; Ettler, Vojtěch; Chrastný, Vladislav; Komárek, Michael; Tejnecký, Václav; Drábek, Ondřej; Penížek, Vít; Galušková, Ivana; Vaněčková, Barbora; Pavlů, Lenka; Ash, Christopher

    2015-01-01

    The environmental stability of Tl-rich sphalerite in two contrasting soils was studied. Rhizospheric conditions were simulated to assess the risk associated with sulfide microparticles entering agricultural (top)soils. The data presented here clearly demonstrate a significant effect of 500 μM citric acid, a model rhizospheric solution, on ZnS alteration followed by enhanced Tl and Zn release. The relative ZnS mass loss after 28 days of citrate incubation reached 0.05 and 0.03 wt.% in Cambisol and Leptosol samples respectively, and was up to 4 times higher, compared to H2O treatments. Incongruent (i.e., substantially increased) mobilization of Tl from ZnS was observed during the incubation time. Generally higher (long-term) stability of ZnS with lower Tl release is predicted for soils enriched in carbonates. Furthermore, the important role of silicates (mainly illite) in the stabilization of mobilized Tl, linked with structural (inter)layer Tl-K exchange, is suggested. Thallium was highly bioavailable, as indicated by its uptake by white mustard; maximum Tl amounts were detected in biomass grown on the acidic Cambisol. Despite the fact that sulfides are thought as relatively stable phases in soil environments, enhanced sulfide dissolution and Tl/trace element release (and bioaccumulation) can be assumed in rhizosphere systems.

  14. 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

  15. 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.

  16. Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil

    PubMed Central

    García-Salamanca, Adela; Molina-Henares, M Antonia; van Dillewijn, Pieter; Solano, Jennifer; Pizarro-Tobías, Paloma; Roca, Amalia; Duque, Estrella; Ramos, Juan L

    2013-01-01

    Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH 8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common. PMID:22883414

  17. Physiological Diversity of the Rhizosphere Diazotroph Assemblages of Selected Salt Marsh Grasses

    PubMed Central

    Bagwell, Christopher E.; Piceno, Yvette M.; Ashburne-Lucas, Amy; Lovell, Charles R.

    1998-01-01

    Rhizosphere diazotroph assemblages of salt marsh grasses are thought to be influenced by host plant species and by a number of porewater geochemical parameters. Several geochemical variables can adversely affect plant productivity and spatial distributions, resulting in strong zonation of plant species and growth forms. This geochemically induced stress may also influence the species compositions and distributions of rhizosphere diazotroph assemblages, but little is currently known about these organisms. The diversity and key physiological features of culturable, O2-tolerant rhizosphere diazotrophs associated with the tall and short growth forms of Spartina alterniflora and with Juncus roemerianus were examined. A total of 339 gram-negative strains were isolated by a root stab culture approach and morphologically and physiologically characterized by using API and BIOLOG tests. Eighty-six distinct groups composed of physiologically similar strains were identified. Of these groups, 72% were shown to be capable of N2 fixation through molecular analyses, and a representative strain was chosen from each diazotroph group for further characterization. Cluster and principal-components analysis of BIOLOG data allowed the designation of physiologically distinct strain groupings. Most of these groups were dominated by strains that were not identifiable to species on the basis of API or BIOLOG testing. Representatives of several families including the Enterobacteriaceae, Vibrionaceae, Azotobacteraceae, Spirillaceae, Pseudomonadaceae, and Rhizobiaceae were recovered, as well as strains with no clear taxonomic affiliations. This study identifies numerous potentially important physiological groups of the salt marsh diazotroph assemblage. PMID:9797277

  18. Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere

    PubMed Central

    Yang, Bo; Wang, Xiao-Mi; Ma, Hai-Yan; Yang, Teng; Jia, Yong; Zhou, Jun; Dai, Chuan-Chao

    2015-01-01

    The endophytic fungus Phomopsis liquidambari performs an important ecosystem service by assisting its host with acquiring soil nitrogen (N), but little is known regarding how this fungus influences soil N nutrient properties and microbial communities. In this study, we investigated the impact of P. liquidambari on N dynamics, the abundance and composition of N cycling genes in rhizosphere soil treated with three levels of N (urea). Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and diazotrophs were assayed using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis at four rice growing stages (S0: before planting, S1: tillering stage, S2: grain filling stage, and S3: ripening stage). A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions. Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages. The root exudates were determined due to their important role in rhizosphere interactions. P. liquidambari colonization altered the exudation of organic compounds by rice roots and P. liquidambari increased the concentration of soluble saccharides, total free amino acids and organic acids in root exudates. Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil. PMID:26441912

  19. 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.

  20. 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

  1. Mass spectrometry imaging: towards mapping the elemental and molecular composition of the rhizosphere

    DOE PAGES

    Veličković, Dušan; Anderton, Christopher R.

    2017-03-22

    In our short review provides perspective regarding the use of mass spectrometry imaging (MSI) to study the rhizosphere. It also serves to complement the multi-omic-focused review by White et al. in this journals’ issue. MSI is capable of elucidating chemical distributions within samples of interest in situ, and thus can provide spatial context to MS omics data in complementary experimental endeavors. Most MSI-based studies of plant-microbe interactions have focused on the phyllosphere and on the “associated rhizosphere” (our term for material that is not removed during harvesting). Sample preparation for these in situ analyses tends to be a limiting factor.more » Our studies, however, have provided valuable insights into the spatial arrangement of proteins, peptides, lipids, and other metabolites within these systems. We intend this short review to be a primer on the fundamentals of MSI and its role in plant-microbe analysis. Finally, we offer a perspective on the future of MSI and its use in understanding the molecular transformations beyond what we call the associated rhizosphere, one which extends to the rest of rhizosphere and into the bulk soil.« less

  2. [Effects of different mulches on rhizosphere temperature, growth, and physiological properties of fluecured tobacco].

    PubMed

    Jia, Zhihong; Yi, Jianhua; Sun, Zaijun

    2006-11-01

    With greenhouse plastic film, rice straw plus greenhouse plastic film, soil-mulching plastic film, rice straw, rice straw plus sun-shading net, and sun-shading net as test mulches, this paper studied their effects on the rhizosphere temperature, growth, and physiological properties of flue-cured tobacco. The results showed that after mulching for 22 days, the accumulative rhizosphere temperature at the depth of 5 cm was the highest (424.75 degrees C) for greenhouse plastic film and the lowest (378.75 degrees C) for rice straw plus sun-shading net, while that at the depth of 15 cm was the highest (396.75 degrees C) for greenhouse plastic film and the lowest (368.31 degrees C) for sun-shading net. With the increase of accumulative rhizosphere temperature, the dry weight of above- and underground parts, photosynthesis, and root vigor of flue-cured tobacco tended to increase, and at the 10th day after mulches removal, root biomass had the largest increment in the treatment of soil-mulching plastic film and the smallest increment in the treatment of rice straw plus sun-shading net.

  3. Potential of siderophore production by bacteria isolated from heavy metal: polluted and rhizosphere soils.

    PubMed

    Hussein, Khalid A; Joo, Jin Ho

    2014-06-01

    Recently, heavy metals have been shown to have a stimulating effect on siderophore biosynthesis in various bacteria. In addition, several studies have found that siderophore production is greater in bacteria isolated from soil near plant roots. The aim of this study was to compare the production of siderophores by bacterial strains isolated from heavy metal-contaminated and uncontaminated soils. Chrome azurol sulphonate was used to detect siderophore secretion by several bacterial strains isolated from heavy metal-contaminated and rhizosphere-uncontaminated soils with both a qualitative disc diffusion method and a quantitative ultraviolet spectrophotometric method. Siderophore production by rhizosphere bacteria was significantly greater than by bacteria isolated from contaminated soil. The Pearson's correlation test indicated a positive correlation between the amount of siderophore produced by bacteria isolated from the rhizosphere using the quantitative and qualitative detection methods and the amount of heavy metal in the soil. However, a significant negative correlation was observed between the amount of siderophore produced by bacteria isolated from heavy metal-contaminated soil and the amount of heavy metal (r value of -0.775, P < 0.001).

  4. In Situ Monitoring of Streptothricin Production by Streptomyces rochei F20 in Soil and Rhizosphere

    PubMed Central

    Anukool, Usanee; Gaze, William H.; Wellington, Elizabeth M. H.

    2004-01-01

    The onset of streptothricin (ST) biosynthesis in Streptomyces rochei F20 was studied by using reverse transcription-PCR (RT-PCR) to detect transcripts of ST genes during growth in liquid medium, soil, and the rhizosphere. In situ results correlated with those obtained in vitro, illustrating the growth phase-dependent manner of ST production by F20. Maximal transcription of ST resistance (sttR) and biosynthesis (sttA) genes occurred during the transition between the exponential and stationary phases of growth, when the specific growth rate (μ) started to decline. A higher level of gene expression of sttR versus sttA was observed in all experiments. In liquid culture, maximal transcript accumulation of the sttA gene was only ca. 40% that of the sttR gene. sttA and sttR mRNAs were detected in soil containing approximately 106 CFU of growing cells g of soil−1. sttR mRNA was detected in sterile and nonsterile rhizosphere colonized with growing mycelium of F20 at 1.2 × 106 and 4.0 × 105 CFU g of soil−1, respectively. However, neither sttR nor sttA transcripts were detected by RT-PCR in the rhizoplane, which supported a lower population density of F20 than the rhizosphere. PMID:15345403

  5. A radioisotope based methodology for plant-fungal interactions in the rhizosphere

    SciTech Connect

    Weisenberger, A. G.; Bonito, G.; Lee, S.; McKisson, J. E.; Gryganskyi, A.; Reid, C. D.; Smith, M. F.; Vaidyanathan, G.; Welch, B.

    2013-10-01

    In plant ecophysiology research there is interest in studying the biology of the rhizosphere because of its importance in plant nutrient-interactions. The rhizosphere is the zone of soil surrounding a plant's root system where microbes (such as fungi) are influenced by the root and the roots by the microbes. We are investigating a methodology for imaging the distribution of molecular compounds of interest in the rhizosphere without disturbing the root or soil habitat. Our intention is to develop a single photon emission computed tomography (SPECT) system (PhytoSPECT) to image the bio-distribution of fungi in association with a host plant's roots. The technique we are exploring makes use of radioactive isotopes as tracers to label molecules that bind to fungal-specific compounds of interest and to image the fungi distribution in the plant and/or soil. We report on initial experiments designed to test the ability of fungal-specific compounds labeled with an iodine radioisotope that binds to chitin monomers (N-acetylglucosamine). Chitin is a compound not found in roots but in fungal cell walls. We will test the ability to label the compound with radioactive isotopes of iodine ({sup 125}I, and {sup 123}I).

  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. 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.

  8. Microbiote shift in the Medicago sativa rhizosphere in response to cyanotoxins extract exposure.

    PubMed

    El Khalloufi, Fatima; Oufdou, Khalid; Bertrand, Marie; Lahrouni, Majida; Oudra, Brahim; Ortet, Philippe; Barakat, Mohamed; Heulin, Thierry; Achouak, Wafa

    2016-01-01

    The bloom-containing water bodies may have an impact due to cyanotoxins production on other microorganisms and aquatic plants. Where such water is being used for crops irrigation, the presence of cyanotoxins may also have a toxic impact on terrestrial plants and their rhizosphere microbiota. For that purpose, PCR-based 454 pyrosequencing was applied to phylogenetically characterize the bacterial community of Medicago sativa rhizosphere in response to cyanotoxins extract. This analysis revealed a wide diversity at species level, which decreased from unplanted soil to root tissues indicating that only some populations were able to compete for nutrients and niches in this selective habitat. Gemmatimonas, Actinobacteria, Deltaproteobacteria and Opitutae mainly inhabited the bulk soil, whereas, the root-adhering soil and the root tissues were inhabited by Gammaproteobacteria and Alphaproteobacteria. The proportion of these populations fluctuated in response to cyanotoxins extract exposure. Betaproteobacteria proportion increased in the three studied compartments, whereas Gammaproteobacteria proportion decreased except in the bulk soil. This study revealed the potential toxicity of cyanotoxins extract towards Actinobacteria, Gemmatimonas, Deltaproteobacteria, and Gammaproteobacteria, however Clostridia, Opitutae and bacteria related with Betaproteobacteria, were stimulated denoting their tolerance. Altogether, these data indicate that crop irrigation using cyanotoxins containing water might alter the rhizosphere functioning.

  9. Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil.

    PubMed

    García-Salamanca, Adela; Molina-Henares, M Antonia; van Dillewijn, Pieter; Solano, Jennifer; Pizarro-Tobías, Paloma; Roca, Amalia; Duque, Estrella; Ramos, Juan L

    2013-01-01

    Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH 8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common.

  10. The rhizosphere microbial community in a multiple parallel mineralization system suppresses the pathogenic fungus Fusarium oxysporum

    PubMed Central

    Fujiwara, Kazuki; Iida, Yuichiro; Iwai, Takashi; Aoyama, Chihiro; Inukai, Ryuya; Ando, Akinori; Ogawa, Jun; Ohnishi, Jun; Terami, Fumihiro; Takano, Masao; Shinohara, Makoto

    2013-01-01

    The rhizosphere microbial community in a hydroponics system with multiple parallel mineralization (MPM) can potentially suppress root-borne diseases. This study focused on revealing the biological nature of the suppression against Fusarium wilt disease, which is caused by the fungus Fusarium oxysporum, and describing the factors that may influence the fungal pathogen in the MPM system. We demonstrated that the rhizosphere microbiota that developed in the MPM system could suppress Fusarium wilt disease under in vitro and greenhouse conditions. The microbiological characteristics of the MPM system were able to control the population dynamics of F. oxysporum, but did not eradicate the fungal pathogen. The roles of the microbiological agents underlying the disease suppression and the magnitude of the disease suppression in the MPM system appear to depend on the microbial density. F. oxysporum that survived in the MPM system formed chlamydospores when exposed to the rhizosphere microbiota. These results suggest that the microbiota suppresses proliferation of F. oxysporum by controlling the pathogen's morphogenesis and by developing an ecosystem that permits coexistence with F. oxysporum. PMID:24311557

  11. Effects of light intensity and water temperature on oxygen release from roots into water lettuce rhizosphere.

    PubMed

    Soda, S; Ike, M; Ogasawara, Y; Yoshinaka, M; Mishima, D; Fujita, M

    2007-01-01

    The oxygen release rate into the rhizosphere by a floating aquatic plant-water lettuce-was determined under various light intensities (0.0-1.2x10(5)lx) and water temperatures (10-35 degrees C). The net specific oxygen release rate was expressed by a model equation comprising the gross oxygen release rate and the rhizosphere respiration terms. Experimental and simulated results show that the net specific oxygen release rate increased with light intensity up to the optimal value, but slight inhibition by higher light intensities was observed at 10-20 degrees C. With increased water temperature, the respiration rate became larger than the gross oxygen release rate. The maximum net specific oxygen release rate of 11.0-12.5mg-O(2)kg-wet(-1)h(-1) was obtained at the optimal condition of about 25 degrees C and 9.0x10(4)-1.1x10(5)lx. The net oxygen release rate was negligible at 35 degrees C at any light intensity because the respiration rate was much greater than the gross oxygen release rate into the rhizosphere.

  12. 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

  13. [Nutrient Characteristics and Nitrogen Forms of Rhizosphere Soils Under Four Typical Plants in the Littoral Zone of TGR].

    PubMed

    Wang, Xiao-feng; Yuan, Xing-zhong; Liu, Hong; Zhang, Lei; Yu, Jian-jun; Yue, Jun-sheng

    2015-10-01

    The Three Gorges Reservoir (TGR), which is the largest water conservancy project ever built in tne world, produced a drawdown area of about 348.93 km2 because of water level control. The biological geochemical cycle of the soil in the drawdown zone has been changed as the result of long-term winter flooding and summer drought and vegetation covering. The loss of soil nitrogen in the drawdown zone poses a threat to the water environmental in TGR. Pengxi river, is an important anabranch, which has the largest drawdown area has been selected in the present study. The four typical vegetation, contained Cynodon dactylon, Cyperus rotundus, Anthium sibiricum and Zea mays L. as the control, were studied to measure nutrient characteristics and nitrogen forms of rhizosphere and non-rhizosphere soils in three distribution areas with different soil types (paddy soil, purple soil and fluvo-aquic soils). The variables measured included organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), hydrolysis N, available P and available K, pH, ion-exchangeable N (IEE-N), weak acid extractable N (CF-N) , iron-manganese oxides N (IMOF-N), organic matter sulfide N (OSF-N), added up four N forms for total transferable N (TF-N) and TN minus TF-N for non-transferable N (NTF-N). The results showed: (1) pH of rhizosphere soil was generally lower than that of non-rhizosphere soil under different vegetation in different type soils because the possible organic acid and H+ released form plant roots and cation absorption differences, and the OM, TP, TN and hydrolysis N of rhizosphere soil were generally higher than those of non-rhizosphere soil, and that the enrichment ratio (ER) of all the four nutrient indicators showed Cyperus rotundus > Cynodon dactylon > Zea mays L. > Anthium sibiricum. Available P showed enrichment in the rhizosphere of three natural vegetations but lose under corn, and available K, TK showed different ER in different conditions. (2) IEF-N CF

  14. 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

  15. 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.

  16. [Effects of nitrogen fertilization and root separation on the plant growth and grain yield of maize and its rhizosphere microorganisms].

    PubMed

    Zhang, Xiang-Qian; Huang, Guo-Qin; Bian, Xin-Min; Zhao, Qi-Guo

    2012-12-01

    A field experiment with root separation was conducted to study the effects of root interaction in maize-soybean intercropping system on the plant growth and grain yield of maize and its rhizosphere microorganisms under different nitrogen fertilization levels (0.1, 0.3, 0.5, and 0.7 g x kg(-1)). Root interaction and nitrogen fertilization had positive effects on the plant height, leaf length and width, and leaf chlorophyll content of maize. Less difference was observed in the root dry mass of maize at maturing stage between the treatments root separation and no root separation. However, as compared with root separation, no root separation under the nitrogen fertilization levels 0.1, 0.3, 0.5, and 0.7 g x kg(-1) increased the biomass per maize plant by 8.8%, 6.3%, 3.6%, and 0.7%, and the economic yield per maize plant by 17.7%, 10.0%, 8.2%, and 0.9%, respectively. No root separation increased the quantity of rhizosphere fungi and azotobacteria significantly, as compared with root separation. With increasing nitrogen fertilization level, the quantity of rhizosphere bacteria, fungi, and actinomycetes presented an increasing trend, while that of rhizosphere azotobacteria decreased after an initial increase. The root-shoot ratio of maize at maturing stage was significantly negatively correlated with the quantity of rhizosphere bacteria, fungi, and actinomycetes, but less correlated with the quantity of rhizosphere azotobacteria. It was suggested that the root interaction in maize-soybean intercropping system could improve the plant growth of maize and increase the maize yield and rhizosphere microbial quantity, but the effect would be decreased with increasing nitrogen fertilization level.

  17. [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.

  18. Enhanced Mineralization of [U-14C]2,4-Dichlorophenoxyacetic Acid in Soil from the Rhizosphere of Trifolium pratense

    PubMed Central

    Shaw, Liz J.; Burns, Richard G.

    2004-01-01

    Enhanced biodegradation in the rhizosphere has been reported for many organic xenobiotic compounds, although the mechanisms are not fully understood. The purpose of this study was to discover whether rhizosphere-enhanced biodegradation is due to selective enrichment of degraders through growth on compounds produced by rhizodeposition. We monitored the mineralization of [U-14C]2,4-dichlorophenoxyacetic acid (2,4-D) in rhizosphere soil with no history of herbicide application collected over a period of 0 to 116 days after sowing of Lolium perenne and Trifolium pratense. The relationships between the mineralization kinetics, the number of 2,4-D degraders, and the diversity of genes encoding 2,4-D/α-ketoglutarate dioxygenase (tfdA) were investigated. The rhizosphere effect on [14C]2,4-D mineralization (50 μg g−1) was shown to be plant species and plant age specific. In comparison with nonplanted soil, there were significant (P < 0.05) reductions in the lag phase and enhancements of the maximum mineralization rate for 25- and 60-day T. pratense soil but not for 116-day T. pratense rhizosphere soil or for L. perenne rhizosphere soil of any age. Numbers of 2,4-D degraders in planted and nonplanted soil were low (most probable number, <100 g−1) and were not related to plant species or age. Single-strand conformational polymorphism analysis showed that plant species had no impact on the diversity of α-Proteobacteria tfdA-like genes, although an impact of 2,4-D application was recorded. Our results indicate that enhanced mineralization in T. pratense rhizosphere soil is not due to enrichment of 2,4-D-degrading microorganisms by rhizodeposits. We suggest an alternative mechanism in which one or more components of the rhizodeposits induce the 2,4-D pathway. PMID:15294813

  19. Survival of Azospirillum brasilense in the Bulk Soil and Rhizosphere of 23 Soil Types

    PubMed Central

    Bashan, Y.; Puente, M. E.; Rodriguez-Mendoza, M. N.; Toledo, G.; Holguin, G.; Ferrera-Cerrato, R.; Pedrin, S.

    1995-01-01

    The survival of Azospirillum brasilense Cd and Sp-245 in the rhizosphere of wheat and tomato plants and in 23 types of plant-free sterilized soils obtained from a wide range of environments in Israel and Mexico was evaluated. Large numbers of A. brasilense cells were detected in all the rhizospheres tested, regardless of soil type, bacterial strain, the origin of the soil, or the amount of rainfall each soil type received prior to sampling. Survival of A. brasilense in soils without plants differed from that in the rhizosphere and was mainly related to the geographical origin of the soil. In Israeli soils from arid, semiarid, or mountain regions, viability of A. brasilense rapidly declined or populations completely disappeared below detectable levels within 35 days after inoculation. In contrast, populations in the arid soils of Baja California Sur, Mexico, remained stable or even increased during the 45-day period after inoculation. In soils from Central Mexico, viability slowly decreased with time. In all soils, percentages of clay, nitrogen, organic matter, and water-holding capacity were positively correlated with bacterial viability. High percentages of CaCO(inf3) and fine or rough sand had a highly negative effect on viability. The percentage of silt, pH, the percentage of phosphorus or potassium, electrical conductivity, and C/N ratio had no apparent effect on bacterial viability in the soil. Fifteen days after removal of inoculated plants, the remaining bacterial population in the three soil types tested began to decline sharply, reaching undetectable levels 90 days after inoculation. After plant removal, percolating the soils with water almost eliminated the A. brasilense population. Viability of A. brasilense in two artificial soils containing the same major soil components as the natural soils from Israel did was almost identical to that in the natural soils. We conclude that A. brasilense is a rhizosphere colonizer which survives poorly in most soils

  20. Impact of a Bacterial Volatile 2,3-Butanediol on Bacillus subtilis Rhizosphere Robustness

    PubMed Central

    Yi, Hwe-Su; Ahn, Yeo-Rim; Song, Geun C.; Ghim, Sa-Youl; Lee, Soohyun; Lee, Gahyung; Ryu, Choong-Min

    2016-01-01

    Volatile compounds, such as short chain alcohols, acetoin, and 2,3-butanediol, produced by certain strains of root-associated bacteria (rhizobacteria) elicit induced systemic resistance in plants. The effects of bacterial volatile compounds (BVCs) on plant and fungal growth have been extensively studied; however, the impact of bacterial BVCs on bacterial growth remains poorly understood. In this study the effects of a well-characterized bacterial volatile, 2,3-butanediol, produced by the rhizobacterium Bacillus subtilis, were examined in the rhizosphere. The nature of 2,3-butanediol on bacterial cells was assessed, and the effect of the molecule on root colonization was also determined. Pepper roots were inoculated with three B. subtilis strains: the wild type, a 2,3-butanediol overexpressor, and a 2,3-butanediol null mutant. The B. subtilis null strain was the first to be eliminated in the rhizosphere, followed by the wild-type strain. The overexpressor mutant was maintained at roots for the duration of the experiment. Rhizosphere colonization by a saprophytic fungus declined from 14 days post-inoculation in roots treated with the B. subtilis overexpressor strain. Next, exudates from roots exposed to 2,3-butanediol were assessed for their impact on fungal and bacterial growth in vitro. Exudates from plant roots pre-treated with the 2,3-butanediol overexpressor were used to challenge various microorganisms. Growth was inhibited in a saprophytic fungus (Trichoderma sp.), the 2,3-butanediol null B. subtilis strain, and a soil-borne pathogen, Ralstonia solanacearum. Direct application of 2,3-butanediol to pepper roots, followed by exposure to R. solanacearum, induced expression of Pathogenesis-Related (PR) genes such as CaPR2, CaSAR8.2, and CaPAL. These results indicate that 2,3-butanediol triggers the secretion of root exudates that modulate soil fungi and rhizosphere bacteria. These data broaden our knowledge regarding bacterial volatiles in the rhizosphere and

  1. Comparison of Survival of Campylobacter jejuni in the Phyllosphere with That in the Rhizosphere of Spinach and Radish Plants

    PubMed Central

    Brandl, Maria T.; Haxo, Aileen F.; Bates, Anna H.; Mandrell, Robert E.

    2004-01-01

    Campylobacter jejuni has been isolated previously from market produce and has caused gastroenteritis outbreaks linked to produce. We have tested the ability of this human pathogen to utilize organic compounds that are present in leaf and root exudates and to survive in the plant environment under various conditions. Carbon utilization profiles revealed that C. jejuni can utilize many organic acids and amino acids available on leaves and roots. Despite the presence of suitable substrates in the phyllosphere and the rhizosphere, C. jejuni was unable to grow on lettuce and spinach leaves and on spinach and radish roots of plants incubated at 33°C, a temperature that is conducive to its growth in vitro. However, C. jejuni was cultured from radish roots and from the spinach rhizosphere for at least 23 and 28 days, respectively, at 10°C. This enteric pathogen also persisted in the rhizosphere of spinach for prolonged periods of time at 16°C, a temperature at which many cool-season crops are grown. The decline rate constants of C. jejuni populations in the spinach and radish rhizosphere were 10- and 6-fold lower, respectively, than on healthy spinach leaves at 10°C. The enhanced survival of C. jejuni in soil and in the rhizosphere may be a significant factor in its contamination cycle in the environment and may be associated with the sporadic C. jejuni incidence and campylobacteriosis outbreaks linked to produce. PMID:14766604

  2. 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.

  3. 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.

  4. 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.

  5. Comparison of survival of Campylobacter jejuni in the phyllosphere with that in the rhizosphere of spinach and radish plants.

    PubMed

    Brandl, Maria T; Haxo, Aileen F; Bates, Anna H; Mandrell, Robert E

    2004-02-01

    Campylobacter jejuni has been isolated previously from market produce and has caused gastroenteritis outbreaks linked to produce. We have tested the ability of this human pathogen to utilize organic compounds that are present in leaf and root exudates and to survive in the plant environment under various conditions. Carbon utilization profiles revealed that C. jejuni can utilize many organic acids and amino acids available on leaves and roots. Despite the presence of suitable substrates in the phyllosphere and the rhizosphere, C. jejuni was unable to grow on lettuce and spinach leaves and on spinach and radish roots of plants incubated at 33 degrees C, a temperature that is conducive to its growth in vitro. However, C. jejuni was cultured from radish roots and from the spinach rhizosphere for at least 23 and 28 days, respectively, at 10 degrees C. This enteric pathogen also persisted in the rhizosphere of spinach for prolonged periods of time at 16 degrees C, a temperature at which many cool-season crops are grown. The decline rate constants of C. jejuni populations in the spinach and radish rhizosphere were 10- and 6-fold lower, respectively, than on healthy spinach leaves at 10 degrees C. The enhanced survival of C. jejuni in soil and in the rhizosphere may be a significant factor in its contamination cycle in the environment and may be associated with the sporadic C. jejuni incidence and campylobacteriosis outbreaks linked to produce.

  6. 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

  7. 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

  8. Effect of Compost on Rhizosphere Microflora of the Tomato and on the Incidence of Plant Growth-Promoting Rhizobacteria

    PubMed Central

    de Brito, Alvarez M. A.; Gagne, S.; Antoun, H.

    1995-01-01

    Four commercial composts were added to soil to study their effect on plant growth, total rhizosphere microflora, and incidence of plant growth-promoting rhizobacteria (PGPR) in the rhizosphere of tomato plants. Three of the compost treatments significantly improved plant growth, while one compost treatment significantly depressed it. Compost amendments caused only small variations in the total numbers of bacteria, actinomycetes, and fungi in the rhizosphere of tomato plants. A total of 709 bacteria were isolated from the four compost treatments and the soil control to determine the percentage of PGPR in each treatment. The PGPR tests measured antagonism to soilborne root pathogens, production of indoleacetic acid, cyanide, and siderophores, phosphate solubilization, and intrinsic resistance to antibiotics. Our results show that the addition of some composts to soil increased the incidence in the tomato rhizosphere of bacteria exhibiting antagonism towards Fusarium oxysporum f. sp. radicis-lycopersici, Pyrenochaeta lycopersici, Pythium ultimum, and Rhizoctonia solani. The antagonistic effects observed were associated with marked increases in the percentage of siderophore producers. No significant differences were observed in the percentage of cyanogens, whereas the percentages of phosphate solubilizers and indoleacetic acid producers were affected, respectively, by one and two compost treatments. Intrinsic resistance to antibiotics was only marginally different among the rhizobacterial populations. Our results suggest that compost may stimulate the proliferation of antagonists in the rhizosphere and confirm previous reports indicating that the use of composts in container media has the potential to protect plants from soilborne root pathogens. PMID:16534902

  9. 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

  10. Draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi).

    PubMed

    Kolton, Max; Green, Stefan J; Harel, Yael Meller; Sela, Noa; Elad, Yigal; Cytryn, Eddie

    2012-10-01

    Here we report the draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi). Flavobacterium spp. are ubiquitous in the rhizospheres of agricultural crops; however, little is known about their physiology. To our knowledge, this is the first published genome of a root-associated Flavobacterium strain.

  11. 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

  12. [Difference of rhizosphere microbe quantity and functional diversity among three flue-cured tobacco cultivars with different resistance].

    PubMed

    Cai, Qiu-hua; Zuo, Jin-xiang; Li, Zhong-huan; Zhang, Ya-ping; Zhao, Yong-gang; Deng, Qiao; Ouyang, Jin; Huang, Jun-jie; Yu, Lu; Zou, Jian; Zhao, Zheng-xiong

    2015-12-01

    Field experiments were conducted in Shilin and Xundian respectively to study the diffe- rence of rhizosphere microbe quantity and functional diversity with plate culture method and Biolog technique among Hongda (high susceptibility, S), Yun87 (middle resistance, MR) and K326 (high resistance, R) , three flue-cured tobacco cultivars with different resistance to bacterial wilt and black shank. The results indicated that the amounts of bacteria, actinomycetes and the total number of microbes in tobacco plants' rhizosphere were positively correlated with the cultivar' s re- sistance, while it was opposite for the fungi. The consistent tendency was obtained not only at 35 d, 55 d and 75 d after transplanting, but also at two experimental sites. Cultivar and experimental con- ditions greatly affected the utilization of six types of carbon source by rhizospheric microbes, as well as the AWCD value. In Xundian site, rhizospheric microbes' utilization of carbohydrates, amino acids, carboxylic acids, polymers,. amines and the AWCD value were all higher at 55 d and 75 d after transplanting for the resistant cultivar than the susceptible one, but it was opposite at 75 d after transplanting for the phenolic acids. In Shilin, significant differences existed among the three culti- vars at 35 d, 55 d and 75 d after transplanting for the indices mentioned above, although they were not consistent with cultivars' resistance. Principal component (PC) analysis even showed that utili- zation of carbon sources by rhizosphere microorganisms differed significantly among the three culti- vars at the two sites, and it was better reflected by PC1 and PC2 at 55 d and 75 d after transplan- ting, respectively. In conclusion, rhizosphere microbial community structure and functional diversity were greatly affected not only by the cultivars' difference in resistance, but also by experimental conditions.

  13. Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest

    PubMed Central

    Yang, Zhenping; Yang, Wenping; Li, Shengcai; Hao, Jiaomin; Su, Zhifeng; Sun, Min; Gao, Zhiqiang; Zhang, Chunlai

    2016-01-01

    As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping crops with peanut

  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. Multitrophic Interaction in the Rhizosphere of Maize: Root Feeding of Western Corn Rootworm Larvae Alters the Microbial Community Composition

    PubMed Central

    Dematheis, Flavia; Zimmerling, Ute; Flocco, Cecilia; Kurtz, Benedikt; Vidal, Stefan; Kropf, Siegfried; Smalla, Kornelia

    2012-01-01

    Background Larvae of the Western Corn Rootworm (WCR) feeding on maize roots cause heavy economical losses in the US and in Europe. New or adapted pest management strategies urgently require a better understanding of the multitrophic interaction in the rhizosphere. This study aimed to investigate the effect of WCR root feeding on the microbial communities colonizing the maize rhizosphere. Methodology/Principal Findings In a greenhouse experiment, maize lines KWS13, KWS14, KWS15 and MON88017 were grown in three different soil types in presence and in absence of WCR larvae. Bacterial and fungal community structures were analyzed by denaturing gradient gel electrophoresis (DGGE) of the16S rRNA gene and ITS fragments, PCR amplified from the total rhizosphere community DNA. DGGE bands with increased intensity were excised from the gel, cloned and sequenced in order to identify specific bacteria responding to WCR larval feeding. DGGE fingerprints showed that the soil type and the maize line influenced the fungal and bacterial communities inhabiting the maize rhizosphere. WCR larval feeding affected the rhiyosphere microbial populations in a soil type and maize line dependent manner. DGGE band sequencing revealed an increased abundance of Acinetobacter calcoaceticus in the rhizosphere of several maize lines in all soil types upon WCR larval feeding. Conclusion/Significance The effects of both rhizosphere and WCR larval feeding seemed to be stronger on bacterial communities than on fungi. Bacterial and fungal community shifts in response to larval feeding were most likely due to changes of root exudation patterns. The increased abundance of A. calcoaceticus suggested that phenolic compounds were released upon WCR wounding. PMID:22629377

  16. 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

  17. 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

  18. Does a rhizospheric microorganism enhance K⁺ availability in agricultural soils?

    PubMed

    Meena, Vijay Singh; Maurya, B R; Verma, Jay Prakash

    2014-01-01

    The potassium solubilizing microorganisms (KSMs) are a rhizospheric microorganism which solubilizes the insoluble potassium (K) to soluble forms of K for plant growth and yield. K-solubilization is carried out by a large number of saprophytic bacteria (Bacillus mucilaginosus, Bacillus edaphicus, Bacillus circulans, Acidothiobacillus ferrooxidans, Paenibacillus spp.) and fungal strains (Aspergillus spp. and Aspergillus terreus). Major amounts of K containing minerals (muscovite, orthoclase, biotite, feldspar, illite, mica) are present in the soil as a fixed form which is not directly taken up by the plant. Nowadays most of the farmers use injudicious application of chemical fertilizers for achieving maximum productivity. However, the KSMs are most important microorganisms for solubilizing of fixed form of K in soil system. The KSMs are an indigenous rhizospheric microorganism which shows effective interaction between soil and plant systems. The main mechanism of KSMs is acidolysis, chelation, exchange reactions, complexolysis and production of organic acid. According to literature, currently negligible use of potassium fertilizer as a chemical form has been recorded in agriculture for enhancing crop yield. Most of the farmers use only nitrogen and phosphorus and not use the K fertilizer due to unawareness so that the problem of K deficiency occurs in rhizospheric soils. The K fertilizer is also costly as compared to other chemical fertilizers. Therefore, the efficient KSMs should be applied for solubilization of a fixed form of K to an available form of K in the soils. This available K can be easily taken up by the plant for growth and development. Our aim of this review is to elaborate on the studies of indigenous K-solubilizing microbes to develop efficient microbial consortia for solubilization of K in soil which enhances the plant growth and yield of crops. This review highlights the future need for research on potassium (K) in agriculture.

  19. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.

    PubMed

    Teixeira, Lia C R S; Peixoto, Raquel S; Cury, Juliano C; Sul, Woo Jun; Pellizari, Vivian H; Tiedje, James; Rosado, Alexandre S

    2010-08-01

    The Antarctic is a pristine environment that contributes to the maintenance of the global climate equilibrium. The harsh conditions of this habitat are fundamental to selecting those organisms able to survive in such an extreme habitat and able to support the relatively simple ecosystems. The DNA of the microbial community associated with the rhizospheres of Deschampsia antarctica Desv (Poaceae) and Colobanthus quitensis (Kunth) BartI (Caryophyllaceae), the only two native vascular plants that are found in Antarctic ecosystems, was evaluated using a 16S rRNA multiplex 454 pyrosequencing approach. This analysis revealed similar patterns of bacterial diversity between the two plant species from different locations, arguing against the hypothesis that there would be differences between the rhizosphere communities of different plants. Furthermore, the phylum distribution presented a peculiar pattern, with a bacterial community structure different from those reported of many other soils. Firmicutes was the most abundant phylum in almost all the analyzed samples, and there were high levels of anaerobic representatives. Also, some phyla that are dominant in most temperate and tropical soils, such as Acidobacteria, were rarely found in the analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Bifidobacterium (phylum Actinobacteria), Arcobacter (phylum Proteobacteria) and Faecalibacterium (phylum Firmicutes). To the best of our knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago.

  20. [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.

  1. 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.

  2. Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status

    PubMed Central

    Yang, Ching-Hong; Crowley, David E.

    2000-01-01

    Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status. PMID:10618246

  3. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status.

    PubMed

    Yang, C H; Crowley, D E

    2000-01-01

    Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.

  4. Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang

    PubMed Central

    Debnath, Rajal; Yadav, Archana; Gupta, Vijai K.; Singh, Bhim P.; Handique, Pratap J.; Saikia, Ratul

    2016-01-01

    Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria abundance. TN was also the significant predictor for less abundant taxonomic groups Chloroflexi, Gemmatimonadetes, and Nitrospirae. Bum La soil harbored less bacterial diversity compared to other sites at lower altitudes. The most abundant phyla at 3% genetic difference were Acidobacteria, Actinobacteria, and Proteobacteria amongst others. Analysis of similarity indicated greater similarity within lower altitudinal than higher altitudinal group (ANOSIM, R = 0.287, p = 0.02). Constraining the ordination with the edaphic factor explained 83.13% of variation. Unique phylotypes of Bradyrhizobium and uncultured Rhizobiales were found in significant proportions at the four regions. With over 1% relative abundance Actinobacteria (42.6%), Acidobacteria (24.02%), Proteobacteria (16.00%), AD3 (9.23%), WPS-2 (5.1%), and Chloroflexi (1.48%) dominated the core microbiome. PMID:27642287

  5. Enhanced Nitrogen Availability in Karst Ecosystems by Oxalic Acid Release in the Rhizosphere.

    PubMed

    Pan, Fujing; Liang, Yueming; Zhang, Wei; Zhao, Jie; Wang, Kelin

    2016-01-01

    In karst ecosystems, a high level of CaCO3 enhances the stabilization of soil organic matter (SOM) and causes nitrogen (N) and/or phosphorus (P) limitation in plants. Oxalic acid has been suggested to be involved in the nutrient-acquisition strategy of plants because its addition can temporarily relieve nutrient limitation. Therefore, understanding how oxalic acid drives N availability may help support successful vegetation restoration in the karst ecosystems of southwest China. We tested a model suggested by Clarholm et al. (2015) where oxalate reacts with Ca bridges in SOM, thus exposing previously protected areas to enzymatic attacks in a way that releases N for local uptake. We studied the effects of oxalic acid, microbial biomass carbon (MBC), and β-1,4-N-acetylglucosaminidase (NAG) on potential N mineralization rates in rhizosphere soils of four plant species (two shrubs and two trees) in karst areas. The results showed that rhizosphere soils of shrubs grown on formerly deforested land had significantly lower oxalic acid concentrations and NAG activity than that of trees in a 200-year-old forest. The levels of MBC in rhizosphere soils of shrubs were significantly lower than those of trees in the growing season, but the measure of shrubs and trees were similar in the non-growing season; the potential N mineralization rates showed a reverse pattern. Positive relationships were found among oxalic acid, MBC, NAG activity, and potential N mineralization rates for both shrubs and trees. This indicated that oxalic acid, microbes, and NAG may enhance N availability for acquisition by plants. Path analysis showed that oxalic acid enhanced potential N mineralization rates indirectly through inducing microbes and NAG activities. We found that the exudation of oxalic acid clearly provides an important mechanism that allows plants to enhance nutrient acquisition in karst ecosystems.

  6. Rhizosphere Inhibition of Cucumber Fusarium Wilt by Different Surfactin- excreting Strains of Bacillus subtilis.

    PubMed

    Jia, Ke; Gao, Yu-Han; Huang, Xiao-Qin; Guo, Rong-Jun; Li, Shi-Dong

    2015-06-01

    Bacillus subtilis B006 strain effectively suppresses the cucumber fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (Foc). The population dynamics of Foc, strain B006 and its surfactin over-producing mutant B841 and surfactin-deficient mutant B1020, in the rhizosphere were determined under greenhouse conditions to elucidate the importance of the lipopeptides excreted by these strains in suppressing Foc. Results showed that B. subtilis strain B006 effectively suppressed the disease in natural soil by 42.9%, five weeks after transplanting, whereas B841 and B1020 suppressed the disease by only 22.6% and 7.1%, respectively. Quantitative PCR assays showed that effective colonization of strain B006 in the rhizosphere suppressed Foc propagation by more than 10 times both in nursery substrate and in field-infected soil. Reduction of Foc population at the cucumber stems in a range of 0.96 log10 ng/g to 2.39 log10 ng/g was attained at the third and the fifth weeks of B006 treatment in nursery substrate. In field-infected soil, all three treatments with B. subtilis suppressed Foc infection, indicated by the reduction of Foc population at a range of 2.91 log10 ng/g to 3.36 log10 ng/g at the stem base, one week after transplanting. This study reveals that the suppression of fusarium wilt disease is affected by the effective colonization of the surfactin-producing B. subtilis strain in the rhizosphere. These results improved our understanding of the biocontrol mechanism of the B. subtilis strain B006 in the natural soil and facilitate its application as biocontrol agent in the field.

  7. Survey of sediment oxygenation in rhizospheres of the saltmarsh grass - Spartina anglica.

    PubMed

    Koop-Jakobsen, Ketil; Fischer, Jan; Wenzhöfer, Frank

    2017-07-01

    Although transport of oxygen via the aerenchyma tissue and subsequent oxygen loss across root surfaces is well-documented for salt marsh grasses, only few studies have measured the oxygenation of sediment surrounding roots and rhizomes. In this study, sediment oxygenation was assessed in situ in rhizospheres of the intertidal salt marsh grass, Spartina anglica - an invading species, vigorously spreading in many wetlands around the world. The rhizospheres of two populations of S. anglica with differing plant morphology growing in different sediment types were investigated in situ using a novel multifiber optode system with 100 oxygen probes. No oxygen was detected inside the rhizospheres at any depth in either location, indicating a limited impact of plant-mediated sediment oxygenation on the bulk anoxic sediment. Subsequent planar optode studies imaging the oxygen content around the roots substantiated these findings showing that sediment oxygenation was present in both locations, but it was confined only to the immediate vicinity of the root tips. The size of the oxic zones surrounding the root tips differed between sediment-types: in S. anglica growing in permeable sandy sediment, oxic root zones extended 1.5mm away from the roots surface compared to only 0.4mm in muddy tidal flat deposit, which had a substantially higher oxygen demand. The oxygen concentration inside the oxic root zones remained stable during continuous light and air-exposure of the aboveground biomass. In comparison, sediment oxygenation generated by burrowing infauna (Hediste diversicolor) showed to be markedly more temporally variability, reaching anoxic conditions multiple times during a 5-h period.

  8. Plant growth promoting potential of bacteria isolated on N free media from rhizosphere of Cassia occidentalis.

    PubMed

    Arun, B; Gopinath, B; Sharma, Shilpi

    2012-09-01

    Plant growth promoting rhizobacteria (PGPR) are an attractive eco-friendly alternative to chemicals in agriculture. While the rhizospheres of crop plants have been well studied with the objective of screening PGPR, weeds, which play an important role in maintaining ecological balance, have largely been ignored. The rhizosphere of a luxuriantly growing, medicinal weed, Cassia occidentalis was analysed by enumerating PGPR on N free media from the most diverse stage of plant (determined by profiles obtained on denaturing gradient gel electrophoresis). Each isolate was tested for other plant growth promotion assays including production of cellulase, indole acetic acid (IAA), ammonia, HCN, siderophore and chitinase to select for ones possessing multi-trait plant growth promoting (PGP) properties. Selected isolates were used for bacterization of Vigna radiata and Vigna mungo to evaluate their efficacy in promoting plant's growth in seedling germination and axenic pot conditions. Thirty five isolates were analysed further for the array of PGP properties they exhibit. A total of 6 isolates were shortlisted on the basis of maximum traits positive, amount of phosphate solubilized and IAA produced. V. radiata responded well to seed bacterization during seedling germination. A maximum increase of approximately 36 and 60 % was observed for shoot and root length, respectively in V. radiata in axenic pot culture over control plants. Extensive branching of roots was also observed with isolate NL, which produced the maximum amount of IAA. Present study investigated the plant growth promoting isolates obtained on N free media in the rhizosphere of C. occidentalis, which have the potential to be used as inoculants for other crops. This provides a new dimension to the significance of weeds in agricultural ecosystems. The study opens up possibilities for utilization of this property of weeds in plant growth promotion, and subsequent enhancement of yield for agricultural crops.

  9. 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.

  10. Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

    NASA Astrophysics Data System (ADS)

    Abdoun, Hamid; McMillan, Mary; Pereg, Lily

    2016-04-01

    Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

  11. Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

    PubMed Central

    Zerbe, Stefan

    2014-01-01

    The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P < 0.05) on 16S rRNA gene diversity revealed significant differences (P < 0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities. PMID:24995302

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  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. Microbial cooperation in the rhizosphere improves liquorice growth under salt stress.

    PubMed

    Egamberdieva, Dilfuza; Wirth, Stephan; Li, Li; Abd Allah, Elsayed Fathi; Lindström, Kristina

    2016-10-26

    Liquorice (Glycyrrhiza uralensis Fisch.) is one of the most widely used plants in food production, and it can also be used as an herbal medicine or for reclamation of salt-affected soils. Under salt stress, inhibition of plant growth, nutrient acquisition and symbiotic interactions between the medicinal legume liquorice and rhizobia have been observed. We recently evaluated the interactions between rhizobia and root-colonizing Pseudomonas in liquorice grown in potting soil and observed increased plant biomass, nodule numbers and nitrogen content after combined inoculation compared to plants inoculated with Mesorhizobium alone. Several beneficial effects of microbes on plants have been reported; studies examining the interactions between symbiotic bacteria and root-colonizing Pseudomonas strains under natural saline soil conditions are important, especially in areas where a hindrance of nutrients and niches in the rhizosphere are high. Here, we summarize our recent observations regarding the combined application of rhizobia and Pseudomonas on the growth and nutrient uptake of liquorice as well as the salt stress tolerance mechanisms of liquorice by a mutualistic interaction with microbes. Our observations indicate that microbes living in the rhizosphere of liquorice can form a mutualistic association and coordinate their involvement in plant adaptations to stress tolerance. These results support the development of combined inoculants for improving plant growth and the symbiotic performance of legumes under hostile conditions.

  18. Diversity of rhizosphere associated entomopathogenic fungi of perennial herbs, shrubs and coniferous trees.

    PubMed

    Fisher, Joanna J; Rehner, Stephen A; Bruck, Denny J

    2011-02-01

    Understanding habitat selection of fungal entomopathogens is critical to improve the efficacy, persistence and cost of these fungi as microbial insecticides. This study sought to determine the prevalence of Metarhizium and Beauveria spp. isolated from the rhizosphere of strawberry, blueberry, grape and Christmas tree crops in the Willamette Valley of Oregon. Entomopathogenic fungi were assigned to thirteen species based on molecular phylogenetic criteria. Four species of Metarhizium were isolated including Metarhizium brunneum, Metarhizium guizhouense, Metarhizium robertsii, and Metarhizium flavoviride var. pemphigi. Nine Beauveria species were isolated including, Beauveria brongniartii, an undescribed species referred to as Clade C and seven phylogenetic species of Beauveria bassiana. Strawberries and blueberries were significantly associated with M. brunneum and Christmas trees with M. guizhouense and M. robertsii. Grapes were significantly associated with B. bassiana phylogenetic species Bbas-16. All of the Metarhizium isolates screened were pathogenic to Otiorhynchus sulcatus larvae in laboratory bioassays but only M. brunneum and M. robertsii caused significant levels of infection. The study results suggest that certain species of Metarhizium and Beauveria are significantly associated with the strawberry, blueberry and Christmas tree rhizosphere and could potentially provide better control of O. sulcatus.

  19. Ecological functions of Trichoderma spp. and their secondary metabolites in the rhizosphere: interactions with plants.

    PubMed

    Contreras-Cornejo, Hexon Angel; Macías-Rodríguez, Lourdes; del-Val, Ek; Larsen, John

    2016-04-01

    Trichodermaspp. are common soil and root inhabitants that have been widely studied due to their capacity to produce antibiotics, parasitize other fungi and compete with deleterious plant microorganisms. These fungi produce a number of secondary metabolites such as non-ribosomal peptides, terpenoids, pyrones and indolic-derived compounds. In the rhizosphere, the exchange and recognition of signaling molecules byTrichodermaand plants may alter physiological and biochemical aspects in both. For example, severalTrichodermastrains induce root branching and increase shoot biomass as a consequence of cell division, expansion and differentiation by the presence of fungal auxin-like compounds. Furthermore,Trichoderma, in association with plant roots, can trigger systemic resistance and improve plant nutrient uptake. The present review describes the most recent advances in understanding the ecological functions ofTrichodermaspp. in the rhizosphere at biochemical and molecular levels with special emphasis on their associations with plants. Finally, through a synthesis of the current body of work, we present potential future research directions on studies related toTrichodermaspp. and their secondary metabolites in agroecosystems.

  20. 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.

  1. [Effects of rhizosphere soil permeability on water and nutrient uptake by maize].

    PubMed

    Niu, Wen-quan; Guo, Chao

    2010-11-01

    Aimed to better understand the significance of soil microenvironment in crop growth, a pot experiment was conducted to investigate the effects of rhizosphere soil permeability on the water and nutrient uptake by maize. Under three irrigation levels (600, 400, and 200 ml per pot), three treatments of soil aeration (no tube aeration as the control, tube aeration every two days, and tube aeration every four days) were installed, and the physiological indices of maize were measured. Under the same irrigation levels, soil aeration increased the plant height, leaf area, chlorophyll contents, promoted nutrient adsorption and increased root vitality markedly. At elongation stage, treatment tube aeration every four days had the highest root vitality (8.24 mg x g(-1) x h(-1)) under the irrigation level 600 ml per pot, being significantly higher (66.7%) than that (4.94 mg x g(-1) x h(-1)) of the control. Soil aeration had no significant effects on the transpiration rate of maize, indicating that rhizosphere soil aeration could raise water and nutrient use efficiency, and improve maize growth.

  2. 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.

  3. [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.

  4. 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.

  5. 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

  6. 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

  7. Using Raman spectroscopy and SERS for in situ studies of rhizosphere bacteria

    NASA Astrophysics Data System (ADS)

    Polisetti, Sneha; Baig, Nameera; Bible, Amber; Morrell-Falvey, Jennifer; Doktycz, Mitchel; Bohn, Paul W.

    2015-08-01

    Bacteria colonize plant roots to form a symbiotic relationship with the plant and can play in important role in promoting plant growth. Raman spectroscopy is a useful technique to study these bacterial systems and the chemical signals they utilize to interact with the plant. We present a Raman study of Pantoea YR343 that was isolated from the rhizosphere of Populus deltoides (Eastern Cottonwood). Pantoea sp. YR343 produce yellowish carotenoid pigment that play a role in protection against UV radiation, in the anti-oxidative pathways and in membrane fluidity. Raman spectroscopy is used to non-invasively characterize the membrane bound carotenoids. The spectra collected from a mutant strain created by knocking out the crtB gene that encodes a phytoene synthase responsible for early stage of carotenoid biosynthesis, lack the carotenoid peaks. Surface Enhanced Raman Spectroscopy is being employed to detect the plant phytoharmone indoleacetic acid that is synthesized by the bacteria. This work describes our recent progress towards utilizing Raman spectroscopy as a label free, non-destructive method of studying plant-bacteria interactions in the rhizosphere.

  8. 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

  9. 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)).

  10. Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland.

    PubMed

    Bai, Yaohui; Liang, Jinsong; Liu, Ruiping; Hu, Chengzhi; Qu, Jiuhui

    2014-01-01

    Microbial communities play a critical role in the degradation of effluent contaminants in constructed wetlands. Many questions remain, however, regarding the role ofmicrobial communities in rhizospheric soil. In this study, we used metagenomic analysis to assess microbial community composition and function in a constructed wetland receiving surface water. The diversity of the microbial community of rhizosphere soil was found to be significantly greater than that of the wetland influent water. This enhancement is likely due to the availability of diverse habitats and nutrients provided by the wetland plants. From function annotation of metagenomic data, a number of biodegradation pathways associated with 14 xenobiotic compounds were identified in soil. Nitrogen fixation, nitrification and denitrification genes were semi-quantitatively analysed. By screening of manganese transformation genes, we found that the biological oxidation of Mn2+ (mainly catalysed by multicopper oxidase) in the influent water yielded insoluble Mn4+, which subsequently precipitated and were incorporated into the wetland soil. These data show that the use of metagenomic analysis can provide important new insights for the study of wetland ecosystems and, in particular, how biologically mediated transformation or degradation can be used to reduce contamination of point and non-point source wastewater.

  11. Phosphate Solubilization Potential of Rhizosphere Fungi Isolated from Plants in Jimma Zone, Southwest Ethiopia

    PubMed Central

    Elias, Firew

    2016-01-01

    Phosphorus (P) is one of the major bioelements limiting agricultural production. Phosphate solubilizing fungi play a noteworthy role in increasing the bioavailability of soil phosphates for plants. The present study was aimed at isolating and characterizing phosphate solubilizing fungi from different rhizospheres using both solid and liquid Pikovskaya (PVK) medium. A total of 359 fungal isolates were obtained from 150 rhizosphere soil samples of haricot bean, faba bean, cabbage, tomato, and sugarcane. Among the isolates, 167 (46.52%) solubilized inorganic phosphate. The isolated phosphate solubilizing fungi belonged to genera of Aspergillus (55.69%), Penicillium spp. (23.35%), and Fusarium (9.58%). Solubilization index (SI) ranged from 1.10 to 3.05. Isolates designated as JUHbF95 (Aspergillus sp.) and JUFbF59 (Penicillium sp.) solubilized maximum amount of P 728.77 μg·mL−1 and 514.44 μg mL−1, respectively, from TCP (tricalcium phosphate) after 15 days of incubation. The highest (363 μg mL−1) soluble-P was released from RP with the inoculation of JUHbF95 in the PVK broth after 10 days of incubation. The present study indicated the presence of diverse plant associated P-solubilizing fungi that may serve as potential biofertilizers. PMID:27688771

  12. Using Raman Spectroscopy and SERS for in-situ studies of rhizosphere bacteria

    SciTech Connect

    Polisetti, Sneha; Baig, Nameera; Bible, Amber N; Morrell-Falvey, Jennifer L; Doktycz, Mitchel John; Bohn, Paul

    2015-01-01

    Bacteria colonize plant roots to form a symbiotic relationship with the plant and can play in important role in promoting plant growth. Raman spectroscopy is a useful technique to study these bacterial systems and the chemical signals they utilize to interact with the plant. We present a Raman study of Pantoea YR343 that was isolated from the rhizosphere of Populus deltoides (Eastern Cottonwood). Pantoea sp. YR343 produce yellowish carotenoid pigment that play a role in protection against UV radiation, in the anti-oxidative pathways and in membrane fluidity. Raman spectroscopy is used to non-invasively characterize the membrane bound carotenoids. The spectra collected from a mutant strain created by knocking out the crtB gene that encodes a phytoene synthase responsible for early stage of carotenoid biosynthesis, lack the carotenoid peaks. Surface Enhanced Raman Spectroscopy is being employed to detect the plant phytoharmone indoleacetic acid that is synthesized by the bacteria. This work describes our recent progress towards utilizing Raman spectroscopy as a label free, non-destructive method of studying plant-bacteria interactions in the rhizosphere.

  13. 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

  14. Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere

    PubMed Central

    Vacheron, Jordan; Moënne-Loccoz, Yvan; Dubost, Audrey; Gonçalves-Martins, Maximilien; Muller, Daniel; Prigent-Combaret, Claire

    2016-01-01

    Plant Growth-Promoting Rhizobacteria (PGPR) enhance plant health and growth using a variety of traits. Effective PGPR strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than PGPR strains with fewer plant-beneficial properties is unknown. Here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. To this end, the co-occurrence of 18 properties involved in enhanced plant nutrition, plant hormone modulation, or pathogen inhibition was analyzed by molecular and biochemical methods in a collection of maize rhizosphere and bulk soil isolates of fluorescent Pseudomonas. Twelve plant-beneficial properties were found among the 698 isolates. Contrarily to expectation, maize preferentially selected pseudomonads with low numbers of plant-beneficial properties (up to five). This selection was not due to the predominance of strains with specific assortments of these properties, or with specific taxonomic status. Therefore, the occurrence of only few plant-beneficial properties appeared favorable for root colonization by pseudomonads. PMID:27610110

  15. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

    PubMed Central

    Naveed, Muhammad; Mubeen, Samavia; khan, SamiUllah; Ahmed, Iftikhar; Khalid, Nauman; Suleria, Hafiz Ansar Rasul; Bano, Asghari; Mumtaz, Abdul Samad

    2014-01-01

    In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization. PMID:25477935

  16. Effect of tree species and mycorrhizal colonization on the archaeal population of boreal forest rhizospheres.

    PubMed

    Bomberg, Malin; Timonen, Sari

    2009-01-01

    Group 1.1c Crenarchaeota are the predominating archaeal group in acidic boreal forest soils. In this study, we show that the detection frequency of 1.1c crenarchaeotal 16S rRNA genes in the rhizospheres of the boreal forest trees increased following colonization by the ectomycorrhizal fungus Paxillus involutus. This effect was very clear in the fine roots of Pinus sylvestris, Picea abies, and Betula pendula, the most common forest trees in Finland. The nonmycorrhizal fine roots had a clearly different composition of archaeal 16S rRNA genes in comparison to the mycorrhizal fine roots. In the phylogenetic analysis, the 1.1c crenarchaeotal 16S rRNA gene sequences obtained from the fine roots formed a well-defined cluster separate from the mycorrhizal ones. Alnus glutinosa differed from the other trees by having high diversity and detection levels of Crenarchaeota both on fine roots and on mycorrhizas as well as by harboring a distinct archaeal flora. The similarity of the archaeal populations in rhizospheres of the different tree species was increased upon colonization by the ectomycorrhizal fungus. A minority of the sequences obtained from the mycorrhizas belonged to Euryarchaeota (order Halobacteriales).

  17. Enhanced phytoextraction of germanium and rare earth elements - a rhizosphere-based approach

    NASA Astrophysics Data System (ADS)

    Wiche, Oliver

    2016-04-01

    Germanium (Ge) and rare earth elements (REEs) are economically valuable raw materials that have become an integral part of our modern high tech society. While most of these elements are not actually rare in terms of general amounts in the earth's crust, they are rarely found in sufficient abundances in single locations for their mining to be economically viable. The average concentration of Ge in soils is estimated at 1.6 μg g-1. The REEs comprise a group of 16 elements including La, the group of lanthanides and Y that are abundant in the earth crust with concentrations varying from 35 μg g-1 (La), 40 μg g-1 (Nd), 6 μg g-1 (Gd) and 3.5 μg g-1 (Er) to 0.5 μg g-1 in Tm. Thus, a promising chance to improve supply of these elements could be phytomining. Unfortunately, bioavailability of Ge and REEs in soils appears to be low, in particular in neutral or alkaline soils. A sequential dissolution analysis of 120 soil samples taken from the A-horizons of soils in the area of Freiberg (Saxony, Germany) revealed that only 0.2% of total Ge and about 0.5% of La, Nd, Gd and Er of bulk concentrations were easily accessible by leaching with NH4-acetate (pH 7). Most of the investigated elements were bound to Fe-/Mn-oxides and silicates and were therefore only poorly available for plant uptake. Here we report an environmentally friendly approach for enhanced phytoextraction of Ge and REEs from soils using mixed cultures of plant species with efficient mechanisms for the acquisition of nutrients in the rhizosphere. The rhizosphere is characterized as the zone in soil sourrounding a plant root that consists of a gradient in chemical, physical and biological soil properties driven by rhizodeposits like carboxylates and protons. Some species like white lupin (Lupinus albus) are able to excrete large amounts of organic acid anions(predominantly citrate and malate) and show a particularly high potential for the acidification of the rhizosphere. In our experiments, mixed cultures

  18. 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

  19. 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.

  20. Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry

    PubMed Central

    Nallanchakravarthula, Srivathsa; Mahmood, Shahid; Alström, Sadhna; Finlay, Roger D.

    2014-01-01

    Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar. PMID:25347069

  1. Stability of Lead Immobilized by Apatite in Lead-Containing Rhizosphere Soil of Buckwheat (Fagopyrum esculentum) and Hairy Vetch (Vicia villosa).

    PubMed

    Katoh, Masahiko; Matsuoka, Hideaki; Sato, Takeshi

    2015-01-01

    This study conducted plant growth experiments using a rhizobox system to understand the growth of buckwheat and hairy vetch as well as the stability of lead immobilized by hydroxyapatite (HAP) in the lead-containing rhizosphere soil. The shoot dry weight of buckwheat did not significantly differ between the lead-containing rhizosphere soil with and without HAP, whereas that of hairy vetch with rhizosphere soil without HAP was reduced. Lead was not accumulated from the rhizosphere soil to the shoots of either plant when HAP was added. The percentage of each lead fraction in sequential extraction was approximately the same through the 3 mm of rhizosphere soils from the root surface and non-planted soil, with and without the addition of HAP. For hairy vetch, the amount of water-soluble lead in the HAP-added rhizosphere soil within 3 mm thickness from the root surface did not increase. However, for buckwheat, the amount of water-soluble lead in the HAP-added rhizosphere soil 1 mm from the root surface increased to the same level as that in the non-planted soil without HAP. Our results suggest that when applying phytostabilization combined with apatite to lead-contaminated soil, the plant that cannot re-mobilize lead should be selected.

  2. Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry.

    PubMed

    Nallanchakravarthula, Srivathsa; Mahmood, Shahid; Alström, Sadhna; Finlay, Roger D

    2014-01-01

    Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

  3. [Community diversity of bacteria and arbuscular mycorrhizal fungi in the rhizosphere of eight plants in Liudaogou watershed on the Loess Plateau China].

    PubMed

    Feng, Ye; Tang, Ming; Chen, Hui; Cong, Wei

    2012-01-01

    Terminal restriction fragment length polymorphism (T-RFLP) was used to examine the community diversity of bacteria and arbuscular mycorrhizal fungi (AMF) and their interrelation in the rhizosphere of 8 plants in the Liudaogou watershed in Shenmu County. The objective was to obtain diversity indices and provide theoretical basis for ecological restoration. Results showed significant variations in the species and abundances of rhizospheric bacteria and AMF associated with 8 plants. Among these, the Shannon diversity index of rhizospheric bacteria was the highest for Robinia pseudoacacia (4.01) and the lowest for Salix babylonica (2.18), whereas the Shannon diversity index of rhizospheric AMF was the highest for Populus simonii (2.07) and the lowest for Hippophae rhamnoides (1.21). Cluster analysis and redundancy analysis indicated a significant difference in associated microbial community structure, while the similarity among community diversity of rhizospheric bacteria and AMF associated with specific plants was also found. There was a significant correlation between diversity indices of bacteria and AMF (P < 0.01). Associated microbial community diversity was influenced primarily by organic matter and total nitrogen content. Our work demonstrated strong impacts of plant species and rhizospheric environment on associated microbial community structure. Due to the high diversity indices of rhizospheric bacteria and AMF, R. pseudoacacia was considered to be a pioneer plant species for vegetation restoration in the Liudaogou watershed.

  4. Effects of Bacillus amyloliquefaciens FZB42 on Lettuce Growth and Health under Pathogen Pressure and Its Impact on the Rhizosphere Bacterial Community

    PubMed Central

    Rändler, Manuela; Schmid, Michael; Junge, Helmut; Borriss, Rainer; Hartmann, Anton; Grosch, Rita

    2013-01-01

    The soil-borne pathogen Rhizoctonia solani is responsible for crop losses on a wide range of important crops worldwide. The lack of effective control strategies and the increasing demand for organically grown food has stimulated research on biological control. The aim of the present study was to evaluate the rhizosphere competence of the commercially available inoculant Bacillus amyloliquefaciens FZB42 on lettuce growth and health together with its impact on the indigenous rhizosphere bacterial community in field and pot experiments. Results of both experiments demonstrated that FZB42 is able to effectively colonize the rhizosphere (7.45 to 6.61 Log 10 CFU g−1 root dry mass) within the growth period of lettuce in the field. The disease severity (DS) of bottom rot on lettuce was significantly reduced from severe symptoms with DS category 5 to slight symptom expression with DS category 3 on average through treatment of young plants with FZB42 before and after planting. The 16S rRNA gene based fingerprinting method terminal restriction fragment length polymorphism (T-RFLP) showed that the treatment with FZB42 did not have a major impact on the indigenous rhizosphere bacterial community. However, the bacterial community showed a clear temporal shift. The results also indicated that the pathogen R. solani AG1-IB affects the rhizosphere microbial community after inoculation. Thus, we revealed that the inoculant FZB42 could establish itself successfully in the rhizosphere without showing any durable effect on the rhizosphere bacterial community. PMID:23935892

  5. Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra.

    PubMed

    Li, Lin; Xing, Ming; Lv, Jiangwei; Wang, Xiaolong; Chen, Xia

    2017-02-21

    Deyeuxia angustifolia (Komarov) Y. L Chang is an herb species originating from the birch forests in the Changbai Mountain. Recently, this species has been found encroaching into large areas in the western slopes of the alpine tundra in the Changbai Mountain, threatening the tundra ecosystem. In this study, we systematically assessed the response of the rhizosphere soil microbial to D. angustifolia encroaching in alpine tundra by conducting experiments for two vegetation types (shrubs and herbs) by real-time PCR and Illumina Miseq sequencing methods. The treatments consisted of D. angustifolia sites (DA), native sites (NS, NH) and encroaching sites (ES, EH). Our results show that (1) Rhizosphere soil properties of the alpine tundra were significantly impacted by D. angustifolia encroaching; microbial nutrient cycling and soil bacterial communities were shaped to be suitable for D. angustifolia growth; (2) The two vegetation community rhizosphere soils responded differently to D. angustifolia encroaching; (3) By encroaching into both vegetation communities, D. angustifolia could effectively replace the native species by establishing positive plant-soil feedback. The strong adaptation and assimilative capacity contributed to D. angustifolia encroaching in the alpine tundra. Our research indicates that D. angustifolia significantly impacts the rhizosphere soil microbial of the alpine tundra.

  6. Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils

    PubMed Central

    Dai, Zhongmin; Hu, Jiajie; Xu, Xingkun; Zhang, Lujun; Brookes, Philip C.; He, Yan; Xu, Jianming

    2016-01-01

    Sensitive responses among bacterial and fungal communities to pyrogenic organic matter (PyOM) (biochar) addition in rhizosphere and bulk soils are poorly understood. We conducted a pot experiment with manure and straw PyOMs added to an acidic paddy soil, and identified the sensitive “responders” whose relative abundance was significantly increased/decreased among the whole microbial community following PyOM addition. Results showed that PyOMs significantly (p < 0.05) increased root growth, and simultaneously changed soil chemical parameters by decreasing soil acidity and increasing biogenic resource. PyOM-induced acidity and biogenic resource co-determined bacterial responder community structure whereas biogenic resource was the dominant parameter structuring fungal responder community. Both number and proportion of responders in rhizosphere soil was larger than in bulk soil, regardless of PyOM types and microbial domains, indicating the microbial community in rhizosphere soil was sensitive to PyOM addition than bulk soil. The significant increased root biomass and length caused by PyOM addition, associated with physiological processes, e.g. C exudates secretion, likely favored more sensitive responders in rhizosphere soil than in bulk soil. Our study identified the responders at fine taxonomic resolution in PyOM amended soils, improved the understanding of their ecological phenomena associated with PyOM addition, and examined their interactions with plant roots. PMID:27824111

  7. [Comparison between transgenic insect-resistant cotton expressing Cry1Ac protein and its parental variety in rhizospheric fungal diversity].

    PubMed

    Pan, Jian-Gang; Jiao, Hai-Hua; Bai, Zhi-Hui; Qi, Hong-Yan; Ma, An-Zhou; Zhuang, Guo-qiang; Zhang, Hong-xun

    2014-11-01

    The dynamics of rhizospheric fungal diversity and biomass at different sampling stages associated with two transgenic insectresistant cottons expressing Cry1Ac protein and their control varieties were studied under greenhouse conditions, followed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time polymerase chain reaction (Q-PCR), in order to evaluate the ecological security of planting transgenic cotton expressing Cry1Ac protein. The results indicated that the fungal superior bands in rhizosphere of transgenic Bt cotton were similar with that of control cotton at four sampling stages, the more obvious difference in the blurred bands among transgenic Bt cotton, JM20 and SHIYUAN321 was detected. The rhizospheric fungal biomass of transgenic Bt cotton SGK321 was significantly lower than that of its parental control cotton at seedling stage, while the slight decrease in fungal biomass of transgenic Bt cotton XP188 was detected at boll forming stage, the ill-defined decrease, even growing tendency in two transgenic Bt cottons was detected at other stages. However, the difference of rhizospheric fungal community compositions and biomass was not only existed between transgenic cotton and its control, but also between SHIYUAN321 and JM20, and the same phenomenon was also detected between transgenic Bt cotton SGK321 and XP188. Hence, Bt protein is not the only incentive resulting in the difference in fungal community composition and diversity, the decrease in biomass between transgenic cotton and untransgenic cotton, different cotton varieties has an effect on them.

  8. Impact of the Spatial Heterogeneity of the Spermosphere and Rhizosphere on Performance of Bacterial Biological Control Agents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The spermosphere and rhizosphere environments are the critical interfaces where many plant-microbe and microbe-microbe interactions occurs that lead to plant disease and the suppression of plant disease by bacterial and other biological control agents. We discuss the spatial heterogeneity of the ph...

  9. Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra

    NASA Astrophysics Data System (ADS)

    Li, Lin; Xing, Ming; Lv, Jiangwei; Wang, Xiaolong; Chen, Xia

    2017-02-01

    Deyeuxia angustifolia (Komarov) Y. L Chang is an herb species originating from the birch forests in the Changbai Mountain. Recently, this species has been found encroaching into large areas in the western slopes of the alpine tundra in the Changbai Mountain, threatening the tundra ecosystem. In this study, we systematically assessed the response of the rhizosphere soil microbial to D. angustifolia encroaching in alpine tundra by conducting experiments for two vegetation types (shrubs and herbs) by real-time PCR and Illumina Miseq sequencing methods. The treatments consisted of D. angustifolia sites (DA), native sites (NS, NH) and encroaching sites (ES, EH). Our results show that (1) Rhizosphere soil properties of the alpine tundra were significantly impacted by D. angustifolia encroaching; microbial nutrient cycling and soil bacterial communities were shaped to be suitable for D. angustifolia growth; (2) The two vegetation community rhizosphere soils responded differently to D. angustifolia encroaching; (3) By encroaching into both vegetation communities, D. angustifolia could effectively replace the native species by establishing positive plant-soil feedback. The strong adaptation and assimilative capacity contributed to D. angustifolia encroaching in the alpine tundra. Our research indicates that D. angustifolia significantly impacts the rhizosphere soil microbial of the alpine tundra.

  10. Quantification of 2,4-diacetylphloroglucinol producing Pseudomonas fluorescens in the plant rhizosphere by real-time PCR.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A real-time PCR SYBR green assay was developed to quantify populations of 2, 4-DAPG-producing (phlD+) Pseudomonas fluorescens in soil and the rhizosphere. Primers were designed to specifically amplify the phlD gene from four different genotypes (A, B, D, and I) of phlD+ P. fluorescens and PCR condit...

  11. Quantification of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains in the plant rhizosphere by real-time PCR.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A real-time PCR SYBR green assay was developed to quantify populations of 2,4-diacetylphloroglucinol (2,4-DAPG)-producing (phlD+) strains of Pseudomonas fluorescens in soil and the rhizosphere. Primers were designed and PCR conditions were optimized to specifically amplify the phlD gene from four di...

  12. 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.

  13. Stability of Chloropyromorphite in Ryegrass Rhizosphere as Affected by Root-Secreted Low Molecular Weight Organic Acids

    PubMed Central

    Wei, Wei; Wang, Yu; Wang, Zheng; Han, Ruiming; Li, Shiyin; Wei, Zhenggui; Zhang, Yong

    2016-01-01

    Understanding the stability of chloropyromorphite (CPY) is of considerable benefit for improving risk assessment and remediation strategies in contaminated water and soil. The stability of CPY in the rhizosphere of phosphorus-deficient ryegrass was evaluated to elucidate the role of root-secreted low molecular weight organic acids (LMWOAs) on the dissolution of CPY. Results showed that CPY treatments significantly reduced the ryegrass biomass and rhizosphere pH. The presence of calcium nitrate extractable lead (Pb) and phosphorus (P) suggested that CPY in the rhizosphere could be bioavailable, because P and Pb uptake by ryegrass potentially provided a significant concentration gradient that would promote CPY dissolution. Pb accumulation and translocation in ryegrass was found to be significantly higher in P-sufficient conditions than in P-deficient conditions. CPY treatments significantly enhanced root exudation of LMWOAs irrigated with P-nutrient solution or P-free nutrient solution. Oxalic acid was the dominant species in root-secreted LMWOAs of ryegrass under P-free nutrient solution treatments, suggesting that root-secreted oxalic acid may be the driving force of root-induced dissolution of CPY. Hence, our work, provides clarifying hints on the role of LMWOAs in controlling the stability of CPY in the rhizosphere. PMID:27494023

  14. Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra

    PubMed Central

    Li, Lin; Xing, Ming; Lv, Jiangwei; Wang, Xiaolong; Chen, Xia

    2017-01-01

    Deyeuxia angustifolia (Komarov) Y. L Chang is an herb species originating from the birch forests in the Changbai Mountain. Recently, this species has been found encroaching into large areas in the western slopes of the alpine tundra in the Changbai Mountain, threatening the tundra ecosystem. In this study, we systematically assessed the response of the rhizosphere soil microbial to D. angustifolia encroaching in alpine tundra by conducting experiments for two vegetation types (shrubs and herbs) by real-time PCR and Illumina Miseq sequencing methods. The treatments consisted of D. angustifolia sites (DA), native sites (NS, NH) and encroaching sites (ES, EH). Our results show that (1) Rhizosphere soil properties of the alpine tundra were significantly impacted by D. angustifolia encroaching; microbial nutrient cycling and soil bacterial communities were shaped to be suitable for D. angustifolia growth; (2) The two vegetation community rhizosphere soils responded differently to D. angustifolia encroaching; (3) By encroaching into both vegetation communities, D. angustifolia could effectively replace the native species by establishing positive plant-soil feedback. The strong adaptation and assimilative capacity contributed to D. angustifolia encroaching in the alpine tundra. Our research indicates that D. angustifolia significantly impacts the rhizosphere soil microbial of the alpine tundra. PMID:28220873

  15. 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.

  16. Comparative analysis of cyanobacteria in the rhizosphere and as endosymbionts of cycads in drought-affected soils.

    PubMed

    Cuddy, William S; Neilan, Brett A; Gehringer, Michelle M

    2012-04-01

    Does the diversity of cyanobacteria in the cycad rhizosphere relate to the cyanobiont species found in the coralloid roots of these ancient plants? The aim of this study was to identify the diversity of soil cyanobacteria occurring in the immediate vicinity of 22 colonized coralloid roots belonging to members of the cycad genera: Macrozamia, Lepidozamia, Bowenia and Cycas. The majority of coralloid roots were sampled at depths > 10 cm below the soil surface. A total of 32 cyanobacterial isolates were cultured and their 16S rRNA gene partially sequenced. Phylogenetic analysis revealed nine operational taxonomic units of soil cyanobacteria comprising 30 Nostoc spp., a Tolypothrix sp. and a Leptolyngbya sp. Microscopy indicated that all isolates were unialgal and confirmed their genus identity. Rhizospheric diversity was compared to existing data on cyanobionts isolated at the same time from the cycad coralloid root. The same isolate was present in both the cycad coralloid root and rhizosphere at only six sites. Phylogenetic evidence indicates that most rhizosphere isolates were distinct from root cyanobionts. This weak relationship between the soil cyanobacteria and cycad cyanobionts might indicate that changes in the soil community composition are due to environmental factors.

  17. 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...

  18. Plant rhizosphere influence on microbial C metabolism: the role of elevated CO2, N availability and root stoichiometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial decomposer C metabolism is considered a factor controlling soil C stability, a key regulator of global climate. The plant rhizosphere is now recognized as a crucial driver of soil C dynamics but specific mechanisms are unclear. Climate change could affect microbial C metabolism via impacts...

  19. Temporal dynamics of microbial communities in the rhizosphere of two genetically modified (GM) maize hybrids in tropical agrosystems.

    PubMed

    Cotta, Simone Raposo; Dias, Armando Cavalcante Franco; Marriel, Ivanildo Evódio; Gomes, Eliane Aparecida; van Elsas, Jan Dirk; Seldin, Lucy

    2013-03-01

    The use of genetically modified (GM) plants still raises concerns about their environmental impact. The present study aimed to evaluate the possible effects of GM maize, in comparison to the parental line, on the structure and abundance of microbial communities in the rhizosphere. Moreover, the effect of soil type was addressed. For this purpose, the bacterial and fungal communities associated with the rhizosphere of GM plants were compared by culture-independent methodologies to the near-isogenic parental line. Two different soils and three stages of plant development in two different periods of the year were included. As evidenced by principal components analysis (PCA) of the PCR-DGGE profiles of evaluated community, clear differences occurred in these rhizosphere communities between soils and the periods of the year that maize was cultivated. However, there were no discernible effects of the GM lines as compared to the parental line. For all microbial communities evaluated, soil type and the period of the year that the maize was cultivated were the main factors that influenced their structures. No differences were observed in the abundances of total bacteria between the rhizospheres of GM and parental plant lines.

  20. Influence of Soil fumigation by Methyl Bromide and Methyl Iodide on Rhizosphere and Phyllosphere Microbial Community Structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizosphere and phyllosphere microbial communities were evaluated on roots and leaves of growth chamber-grown lettuce (Lactuca sativa (L.) cv. Green Forest) plants by culture-dependent and -independent methods after soil fumigation. Denaturing gradient gel electrophoresis (DGGE) with 16S rRNA primer...

  1. Water-Limiting Conditions Alter the Structure and Biofilm-Forming Ability of Bacterial Multispecies Communities in the Alfalfa Rhizosphere

    PubMed Central

    Bogino, Pablo; Abod, Ayelén; Nievas, Fiorela; Giordano, Walter

    2013-01-01

    Biofilms are microbial communities that adhere to biotic or abiotic surfaces and are enclosed in a protective matrix of extracellular compounds. An important advantage of the biofilm lifestyle for soil bacteria (rhizobacteria) is protection against water deprivation (desiccation or osmotic effect). The rhizosphere is a crucial microhabitat for ecological, interactive, and agricultural production processes. The composition and functions of bacterial biofilms in soil microniches are poorly understood. We studied multibacterial communities established as biofilm-like structures in the rhizosphere of Medicago sativa (alfalfa) exposed to 3 experimental conditions of water limitation. The whole biofilm-forming ability (WBFA) for rhizospheric communities exposed to desiccation was higher than that of communities exposed to saline or nonstressful conditions. A culture-dependent ribotyping analysis indicated that communities exposed to desiccation or saline conditions were more diverse than those under the nonstressful condition. 16S rRNA gene sequencing of selected strains showed that the rhizospheric communities consisted primarily of members of the Actinobacteria and α- and γ-Proteobacteria, regardless of the water-limiting condition. Our findings contribute to improved understanding of the effects of environmental stress factors on plant-bacteria interaction processes and have potential application to agricultural management practices. PMID:24223979

  2. 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.

  3. 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

  4. 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

  5. Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities.

    PubMed

    Zancarini, Anouk; Mougel, Christophe; Voisin, Anne-Sophie; Prudent, Marion; Salon, Christophe; Munier-Jolain, Nathalie

    2012-01-01

    Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM). First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability.

  6. 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

  7. Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments.

    PubMed

    Sliwinski, Marek K; Goodman, Robert M

    2004-03-01

    To explore whether the crenarchaeal consortium found in the rhizosphere is distinct from the assemblage of crenarchaeotes inhabiting bulk soil, PCR-single-stranded-conformation polymorphism (PCR-SSCP) profiles were generated for 76 plant samples collected from native environments. Divergent terrestrial plant groups including bryophytes (mosses), lycopods (club mosses), pteridophytes (ferns), gymnosperms (conifers), and angiosperms (seed plants) were collected for this study. Statistical analysis revealed significant differences between rhizosphere and bulk soil PCR-SSCP profiles (Hotelling paired T(2) test, P < 0.0001), suggesting that a distinct crenarchaeal consortium is associated with plants. In general, phylotype richness increased in the rhizosphere compared to the corresponding bulk soil, although the range of this increase was variable. Examples of a major change in rhizosphere (versus bulk soil) PCR-SSCP profiles were detected for all plant groups, suggesting that crenarchaeotes form associations with phylogenetically diverse plants in native environments. In addition, examples of minor to no detectable difference were found for all terrestrial plant groups, suggesting that crenarchaeal associations with plants are mediated by environmental conditions.

  8. Comparison of Crenarchaeal Consortia Inhabiting the Rhizosphere of Diverse Terrestrial Plants with Those in Bulk Soil in Native Environments

    PubMed Central

    Sliwinski, Marek K.; Goodman, Robert M.

    2004-01-01

    To explore whether the crenarchaeal consortium found in the rhizosphere is distinct from the assemblage of crenarchaeotes inhabiting bulk soil, PCR-single-stranded-conformation polymorphism (PCR-SSCP) profiles were generated for 76 plant samples collected from native environments. Divergent terrestrial plant groups including bryophytes (mosses), lycopods (club mosses), pteridophytes (ferns), gymnosperms (conifers), and angiosperms (seed plants) were collected for this study. Statistical analysis revealed significant differences between rhizosphere and bulk soil PCR-SSCP profiles (Hotelling paired T2 test, P < 0.0001), suggesting that a distinct crenarchaeal consortium is associated with plants. In general, phylotype richness increased in the rhizosphere compared to the corresponding bulk soil, although the range of this increase was variable. Examples of a major change in rhizosphere (versus bulk soil) PCR-SSCP profiles were detected for all plant groups, suggesting that crenarchaeotes form associations with phylogenetically diverse plants in native environments. In addition, examples of minor to no detectable difference were found for all terrestrial plant groups, suggesting that crenarchaeal associations with plants are mediated by environmental conditions. PMID:15006809

  9. Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a mediterranean forest after a wildfire.

    PubMed

    Cobo-Díaz, José F; Fernández-González, Antonio J; Villadas, Pablo J; Robles, Ana B; Toro, Nicolás; Fernández-López, Manuel

    2015-05-01

    Wildfires are frequent in the forests of the Mediterranean Basin and have greatly influenced this ecosystem. Changes to the physical and chemical properties of the soil, due to fire and post-fire conditions, result in alterations of both the bacterial communities and the nitrogen cycle. We explored the effects of a holm oak forest wildfire on the rhizospheric bacterial communities involved in the nitrogen cycle. Metagenomic data of the genes involved in the nitrogen cycle showed that both the undisturbed and burned rhizospheres had a conservative nitrogen cycle with a larger number of sequences related to the nitrogen incorporation pathways and a lower number for nitrogen output. However, the burned rhizosphere showed a statistically significant increase in the number of sequences for nitrogen incorporation (allantoin utilization and nitrogen fixation) and a significantly lower number of sequences for denitrification and dissimilatory nitrite reductase subsystems, possibly in order to compensate for nitrogen loss from the soil after burning. The genetic potential for nitrogen incorporation into the ecosystem was assessed through the diversity of the nitrogenase reductase enzyme, which is encoded by the nifH gene. We found that nifH gene diversity and richness were lower in burned than in undisturbed rhizospheric soils. The structure of the bacterial communities involved in the nitrogen cycle showed a statistically significant increase of Actinobacteria and Firmicutes phyla after the wildfire. Both approaches showed the important role of gram-positive bacteria in the ecosystem after a wildfire.

  10. Identification and onion pathogenicity of Burkholderia cepacia complex isolates from the onion rhizosphere and onion field soil.

    PubMed

    Jacobs, Janette L; Fasi, Anthony C; Ramette, Alban; Smith, James J; Hammerschmidt, Raymond; Sundin, George W

    2008-05-01

    Burkholderia cepacia complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on B. cepacia complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative B. cepacia complex isolates were recovered on Pseudomonas cepacia azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative B. cepacia complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and recA sequences and restriction fragment length polymorphism analysis of the recA sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species B. cepacia (160), B. cenocepacia (480), B. ambifaria (623), and B. pyrrocinia (27). The majority of isolates identified as B. cepacia (85%), B. cenocepacia (90%), and B. ambifaria (76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of recA sequences from representative B. cepacia complex type and panel strains, along with isolates collected in this study, revealed that the B. cenocepacia isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple B. cepacia complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source

  11. Field and laboratory assessments on dissolution and fractionation of Pb from spent and unspent shots in the rhizosphere soil.

    PubMed

    Hashimoto, Yohey

    2013-11-01

    The objective of this study was to determine the effect of plant root growth on Pb dissolution from shot under laboratory and field-scale conditions. For a laboratory study, a 100-d incubation experiment was conducted to assess Pb dissolution from unspent shot (new) and spent shot (>10yr in fields) in rhizosphere and non-rhizosphere (bulk) soils using the Toxicity Characteristic Leaching Procedure (TCLP) and sequential extraction methods. This study found that increasing the soil pH value to 7.5 by liming significantly reduced Pb dissolution from unspent and spent shot (<5mgL(-1)). Dissolution of Pb from shot was induced more in rhizosphere than bulk soils. Regardless of shot types, the averaged TCLP-Pb concentration in acidic and limed soils was 12.9- and 8.1-fold greater in rhizosphere than in bulk soils, respectively. For a field-scale investigation, a total of 31 individual plant samples of 6 different species and their rhizosphere soils were collected from a clay-target shooting range (<35000mgPbkg(-1)). The Pb concentration in plant aboveground tissues depended on species with a mean value of 72mgkg(-1) (15-254mgkg(-1)), which was far smaller than that reported in previous studies. Regardless of high soil Pb levels, aboveground tissue Pb concentrations of Solidago altissima (i.e., Canada goldenrod, 15mgkg(-1)) and Andropogon virginicus (i.e., broomsedge, 18mgkg(-1)) were below the toxicity threshold, suggesting that these indigenous species could have phytostabilization potentials. The limited Pb accumulation by vegetation was attributed to the abundance of soil calcite derived from spent clay-target fragments.

  12. 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.

  13. 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.

  14. [Effect of ectomycorrhizae on heavy metals sequestration by thermostable protein in rhizosphere of Pinus tabulaeformis under Cu and Cd stress].

    PubMed

    Zhang, Ying-Wei; Chai, Li-Wei; Wang, Dong-Wei; Wang, Jie; Huang, Yi

    2014-03-01

    Copper and cadmium in soil is a severe soil pollution problem in China. It is effective to remediate the soil by sequestrating Cu and Cd with tolerant plant and microorganism. Ectomycorrhizae could exude a large number of organic matter to reduce the biological effectiveness of heavy metals. Therefore, under Cu or Cd stress, thermostable protein in rhizosphere exuded by roots of pine seedling (Pinus tabulaeformis) associated with ectomycorrhizal fungi (Xerocomus chrysenteron) can have the potential of sequestration for heavy metals. The results illustrated that the association didn't impact on exudation of thermostable protein but treated with different concentrations of Cu, the total thermostable protein (TTP) and easily extracted thermostable protein (EETP) in mycorrhizal rhizosphere increased by 2.64 to 11.79 times compared with non-mycorrhizal one. While treated with Cd, it was 1.49 to 7.56 times. Further analysis of metal content in rhizosphere showed that association significantly increased the Cu sequestration in mycorrhizal rhizosphere where relative content of Cu was 1.81 to 2.75 times higher than those in non-mycorrhizal rhizosphere while most of Cu was sequestrated by thermostable protein, 4.19 to 43.00 times higher in protein than in root cell. Meanwhile results of Cd treatments showed a similar trend with Cu treatments. That indicated that under excessive heavy metals stress, ectomycorrhizal association facilitated the exudation of thermostable protein so as to extend the capacity of sequestration for excessive heavy metals and mitigate the phytotoxicity from heavy metals polluted soil.

  15. 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

  16. 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

  17. Life on the energetic edge: Iron oxidation by circumneutral lithotrophic bacteria in the wetland plant rhizosphere

    NASA Astrophysics Data System (ADS)

    Neubauer, S. C.; Emerson, D.; Megonigal, J. P.; Weiss, J. V.

    2002-05-01

    We have discovered a phylogenetically and genotypically coherent group of obligately lithotrophic Fe-oxidizing bacteria that grow at neutral pH and are globally distributed in a range of habitats, from the rhizosphere of freshwater wetlands to deep-sea hydrothermal vents. We have initiated bioreactor studies using pure cultures of these organisms to determine the significance of microbial Fe(II) oxidation at circumneutral pH and identify the biotic and abiotic variables that affect the partitioning between microbial and chemical oxidation. These studies have focused on strain BrT, which was isolated from an iron oxide precipitate in rhizosphere of a wetland plant. In one set of experiments, Fe(II) oxidation rates were measured before and after cultures of strain BrT were poisoned with sodium azide. These experiments indicated that 18 to 53 % of total iron oxidation was due to microbial metabolism. In a second set of experiments, Fe(II) was constantly added to bioreactors inoculated with live cells, killed cells, or no cells. A statistical model fit to the experimental data demonstrated that metabolic Fe(II) oxidation accounted for up to 62 % of total oxidation. Total Fe(II) oxidation rates in these experiments were strongly limited by the rate of Fe(II) delivery to the system, and were also influenced by O2 and total iron concentrations. Additionally, the model suggested that the microbes inhibited rates of abiotic Fe(II) oxidation, perhaps by binding Fe(II) to bacterial exopolymers. The net effect of strain BrT was to accelerate total oxidation rates by up to 18 % versus cell-free treatments. Using two independent techniques, we demonstrated that strain BrT actively metabolizes Fe(II) and can account for up to 50 to 60 % of total Fe(II) oxidation in laboratory cultures. These results suggest that neutrophilic Fe(II)-oxidizing bacteria may compete for limited O2 in the rhizosphere and influence the biogeochemistry of other elements including carbon, phosphorus, and

  18. Bacillus amyloliquefaciens SB14 from rhizosphere alleviates Rhizoctonia damping-off disease on sugar beet.

    PubMed

    Karimi, Elham; Safaie, Naser; Shams-Baksh, Masoud; Mahmoudi, Bagher

    2016-11-01

    The use of biocontrol strains recently has become a popular alternative to conventional chemical treatments. A set of bacteria isolated from sugar beet rhizosphere and from roots and shoots of apple and walnut were evaluated for their potential to control sugar beet seedling damping-off caused by R. solani AG-4 and AG2-2.The results of in vitro assays concluded that three isolates, SB6, SB14, SB15, obtained from rhizosphere of sugar beet and five isolates, AP2, AP4, AP6, AP7, AP8, obtained from shoots and roots of apple were the most effective antagonists that inhibited the mycelial growth of both R. solani isolates. Combination of several biochemical tests and partial sequencing of 16S rRNA and gyrBgenes revealed that eight efficient bacterial isolates could be assigned to the genus Bacillus and all could tolerate high temperatures and salt concentrations in their vegetative growth. The potential biocontrol activity of the eight bacterial antagonists were tested in greenhouse condition. The results indicated that four strains,B. amyloliquefaciens SB14, B. pumilus SB6,B. siamensis AP2 and B. siamensisAP8 exerted a significant influence on controlling of seedling damping-off and performed significantly better than others.However, the treatment of the seeds with bacteria was most effective when the isolate SB14 was used, which significantly controlled damping-off disease by 58% caused by R. solani AG-4 and by 52.5% caused by R. solani AG-2-2. This indicates that the use of beneficial bacterial native to the host plant may increase the success rate in screening biocontrols, because these microbes are likely to be better adapted to their host and its associated environmental conditions than are strains isolated from other plant species grown in different environmental conditions. We can infer from the results reported here that sugar beet plantsmay recruitbeneficial microbes to the rhizosphere to help them solve context-specific challenges.

  19. 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.

  20. Rhizosphere anode model explains high oxygen levels during operation of a Glyceria maxima PMFC.

    PubMed

    Timmers, Ruud A; Strik, David P B T B; Arampatzoglou, Cristina; Buisman, Cees J N; Hamelers, Hubertus V M

    2012-03-01

    In this paper, the effect of root oxygen loss on energy recovery of the plant microbial fuel cell (PMFC) is described. In this manner, advanced understanding of competing processes within the rhizosphere-anode interface was provided. A microscopic model was developed on the basis of exudation, oxygen loss, biological oxidation, and biological current generation. The model was successfully validated by comparison to oxygen concentration profiles, volatile fatty acid profiles, and chemical oxygen demand profiles measured in the anode compartment. The model predicted oxic zones around roots in the anode of the plant microbial fuel cell. Results show no direct link between current generation and photosynthesis. This was consistent with the model which predicted that current was generated via hydrolysis of root-derived organic compounds. This result means that to optimize energy recovery of a PMFC, the plant selection should focus on high root biomass production combined with low oxygen loss.

  1. Isolation and characterization of phosphate-solubilizing bacteria from seagrass rhizosphere soil

    NASA Astrophysics Data System (ADS)

    Ghosh, Upasana; Subhashini, Ponnambalam; Dilipan, Elangovan; Raja, Subramanian; Thangaradjou, Thirunavukarassu; Kannan, Lakshmanan

    2012-03-01

    Phosphate-solubilizing bacterial strains (6 Nos.) were isolated from the rhizosphere soils of two seagrasses ( Halophila ovalis (R. Br.) Hook and Halodule pinifolia (Miki) Hartog) in the Vellar estuary. Experimental studies found that the strain PSSG6 was effective in phosphate solubilization with Phosphate Solubilization efficiency index E = 375 ± 8.54, followed by the strain PSSG5 with Phosphate Solubilization efficiency index E = 275 ± 27.3. Of the 6 strains isolated, the strains PSSG4 and PSSG5 belonged to the genus Bacillus, and PSSG1, PSSG2 and PSSG3 were identified as Citrobacter sp., Shigella sp., and Klebsiella sp., respectively, by conventional method, and PSSG6 was identified as Bacillus circulans using conventional and molecular methods.

  2. Interactions between plant and rhizosphere microbial communities in a metalliferous soil.

    PubMed

    Epelde, Lur; Becerril, José M; Barrutia, Oihana; González-Oreja, José A; Garbisu, Carlos

    2010-05-01

    In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems.

  3. 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

  4. Isolation, characterization and screening of rhizospheric bacteria of Pittosferum resiniferum Hemsl.

    NASA Astrophysics Data System (ADS)

    Hanirah, R.; Piakong, M. T.; Syaufi, L.

    2015-04-01

    The bacterial rhizosphere species of host plant, Petroleum Nut (Pittosferum resiniferum) were isolated and characterized morphologically. The isolates were designated as, TSArp- Cr2, TSArp- Cr3, TSArp- Cr4, TSArp- Cr5, TSArp- Cr6 and TSArp- Cr7. All of the species were tested on three different concentration of phenol (1mM, 3mM and 5mM). Only species TSArp- Cr4 and TSArp- Cr6 growth were detected. The highest growth is 6Log10CFU/ml in 1mM by TSA-Cr4. The lowest reading was 3.6 Log10CFU/ml in 3mM by TSA-Cr6. Species TSArp- Cr4 has higher tolerance on phenol compared to TSArp- Cr6

  5. Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

    PubMed Central

    Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

    2013-01-01

    Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

  6. 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.

  7. Effects of VA mycorrhiza formation on plant nitrogen uptake and rhizosphere bacteria

    SciTech Connect

    Ames, R.N.

    1983-01-01

    Mycorrhizal and nonmycorrhizal sorghum plants were grown in pots at three levels of fertilizer nitrogen ((NH/sub 4/)/sub 2/SO/sub 4/) which had been enriched with /sup 15/N. Root colonization by Glomus mosseae did not affect plant growth or total N uptake, but significant reductions in mycorrhizal plant /sup 15/N:/sup 14/N ratios and increased 'A' values were found. This suggested that mycorrhizal plants had access to an N source which was less available to nonmycorrhizal plants. In two additional experiments, mycorrhizal and nonmycorrhizal celery plants were grown in pots which allowed VAM fungal hyphae, but not roots, to have direct access to /sup 15/N-enriched organic or inorganic N sources. Root dry weight was significantly reduced in mycorrhizal plants. Mycorrhizal plants had significantly greater shoot and root /sup 15/N content than nonmycorrhizal plants. Number and length of VAM fungal hyphae crossing into the area of /sup 15/N placement were positively correlated with mycorrhizal plant /sup 15/N content in the inorganic-N but not organic-N treatment. In a fourth experiment, the effect of G. mosseae on the rhizosphere populations of five bacterial isolates associated with blue grama (Bouteloua gracilis) was examined. No significant differences in bacterial populations were found in nonrhizosphere soil samples from pots of mycorrhizal and nonmycorrhizal plants. One bacterial isolate was significantly increased in number, while a different isolate and total bacterial populations were significantly reduced by the presence of the mycorrhizal fungus. The results suggest that root colonization by VAM fungi can alter rhizosphere bacterial populations.

  8. Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China

    PubMed Central

    Lv, Fenglian; Xue, Sha; Wang, Guoliang; Zhang, Chao

    2017-01-01

    Atmospheric nitrogen (N) deposition profoundly alters the soil microbial communities and will thus affect nutrient cycles. The effects of N availability on microbial community, however, are not clear. We used PLFA analysis to evaluate the effects of a gradient of N addition (0, 2.8, 5.6, 11.2, and 22.4 g N m-2 y-1) for three years on the rhizospheric microbial community of Pinus tabuliformis seedlings. The main factors influencing the community were quantified using structural equation modelling and redundancy analysis. At the microbial-community level, N addition increased the total phospholipid fatty acids content by increasing the dissolved organic carbon (DOC) and root biomass. Increases in soil microbial biomass carbon and N, however, was attributed to the increased DOC, N content and decreased pH. At the microbial-groups level, Fungal, arbuscular mycorrhizal fungal (AMF), gram-positive bacterial (GP) abundances and the GP:GN ratio first increased and then decreased with N addition. Nitrogen addition increased the abundances of bacteria, fungi, and actinomycetes mainly by increasing the DOC content and decreasing root biomass. Additionally, the decrease of pH and ammonium N caused by N addition increased the fungal abundances and reduced actinomycete abundances, respectively. Nitrogen addition shifted the rhizospheric microbial community mainly by altering the DOC content and root biomass. The current rate of N deposition (2.5 g N m-2 y-1) benefits plant growth and increases the abundances of fungi, arbuscular mycorrhizal fungi, GP, actinomycetes and the GP:GN ratio. PMID:28234932

  9. Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

    PubMed Central

    Xiao, Chunping; Yang, Limin; Zhang, Lianxue; Liu, Cuijing; Han, Mei

    2015-01-01

    Background Panax ginseng cannot be cultivated on the same land consecutively for an extended period, and the underlying mechanism regarding microorganisms is still being explored. Methods Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and BIOLOG methods were used to evaluate the microbial genetic and functional diversity associated with the P. ginseng rhizosphere soil in various cultivation ages and modes. Results The analysis of microbial diversity using PCR-DGGE showed that microbial communities were significantly variable in composition, of which six bacterial phyla and seven fungal classes were detected in P. ginseng soil. Among them, Proteobacteria and Hypocreales dominated. Fusarium oxysporum, a soilborne pathogen, was found in all P. ginseng soil samples except R0. The results from functional diversity suggested that the microbial metabolic diversity of fallow soil abandoned in 2003 was the maximum and transplanted soil was higher than direct-seeding soil and the forest soil uncultivated P. ginseng, whereas the increase in cultivation ages in the same mode led to decreases in microbial diversity in P. ginseng soil. Carbohydrates, amino acids, and polymers were the main carbon sources utilized. Furthermore, the microbial diversity index and multivariate comparisons indicated that the augmentation of P. ginseng cultivation ages resulted in decreased bacterial diversity and increased fungal diversity, whereas microbial diversity was improved strikingly in transplanted soil and fallow soil abandoned for at least one decade. Conclusion The key factors for discontinuous P. ginseng cultivation were the lack of balance in rhizosphere microbial communities and the outbreak of soilborne diseases caused by the accumulation of its root exudates. PMID:26843819

  10. CHARACTERIZATION AND BIOCONTROL POTENT OF STREPTOMYCES SP. ISOLATED FROM THE RHIZOSPHERE OF ONONIS ANGUSTISSIMA LAM.

    PubMed

    Ghadbane, M; Belhadj, H; Medjekal, S; Harzallah, D

    2015-01-01

    A total of 40 actinomycetes isolated from rhizosphere soils of Ononis angustissima Lam. were in vitro tested for their antagonism against deferent pathogenic microorganisms by streak assay. Among the isolates, four (21, 2A26, 1B10 and 2C34) present a potent antagonism against both pathogenic bacteria and fungi, they were selected, identified by 16S rDNA sequence analysis and phenotypic properties, and tested for their antimicrobial activity as well as their biocontrol potential against Chickpea (Cicer arietinum L.) pathogenic fungus (Fusarium oxysporum). Cultural characteristic studies strongly suggested that these strains belong to the genus Streptomyces. The four Streptomyces sp., solubilize phosphate and produce extracellular fungal cell-wall degrading enzymes chitinase and protease, as well as a marked production of acid-β-indole acetic (AIA). The nucleotide sequence of the 16S rRNA gene of Streptomyces sp. strains 21, 2A26, 1B10 and 2C34 exhibited close similarity (62-75%) with Streptomyces parvulus MARS 16S rRNA genes. The inhibition was higher against fungi and Gram+ bacteria, while Gram- bacteria were less inhibited. The growth of the plant pathogenic fungus Fusarium oxysporum was considerably inhibited in the presence of the strains 21, 2A26, 1B10 and 2C34 culture supernatant. These studies revealed that the presence of the Streptomyces strains in the soil significantly promoted the growth of the Chickpea plants. These results indicate that the Streptomyces strains isolated for rhizosphere from Ononis angustissima Lam. growing in arid conditions in southern Algeria (Sahara) could be an interesting source for antimicrobial bioactive substances and as biocontrol agents.

  11. Host identity impacts rhizosphere fungal communities associated with three alpine plant species.

    PubMed

    Becklin, Katie M; Hertweck, Kate L; Jumpponen, Ari

    2012-04-01

    Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect

  12. Selenium addition alters mercury uptake, bioavailability in the rhizosphere and root anatomy of rice (Oryza sativa)

    PubMed Central

    Wang, Xun; Tam, Nora Fung-Yee; Fu, Shi; Ametkhan, Aray; Ouyang, Yun; Ye, Zhihong

    2014-01-01

    Background and Aims Mercury (Hg) is an extremely toxic pollutant, especially in the form of methylmercury (MeHg), whereas selenium (Se) is an essential trace element in the human diet. This study aimed to ascertain whether addition of Se can produce rice with enriched Se and lowered Hg content when growing in Hg-contaminated paddy fields and, if so, to determine the possible mechanisms behind these effects. Methods Two cultivars of rice (Oryza sativa, japonica and indica) were grown in either hydroponic solutions or soil rhizobags with different Se and Hg treatments. Concentrations of total Hg, MeHg and Se were determined in the roots, shoots and brown rice, together with Hg uptake kinetics and Hg bioavailability in the soil. Root anatonmy was also studied. Key Results The high Se treatment (5 μg g–1) significantly increased brown rice yield by 48 % and total Se content by 2·8-fold, and decreased total Hg and MeHg by 47 and 55 %, respectively, compared with the control treatments. The high Se treatment also markedly reduced ‘water-soluble’ Hg and MeHg concentrations in the rhizosphere soil, decreased the uptake capacity of Hg by roots and enhanced the development of apoplastic barriers in the root endodermis. Conclusions Addition of Se to Hg-contaminated soil can help produce brown rice that is simultaneously enriched in Se and contains less total Hg and MeHg. The lowered accumulation of total Hg and MeHg appears to be the result of reduced bioavailability of Hg and production of MeHg in the rhizosphere, suppression of uptake of Hg into the root cells and an enhancement of the development of apoplastic barriers in the endodermis of the roots. PMID:24948669

  13. Plant rhizosphere effects on metal mobilization and transport. 1998 annual progress report

    SciTech Connect

    Fan, T.W.M.

    1998-06-01

    'Information on the mechanism of how plants mobilize, uptake, and metabolize metal ions is very limited. Especially deficient is the understanding of these processes involving pollutant metal ions and interactions among these ions. Based on the current knowledge regarding nutrient ions, it is clear that elucidation of rhizospheric processes such as exudation of organic ligands by plant roots and plant metabolism/adaptation involving these biogenic chelators is critically important. A mechanistic insight into these processes will advance knowledge in microbe-plant host interactions and how metal ions are mobilized, immobilized, and sequestered by these interactions. This, in turn, is essential to applications such as phytobioremediation and microbioremediation of metal ion pollution. Root exudation also serves many other important rhizosphere functions including energy supply for microbial degradation of organic pollutants, structuring of microbial community, and the formation of soil humic materials which are considered to be a major sink for both organic and inorganic pollutants. How root exudates function is critically dependent on the chemical nature of exudate components. Therefore, a comprehensive characterization of all major exudate components, regardless of their chemical class, should facilitate the development and implementation of bioremediation for both organic and inorganic pollutants. Therefore, the objectives of this project are: (1) To obtain a comprehensive composition of major organic components in plant root exudates as a function of different metal ions; (2) To examine plant metabolic response(s) to these metal ion treatments, with emphasis on biosynthetic pathways of organic ligands; and (3) To investigate the effect(s) of soil microbial (e.g. mycorrhizae) association on (1) and (2).'

  14. 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

  15. [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.

  16. Field Demonstration of Rhizosphere-Enhanced Treatment of Organics-Contaminated Soils on Native American Lands with Application to Northern FUD Sites

    DTIC Science & Technology

    2004-11-01

    M., C.R. Woolard, J. F. Braddock, and C. M. Reynolds. 1997. Enhancement and inhibition of soil petroleum biodegradation through the use of...Rhizosphere- Enhanced Treatment of Organics- Contaminated Soils on Native American Lands with Application to Northern FUD Sites November 2004 Report...rhizosphere- enhanced bioremediation of petroleum, oils , and lubricants (POL) at three cold sites in Alaska. The demonstrations evaluated the use of

  17. ESTCP Cost and Performance Report: Field Demonstration of Rhizosphere-Enhanced Treatment of Organics-Contaminated Soils on Native American Lands with Application to Northern FUD Sites

    DTIC Science & Technology

    2004-06-01

    England. Reynolds, C.M., P. Bhunia, and B.A. Koenen. 1997. Soil Remediation demonstration Project: Biodegradation of Heavy Fuel Oils . Special Report...TITLE AND SUBTITLE ESTCP Cost and Performance Report: Field Demonstration of Rhizosphere- Enhanced Treatment of Organics-Contaminated Soils on Native...1011, “Field Demonstration of Rhizosphere- Enhanced Treatment of Organics-Contaminated Soils on Native American Lands with Application to Northern

  18. Diversity and distribution of 16S rRNA and phenol monooxygenase genes in the rhizosphere and endophytic bacteria isolated from PAH-contaminated sites

    PubMed Central

    Peng, Anping; Liu, Juan; Ling, Wanting; Chen, Zeyou; Gao, Yanzheng

    2015-01-01

    This is the first investigation of the diversity and distribution of 16S rRNA and phenol monooxygenase (PHE) genes in endophytic and rhizosphere bacteria of plants at sites contaminated with different levels of PAHs. Ten PAHs at concentrations from 34.22 to 55.29 and 45.79 to 97.81 mg·kg−1 were measured in rhizosphere soils of Alopecurus aequalis Sobol and Oxalis corniculata L., respectively. The diversity of 16S rRNA and PHE genes in rhizosphere soils or plants changed with varying PAH pollution levels, as shown based on PCR-DGGE data. Generally, higher Shannon-Weiner indexes were found in mild or moderate contaminated areas. A total of 82 different bacterial 16S rRNA gene sequences belonging to five phyla; namely, Acfinobacteria, Proteobacteria, Chloroflexi, Cyanophyta, and Bacteroidetes, were obtained from rhizosphere soils. For the 57 identified PHE gene sequences, 18 were excised from rhizosphere bacteria and 39 from endophytic bacteria. The copy numbers of 16S rRNA and PHE genes in rhizosphere and endophytic bacteria varied from 3.83 × 103 to 2.28 × 106 and 4.17 × 102 to 1.99 × 105, respectively. The copy numbers of PHE genes in rhizosphere bacteria were significantly higher than in endophytic bacteria. Results increase our understanding of the diversity of rhizosphere and endophytic bacteria from plants grown in PAH-contaminated sites. PMID:26184609

  19. Changes in the species composition of the rhizosphere and phyllosphere of sugar beet under the impact of biological preparations based on endophytic bacteria and their metabolites

    NASA Astrophysics Data System (ADS)

    Pusenkova, L. I.; Il'yasova, E. Yu.; Lastochkina, O. V.; Maksimov, I. V.; Leonova, S. A.

    2016-10-01

    The species structure of the mycobiota in the rhizosphere and phyllosphere of sugar beet in ontogenesis was studied. The treatment of the plants with biopreparations based on endophytic bacteria and their metabolites (Phytosporin-M, Vitaplan, and Albit) were shown to create conditions for the colonization of the plant rhizosphere and phyllosphere by bacteria-antagonists displacing phytopathogenic microorganisms and stimulating plant growth, which induces the transformation of the microbial cenosis.

  20. Diversity and distribution of 16S rRNA and phenol monooxygenase genes in the rhizosphere and endophytic bacteria isolated from PAH-contaminated sites

    NASA Astrophysics Data System (ADS)

    Peng, Anping; Liu, Juan; Ling, Wanting; Chen, Zeyou; Gao, Yanzheng

    2015-07-01

    This is the first investigation of the diversity and distribution of 16S rRNA and phenol monooxygenase (PHE) genes in endophytic and rhizosphere bacteria of plants at sites contaminated with different levels of PAHs. Ten PAHs at concentrations from 34.22 to 55.29 and 45.79 to 97.81 mg·kg-1 were measured in rhizosphere soils of Alopecurus aequalis Sobol and Oxalis corniculata L., respectively. The diversity of 16S rRNA and PHE genes in rhizosphere soils or plants changed with varying PAH pollution levels, as shown based on PCR-DGGE data. Generally, higher Shannon-Weiner indexes were found in mild or moderate contaminated areas. A total of 82 different bacterial 16S rRNA gene sequences belonging to five phyla; namely, Acfinobacteria, Proteobacteria, Chloroflexi, Cyanophyta, and Bacteroidetes, were obtained from rhizosphere soils. For the 57 identified PHE gene sequences, 18 were excised from rhizosphere bacteria and 39 from endophytic bacteria. The copy numbers of 16S rRNA and PHE genes in rhizosphere and endophytic bacteria varied from 3.83 × 103 to 2.28 × 106 and 4.17 × 102 to 1.99 × 105, respectively. The copy numbers of PHE genes in rhizosphere bacteria were significantly higher than in endophytic bacteria. Results increase our understanding of the diversity of rhizosphere and endophytic bacteria from plants grown in PAH-contaminated sites.

  1. 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.

  2. [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

  3. 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

  4. Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates.

    PubMed

    Gschwendtner, Silvia; Esperschütz, Jürgen; Buegger, Franz; Reichmann, Michael; Müller, Martin; Munch, Jean Charles; Schloter, Michael

    2011-06-01

    A high percentage of photosynthetically assimilated carbon is released into soil via root exudates, which are acknowledged as the most important factor for the development of microbial rhizosphere communities. As quality and quantity of root exudates are dependent on plant genotype, the genetic engineering of plants might also influence carbon partitioning within the plant and thus microbial rhizosphere community structure. In this study, the carbon allocation patterns within the plant-rhizosphere system of a genetically modified amylopectin-accumulating potato line (Solanum tuberosum L.) were linked to microbial degraders of root exudates under greenhouse conditions, using (13)C-CO(2) pulse-chase labelling in combination with phospholipid fatty acid (PLFA) analysis. In addition, GM plants were compared with the parental cultivar as well as a second potato cultivar obtained by classical breeding. Rhizosphere samples were obtained during young leaf developmental and flowering stages. (13)C allocation in aboveground plant biomass, water-extractable organic carbon, microbial biomass carbon and PLFA as well as the microbial community structure in the rhizosphere varied significantly between the natural potato cultivars. However, no differences between the GM line and its parental cultivar were observed. Besides the considerable impact of plant cultivar, the plant developmental stage affected carbon partitioning via the plant into the rhizosphere and, subsequently, microbial communities involved in the transformation of root exudates.

  5. 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.

  6. Effects of Inoculation with PGPR Bacillus and Pisolithus tinctorius on Pinus pinea L. Growth, Bacterial rhizosphere Colonization, and Mycorrhizal Infection.

    PubMed

    Probanza, A.; Mateos, J.L.; Lucas García, J.A.; Ramos, B.; De Felipe, M.R.; Gutierrez Mañero, F.J.

    2001-02-01

    The effect of co-inoculation with Pisolithus tinctorius and a PGPR belonging to the genus Bacillus (Bacillus licheniformis CECT 5106 and Bacillus pumilus CECT 5105) in enhancing growth of Pinus pinea plants and the changes that occurred in rhizosphere microbial communities and the degree of mycorrhization were evaluated. Both bacterial strains of Bacillus promote the growth of Pinus pinea seedlings, but this biological effect does not imply a synergic effect with mycorrhizal infection. However, the positive response to mycorrhiza in a longer-term experiment it could be expected. The introduction of both inocula causes an alteration in the microbial rhizosphere composition, despite the low levels of inocula that were found at the end of the assay.

  7. Synergism between Phyllobacterium sp. (N(2)-fixer) and Bacillus licheniformis (P-solubilizer), both from a semiarid mangrove rhizosphere.

    PubMed

    Rojas, A; Holguin, G; Glick, B R.; Bashan, Y

    2001-04-01

    Mangrove seedlings were treated with a mixture of two bacterial species, the slow-growing, N(2)-fixing bacterium Phyllobacterium sp. and the fast-growing, phosphate-solubilizing bacterium Bacillus licheniformis, both isolated from the rhizosphere from black, white, and red mangroves of a semiarid zone. Nitrogen fixation and phosphate solubilization increased when the mixture was used compared to the effects observed when adding individual cultures, notwithstanding that there was no increase in bacterial multiplication under these conditions. Inoculation of black mangrove seedlings in artificial seawater showed the mixture performed somewhat better than inoculation of the individual bacterium; more leaves were developed and higher levels of (15)N were incorporated into the leaves, although the total nitrogen level decreased. This study demonstrates that interactions between individual components of the rhizosphere of mangroves should be considered when evaluating these bacteria as plant growth promoters.

  8. [Effects of Green Manure Intercropping and Straw Mulching on Winter Rape Rhizosphere Soil Organic Carbon and Soil Respiration].

    PubMed

    Zhou, Quan; Wang, Long-chang; Xiong, Ying; Zhang, Sai; Du, Juan; Zhao, Lin-lu

    2016-03-15

    Under the background of global warming, the farmland soil respiration has become the main way of agricultural carbon emissions. And green manure has great potential to curb greenhouse gas emissions and achieve energy conservation and emissions reduction. However, in purple soil region of Southwest, China, soil respiration under green manure remains unclear, especially in the winter and intercropping. Through the green manure ( Chinese milk vetch) intercropping with rape, therefore, we compared the effects of rape rhizosphere under straw mulching. The soil organic carbon and soil respiration were examined. The results showed, compared with straw mulching, root separation was the major influencing factors of soil organic carbon on rape rhizosphere. Soil organic carbon was significantly decreased by root interaction. In addition, straw mulching promoted while green manure intercropping inhibited the soil respiration. Soil respiration presented the general characteristics of fall-rise-fall due to the strong influence of rape growth period. Therefore, it showed a cubic curve relationship with soil temperature.

  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. Sustainable biodegradation of phenol by Acinetobacter calcoaceticus P23 isolated from the rhizosphere of duckweed Lemna aoukikusa.

    PubMed

    Yamaga, Fumiko; Washio, Kenji; Morikawa, Masaaki

    2010-08-15

    Phenol-degrading bacteria were isolated from the rhizosphere of duckweed (Lemna aoukikusa) using an enrichment culture method. One of the isolates, P23, exhibited an excellent ability to degrade phenol and attach to a solid surface under laboratory conditions. Phylogenetic analysis revealed that P23 belongs to the genera Acinetobacter and has the highest similarity to Acinetobacter calcoaceticus. P23 rapidly colonized on the surface of sterilized duckweed roots and formed biofilms, indicating that the conditions provided by the root system of duckweed are favorable to P23. A long-term performance test (160 h) showed that continuous removal of phenol can be attributed to the beneficial symbiotic interaction between duckweed and P23. P23 is the first growth-promoting bacterium identified from Lemna aoukikusa. The results in this study suggest the potential usefulness of dominating a particular bacterium in the rhizosphere of duckweeds to achieve efficient and sustainable bioremediation of polluted water.

  11. Diversity of bacterial endophytes in roots of Mexican husk tomato plants (Physalis ixocarpa) and their detection in the rhizosphere.

    PubMed

    Marquez-Santacruz, H A; Hernandez-Leon, R; Orozco-Mosqueda, M C; Velazquez-Sepulveda, I; Santoyo, G

    2010-12-07

    Endophytic bacterial diversity was estimated in Mexican husk tomato plant roots by amplified rDNA restriction analysis and sequence homology comparison of the 16S rDNA genes. Sixteen operational taxonomic units from the 16S rDNA root library were identified based on sequence analysis, including the classes Gammaproteobacteria, Betaproteobacteria, Actinobacteria, and Bacilli. The predominant genera were Stenotrophomonas (21.9%), Microbacterium (17.1%), Burkholderia (14.3%), Bacillus (14.3%), and Pseudomonas (10.5%). In a 16S rDNA gene library of the same plant species' rhizosphere, only common soil bacteria, including Stenotrophomonas, Burkholderia, Bacillus, and Pseudomonas, were detected. We suggest that the endophytic bacterial diversity within the roots of Mexican husk tomato plants is a subset of the rhizosphere bacterial population, dominated by a few genera.

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

    PubMed Central

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

    2014-01-01

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

  13. 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.

  14. Colonization of Wheat Roots by an Exopolysaccharide-Producing Pantoea agglomerans Strain and Its Effect on Rhizosphere Soil Aggregation

    PubMed Central

    Amellal, N.; Burtin, G.; Bartoli, F.; Heulin, T.

    1998-01-01

    The effect of bacterial secretion of an exopolysaccharide (EPS) on rhizosphere soil physical properties was investigated by inoculating strain NAS206, which was isolated from the rhizosphere of wheat (Triticum durum L.) growing in a Moroccan vertisol and was identified as Pantoea aglomerans. Phenotypic identification of this strain with the Biotype-100 system was confirmed by amplified ribosomal DNA restriction analysis. After inoculation of wheat seedlings with strain NAS206, colonization increased at the rhizoplane and in root-adhering soil (RAS) but not in bulk soil. Colonization further increased under relatively dry conditions (20% soil water content; matric potential, −0.55 MPa). By means of genetic fingerprinting using enterobacterial repetitive intergenic consensus PCR, we were able to verify that colonies counted as strain NAS206 on agar plates descended from inoculated strain NAS206. The intense colonization of the wheat rhizosphere by these EPS-producing bacteria was associated with significant soil aggregation, as shown by increased ratios of RAS dry mass to root tissue (RT) dry mass (RAS/RT) and the improved water stability of adhering soil aggregates. The maximum effect of strain NAS206 on both the RAS/RT ratio and aggregate stability was measured at 24% average soil water content (matric potential, −0.20 MPa). Inoculated strain NAS206 improved RAS macroporosity (pore diameter, 10 to 30 μm) compared to the noninoculated control, particularly when the soil was nearly water saturated (matric potential, −0.05 MPa). Our results suggest that P. agglomerans NAS206 can play an important role in the regulation of the water content (excess or deficit) of the rhizosphere of wheat by improving soil aggregation. PMID:9758793

  15. 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

  16. [Effects of cotton stalk biochar on microbial community structure and function of continuous cropping cotton rhizosphere soil in Xinjiang, China].

    PubMed

    Gu, Mei-ying; Tang, Guang-mu; Liu, Hong-liang; Li, Zhi-qiang; Liu, Xiao-wei; Xu, Wan-li

    2016-01-01

    In this study, field trials were conducted to examine the effects of cotton stalk biochar on microbial population, function and structural diversity of microorganisms in rhizosphere soil of continuous cotton cropping field in Xinjiang by plate count, Biolog and DGGE methods. The experiment was a factorial design with four treatments: 1) normal fertilization with cotton stalk removed (NPK); 2) normal fertilization with cotton stalk powdered and returned to field (NPKS); 3) normal fertilization plus cotton stalk biochar at 22.50 t · hm⁻² (NPKB₁); and 4) normal fertilization plus cotton stalk biochar at 45.00 t · hm⁻² (NPKB₂). The results showed that cotton stalk biochar application obviously increased the numbers of bacteria and actinomycetes in the rhizospheric soil. Compared with NPK treatment, the number of fungi was significantly increased in the NPKB₁treatment, but not in the NPKB₂ treatment. However, the number of fungi was generally lower in the biochar amended (NPKB₁, NPKB₂) than in the cotton stalk applied plots (NPKS). Application of cotton stalk biochar increased values of AWCD, and significantly improved microbial richness index, suggesting that the microbial ability of utilizing carbohydrates, amino acids and carboxylic acids, especially phenolic acids was enhanced. The number of DGGE bands of NPKB₂ treatment was the greatest, with some species of Gemmatimonadetes, Acidobacteria, Proteobacteria and Actinobacteria being enriched. UPGMC Cluster analysis pointed out that bacterial communities in the rhizospheric soil of NPKB₂ treatment were different from those in the NPK, NPKS and NPKB₁treatments, which belonged to the same cluster. These results indicated that application of cotton stalk biochar could significantly increase microbial diversity and change soil bacterial community structure in the cotton rhizosphere soil, thus improving the health of soil ecosystem.

  17. 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.

  18. Understanding Trichoderma in the root system of Pinus radiata: associations between rhizosphere colonisation and growth promotion for commercially grown seedlings.

    PubMed

    Hohmann, Pierre; Jones, E Eirian; Hill, Robert A; Stewart, Alison

    2011-08-01

    Two Trichoderma isolates (T. hamatum LU592 and T. atroviride LU132) were tested for their ability to promote the growth and health of commercially grown Pinus radiata seedlings. The colonisation behaviour of the two isolates was investigated to relate rhizosphere competence and root penetration to subsequent effects on plant performance. Trichoderma hamatum LU592 was shown to enhance several plant health and growth parameters. The isolate significantly reduced seedling mortality by up to 29%, and promoted the growth of shoots (e.g. height by up to 16%) and roots (e.g. dry weight by up to 31%). The introduction of LU592 as either seed coat or spray application equally improved seedling health and growth demonstrating the suitability of both application methods for pine nursery situations. However, clear differences in rhizosphere colonisation and root penetration between the two application methods highlighted the need for more research on the impact of inoculum densities. When spray-applied, LU592 was found to be the predominant Trichoderma strain in the plant root system, including bulk potting mix, rhizosphere and endorhizosphere. In contrast, T. atroviride LU132 was shown to colonise the root system poorly, and no biological impact on P. radiata seedlings was detected. This is the first report to demonstrate rhizosphere competence as a useful indicator for determining Trichoderma bio-inoculants for P. radiata. High indigenous Trichoderma populations with similar population dynamics to the introduced strains revealed the limitations of the dilution plating technique, but this constraint was alleviated to some extent by the use of techniques for morphological and molecular identification of the introduced isolates.

  19. 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

  20. Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline

    PubMed Central

    Hilton, Sally; Bennett, Amanda J.; Keane, Gary; Bending, Gary D.; Chandler, David; Stobart, Ron; Mills, Peter

    2013-01-01

    Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality. PMID:23573215

  1. Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline.

    PubMed

    Hilton, Sally; Bennett, Amanda J; Keane, Gary; Bending, Gary D; Chandler, David; Stobart, Ron; Mills, Peter

    2013-01-01

    Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality.

  2. 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

  3. Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

    PubMed Central

    Dunfield, Kari E.; Germida, James J.

    2003-01-01

    The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified

  4. How do microorganisms influence trace element uptake by plants? Screening in an agar model rhizosphere.

    NASA Astrophysics Data System (ADS)

    Marchetti, M.; Robinson, B. H.; Evangelou, M. W. H.; Vachey, A.; Schwitzguebel, J. P.; Bernier-Latmani, R.; Schulin, R.

    2009-04-01

    Trace elements (TE) are essential for humans and plants, but they may be toxic if their concentration is too high. For this reason, the management of TE in soils is very important. In some cases it may be necessary to increase the uptake of nutrients or TE by plants, for example in a biofortification perspective. Conversely, in some other cases TE uptake by plants should be decreased, for instance to avoid heavy metals entering the food chain via edible crops. Microorganisms living in the rhizosphere affect trace element (TE) uptake by plants. However, due to the complexity of this space and the variety of microorganisms that occur there, it is difficult to isolate the effect of any particular strain. To overcome this hurdle, we developed a system in which we grew plants under sterile conditions in agar and inoculated their rhizosphere with a single, well-defined microbial strain. For many years, agar has been used as a growth substrate for microorganisms and plant tissues. It is cheap, easy to use, and can be autoclaved to ensure its sterility. Because of its widespread use, an experiment conducted using this substrate can be reproduced under the same conditions in any laboratory. In contrast to soil, there is little interaction between the trace elements and the agar matrix. There are many studies investigating the influence of microorganisms on TE uptake by plants. However, so far only a small variety of microorganisms has been tested on few plant species. Therefore, the first objective of our research was to develop a method to rapidly screen a large variety of microorganisms on various plant species. Once this goal was achieved, we sought to study the effect of single, well-defined microbial strains on TE uptake by sunflower and wheat. The substrate for plants growth was a 10% agar solution prepared with modified Hoagland's solution and a TE solution containing 1 mg/kg Pb and molar equivalents of Cu, Ni and Zn. The agar solution was autoclaved and poured into

  5. 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

  6. 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 pr